Difference between revisions of "Team:UCAS-China/Contributions"

 
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<h1> Team Accomplishments</h1>
 
  
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<h2>CONTRIBUTIONS:<h2>
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<h2>CONTRIBUTIONS</h2>
 
<p>We participated in the InterLab study, which helped to reduce the lab-to-lab variability around the world. We also put forward new ideas of the tandem expression of chromoproteins, to get new colors, which would greatly enrich the colors and the BioBrick parts in the Registry. Then using the RGB system[1] which was central to our project, we characterized the Red-, Green-,Blue light sensors (Cph8, YF1, CcaSR) which had already existed in the registry(BBa_K1886006, BBa_K1053210, BBa_K2598005), by exploring the relationship between the fluorescent intensity with the wavelengths and intensity of input light.  
 
<p>We participated in the InterLab study, which helped to reduce the lab-to-lab variability around the world. We also put forward new ideas of the tandem expression of chromoproteins, to get new colors, which would greatly enrich the colors and the BioBrick parts in the Registry. Then using the RGB system[1] which was central to our project, we characterized the Red-, Green-,Blue light sensors (Cph8, YF1, CcaSR) which had already existed in the registry(BBa_K1886006, BBa_K1053210, BBa_K2598005), by exploring the relationship between the fluorescent intensity with the wavelengths and intensity of input light.  
 
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<h2>INTERLAB<h2>
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<h2>INTERLAB</h2>
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<h4>Summary
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<h4>Summary</h4>
  
 
<p>Interlab is a global collaboration through which the Measurement Committee aim to improve the measurement tools available to both the iGEM community and the synthetic biology community as a whole. This year, the Committee along with teams all over the world aimed to reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD.</p>
 
<p>Interlab is a global collaboration through which the Measurement Committee aim to improve the measurement tools available to both the iGEM community and the synthetic biology community as a whole. This year, the Committee along with teams all over the world aimed to reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD.</p>
  
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<h4>Procedure
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<h4>Procedure</h4>
 
<p>In order to compute the cell count in samples, two orthogonal approaches were exploited. (detailed protocol was provided in https://2018.igem.org/Measurement/InterLab/Plate_Reader)</p>
 
<p>In order to compute the cell count in samples, two orthogonal approaches were exploited. (detailed protocol was provided in https://2018.igem.org/Measurement/InterLab/Plate_Reader)</p>
 
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<h2>Software:<h2>
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<h4>Results<h4>
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<p>Our software was designed by Yun DONG and Shiyang WANG. The software was written by Shiyang WANG.</p>
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<img class="img-responsive img-center" width="600px;" src="https://static.igem.org/mediawiki/2018/a/a2/T--UCAS-China--interlab1.jpg">
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<h5>Fig 1. Particle standard curve of Silica beads for Abs​600  calibration</h5>
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<img class="img-responsive img-center" width="600px;" src="https://static.igem.org/mediawiki/2018/9/91/T--UCAS-China--interlab2.jpg">
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<h5>Fig 2. Fluorescein standard curve for fluorescence calibration</h5>
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<br></center><br>
  
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<h2>Modelling:<h2>
 
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<p>Our modeling work was mainly accomplished by Liangpu Wang, with the help of Shiyang WANG.</p>
 
  
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<h2>Human Practice:<h2>
 
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<p>Yun DONG is the leader of our HP Squad. She accomplished most of the contact and interview work and record every HP activity. Jiachen HU and Yaru TIAN made the educational videos. Yufei SHAN contacted the educational speech in the primary school and some meet-ups. Yuanli GAO, Ziyi ZHAO, Zepeng XU, Yiyi WANG, Liangpu WANG, Yuyan NI, Zhaoying PAN also contributed to the HP work.</p>
 
  
  
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<h2>Wiki:<h2>
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<h2>TANDEM EXPRESSION OF CHROMOPROTEINS</h2>
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<p>Our wiki was designed by Shiyang WANG, Yaru TIAN and Yufei SHAN. The coding work was finished by Yuanli GAO, Shiyang WANG, with the help of Fankang Meng. The paperwork was finished by the joint effort of Yuanli GAO, Yun Dong, Ziyi ZHAO, Zpeng XU, Yiyi WANG, Liangpu WANG, Yuyan NI, Zhaoying PAN, and finally summarized and modified by Yuanli GAO.</p>
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<p>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, 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 to produce more colors from limited chromoproteins, which would greatly enrich the colors and the BioBrick parts in the Registry. (More information, please see <a href= "https://2018.igem.org/Team:UCAS-China/Validated_contribution">Valid Contribution & Proof of Concept</a>)</p>
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<img class="img-responsive img-center" width="600px;" src="https://static.igem.org/mediawiki/2018/a/a5/T--UCAS-China--color4.png">
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<h5>Figure 3. The color spectrum built from chromoproteins and their tandem expression products.</h5>
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<h2>Art work:<h2>
 
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<p>Our art work was accomplished by our excellent art designer Yaru TIAN, Yufei SHAN, while Shiyang WANG participated in the discussion.</p>
 
