Team:RDFZ-China/Notebook

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  Description Design Modelling InterLab Result Protocol Notebook
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  Biosafety & DIY Bio Public Engagement
• Part
  Basic Composite Improvement Measurement
• Safety
• Valhalla
• Team
  School Members Collaboration Attribution & Acknowledgement
• Achievement

• • What are we facing?
  • Predecessors
  • Project Xscape
  • For Fermentation
  • For Therapy
  • Metabolic Stress
  • DIY Bio and Biosafety
  • Community and Future
  • References

What are we facing?

Biosafety has always been a major concern to the public, to the companies and to the researchers. Doubts and worries were raised just as genetic technology was invented. With the rapid growth of synthetic biology and the iGEM community, and more and more synthetic biology products being built with widely distributed DNA toolkits or the inexpensive DNA synthesis service(Synthetic and Will); we are facing the unprecedented biosafety issue of unwanted leakage of synthetic biology products to the environment that may cause unexpected but likely disastrous problems.

Predecessors

For decades, researchers were striving to build biosafety devices through auxotrophy or external inducive kill switches(Lee et al.); of the latter holins and restriction enzymes are most commonly used. Most failures of the previous devices were due to mutations and evolution of immunity(Moe-Behrens et al.) .

The two major threats of engineered microbes’ leakage are the possible horizontal gene transfer which will lead to the spread of recombinant DNA to the ecosystem, or the fact that engineered bacteria could contaminate or overrun the natural habitat.(Wright et al.))

Project Xscape

Under this circumstance, this year we decided to be a fundamentalist to synthetic biology, using genetic circuits and logic gates to establish biosafety devices which can apply to real-world situations.

Since cell death and lysis mean there is a continual presence of free DNA in the environment, holins, which are most widely used are excluded from our choices, and colicin E2 nucleases (Darmstadt iGEM2016) came into our site. We choose site non-specific nucleases since the entire genome and plasmids needed to be entirely digested to prevent the spread, and we use nucleases from a different family to prevent the possible evolution of nuclease inhibitors. Artificial DNA, RNA, and amino acids are a good solution, but due to its high cost so far, it is not applicable to most of the user.

For fermentation

The first device we build is for the fermentation; we want to execute any escaped engineered bacteria from the fermenter, whether the escape happened accidentally or intentionally. We used two environment factors to monitor the bacteria’s situation: temperature and population density, thet are both high and tunable in the fermenter, so our device will initiate when temperature and density are both low. We used thermal sensitive regulator (NUS iGEM2017)(Piraner et al.) and quorum sensing regulator (MIT iGEM2004) (Canton et al.)as our sensor, with sRNA(Storz et al.) and tetR family repressor PhlF(Glasgow iGEM2015)(Stanton et al.) as the signal inverter. We added an integrase (Peking iGEM2017) controlled by the thermal sensitive regulator which will enable the promoter of a lethal gene to potentially express when temperature rise in the fermenter so that bacteria can survive at the very beginning. Also, we built a model to stimulate the minimum autoinducer required at the beginning of the fermentation, same as the purpose of integrase. This model is for keeping bacteria alive at the very beginning of fermentation. Together they form a NOR gate that will lead to cell death through genome degradation when both temperature and density decrease.

For Therapy

The second device we build is for therapeutic bacteria. The device can carry out noninvasive tracing through ultrasound imaging of the gas vesicle(Shapiro et al.), release the drug (from SHSBNU 2017) controlled by a thermosensitive regulator at nidus by ultrasound tissue heating, and heat to a higher temperature to release nuclease and kill the bacteria after it finishes its mission.

For Metabolic Stress

We applied capacity monitor (Ceroni et al.) to quantify the expression burden of all our systems, and to reduce the metabolic stress, we designed another device for fermentation which used a LuxR repressive promoter (Peking iGEM2011) and cold-regulated 5’UTR region (Ionis Paris 2017). This device only involves one transcriptional regulator, which will be less energy consuming.

