合成生物电路

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此词条暂由袁一博翻译,翻译字数共956,未经人工整理和审校,带来阅读不便,请见谅。 由CecileLi初步审校

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模板:Synthetic biology

文件:Lac Operon.svg
The lac operon is a natural biological circuit on which many synthetic circuits are based. Top: Repressed, Bottom: Active.
文件:Lac Operon.svg
Lac Operon 是一种天然的生物电路,许多合成电路都是以它为基础的。 上图: 压抑状态,下图: 活跃状态。< br/> 1: RNA polymerase, 2: Repressor, 3: Promoter, 4: Operator, 5: Lactose, 6: lacZ, 7: lacY, 8: lacA.
1: RNA polymerase, 2: Repressor, 3: Promoter, 4: Operator, 5: Lactose, 6: lacZ, 7: lacY, 8: lacA.

1: RNA 聚合酶,2: 抑制子,3: 启动子,4: 操作者,5: 乳糖,6: lacZ,7: lacY,8: lacA ]


Synthetic biological circuits are an application of synthetic biology where biological parts inside a cell are designed to perform logical functions mimicking those observed in electronic circuits. The applications range from simply inducing production to adding a measurable element, like GFP, to an existing natural biological circuit, to implementing completely new systems of many parts.[1]

Synthetic biological circuits are an application of synthetic biology where biological parts inside a cell are designed to perform logical functions mimicking those observed in electronic circuits. The applications range from simply inducing production to adding a measurable element, like GFP, to an existing natural biological circuit, to implementing completely new systems of many parts.

合成生物电路作为对合成生物学的一种应用,通过利用细胞内的生物部件(细胞器)执行电子电路的逻辑功能。合成生物电路的应用范围十分广泛,例如,简单的诱导增殖到促使可观测的元素色荧光蛋白等的生成、利用现存自然生物电路、构建许多部分以组成全新系统等。

文件:Protein translation.gif
A ribosome is a biological machine.核糖体是一个细胞器。
A ribosome is a biological machine.

[核糖体是一种细胞器]

The goal of synthetic biology is to generate an array of tunable and characterized parts, or modules, with which any desirable synthetic biological circuit can be easily designed and implemented.[2] These circuits can serve as a method to modify cellular functions, create cellular responses to environmental conditions, or influence cellular development. By implementing rational, controllable logic elements in cellular systems, researchers can use living systems as engineered "biological machines" to perform a vast range of useful functions.[1]

The goal of synthetic biology is to generate an array of tunable and characterized parts, or modules, with which any desirable synthetic biological circuit can be easily designed and implemented. These circuits can serve as a method to modify cellular functions, create cellular responses to environmental conditions, or influence cellular development. By implementing rational, controllable logic elements in cellular systems, researchers can use living systems as engineered "biological machines" to perform a vast range of useful functions. The second, by Michael Elowitz and Stanislas Leibler, showed that three repressor genes could be connected to form a negative feedback loop termed the Repressilator that produces self-sustaining oscillations of protein levels in E. coli.

合成生物学旨在生成一系列可调谐和特征化的部件或模块。利用这些部件或模块,我们可以依据设想轻易设计合成并搭建生物电路。这些电路可以用来改善细胞功能,生成针对环境条件的细胞响应,或影响细胞的生长。通过向细胞系统中插入合理、可控的逻辑元素,研究人员可以将活体系统作为工程化的“生物机器”一样运用其许多实用功能。迈克尔·埃洛维茨(Michael Elowitz)和斯坦尼斯拉斯·雷布勒(Stanislas Leibler)的另一项研究表明,三个阻遏基因可以相互联结从而形成一个负反馈环路,被称为抑制震荡子(Repressilator),它可以在大肠杆菌中促成蛋白质水平的自维持振荡。

History 发展历程

Currently, synthetic circuits are a burgeoning area of research in systems biology with more publications detailing synthetic biological circuits published every year. There has been significant interest in encouraging education and outreach as well: the International Genetically Engineered Machines Competition manages the creation and standardization of BioBrick parts as a means to allow undergraduate and high school students to design their own synthetic biological circuits.

