Team:UCAS-China/Description

DESCRIPTION

One hundred years ago, there was a young boy who was seeking a unique rose for his beloved girl. It was a freezing winter night, and all roses had died. After a long time searching in the withered rose bush, the young boy was desperate. Touched by his true love, a nightingale, who heard and understood his wish, sang all night under the cold moonlight. Just before dawn, a rose stained with the blood of the nightingale, bloomed, bright and fragrant.

The writer Oscar Wilde, created a red rose for true love out of the nightingale’s song under moonlight.[1] To Wilde, the unique rose stained with blood of the nightingale is the symbol of love and true art. To us UCAS-China iGEM team, the touching story should be passed down to our generation and explained in a scientific and creative way using the tools of synthetic biology. Furthermore, as Wilde conveyed in the story, the barrier and combination of art and science still remain worthy of discussion, so we also explored in depth the relationship of art and science in the Human Practices section.


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Our project combines the four elements - music (the song of the nightingale), light (the moonlight), color (the stained rose) and odor (the rose fragrance). In our project every iGEMer is able to create his/her own rose with unique soul, together to form our rose forest in the junction of art and science!

DESIGN

In our project, E. coli needed light and sound as inputs to produce color and odor as outputs. The process was mainly divided into three parts: sound to light, light to color, and light to odor. The light-color and light-odor conversions were achieved with the RGB system[2] which was based on the phage RNAP system as a resource allocator. As for the sound-light conversion, we developed a software that allowed users to upload their own music to generate their unique dynamic pictures, with which people could color and ‘ensoul’ their own roses.


LIGHT TO COLOR

Firstly, we introduced the RGB system to stain our rose using light. The RGB system mainly consists of four modules: a sensor array, circuits, a resource allocator and actuators. The sensor array combines 3 light sensors, Cph8*, YF1 and CcasR, which can respond to lights of different wavelengths. CcasR can sense and be switched on by green (535nm) light. Cph8* is switched off by red (650nm) light, while YF1 is switched off by blue (470nm) light.


To activate gene expression, the signals from the red- and blue- light sensors need to be inverted, which is done by connecting them to NOT gates in circuits.


The resource allocator which connects the circuits and actuators, is based on a split-RNA polymerase system. In the system, the sigma fragments activated by light sensors can combine with the constitutively expressed non-active ‘core’ fragment to form complete RNA polymerases, then activates the expression of actuators accordingly. For more information on the circuit design, see LIGHT TO COLOR .


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The actuators we chose were three kinds of color protein: fluorescent protein, chromoprotein and enzyme which can produce colorful products. Although more and more fluorescent proteins and chromoproteins are edited to generate more and more colors, the number of colors produced by organisms is still limited by the number of the kinds of proteins. Once a new color is needed, researchers have to modify the chromophores of the proteins, which takes much time and effort.


So how do we create more colors in a reasonable and convenient way? Here, we put forward a new concept—mixing color into bacterial cells! Unlike the mix of different bacterial cells which produce different colors as the previous iGEM teams have done[4], we used tandem expression and RGB system to control the ratios of the expression of different colors in bacterial cells, to achieve mixing color in bacterial cells, and stain our roses with more bright colors.


We built hardware to generate lights with smooth distribution on the plates and controlled intensity, to activate our system to produce predictable colors. Our final hardware is designed and built to illuminate our bacteria on the plates, with the help of a projector, to achieve the interaction between users and our E.coli. More information see HARDWARE.


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LIGHT TO ODOR

Our roses are colorful now, but only with added fragrance can the rose bloom more vivid, appealing and with a soul as a real rose. So this is our second part, light to odor, making our roses more soulful and real. We first tried to use CRISPR/Cas9 gene-editing system[5] to knock out the original gene of E. coli producing smell to prevent E. coli from giving off a nasty and unpleasant smell. Then based on the light-control system, we changed the actuators with genes which could produce various kinds of odors.


The inherent unpleasant odor of E. coli comes from indole produced naturally in the cells’ metabolic process. In the L-tryptophan degradation pathway, Tryptophanase, encoded by tnaA gene[6], degraded L-tryptophan of indole, which produces the odor in high concentration.


L-tryptophan + H2O = indole + pyruvate + NH3. (The enzyme needs Co-factor: pyridoxal 5'-phosphate)


We first tried to knock out the tnaA gene in the genome of E. coli, then we replaced the actuators in the RGB system with genes which could produce various kinds of fragrance. We devoted ourselves to introducing diversified odor to make our roses not only vivid ones with traditional flower fragrance, but unique ones with more kinds of odor like lemon and rain[7]. Thus we can use light to control the fragrance of E.coli, and the function of our system was tested by HPLC. (See LIGHT TO ODOR).


SOUND TO LIGHT

We could paint a colorful and fragrant rose with light , but it was sound that brought a unique soul to the rose. To create his/her rose with a unique soul, we developed an online software—Orpheus—to convert music into unique colorful pictures. The users could choose their music or their own voice, and the pictures that they want to ensoul, to color the pictures with random colorful dots. When the music is input, after a specified time, the sound waves will be read and the amplitude and frequency of the music will be extracted. The diameter and the color of the dots vary with the amplitude and frequency of the music, and the pictures thus they are painted with beautiful colors. (see SOUND TO LIGHT).


THE COMBINATION OF ART & SCIENCE!

As Wilde conveyed in his story, the barrier and combination of art and science still remain worth discussing, so we explored in depth the relationship of art and science in the Human Practices section. One prime barrier of outstanding art and science is the stereotype of defining art as being too selfish and far from the public and science as only about reality with no emotion. We surveyed university students from science and art backgrounds, and to our surprise we found the unconventional idea that the integration of art and science has been well-accepted among the younger generation.


Encouraged by our survey , we interviewed many university professors who are experienced in popularization of both art and science, and also communicated with artists in the AS Research Center. During this investigative interview process we gradually got motivated and had a clearer idea of our story to explore the junction of art and science.(see HUMAN PRACTICES).


More than a hundred years ago, in Wilde’s story, the rose was thrown into the gutter. But today, we UCAS-China iGEMers have picked the rose back up from the gutter, to offer everyone the chance to create their own rose. Inspired by idealism and stirred by imagination, facilitated by scientific gene circuits we develop a practical kit expecting that our work will inaugurate a new era of art and science further inspiring young scientists for future generations.


References

[1]Oscar Wilde, 1995, Happy Prince and Other Tales. Everyman's Library, 96

[2] Fernandez-Rodriguez J, Moser F, Song M, et al. Engineering RGB color vision into Escherichia coli[J]. Nature Chemical Biology, 2017, 13(7):706-708.

[3] Segallshapiro T H, Meyer A J, Ellington A D, et al. A 'resource allocator' for transcription based on a highly fragmented T7 RNA polymerase.[J]. Molecular Systems Biology, 2014, 10(7):742.

[4] http://2010.igem.org/Team:KIT-Kyoto

[5] Cong L, Zhang F. Genome Engineering Using CRISPR-Cas9 System[J]. Methods in Molecular Biology, 2015, 1239(11):197.

[6]Li G, Young K D. Indole production by the tryptophanase TnaA in Escherichia coli is determined by the amount of exogenous tryptophan[J]. Microbiology-sgm, 2013, 159(2):402-410.

[7] http://2014.igem.org/Team:Paris_Bettencourt