Team:HZAU-China/Detailed-Attributions

attribution

Team member list
Main
Description
Design
Proof
Demonstrate
Measurement
Experiments-chassis_integration
Experiments-Light_control
Experiments-Motility
Model
Software
Hardware
Part

Detailed-Attributions

Team member list
Name	Major	Grade
Wen Wang	bioscience	Junior
Kangjian Hua	bioinformatics	Junior
Jin Xiao	bioinformatics	Junior
Bocheng Cheng	bioinformatics	Junior
Xinran Zhao	Bioengineering	Junior
Zewen Ding	Bioengineering	sophomore
Wenqi Huang	Biotechnology	sophomore
Jun Li	bioscience	sophomore
Pan Chu	bioengineering	sophomore
Weitong Zhang	bioinformatics	sophomore
Haimen Li	bioscience	sophomore
Boyao Zhang	Biotechnology	Junior
Qiqi Xiong	Biotechnology	freshmen
Yichi Zhang	bioinformatics	freshmen
Luyao Zhang	Landscape and gardening	freshmen
Wentao Yu	Biotechnology	freshmen
Anqi Zhou	Biotechnology	freshmen
Zhujun Zia	Bioengineering	freshmen
Tengteng Wang	Bioengineering	sophomore
Kening Chen	Biotechnology	sophomore
Yang Bai	Automation	sophomore
Zhihao Li	Automation	sophomore

https://2016.igem.org/Team:HZAU-China

In the homepage

Figures are designed by Kening Chen.
Animation Video (Designed by Kangjian Hua; Narrated by Xinran Zhao)

https://2016.igem.org/Team:HZAU-China/Description

In Description page

Figure 1. Augmented reality. (Designed by Kening Chen);
Figure 2. Welcome to BioPaFiAR! (Designed by Tengteng Wang);
Figure 3. Bio-pattern formation in Nature. (Designed by Tengteng Wang);
Figure 4. The "band-detect" gene networks. (Quoted from S. Basu, Y. Gerchman, C. H. Collins, F. H. Arnold, R. Weiss, A synthetic multicellular system for programmed pattern formation. Nature 434, 1130-1134. (2005);
Figure 5. Density-sensing and Motility-control. (Quoted from Chenli liu, et al. Sequential Establishment of Stripe Patterns in an Expanding Cell Population. Science 334, 238. (2011));
Figure 6. The mechanisms of bacteria motility and the role of protein cheZ. (Designed by Pan Chu, Tengteng Wang);
Figure 7. The working mechanisms of the TCS circuits. (Designed by Pan Chu, Tengteng Wang (inspired by: E. J. Olson, L. A. Hartsough, B. P. Landry, R. Shroff, J. J. Tabor, Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals. Nature Methods 11, 449-455. (2014));
Figure 8. The working mechanisms of Riboswitches. (Designed by Pan Chu)
Figure 9. The hardware devices to quantify light-switchable TCS. (Photo taken by Pan Chu);
Figure 10. Illustration for the BioPaFiAR hardware device. (Photo taken by Pan Chu);
Figure 11. The software GUIs. (Designed by Kangjian Hua, Bocheng Chen).

https://2016.igem.org/Team:HZAU-China/Design

In Design page

Figure 1. Overall Design Circuit. (Designed by Tengteng Wang, Kangjian Hua);
Figure 2. “Traffic Light Circuit”. (Designed by Tengteng Wang, Pan Chu);
Figure 3. (Designed by Tengteng Wang, Pan Chu);
Figure 4. CcaS/CcaR TCS. (Designed by Tengteng Wang, Pan Chu);
Figure 5. (Designed by Tengteng Wang, Pan Chu);
Figure 5. Schematic of riboswitches. (Designed by Pan Chu, Figure 5.b was quoted from H. Zhou et al., Characterization of a natural triple-tandem c-di-GMP riboswitch and application of the riboswitch-based dual-fluorescence reporter. Sci Rep 6, 20871 (2016).).

https://2016.igem.org/Team:HZAU-China/Proof

In Proof page

Figure 1. Riboswitches modeling. (Designed by Bocheng cheng, Pan Chu);
Figure 2. The kinetics of cheZ. (Designed by Bocheng cheng, Pan Chu);
Figure 3. Motility modeling. (Designed by Bocheng cheng, Kangjian Hua);
Figure 4. Proof of the Bacterial Motility Device. (This experiment was designed and finished by Wen Wang , Zewen Ding and Wenqi Huang);
Figure 5. Proof of the Light-Switchable TCS Device. (This experiment was designed and finished by Boyao Zhang and Jun Li);
Figure 6. Optimization of the CcaS-CcaR System. (This experiment was designed and finished by Boyao Zhang and Jun Li);
Figure 7. Proof of the Riboswitch Device. (This experiment was designed and finished by Pan Chu and Anqi Zhou);
Figure 8. The differences of motility between riboswitch(+) and riboswitch(-). (This experiment was designed and finished by Pan Chu and Wenqi Huang).

