of optogenetics tools in computing networks.
转录因子可以作为逻辑电路或其它分子传感器或调节活性中介的输入。到目前，大部分的生物计算电路中，它们已被用来作为小分子的浓度传感器。此外，光传感技术用于细菌电路来实现边缘检测，和哺乳动物细胞中来激活基因治疗产品。这些例子指出了光遗传学工具在计算网络潜在用途。
Logical integration of endogenously expressed transcription factor activities for cell surveillance and control purposes still remains a major challenge. In a recent development, endogenous transcriptional activity was sensed indirectly by endogenous promoters driving separate components of a yeast two-hybrid activator with the purpose of identifying and destroying cultured cancer cells in which both promoters are active at the same time.
逻辑集成的内源性表达的转录因子用于细胞监视和控制的目的仍然是一个重大的挑战。在最近的发展中，为了识别和摧毁培养的癌细胞，他们的启动子活跃在同一时间，通过内源启动子驱动酵母双杂交剂的单独部分，间接检测内源性转录的活性。
Protein-based switches that do not involve transcription factors are ubiquitous in nature, but their engineering has lagged behind. Studies have shown that signalling processes such as mating and osmolarity pathways in yeast and two-component signalling in bacteria can be rewired. In recent work, the mating pathway in type a yeast cells was manipulated genetically by placing some of the pathway’s components under chemical induction, thereby implementing two-input gates such as [pheromone-α] AND [inducer] → GFP (FIG. 6b).
不涉及转录因子的基于蛋白的开关在自然界是无处不在，但他们的设计已经落后。
研究表明，信令流程如在酵母和细菌的双组分信号的交配和渗透性途径可以重新布线。在最近的工作中，通过在化学诱导下对一些组件进行基因操作实现酵母细胞的交配途径的排版，从而实现双输入门如[pheromone-α] AND [inducer] → GFP（图6b）。
图 6-b
‘Sender’ type-α strains were engineered to secrete pheromone-α following chemical stimulation, allowing co-cultured ‘sender’ and ‘receiver’ strains to generate complex logic circuits linking up to three chemical inputs to two fluorescent outputs. Despite these successes, we are far from having a kit of engineered enzymes to design de novo signalling circuits or proteins that are capable of integrating multiple inputs (similar to histones or p53 (REF. 97)). “发件人”type-α菌株在化学刺激下分泌pheromone-α，允许共同培养“发件人”和“接收”菌株产生复杂的逻辑电路，连接多达三个化学输入到两个荧光输出。尽管有了这些成就，我们离一个设计重始信号的工程酶工具包和能够集成多输入的蛋白质（类似于组蛋白和p53（参考文献97））还很远。
Another class of useful switches is based on protein interactions. One of the first studies in this direction showed a modular platform for controlling protein
function with two independent protein inputs, resulting in various logic behaviours. Yeast two- and three-hybrid systems can implement AND logic, and many ‘split’ protein systems — in which the original functional protein is split into two peptides that then interact through add-on binding moieties to reconstruct the function — were devised to achieve a similar two-input AND effect.
另一类有用的开关是基于蛋白质的相互作用。在这个方向上的第一个研究显示了，一个模块化平台用于有两个独立的蛋白质输入的蛋白质控制，结果得到了各种逻辑行为。酵母双杂交和三杂交系统可以实现与逻辑，许多“分裂”蛋白系统——原有的功能蛋白分为两个肽，然后通过扩展结合部分的互动来重建功能，被设计来实现得到类似双输入与门的效果。
Finally, protein degradation is an ‘off ’ switch that does not require transcription or translation machinery. Site-specific proteases from orthologous sources were shown to be useful in this respect. Yet scaling and generalizing these approaches remain major challenges that require improved tools for protein structure and interaction prediction.
最后，蛋白质降解是一个断开开关，不需要转录或翻译机制。来源于直系同源的位点专一的蛋白酶被证明在这方面是有用的。然而，缩放和推广这些方法仍然是主要的挑战，需要改进用于预测蛋白质结构和相互作用的工具。
To summarize, the approaches that have delivered the largest computations so far are based on simple, natural-like switching, such as transcription regulation with transcription factors and post-transcriptional regulation by RNAi. Transcriptional regulation is amenable to cascading, whereas in post-transcriptional regulation the size grows laterally in a normal-form-like
circuitry. Other approaches require a great deal of engineering of individual elements and thus have only been shown to work for a small number of inputs; their potential for scaling up remains the subject of future work.
总而言之，到目前为止交付最大计算量的都是基于简单的、倾向于自然的开关，如转录因子的转录调控和RNAi的转录后调控。转录调控可以实现级联，而在转录后调节中，正常电路的大小会横向生长。其他方法所需要的个体元素的设计量很大，因此只有输入很少的工作得到了验证；规模扩大的潜力仍然是未来工作的主旨。
Experimental state machines 状态机实验
Self-assembly as biochemical Turing computation 自组装生物图灵的计算 Self-assembly — a hallmark of complexity — is ubiquitous in biology. Computer science has shown that self-assembly processes can be described as computations and that any computation can be implemented with self-assembling building blocks. In particular, rectangular tiles with differently coloured edges that stick together when their edges match can encode a Turing machine program and can assemble into intricate two-dimensional pat-terns (Supplementary Information S1 (figure)). Molecular implementation of this concept was first proposed and implemented for a periodic pattern of planar DNA tiles (FIG. 7a) and later for an aperiodic assembly that computed four consecutive XOR operations.
自组装—复杂性的标志—在生物中无处不在。计算机科学研究表明，自组装的过程可以被描述为计算，任何计算也可以通过自组装建筑模块实现。特别是，不同边界着色的长方形瓷砖，当他们的边界匹配可以编码一个图灵程序，或者可以组装成复杂的二维模型时，他们会粘合在一起（补充信息S1（图））。这一概念的
分子实现首次被提出，并用这种概念实现了平面DNA瓷砖的周期方向图（图7a），后来的非周期性自组装计算了四个连续的异或运算。
图 7-a
Algorithmic two-dimensional assembly has been extensively studied using counting as a benchmark because incremental counting is encoded in a small-size Turing machine program. Multiple challenges, such as error propagation, had to be overcome for experimental realization. Recently, counting to 12 with minimal errors has been achieved.
算术的二维组件已经被广泛的视为一个基准，因为增量计数是用一个小型的图灵程序编码的。但仍存在多重挑战，如误差蔓延，为了试验验证必须克服。最近，