  
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<h1>Supports<h1>
 
  
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<h2>General support:<h2>
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<h2>CHARACTERIZATION OF SENSORS</h2>
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<p>University of Chinese Academy of Sciences</p>
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<p>College of Life Sciences, University of Chinese Academy of Sciences</p>
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<p>Institute of Biophysics, Chinese Academy of Sciences</p>
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<p>Institute of Microorganism, Chinese Academy of Sciences</p>
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<h2>Project support and advice<h2>
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<p>We used our RGB system to further characterize the red-, green-, blue-light sensors (BBa_K1886006, BBa_K1053210, BBa_K2598005), which had already existed in the registry, because the expression of red-, green-, blue-fluorescent proteins would change according to the excitation degrees of red-, green, blue-sensors. (More information, please see <a href= "https://2018.igem.org/Team:UCAS-China/LightToColor">LIGHT TO COLOR</a>) </p><br>
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<p>Prof. Christopher A Voigt generously </p>
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<p>Prof. Xiaohong LIU generously provided advice on project design and experiment design.</p>
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<img class="img-responsive img-center" width="1000px;" src="https://static.igem.org/mediawiki/2018/b/b2/T--UCAS-China--color12.jpg">
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<p>Prof. Chunbo LOU generously provided advice on project design and experiment design.</p>
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<h5>Figure 4. The flow cytometry results shows the distribution of the cells in fluorescence intensity. BV421 represented the blue-fluorescence intensity, while the FITC-A represented the green-fluorescence intensity and Pe-TxR-A represented the red-fluorescence intensity. The horizontal axis shew the fluorescence intensity, while the vertical axis shew the number of bacteria cells.</h5>
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<p>Prof. Jiangyun Wang generously provided advice on project design and experiment design.</p>
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<p>Prof. Pingsheng LIU accepted our interview and provided advice on project design. </p>
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<p>Prof. Jun YU accepted our interview and provided advice on project design. </p>
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<p>Prof. Christopher A. Voigt generously supported our project and sent us the plasmids pJFR1-5 and the E.coli strain JF1.</p>
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<p>Fankang Meng attended our project defense and gave detailed advice. Zhi SUN gave detailed advice on our project.</p>
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<h2>Fundraising help and advice:<h2>
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<p>College of Life Sciences, University of Chinese Academy of Sciences</p>
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<h2>Lab support:<h2>
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<p>Prof. Jiangyun WANG, IBP, CAS provided his lab for our experiments.</p>
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<p>Prof. Chunbo LOU, IM, CAS provided his lab for our experiments.</p>
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<p>College of Life Sciences, University of Chinese Academy of Sciences, provided a lab for experiments.</p>
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<p>Prof. Xiaohong LIU and Fankang MENG helped in laboratory management.</p>
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<h2>Difficult technique support:<h2>
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<p>Fankang MENG provided important advice and instructions in laboratory.</p>
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<p>Fankang MENG gave consistent help and instructions on FCM analysis.</p>
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<p>Hao GUO gave consistent help and instructions on HPLC analysis.</p>
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<p>Yeqing ZONG gave help and instructions on qPCR analysis.</p>
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<p>Xiangyu JI gave help and instructions on the Crisper-Cas9 technique.</p>
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<h2>Hardware support:<h2>
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<p>Yeqing ZONG gave help and instructions on the design of our hardware.</p>
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<h2>Wiki support:<h2>
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<p>Lewis Sandler proofread our paperwork for wiki.</p>
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<h2>Presentation coaching:<h2>
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<p>Prof. Jiangyun WANG coached us in our presentation.</p>
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<p>Prof. Xiaohong LIU coached us in our presentation.</p>
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<p>Fankang MENG coached us in our presentation.</p>
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<p>Lewis Sandler coached us in our presentation.</p>
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<h2>Human Practice support:<h2>
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<p> Education:</p>
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<p>Anmin Primary School provided the chances of education.</p>
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<p>XingKong volunteering association of UCAS helped us contact schools.</p>
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<p>Prof. Yanmei LIU helped arranged speech in summer camp.</p>
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<p>Jiahui MA helped arranged speech in summer camp.</p>
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<p>Students from UCAS high-school student summer camp supported our speech.</p>
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<p> Collaboration:</p>
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<p>ZJUT-China shared ideas and offered advice in bilateral meet-up.</p>
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<p>BNDS_CHINA shared ideas and offered advice in bilateral meet-up.</p>
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<p>Peking invited us to the meet-up.</p>
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<p>Peking, BIT_China, BNU-China, Tsinghua and OUC-China shared ideas and offered advice in the meet-up held by Peking.</p>
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<p>BNU-China work with us to finish the calendar.</p>
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<p>BNU-China, NKU_CHINA, TJU_China , Tsinghua, TUST_China attended meet-up held by us and shared ideas and offered advice.</p>
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<p>TUST_China co-organized Beijing-Tianjin iGEM Alliance Establishing Conference.</p>
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<p>BNU-China, NKU_CHINA, TJU_China , TUST_China joined us to established Beijing-Tianjin iGEM Alliance.</p>
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<p>TUST_China proposed to make science videos or cartoons in Beijing-Tianjin iGEM Alliance Establishing Conference.</p>
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<p>TJU_China proposed to share HP resources such as chances to collaborate with TV station in Beijing-Tianjin iGEM Alliance Establishing Conference.</p>
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<p>BNU-China proposed to interview experts from fields like biosafety, ethics or law together in Beijing-Tianjin iGEM Alliance Establishing Conference.</p>
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<p>NKU_CHINA proposed to held education activities together and make toys or games relating to synthetic biology in Beijing-Tianjin iGEM Alliance Establishing Conference.</p>
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<p>Prof. Xiaohong LIU attended Beijing-Tianjin iGEM Alliance Establishing Conference and gave advice.</p>
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<p>Fankang MENG attended Beijing-Tianjin iGEM Alliance Establishing Conference and gave advice.</p>
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<p> Interview:</p>
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<p>Ruiling CAI helped prepare the interview and gave advice.</p>
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<p>Baichan SAN accepted our interview and provided advice from artistic perspective.</p>
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<p>Prof. Pingsheng LIU accepted our interview and provided advice on project design.</p>
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<p>Prof. Jun YU accepted our interview and provided advice on project design.</p>
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<p>Art and Science Research Center gave advice and supported us in our artistic design.</p>
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<p> Public engagement: </p>
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<p>China Association for Science and Technology accepted our activity declaration in National Science Day.</p>
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<p>Students from UCAS and BNDS participated in our bacterial painting activity.</p>
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<p>Prof. Lewis Sandler invited us to have a podcast with him.</p>
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<p> Safety:</p>
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<p>Fankang MENG supported us in our biosafety design.</p>
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<p> Integrated:</p>
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<p>Yili Hamujiang, Shujie XIE, Chengyuan YANG helped us in domino video shooting.</p>
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<p>Xiaoding SUN gave advice in domino video shooting.</p>
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<p>Fengzhi Li and Yili Hamujiang helped edit the domino video.</p>
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<p>Institute of Physics CAS held the 3 minutes for science competition.</p>
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<p>Committee of 3 minutes for science competition accepted and approved our video.</p>
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Latest revision as of 02:33, 18 October 2018