目前,合成生物电路是系统生物学研究的一个新兴领域,每年都有许多新的刊物详细介绍合成生物电路。外界也对合成生物电路的教育引导和促进推广等方面有着浓厚的兴趣,如国际基因工程机器竞赛,它通过倡导生物积木零件的创造和标准化的方式鼓励本科生和高中生来设计自己的合成生物电路。

The first natural gene circuit studied in detail was the lac operon. In studies of diauxic growth of E. coli on two-sugar media, Jacques Monod and Francois Jacob discovered that E.coli preferentially consumes the more easily processed glucose before switching to lactose metabolism. They discovered that the mechanism that controlled the metabolic "switching" function was a two-part control mechanism on the lac operon. When lactose is present in the cell the enzyme β-galactosidase is produced to convert lactose into glucose or galactose. When lactose is absent in the cell the lac repressor inhibits the production of the enzyme β-galactosidase to prevent any inefficient processes within the cell. The first natural gene circuit studied in detail was the lac operon. In studies of diauxic growth of E. coli on two-sugar media, Jacques Monod and Francois Jacob discovered that E.coli preferentially consumes the more easily processed glucose before switching to lactose metabolism. They discovered that the mechanism that controlled the metabolic "switching" function was a two-part control mechanism on the lac operon. When lactose is present in the cell the enzyme β-galactosidase is produced to convert lactose into glucose or galactose. When lactose is absent in the cell the lac repressor inhibits the production of the enzyme β-galactosidase to prevent any inefficient processes within the cell. 科学家们细致研究的第一个天然基因电路是乳糖操纵子。贾克斯·莫诺德(Jacques Monod)和弗朗索瓦·雅各布(Francois Jacob)在研究大肠杆菌在双糖培养基上的二次生长时发现,大肠杆菌在转换为乳糖代谢之前,会优先消耗更易加工的葡萄糖。他们发现控制代谢“转换”功能的机制是对乳糖操纵子的一种二分控制机制。当乳糖存在于细胞中时,β-半乳糖苷酶就会表达出来,从而将乳糖转化为葡萄糖或半乳糖。当细胞中缺乏乳糖时,乳糖阻遏物便会抑制β-半乳糖苷酶的表达,从而阻止细胞内效率低下的过程。


The lac operon is used in the biotechnology industry for production of recombinant proteins for therapeutic use. The gene or genes for producing an exogenous protein are placed on a plasmid under the control of the lac promoter. Initially the cells are grown in a medium that does not contain lactose or other sugars, so the new genes are not expressed. Once the cells reach a certain point in their growth, Isopropyl β-D-1-thiogalactopyranoside (IPTG) is added. IPTG, a molecule similar to lactose, but with a sulfur bond that is not hydrolyzable so that E. Coli does not digest it, is used to activate or "induce" the production of the new protein. Once the cells are induced, it is difficult to remove IPTG from the cells and therefore it is difficult to stop expression. The lac operon is used in the biotechnology industry for production of recombinant proteins for therapeutic use. The gene or genes for producing an exogenous protein are placed on a plasmid under the control of the lac promoter. Initially the cells are grown in a medium that does not contain lactose or other sugars, so the new genes are not expressed. Once the cells reach a certain point in their growth, Isopropyl β-D-1-thiogalactopyranoside (IPTG) is added. IPTG, a molecule similar to lactose, but with a sulfur bond that is not hydrolyzable so that E. Coli does not digest it, is used to activate or "induce" the production of the new protein. Once the cells are induced, it is difficult to remove IPTG from the cells and therefore it is difficult to stop expression.