https://2016.igem.org/Team:HZAU-China/Demonstrate

In Demonstration page

Movie 1. (Film: Kangjian Hua ; performance: Boyao Zhang)

https://2016.igem.org/Team:HZAU-China/Measurement

In Measure page

Figure 1.Quantification on sfGFP fluorescence in PCB optimization. (This experiment was designed and finished by Boyao Zhang and Jun Li);
Figure 2. Fluorescence assay in different chassis strain B,C,D. (This experiment was designed and finished by Boyao Zhang and Jun Li);
Figure 3. Characterization in PcpcG2 optimization. (This experiment was designed and finished by Boyao Zhang and Jun Li);
Figure 4. Phenotype of pleD expression. (This experiment was designed and finished by Pan Chu);
Figure 5. Quantification on riboswitches. (This experiment was designed and finished by Pan Chu and Anqi Zhou);
Figure 6. cheZ-GFP overlapping extension fragment. (This experiment was designed and finished by Wen Wang , Zewen Ding and Wenqi Huang);
Figure 7. Quantification on function of CheZ in swarming assay. (This experiment was designed and finished by Wen Wang , Zewen Ding and Wenqi Huang);
Figure 8. Quantification on relationship between promoter strength and swarming ability. (This experiment was designed and finished by Wen Wang , Zewen Ding and Wenqi Huang);
Figure 9. Normalization of swarming rate. (This experiment was designed and finished by Wen Wang , Zewen Ding and Wenqi Huang)

https://2016.igem.org/Team:HZAU-China/Experiments-chassis_integration

In this page

Figure 1. Mechanism of λ Red recombination. (Design: Boyao Zhang; Drawn by: Tengteng Wang );
Figure 2. Mechanism of Cre/Lox recombination. (Design: Boyao Zhang; Drawn by: Tengteng Wang );
Figure3. Plasmid: pSC101-BAD-gbaA-tet, pR6K-lox-kan-lox-new, pSC101-BAD-Cre-tet (Design: Boyao Zhang; Drawn by: Tengteng Wang );
Figure 4. EnvZ gene disruption. ( This experiment was designed and finished by Boyao Zhang and Pan Chu);
Figure 5. Resistance test on resistance gene elimination, Kan (upper plates),Tet (lower plates). ( This experiment was designed and finished by Boyao Zhang and Pan Chu);
Figure 6. PCR verification of resistant gene elimination. (This experiment was designed and finished by Boyao Zhang and Pan Chu).

https://2016.igem.org/Team:HZAU-China/Experiments-Light_control

In this page

Figure 1. Mechanism of λ Red recombination (quote from J. J. Tabor, A. Levskaya, C. A. Voigt, Multichromatic control of gene expression in Escherichia coli. Journal of molecular biology 405, 315-324 (2011));
Table 1. Strains used in this work (Tabulated by: Jun Li and Boyao Zhang);
Figure 2. (Design: Boyao Zhang; Drawn by: Tengteng Wang );
Table 2. Plasmids used in this study. (Tabulated by: Jun Li and Boyao Zhang);
Table 3. Plasmid assembly detailed descriptions. (Tabulated by: Jun Li and Boyao Zhang);
Table 4. The protocol of Multi-Mode Reader (Tabulated by: Jun Li and Boyao Zhang);
Figure 3. Measurement on sfGFP fluorescence in PCB optimization. (This experiment was designed and finished by Boyao Zhang and Jun Li);
Figure 4. Fluorescence assay in different chassis strain B,C,D. (This experiment was designed and finished by Boyao Zhang and Jun Li);
Figure 5. Measurement on fluorescence in PcpcG2 optimization. (This experiment was designed and finished by Boyao Zhang and Jun Li)

https://2016.igem.org/Team:HZAU-China/Experiments-Motility

In this page

Figure 1. Mechanism of motility. (quote from : S. Schulmeister, M. Ruttorf, S. Thiem, D. Kentner, D. Lebiedz, V. Sourjik, Protein exchange dynamics at chemoreceptor clusters in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 105, 6403-6408 (2008));
Figure 2. (This experiment was designed and finished by Wen Wang , Zewen Ding and Wenqi Huang);
Figure 3. CL1 means the E.coli K12 mg1655 cheZ lacking strain as the negative control. CK means CL1 strain transformed with BBa_K819010. CZ means CL1 transformed with our constructed Biobrick, BBa_K2012007. (This experiment was designed and finished by Wen Wang , Zewen Ding and Wenqi Huang);
Figure 4. (This experiment was designed and finished by Wen Wang , Zewen Ding and Wenqi Huang);
Figure 5. (This experiment was designed and finished by Wen Wang , Zewen Ding and Wenqi Huang);
Figure 1. Mechanism of riboswitch. (Design and Draw: Pan Chu);
Figure 2. PSB4A5-735F & peT-Ptac-pleD (Design: Pan Chu; Draw: Tengteng Wang);
Figure 3. Phenotype of pleD expression (This experiment was designed and finished by Pan Chu);
(Note: This work was done by our team member; the protocol referred to H. Zhou et al., Characterization of a natural triple-tandem c-di-GMP riboswitch and application of the riboswitch-based dual-fluorescence reporter. Sci Rep 6, 20871 (2016); but there are some differences between our protocol and the protocol in that paper.)
Figure 4. Characterization of riboswitch. (This experiment was designed and finished by Pan Chu, Anqi Zou and Luyao Zhang);
(Note: This work was done by our team member; we re-construction all plasmids. assembly method: Bio-brick assembly.)

