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Synthetic Biology: What's Hindering Us?

Efforts in synthetic biology have been primarily focused on the creation and perfection of biological modules and systems in order to achieve specific functions. Since first demonstrated by the bacterial toggle switch and the Repressilator in 2000, synthetic biologists now possess the ability to engineer and manipulate genetic circuits, metabolic pathways, and even entire genomes.

In genetic engineering, chemicals are frequently employed as signals to control molecular and cellular behavior. However, because chemicals deliver information only by diffusion, chemical signals are seriously limited by the short-range interactions. Another serious issue regarding chemical signals is the complexity of the process in fully eradicating them, making it difficult for the system to reset. Additionally, the cytotoxicity, high cost, and narrow dynamic range of chemicals urge synthetic biologists to find more spatiotemporally specific and environmental friendly alternatives.

Figure 1. Comparison of chemical signal and light signal

Optogenetics: Inspiring Synthetic Biology

Literally, optogenetics refers to the genetic strategies which employ light as the input signal in the place of chemical signals. During the last decade, optogenetics has made significant impact on life sciences and other practices^[1]. It has evolved rapidly, with light-switchable promoters^[2], light-induced protein-protein interaction^[3], light-activated ion channelsand^[4] eventually, light-controlled animal behavior, and so on. The spatiotemporal specificity of light signals allows for precise manipulation and long range interaction without physical contact. Besides its incredible range of functions, light resources are also cheaper, more sustainable, and environmentally friendly. These properties together make optogenetic tools attractive for synthetic biologists.

Figure 2. Evolution of Optogenetics^[6]

Light as a signal may carry massive information. The wavelength, intensity, frequency and spatial-temporal patterns of light are all informations encoded in a physical manner. Plus light signals possess a Bool-logic-like dynamic behavior and does not require any medium for its propagation, it would be much more enabling in transmitting accurate and complex information than the frequently investigated chemical signals. (In fact, natural biological systems has already explored this advantage to an astonishing extent. Think of our vision! )

Thus using light as a signal, we may program cellular behaviors to achieve, say, cell-cell communication that does not require physical contact. To communicate through light, first cells must be able to sense light, which means we need to develop a light sensor. And to realize this new generation of light communication that has never been implemented before, the sensor itself must make a big difference.

Reference

1. Miesenbock, G. (2011) Optogenetic control of cells and circuits. Annu. Rev. Cell. Dev. Biol., 27: 731: 758
2. Shimizu-Sato, S., Huq, E., et al. (2002) A light-switchable gene promoter system. Nat. Biotechnol., 20(10): 1041: 1044
3. Levskaya, A., Weiner, O.D., et al. (2009) Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature, 461(7266): 997: 1001.
4. Zemelman, B.V., Lee, G.A., et al. (2002) Selective photostimulation of genetically chARGed neurons. Neuron, 33(1): 15: 22
5. Ohlendorf, R., Vidavski, R.R., et al. (2012) From dusk till dawn: one-plasmid systems for light-regulated gene expression. J. Mol. Biol. 416(4): 534: 542
6. http://www.stanford.edu/group/dlab/optogenetics/