乳糖控制因子可用于生物技术工业生产治疗用重组蛋白。在乳糖控制因子的作用下,用于产生外源蛋白的基因被插入到质粒上。最初,细胞是在不含乳糖或其他糖类的培养基中生长的,因此新的基因不表达。一旦细胞达到生长的某个点,乳糖控制因子就向其中加入异丙基β- d -1-硫代半乳糖苷(IPTG)。IPTG是一种类似乳糖的分子,但它的硫键并不能水解,所以大肠杆菌无法消化它。IPTG被用来激活或“诱导”新蛋白质的产生。一旦细胞被诱导,IPTG便很难从细胞中去除,因此也很难停止表达。

Both immediate and long term applications exist for the use of synthetic biological circuits, including different applications for metabolic engineering, and synthetic biology. Those demonstrated successfully include pharmaceutical production, and fuel production. However methods involving direct genetic introduction are not inherently effective without invoking the basic principles of synthetic cellular circuits. For example, each of these successful systems employs a method to introduce all-or-none induction or expression. This is a biological circuit where a simple repressor or promoter is introduced to facilitate creation of the product, or inhibition of a competing pathway. However, with the limited understanding of cellular networks and natural circuitry, implementation of more robust schemes with more precise control and feedback is hindered. Therein lies the immediate interest in synthetic cellular circuits.

合成生物电路的近期和长期应用都存在于代谢工程学和合成生物学在内等多重领域中。这些成功的案例包括制药生产和燃料生产。然而,如果不引用合成细胞电路的基本原理,涉及直接基因导入的方法就不会自然发生作用。例如,每个成功的系统都需要使用一种方法来引入是或否的诱导或表达。作为一种生物电路,可以通过引入简单的阻遏物或启动子来促进产物的生成,或抑制竞争途径。然而,由于对蜂窝网络和自然电路的了解有限,实施更精确的控制和反馈更具鲁棒性的方案面临着阻碍。人工合成蜂窝电路的最大潜藏利益就在于此。


Two early examples of synthetic biological circuits were published in Nature in 2000. One, by Tim Gardner, Charles Cantor, and Jim Collins working at Boston University, demonstrated a "bistable" switch in E. coli. The switch is turned on by heating the culture of bacteria and turned off by addition of IPTG. They used GFP as a reporter for their system.[3] The second, by Michael Elowitz and Stanislas Leibler, showed that three repressor genes could be connected to form a negative feedback loop termed the Repressilator that produces self-sustaining oscillations of protein levels in E. coli.[4] Two early examples of synthetic biological circuits were published in Nature in 2000. One, by Tim Gardner, Charles Cantor, and Jim Collins working at Boston University, demonstrated a "bistable" switch in E. coli. The switch is turned on by heating the culture of bacteria and turned off by addition of IPTG. They used GFP as a reporter for their system. The second, by Michael Elowitz and Stanislas Leibler, showed that three repressor genes could be connected to form a negative feedback loop termed the Repressilator that produces self-sustaining oscillations of protein levels in E. coli.

2000年,《自然》杂志发表了两个合成生物电路的早期例子。波士顿大学的蒂姆·加德纳、查尔斯·康托和吉姆·柯林斯研究了一种大肠杆菌的“双稳态”开关。通过加热细菌培养物打开开关,加入IPTG关闭开关。他们使用GFP作为他们系统的记者。第二项研究是由迈克尔·埃洛维茨(Michael Elowitz)和斯坦尼斯拉斯·莱布勒(Stanislas Leibler)提出的,他们发现三个抑制因子基因可以连接在一起,形成一个负反馈回路,称为抑制因子,它可以在大肠杆菌中产生自维持的蛋白质水平的振荡。

Development in understanding cellular circuitry can lead to exciting new modifications, such as cells which can respond to environmental stimuli. For example, cells could be developed that signal toxic surroundings and react by activating pathways used to degrade the perceived toxin. To develop such a cell, it is necessary to create a complex synthetic cellular circuit which can respond appropriately to a given stimulus.

对细胞电路理解的深入可以促成惊人的新修正作用,如可以对环境刺激作出反应的细胞、使细胞具有可以警示当前处于有毒环境,并通过激活用于降解感知毒素的途径来进行反应的功能等。为了研制这样一个细胞,我们有必要创建一个复杂的合成细胞电路,从而可以适当地响应给定的刺激。


Currently, synthetic circuits are a burgeoning area of research in systems biology with more publications detailing synthetic biological circuits published every year.[5] There has been significant interest in encouraging education and outreach as well: the International Genetically Engineered Machines Competition[6] manages the creation and standardization of BioBrick parts as a means to allow undergraduate and high school students to design their own synthetic biological circuits.