https://2016.igem.org/Team:HZAU-China/Model

In this page

Figure 1. Gene circuit. (Designed by Pan Chu, Tengteng Wang (imitate E. J. Olson, L. A. Hartsough, B. P. Landry, R. Shroff, J. J. Tabor, Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals. Nature Methods 11, 449-455. (2014));
Figure 2. Green light. (Bocheng Cheng);
Figure 3. Red light. (Bocheng Cheng);
Figure 4. The concentration of CheZ. (Bocheng Cheng);
Figure 5. The 2D plane of bacteria diffusion. (Bocheng Cheng);
Movie 1. Visualization for the R-M model of bacteria diffusion.(Kangjian Hua);
Figure 6. Pikachu,a famous cartoon character. (Kangjian Hua);
Movie 2. Visualization for the R-M model of bacteria diffusion in a restricted area using Pikachu as the target pattern. (Kangjian Hua);
Movie 3. Visualization for the R-M model of bacteria diffusion with dynamic regulation using Pikachu as the target pattern. (Kangjian Hua);
Figure 7. Moore neighbors. (Bocheng Cheng);
Figure 8. Breeding process. (Bocheng Cheng);
Figure 9. CA program. (Bocheng Cheng);

https://2016.igem.org/Team:HZAU-China/Software

In this page

Figure 1. Colony radius calculation software. (Kangjian Hua);
Figure 2. Motility dynamic model software. (Kangjian Hua);
Figure 3. The GUI for the colony motion simulation software. (Bocheng Cheng);
Movie 1. Hardware device demo. (Kangjian Hua);
Figure 4. Illustration for the working process of the BioPaFiAR software. (Bocheng Cheng and Kangjian Hua)

https://2016.igem.org/Team:HZAU-China/Hardware

In this page

Figure 1. Modules in the BioPaFiAR device. (Pan Chu);
Figure 2. The flowchart for the temperature control software.(Drawn by: Kangjian Hua);
Figure 3. The BioPaFiAR driver program test with a piece of paper as the target pattern. ( Bocheng Cheng and Kangjian Hua);
Figure 4. The BioPaFiAR driver program test with a real bacteria colony. (Kangjian Hua);
Movie 1. (Film: Kangjian Hua ; performance: Boyao Zhang);
Figure 5. The inside demo of the BioPaFiAR hardware device (Kangjian Hua);
Figure 6. Parts and finished product of the LPA device. (Shot by: Pan Chu);
Figure 7. Schematic of circuit board microcontroller (Quote from: K. Gerhardt et al., An open-hardware platform for optogenetics and photobiology. bioRxiv, 055053. (2016) );
Figure 8. The LED driver stage can be controlled by microcontroller to regulate the intensity of LEDs. (Quote from: K. Gerhardt et al., An open-hardware platform for optogenetics and photobiology. bioRxiv, 055053. (2016) );
Figure 9. The final PCB plate printed as described above. This is our DIY PCB plate. (Shot by: Bocheng Cheng);
Figure 10.a (Quote from: K. Gerhardt et al., An open-hardware platform for optogenetics and photobiology. bioRxiv, 055053. (2016) ) Figure 10.b (Shot by: Kanjian Hua);
Figure 11. (Bocheng Chen);
Figure 12. Different situations when compiling the firmware. (Quote from: K. Gerhardt et al., An open-hardware platform for optogenetics and photobiology. bioRxiv, 055053. (2016) );
Figure 13. The file was downloaded from http://iris.taborlab.rice.edu;
Figure 14. (This experiment was designed and finished by Jun Li)

http://parts.igem.org/Part:BBa_K2012000

Figure 1 (Designed and Drawn by: Pan Chu);
Figure 2. Schematic of riboswitches (Designed and Drawn by: Pan Chu);
Figure 3. Characterization of Riboswitch (This experiment was designed and finished by Pan Chu)

http://parts.igem.org/Part:BBa_K2012013

Figure 1, 2 & 3 (This experiment was designed and finished by Wen Wang , Zewen Ding and Wenqi Huang)

http://parts.igem.org/Part:BBa_K2012002

Figure 1. (This experiment was designed and finished by Pan Chu)

http://parts.igem.org/Part:BBa_K2012007

Figure 1, 2 (This experiment was designed and finished by Wen Wang , Zewen Ding and Wenqi Huang)

http://parts.igem.org/Part:BBa_K2012015

Figure 1. (This experiment was designed and finished by Jun Li and Boyao Zhang)

http://parts.igem.org/Part:BBa_K2012023

Figure 1. (This experiment was designed and finished by Wen Wang , Zewen Ding and Wenqi Huang)