Team:HIT-Harbin/Humanpractices

         This year, we aim at enhancing our efforts for the publicity of synthetic boilogy. At the mean time, we actively helped the other two universities in Heilongjiang Province on the experience of iGem.

Since HIT is an engineering university which is strict in qualifications for graduates and makes every endeavor in educating students, we have solid foundation of engineering. Thus, our publicity contributes to the more promising development of the idea which combines synthetic biology together with engineering, and attracts more scholars to engage in relative researches so that guarantee the future development of synthetic biology. In order to reach our goals, our team successfully organized a preliminary at HIT and held the meet-up during summer vacation where we, joined by Northeast Agricultural University and Northeast Forestry University, discussed the design and progress of our projects. We also invited Dr. Andrew Harrison and many other professors (for the whole name list click here) to give us lectures on biology and calculation. What’s more, in this semester, bisides the course “Simulation, Design and Implementation of Biologic Circuits based on BioBricks” by Pro. Dechang Xu, we started a new course - “Synthetic Biology” where Pro. Mario instructs our students what is synthetic biology and how to do modeling. In the aspect of online service, we developed a platform via wechat so that we have an access to discuss about safety issues with others. Besides, we set up a social network site especially for scientists which do goods to the exchanging of materials and communication. With all our efforts, we have already whetted an upsurge in researches of synthetic biology.

1.       Preliminary

In order to strengthen the effects of synthetic biology at HIT and make our students get to know biology, meanwhile recruit fresh staffs, after 2 months’ preparation and discussion supported by School of Undergraduate and Office of Academic Affairs, we held the great preliminary to select our new teammates. Participants added up to about 60 students, including the students from School of Live Science, School of Food Science and Engineering, School of Municipal and Environment Engineering and School of Astronautics. The competition is divided into two parts, namely, experimental competition and modeling competition. The former asks our participants to assemble E.coli that can illuminate. The latter contains three modeling problems about biology. In the end, we awarded four gold, three silver and five bronze. All of the procedures were publicized on the website of HIT so that synthetic biology and iGem can gain more population.

2． Meet up

During the summer vacation, iGem advocates more communication and interaction between teams. Though we did not register a meet-up officially, we held a meet up in a small scale with another two local universities. We invited more than 50 professors and students from Northeast Agricultural University and Northeast Forestry University. Our three teams introduced each of our projects and progresses. Meanwhile, we invited some professors who are versed in biology and modeling to inform us the latest development of technology. The meet-up lasted for a whole day long. We also prepared lunch, dinner and snacks for all participants. We are sure that everybody enjoyed that day. The meet-up came to a termination in a harmonious atmosphere.

3.       Two new courses

Bisides the course “Simulation, Design and Implementation of Biologic Circuits based on BioBricks” by Pro. Dechang Xu, we started a new course - “Synthetic Biology” where Pro. Mario instructs our students what is synthetic biology and how to do modeling.

The course taught by Pro. Xu focuses on practical application, which contains modeling and experiments.

Pro. Xu’s course underlines practical application, which is divided into modeling section and experiments section. For the modeling section, typically it takes two classes to introduce the models and simulations for systematic biology, together with system analysis and standard of systematic biology. This course also requires students to choose a kind of valuable microorganism to do genome-scale metabolic network modeling as a project.

For the experiment section, led by instructor Dai, those students who had never entered biology laboratory will get familiar with the operations with the basic equipment. After that, they will be asked to finish a project individually where green fluorescent protein is expected to express in E.coli.

This course has already been opened for six semesters up till now. Skills about synthetic biology have been imparted to more than a hundred students from a variety of Schools.

The course taught by Pro. Mario focuses on the accumulation of theory and basic knowledge, which explain the theories about experiments and modeling of synthetic biology in detail.

Following is the syllabus:

•        Foundational ideas of Synthetic Biology. Examples of gene circuits.

•        Modeling synthetic circuits: Mass-action kinetics, Hill-functions, and Michaelis-Menten kinetics.

•        Modeling stochastic processes: an introduction.

•        The Chemical Master Equation.

•        Modeling large networks: Rule-based modeling approach.

•        Circuit analysis: steady-state and circuit stability; data fitting; optimization of parameter values; sensitivity analysis; model reduction; robustness.

•        Understanding robustness: the bacterial chemotaxis.

•        Circuit motifs: constitutive gene expression; negative autoregulation; positive autoregulation; oscillatory systems; Boolean gates (transcription and translation regulation); Feed-Forward Loops; gene cascades; cell consortia; delay ODEs; spatial modeling; pathway re-engineering.

•        Wet-lab techniques: general procedure to construct synthetic circuits in yeast cells; shuttle vectors; PCR; DNA isothermal assembly; plasmid digestion and DNA ligation; the BioBrick DNA composition method; yeast cell transformation; circuit read-out measurements: FACS, real-time PCR, Western Blotting.