Currently, synthetic circuits are a burgeoning area of research in systems biology with more publications detailing synthetic biological circuits published every year.[5] There has been significant interest in encouraging education and outreach as well: the International Genetically Engineered Machines Competition[6] manages the creation and standardization of BioBrick parts as a means to allow undergraduate and high school students to design their own synthetic biological circuits.

目前,合成电路是系统生物学研究的一个新兴领域,每年都有更多的出版物详细介绍合成生物电路。外界对其在鼓励教育和推广方面也有很大的兴趣:国际基因工程机器竞赛管理着生物砖部件的创造和标准化,着使得本科生和高中生能够设计自己的合成生物电路。

Given synthetic cellular circuits represent a form of control for cellular activities, it can be reasoned that with complete understanding of cellular pathways, "plug and play" synthetic cells can be developed implementing only the pathways necessary for cell survival reproduction. From this cell, to be thought of as a minimal genome cell, one can add pieces from the toolbox to create a well defined pathway with appropriate synthetic circuitry for an effective feedback system. Because of the basic ground up construction method, and the proposed database of mapped circuitry pieces, techniques mirroring those used to model computer or electronic circuits can be used to redesign cells and model cells for easy troubleshooting and predictive behavior and yields.

鉴于合成细胞电路代表了一种控制细胞活动的形式,可以推断,只要完全了解细胞通路,就可以开发出只执行细胞生存繁殖所必需的通路的“即插即用”的合成细胞。在这个被认为是一个最小的基因组细胞中,我们可以添加工具箱中的片段,为一个有效的反馈系统创造一个拥有合适的合成电路的良定路径。细胞基础重构方法以及映射电路片的数据库,可以用于模拟计算机或电子电路的技术可用于重新设计细胞和模型细胞,以便排除故障和预测行为与产量。

Interest and goals 研究方向和目标

Both immediate and long term applications exist for the use of synthetic biological circuits, including different applications for metabolic engineering, and synthetic biology. Those demonstrated successfully include pharmaceutical production,[7] and fuel production.[8] However methods involving direct genetic introduction are not inherently effective without invoking the basic principles of synthetic cellular circuits. For example, each of these successful systems employs a method to introduce all-or-none induction or expression. This is a biological circuit where a simple repressor or promoter is introduced to facilitate creation of the product, or inhibition of a competing pathway. However, with the limited understanding of cellular networks and natural circuitry, implementation of more robust schemes with more precise control and feedback is hindered. Therein lies the immediate interest in synthetic cellular circuits. Both immediate and long term applications exist for the use of synthetic biological circuits, including different applications for metabolic engineering, and synthetic biology. Those demonstrated successfully include pharmaceutical production,[7] and fuel production.[8] However methods involving direct genetic introduction are not inherently effective without invoking the basic principles of synthetic cellular circuits. For example, each of these successful systems employs a method to introduce all-or-none induction or expression. This is a biological circuit where a simple repressor or promoter is introduced to facilitate creation of the product, or inhibition of a competing pathway. However, with the limited understanding of cellular networks and natural circuitry, implementation of more robust schemes with more precise control and feedback is hindered. Therein lies the immediate interest in synthetic cellular circuits.

合成生物电路在代谢工程和合成生物学等许多领域中,都具有短期和长期应用。成功的案例有制药生产和燃料生产等。然而,如果不运用合成细胞电路的基本原理,直接引入基因的方法本身便是无效的。例如,每一个成功的系统都使用了一种独特的方法来引入是或非的归纳或表达式。这种生物电路通过引入简单的抑制子或启动子来促进产物的生成,或抑制竞争途径。然而,由于人们对蜂窝网络和自然电路的了解有限,实现具有更精确的控制和反馈的、更具鲁棒性的方案必然受到阻碍。这也是合成细胞电路的直接利益所在。