DIY bio and Biosafey

Back to the growing and glowing synthetic biology community, despite the current majority doing it on campus, more and more people are starting it at home, and they call themselves Genehacker or DIY biologists. The lack of sufficient training and efficient surveillance will be a time bomb for which we do know that monstrous harmful bioproducts will be made someday in the future, and indeed, it will be a significant threat to the current biosafety basis. Recall our memory to iGEM2009, Peking surveyed DIY bio, almost ten years later, we conducted a similar DIY bio-survey. We tried to order materials for molecular experiments, using the delivery address to our home, and the result was quite shocking that we can buy almost everything for the molecular experiment, from the internet. Then, we went through relevant laws and regulations throughout the world, in which we found no laws related to credit certification and the address certification about the people who book the biology reagent. Most of the laws are about the quality certification and how they would serve the user after they bought this. We interviewed the Director of a center for disease control and prevention. He said that in his experiment with the disease caused by the bacteria leak, vast impacts such as environmental pollution had been observed. and our country has been making great effort towards elimenating such leakage accidents and incidents. He said it is not easy to solve the problem with hard work, rather it needs the cooperation between all the countries. He made an example of 731 army during the second world war two, in which the outbreak of pathogens caused significant physical and social harm. We are still on our way to win the battle, and the effort still needs to be put in.

Community and Future

Also, we hosted two major meeting in Beijing. In a biosafety forum in October, we invited a team leader who runs his high school lab, lab teachers from a university lab, and a former team member from Peking iGEM2009, who participated in their DIY bio investigation ten years ago.

We concluded that the development of DIY bio should be taken seriously, and the permanent way to solve its safety and security concerns is through implanting biosafety awareness into our academic culture. Also, as iGEMers, we should strive to be the considerate and responsible leaders in our community, to ensure the biosafety issue has been taken properly. Another meeting was with biology Olympians all over China, in which we discussed the future of biology community during the meeting, especially with more and more high school iGEM teams coming up in China contrasted with the lack of relevant instruction and education to the students. We came up with the idea of setting up a collaboration between schools to share and overcome difficulties hand in hand. This kind of meeting will be continued after iGEM2018, since the community usually grows fast after every iGEM season.

Hopefully, years later, biosafety awareness and considerations can be seriously taken in communities, laboratory studies, and real-world applications.

References

Canton, Barry, et al. “Refinement and Standardization of Synthetic Biological Parts and Devices.” Nature Biotechnology, vol. 26, no. 7, 2008, pp. 787–93, doi:10.1038/nbt1413.

Ceroni, Francesca, et al. “Quantifying Cellular Capacity Identifies Gene Expression Designs with Reduced Burden.” Nature Methods, vol. 12, no. 5, 2015, pp. 415–18, doi:10.1038/nmeth.3339.

Lee, Jeong Wook, et al. “Next-Generation Biocontainment Systems for Engineered Organisms.” Nature Chemical Biology, Springer US, 2018, p. 1, doi:10.1038/s41589-018-0056-x.

Moe-Behrens, Gerd H. G., et al. “Preparing Synthetic Biology for the World.” Frontiers in Microbiology, vol. 4, no. JAN, 2013, pp. 1–10, doi:10.3389/fmicb.2013.00005.

Piraner, Dan I., et al. “Tunable Thermal Bioswitches for in Vivo Control of Microbial Therapeutics.” Food, Pharmaceutical and Bioengineering Division 2017 - Core Programming Area at the 2017 AIChE Annual Meeting, vol. 2, no. November, Nature Publishing Group, 2017, pp. 695–702, doi:10.1038/nchembio.2233.

Shapiro, Mikhail G., et al. “Biogenic Gas Nanostructures as Ultrasonic Molecular Reporters.” Nature Nanotechnology, vol. 9, no. 4, Nature Publishing Group, 2014, pp. 311–16, doi:10.1038/nnano.2014.32.

Stanton, Brynne C., et al. “Genomic Mining of Prokaryotic Repressors for Orthogonal Logic Gates.” Nature Chemical Biology, vol. 10, no. 2, 2014, pp. 99–105, doi:10.1038/nchembio.1411.

Storz, Gisela, et al. “Regulation by Small RNAs in Bacteria: Expanding Frontiers.” Molecular Cell, vol. 43, no. 6, 2011, pp. 880–91, doi:10.1016/j.molcel.2011.08.022.

Synthetic, How, and Biology Will. “Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves.” Choice Reviews Online, 2013, doi:10.5860/CHOICE.50-3835.

Wright, Oliver, et al. “Building-in Biosafety for Synthetic Biology.” Microbiology (United Kingdom), vol. 159, no. PART7, 2013, pp. 1021–35, doi:10.1099/mic.0.066308-0.