@@ Line 21: / Line 21: @@
 <div class="PKU_context floatR">
 <h3 id="title2">Optogenetics: Inspiring Synthetic Biology </h3>
-<p>Literally, optogenetics refers to the genetic strategies which employ light as the input signal in the place of chemical signals. During the last decade, optogenetics has made significant impact on life sciences and other practices. It has evolved rapidly, with light-switchable promoters, light-induced protein-protein interaction, light-activated ion channels and eventually, light-controlled animal behavior, and so on. The spatiotemporal specificity of light signals allows for precise manipulation and long range interaction without physical contact. Besides its incredible range of functions, light resources are also cheaper, more sustainable, and environmentally friendly. These properties together make optogenetic tools attractive for synthetic biologists.
+<p>Literally, optogenetics refers to the genetic strategies which employ light as the input signal in the place of chemical signals. During the last decade, optogenetics has made significant impact on life sciences and other practices<sup><a href="#ref1" title=" Miesenbock, G. (2011). Optogenetic control of cells and circuits." Annu Rev Cell Dev Biol 27: 731-758.>[1]</a></sup>. It has evolved rapidly, with light-switchable promoters<sup><a href="#ref2" title=" Shimizu-Sato, S., E. Huq, et al. (2002). A light-switchable gene promoter system". Nat Biotechnol 20(10): 1041-1044.>[2]</a></sup>, light-induced protein-protein interaction<sup><a href="#ref3" title=" Levskaya, A., O. D. Weiner, et al. (2009). Spatiotemporal control of cell signalling using a light-switchable protein interaction." Nature 461(7266): 997-1001.>[3]</a></sup>, light-activated ion channelsand<sup><a href="#ref4" title=" Zemelman, B. V., G. A. Lee, et al. (2002). Selective photostimulation of genetically chARGed neurons". Neuron 33(1): 15-22.>[4]</a></sup>  eventually, light-controlled animal behavior, and so on. The spatiotemporal specificity of light signals allows for precise manipulation and long range interaction without physical contact. Besides its incredible range of functions, light resources are also cheaper, more sustainable, and environmentally friendly. These properties together make optogenetic tools attractive for synthetic biologists.
 </p>
 <div class="floatC">
-   <img src="/wiki/images/a/aa/Peking2012_Optogenetics.jpg" alt="[Fig 2.]" style="width:450px;"/>
+   <img src="/wiki/images/4/40/Peking2012_SA_Optogenetics.jpg" alt="[Fig 2.]" style="width:450px;"/>
    <p class="description" style="text-align:center;font-style:normal;">
-Figure 2. Evolution of Optogenetics.</p>
+Figure 2. Evolution of Optogenetics<sup><a href="#ref6">[6]</a><sup></p>
+<p>Light as a signal may carry massive information. The wavelength, intensity, frequency and spatial-temporal patterns of light are all informations encoded in a physical manner. Plus light signals possess a Bool-logic-like dynamic behavior and does not require any medium for its propagation, it would be much more enabling in transmitting accurate and complex information than the frequently investigated chemical signals. (In fact, natural biological systems has already explored this advantage to an astonishing extent. Think of our vision! ) <br/><br/>
+Thus using light as a signal, we may program cellular behaviors to achieve, say, cell-cell communication that does not require physical contact. To communicate through light, first cells must be able to sense light, which means we need to develop a light sensor. And to realize this new generation of light communication that has never been implemented before, the sensor itself must make a big difference.</p>
 </div>
- <p>However, current optogenetic tools are far from satisfactory for synthetic biology applications. In the next section, we will systematically analyze the current optogenetic methods and raise issues that our <i>Luminesensor</i> needs to circumvent.
-</p>
 </div>
-<div class="PKU_context floatR">
- <h3 id="title3">Issues of Current Optogenetic Methods</h3>
- <p>
-We carefully selected 15 representative optogenetic methods, ranging from those used in prokaryotes to those in eukaryotes. By statistically evaluating the modularity, sensitivity, and dynamic range of these optogenetics methods, we have come to address these four issues of current optogenetics approaches:
- </p>
- <div class="floatR">
-   <br /><br /><br />
-  <img src="/wiki/images/5/5b/Peking2012_effect_of_laser_1.jpg" alt="[Fig 3.]" style="width:200px;"/>
-  <p class="description" style="width:200px;">
-   Figure 3. The inhibitory effect of lasers on bacterial growth.
-  </p>
- </div>
- <p>
-<B>1. Low Sensitivity</b>
- <br /><BR>
-To minimize the influence on cell growth, strong light needs to be avoided for practical applications. Nearly 50% of current 15 optogenetic tools employ lasers as the light source. We demonstrated the lethal effect of lasers by illuminating a lawn of E.coli with a laser pointer. As clearly shown in Figure 2, no bacterial growth could be found on the spot that was illuminated. Only about 25% of the 15 optogenetics tools are able to sense natural light (~1W/m<sup>2</sup>), a biologically friendly and much more sustainable source of light (Figure 3, 4).
- <br /> <br />
-<b>2. Narrow Dynamic Range</b>
- <br /><BR>