Development in understanding cellular circuitry can lead to exciting new modifications, such as cells which can respond to environmental stimuli. For example, cells could be developed that signal toxic surroundings and react by activating pathways used to degrade the perceived toxin.[9] To develop such a cell, it is necessary to create a complex synthetic cellular circuit which can respond appropriately to a given stimulus. Development in understanding cellular circuitry can lead to exciting new modifications, such as cells which can respond to environmental stimuli. For example, cells could be developed that signal toxic surroundings and react by activating pathways used to degrade the perceived toxin.[9] To develop such a cell, it is necessary to create a complex synthetic cellular circuit which can respond appropriately to a given stimulus.

对细胞电路方面的学科的深入了解可以促成惊人的新修正方法,例如,细胞可以对环境刺激作出反应。处于有毒环境时,细胞可以发出信号,并通过激活降解对所感知毒素的途径进行反应。要形成这样的细胞,就必须创造一个复杂的合成细胞电路,能够对给定的刺激做出适当的反应。

Repressilator

抑制震荡子


Mammalian tunable synthetic oscillator

哺乳动物可调谐合成振荡器

Given synthetic cellular circuits represent a form of control for cellular activities, it can be reasoned that with complete understanding of cellular pathways, "plug and play"[1] cells with well defined genetic circuitry can be engineered. It is widely believed that if a proper toolbox of parts is generated,[10] synthetic cells can be developed implementing only the pathways necessary for cell survival reproduction. From this cell, to be thought of as a minimal genome cell, one can add pieces from the toolbox to create a well defined pathway with appropriate synthetic circuitry for an effective feedback system. Because of the basic ground up construction method, and the proposed database of mapped circuitry pieces, techniques mirroring those used to model computer or electronic circuits can be used to redesign cells and model cells for easy troubleshooting and predictive behavior and yields.

Given synthetic cellular circuits represent a form of control for cellular activities, it can be reasoned that with complete understanding of cellular pathways, "plug and play"[1] cells with well defined genetic circuitry can be engineered. It is widely believed that if a proper toolbox of parts is generated,[10] synthetic cells can be developed implementing only the pathways necessary for cell survival reproduction. From this cell, to be thought of as a minimal genome cell, one can add pieces from the toolbox to create a well defined pathway with appropriate synthetic circuitry for an effective feedback system. Because of the basic ground up construction method, and the proposed database of mapped circuitry pieces, techniques mirroring those used to model computer or electronic circuits can be used to redesign cells and model cells for easy troubleshooting and predictive behavior and yields.

假定合成细胞电路代表了一种控制细胞活动的形式,那么我们就可以推论,在完全理解细胞通路的情况下,具有明确定义的遗传电路的“即插即用”的细胞可以被制造出来。人们普遍认为,如果能够生成一个适当的工具部件,那么就可以将合成细胞改造为只执行细胞生存繁殖所需的生命过程。从这个被认为是最小的基因组细胞的细胞中,我们可以从工具箱中添加一些片段,创建一个具有适当的合成电路的良定通路,从而形成一个有效的反馈系统。由于基本的自底向上的方法,以及提出的映射电路片段的数据库,那些用于构建计算机或电子电路的技术可以用于重新设计单元和模型单元,以便于排除故障以及预测行为和产量。

Bacterial tunable synthetic oscillator

细菌可调谐合成振荡器


Coupled bacterial oscillator

耦合细菌振荡器

Example circuits 电路示例

Globally coupled bacterial oscillator

球状耦合细菌振荡器


Elowitz et al. and Fung et al. created oscillatory circuits that use multiple self-regulating mechanisms to create a time-dependent oscillation of gene product expression.