CONTRIBUTIONS

We participated in the InterLab study, which helped to reduce the lab-to-lab variability around the world. We also put forward new ideas of the tandem expression of chromoproteins, to get new colors, which would greatly enrich the colors and the BioBrick parts in the Registry. Then using the RGB system[1] which was central to our project, we characterized the Red-, Green-,Blue light sensors (Cph8, YF1, CcaSR) which had already existed in the registry(BBa_K1886006, BBa_K1053210, BBa_K2598005), by exploring the relationship between the fluorescent intensity with the wavelengths and intensity of input light.

INTERLAB

Summary

Interlab is a global collaboration through which the Measurement Committee aim to improve the measurement tools available to both the iGEM community and the synthetic biology community as a whole. This year, the Committee along with teams all over the world aimed to reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or colony-forming units (CFUs) instead of OD.

Procedure

In order to compute the cell count in samples, two orthogonal approaches were exploited. (detailed protocol was provided in https://2018.igem.org/Measurement/InterLab/Plate_Reader)

  • Converting between absorbance of cells to absorbance of a known concentration of beads:

    • In this year’s Measurement Kit, we were provided with a sample containing silica beads that were roughly the same size and shape as a typical E. coli cell. As we knew the concentration of the beads, we could convert absorbance measurements into a universal, standard “equivalent concentration of beads” measurement.

  • Counting colony-forming units (CFUs) from the sample:

    • Since each colony began with a single cell, by counting the colonies cell numbers in certain volume of media could be determined. We were required to determine the number of CFUs in positive and negative control samples in order to compute a conversion factor from absorbance to CFU.

Results

Fig 1. Particle standard curve of Silica beads for Abs​600 calibration


Fig 2. Fluorescein standard curve for fluorescence calibration


TANDEM EXPRESSION OF CHROMOPROTEINS

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, 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 to produce more colors from limited chromoproteins, which would greatly enrich the colors and the BioBrick parts in the Registry. (More information, please see Valid Contribution & Proof of Concept)

Figure 3. The color spectrum built from chromoproteins and their tandem expression products.


CHARACTERIZATION OF SENSORS

We used our RGB system to further characterize the red-, green-, blue-light sensors (BBa_K1886006, BBa_K1053210, BBa_K2598005), which had already existed in the registry, because the expression of red-, green-, blue-fluorescent proteins would change according to the excitation degrees of red-, green, blue-sensors. (More information, please see LIGHT TO COLOR)


Figure 4. The flow cytometry results shows the distribution of the cells in fluorescence intensity. BV421 represented the blue-fluorescence intensity, while the FITC-A represented the green-fluorescence intensity and Pe-TxR-A represented the red-fluorescence intensity. The horizontal axis shew the fluorescence intensity, while the vertical axis shew the number of bacteria cells.