-For a control system, the dynamic range (fold change of output in response to input signal) is an essential parameter used to evaluate the control efficiency. Among the 15 optogenetic methods, few have a dynamic range that reaches 100-fold (Figure 3b). In application, systems with narrow dynamic ranges will be easily interfered by the intrinsic and extrinsic noises. The main motive for having narrow dynamic range is due to the fact that most of the methods utilize a complex signal cascade where high basal level is inevitable.
- </p>
- <div class="floatC">
-  <img src="/wiki/images/e/ee/Peking2012_YL_overview_sensitivity_dynamic_range.png" alt="[Fig 3b.]" style="width:600px;"/>
-  <p class="description" style="text-align:center;font-style:normal;">
-Figure 4. The sensitivity and dynamic range of the 15 optogenetic methods.
-  </p>
- </div>
- <p>
- <br /> <br />
-<b>3. Dependency on Exogenous Chromophores</b>
- <br /><BR>
-Many optogenetic methods require the supplement of exogenous chromophores, e.g. phycocyanobilin (PCB) and caged amino acids. This leads to two major problems: <br />
-(1) The exogenous chromophores may be incompatible with the endogenous components, and observed in some cases, even have cytotoxity; <br />
-(2) The uneven diffusion of chromophores, in many cases, makes the output unpredictable.
- <br /> <br />
-<b>4. Limited Application in Prokaryotes</b>
- <br /><BR>
-Another serious issue concerns the limited application of optogenetic methods in prokaryotes. The rapidly reproducing prokaryote plays a very significant role in both fundamental research and industrial application of synthetic biology. In many methods, only proof of concept is provided without considering practical application.  <br />Low sensitivity, narrow dynamic range, and the need for exogenous chromophores, as mentioned above, are the obstacles for a broader and more practical application of optogenetics in synthetic biology.
- </p>
-</div>
-<div class="PKU_context floatR">
-<h3 id="title4">A New Generation of Optogenetic Tool: <br/>The <i>Luminesensor</i></h3>
-<p>
-By gaining insight into the current optogenetic methods, Peking iGEM team speculates that rationally designing a robust and ultra-sensitive transcription regulator that works in prokaryotes will circumvent all the issues mentioned above. High sensitivity allows for dimmer, cheaper, and safer light as the source of signals. Because the light sensitive transcription regulator functions directly on the gene expression, the basal level will also be low enough to guarantee a high dynamic range.
-<BR><BR>
-Indeed, as you will see later, such an ultrasensitive and efficient optogenetic tool has been successfully designed. Moreover, we endeavored to explore the full proficiency of our <i>Luminesensor</i> and raised a new generation of optogenetic tool with broader applications on the manipulation of biochemical process, cellular behavior, and even, inter-cellular communication.
-</p>
-</div>
 <div class="PKU_context floatR">
@@ Line 88: / Line 38: @@
   <p></p>
   <ul class="refer"><li id="ref1">
-. Wu, Y. I., D. Frey, et al. (2009). "A genetically encoded photoactivatable Rac controls the motility of living cells." Nature 461(7260): 104-108.<br>
+. Miesenbock, G. (2011) Optogenetic control of cells and circuits. <i>Annu. Rev. Cell. Dev. Biol.</i>, 27: 731: 758<br />
-.Shimizu-Sato, S., E. Huq, et al. (2002). "A light-switchable gene promoter system." Nat Biotechnol 20(10): 1041-1044.<br>
+  </li><li id = "ref2">
-.Moglich, A., R. A. Ayers, et al. (2009). "Design and signaling mechanism of light-regulated histidine kinases." J Mol Biol <br>
+. Shimizu-Sato, S., Huq, E., <i>et al</i>. (2002) A light-switchable gene promoter system. <i>Nat. Biotechnol.</i>, 20(10): 1041: 1044<br />
-.Gradinaru, V., F. Zhang, et al. (2010). "Molecular and cellular approaches for diversifying and extending optogenetics." Cell 141(1): 154-165.<br>
+  </li><li id = "ref3">
-.Ohlendorf, R., R. R. Vidavski, et al. (2012). "From dusk till dawn: one-plasmid systems for light-regulated gene expression." J Mol Biol 416(4): 534-542.<br>
+. Levskaya, A., Weiner, O.D., <i>et al.</i> (2009) Spatiotemporal control of cell signalling using a light-switchable protein interaction. <i>Nature</i>, 461(7266): 997: 1001.<br />
-.Miesenbock, G. (2011). "Optogenetic control of cells and circuits." Annu Rev Cell Dev Biol 27: 731-758.<br>
+  </li><li id = "ref4">
-.Zemelman, B. V., G. A. Lee, et al. (2002). "Selective photostimulation of genetically chARGed neurons." Neuron 33(1): 15-22.<br>
+. Zemelman, B.V., Lee, G.A., <i>et al.</i> (2002) Selective photostimulation of genetically chARGed neurons. <i>Neuron</i>, 33(1): 15: 22<br />
-.Levskaya, A., O. D. Weiner, et al. (2009). "Spatiotemporal control of cell signalling using a light-switchable protein interaction." Nature 461(7266): 997-1001.<br>
+  </li><li id = "ref5">
-.Toettcher, J. E., C. A. Voigt, et al. (2011). "The promise of optogenetics in cell biology: interrogating molecular circuits in space and time." Nat Methods 8(1): 35-38.<br>
+. Ohlendorf, R., Vidavski, R.R., <i>et al.</i> (2012) From dusk till dawn: one-plasmid systems for light-regulated gene expression. <i>J. Mol. Biol.</i> 416(4): 534: 542<br />
+  </li><li id = "ref6">
+. http://www.stanford.edu/group/dlab/optogenetics/
   </li></ul>