埃洛维茨等人。和 Fung 等人。创造的振荡电路,使用多种自我调节机制,创造一个时间相关的振荡基因产品表达。

Oscillators 振荡器

  1. Repressilator
  1. Mammalian tunable synthetic oscillator
Toggle-switch

拨动开关

  1. Bacterial tunable synthetic oscillator

Gardner et al. used mutual repression between two control units to create an implementation of a toggle switch capable of controlling cells in a bistable manner: transient stimuli resulting in persistent responses If Signal A AND Signal B are present, then the desired gene product will result. All promoters shown are inducible, activated by the displayed gene product. Each signal activates expression of a separate gene (shown in light blue). The expressed proteins then can either form a complete complex in cytosol, that is capable of activating expression of the output (shown), or can act separately to induce expression, such as separately removing an inhibiting protein and inducing activation of the uninhibited promoter.]]

加德纳等人使用两个控制单元之间的相互抑制来创建一个能够以双稳态方式控制细胞的拨动开关的实现: 如果接收到信号 A 和信号 B ,那么期望的基因产物将被表达出来。所有显示出的启动子都是诱导性的,并被表达的基因产物激活。每个信号激活一个单独基因的表达(如浅蓝色所示)。然后,表达的蛋白质可以在细胞溶胶中形成一个完整的能够激活输出的表达(如图所示)的复合体,或者可以单独作用诱导表达,例如单独去除抑制蛋白和诱导激活不受抑制的启动子。

  1. Coupled bacterial oscillator

耦合细菌振荡器

  1. Globally coupled bacterial oscillator

球状耦合细菌振荡器

The logical [[OR gate.

逻辑的[或门。

Elowitz et al. and Fung et al. created oscillatory circuits that use multiple self-regulating mechanisms to create a time-dependent oscillation of gene product expression.埃洛维茨等人和冯等人创造了一种振荡电路,它使用多个自调节机制来形成基因表达的依赖于时间的振荡器。[11][12]


Bistable switches 双稳态开关

Synthetic gene circuits can control gene expression heterogeneity and can be controlled independently of the gene expression mean.

合成基因电路可以控制基因表达的异质性,并且可以独立于基因表达方式进行控制。

  1. Toggle-switch

Gardner et al. used mutual repression between two control units to create an implementation of a toggle switch capable of controlling cells in a bistable manner: transient stimuli resulting in persistent responses[3].

 --CecileLi(讨论)  【审校】补充翻译:Gardner等人利用两个控制单元之间的相互抑制来实现一个能够以双稳态方式控制细胞的拨动开关:瞬态刺激导致持续反应[13]

Engineered systems are the result of implementation of combinations of different control mechanisms. A limited counting mechanism was implemented by a pulse-controlled gene cascade and application of logic elements enables genetic "programming" of cells as in the research of Tabor et al., which synthesized a photosensitive bacterial edge detection program.

工程系统是不同控制机制组合的结果。脉冲控制基因级联实现了有限计数机制,逻辑元件的应用实现了细胞的遗传“编程”,例如泰伯等人合成了一个光敏细菌边缘检测程序。

Logical operators 逻辑运算

文件:SynBioCirc-AndLogicGate.jpg
The logical AND gate.逻辑与门[14][15] If Signal A AND Signal B are present, then the desired gene product will result. All promoters shown are inducible, activated by the displayed gene product. Each signal activates expression of a separate gene (shown in light blue). The expressed proteins then can either form a complete complex in cytosol, that is capable of activating expression of the output (shown), or can act separately to induce expression, such as separately removing an inhibiting protein and inducing activation of the uninhibited promoter.如果信号 A 和信号 B 产生,那么期望的基因产物将被表达出来。所有显示出的启动子都是诱导性的,并被表达的基因产物激活。每个信号激活一个单独基因的表达(如浅蓝色所示)。表达的蛋白质可以在细胞溶胶中形成一个完整的能够激活输出的表达(如图所示)的复合体,或者可以单独作用诱导表达,例如分别去除抑制蛋白和诱导激活不受抑制的启动子。


Computational design and evaluation of DNA circuits to achieve optimal performance

实现最佳性能的 DNA 电路的计算设计和评估

文件:SynBioCirc-OrLogicGate.jpg
The logical OR gate.逻辑或门[14][15] If Signal A OR Signal B are present, then the desired gene product will result. All promoters shown are inducible. Either signal is capable of activating the expression of the output gene product, and only the action of a single promoter is required for gene expression. Post-transcriptional regulation mechanisms can prevent the presence of both inputs producing a compounded high output, such as implementing a low binding affinity ribosome binding site.如果信号 A 或信号 B 产生,那么期望的基因产物将被表达出来。所有显示出的启动子都是诱导性的。无论何种信号,都能激活基因产物的表达,并且只需一个启动子就可以产生这种表达。转录后的调节机制可以阻止产生复合高产出的两个输入信号的产生,比如插入一个低结合亲和力的核糖体结合点。


Recent developments in artificial gene synthesis and the corresponding increase in competition within the industry have led to a significant drop in price and wait time of gene synthesis and helped improve methods used in circuit design. At the moment, circuit design is improving at a slow pace because of insufficient organization of known multiple gene interactions and mathematical models. This issue is being addressed by applying computer-aided design (CAD) software to provide multimedia representations of circuits through images, text and programming language applied to biological circuits. Some of the more well known CAD programs include GenoCAD, Clotho framework and j5. GenoCAD uses grammars, which are either opensource or user generated "rules" which include the available genes and known gene interactions for cloning organisms. Clotho framework uses the Biobrick standard rules.

最近在人工基因合成法领域的发展和行业内竞争的相应增加已经导致了基因合成的价格和等待时间的显著下降,并且帮助改进了电路设计中使用的方法。目前,由于对已知的多基因相互作用和数学模型的架构不足,电路设计正在缓慢地改进。这个问题目前通过应用计算机辅助设计(CAD)软件,利用图像、文本和应用于生物电路的编程语言来提供电路的多媒体表示来解决。一些更著名的 CAD 程序包括 GenoCAD,Clotho框架和 j5。GenoCAD 使用语法,这些语法要么是开源的,要么是用户生成的“规则” ,其中包括克隆生物的可用基因和已知的基因相互作用。Clotho框架使用“生物积木”标准规则。

文件:SynBioCirc-NandLogicGate.jpg
The logical Negated AND gate.逻辑非门[14][15] If Signal A AND Signal B are present, then the desired gene product will NOT result. All promoters shown are inducible. The activating promoter for the output gene is constitutive, and thus not shown. The constitutive promoter for the output gene keeps it "on" and is only deactivated when (similar to the AND gate) a complex as a result of two input signal gene products blocks the expression of the output gene.如果信号 A 和信号 B 产生,那么期望的基因产物不会被表达出来。所有显示出的启动子都是诱导性的。输出基因的活性启动子是本构的,因而不会显示出来。输出基因的本构启动子让它始终被表达,只有在两个输入信号基因的产物阻滞输出基因的表达,形成一个复合体时,输出基因才失活。


Analog tuners 模拟调谐器

Using negative feedback and identical promoters, linearizer gene circuits can impose uniform gene expression that depends linearly on extracellular chemical inducer concentration.

线性化电路使用负反馈和完全相同的启动子,可以利用线性依赖于细胞外化学诱导物浓度的统一基因的表达。[16]


Controllers of gene expression heterogeneity 基因表达异质性的控制

Synthetic gene circuits can control gene expression heterogeneity and can be controlled independently of the gene expression mean.

合成基因电路可以控制基因表达的异质性,并且可以独立于基因表达均值来控制。[17]


Other engineered systems 其他工程系统

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Engineered systems are the result of implementation of combinations of different control mechanisms. A limited counting mechanism was implemented by a pulse-controlled gene cascade[18] and application of logic elements enables genetic "programming" of cells as in the research of Tabor et al., which synthesized a photosensitive bacterial edge detection program.[19]

 --CecileLi(讨论)  【审校】补充翻译:工程系统是执行不同控制机制组合的结果。脉冲控制的基因级联实现了有限的计数机制,逻辑元件的应用使细胞的基因“编程”成为可能,正如Tabor等人的研究所述,科学家们已合成了一种光敏细菌边缘检测程序。

Category:Synthetic biology

类别: 合成生物学


This page was moved from wikipedia:en:Synthetic biological circuit. Its edit history can be viewed at 合成生物电路/edithistory

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