Difference between revisions of "Team:NDNF China/Description"

Background

New materials, new fuels, new therapies; new attire, new food and new ways of living.

Ever since the dawning of the synbio era near two decades ago, we have all been witness to its world-changing potential:

lab grown meat has offered new insight into providing eco-friendly and cruelty-free sources of protein; engineered bacteria that are able to synthesize artificial leather and dyes have the potential to overturn the fashion industry; more recent advances in bio-sensing and processing are producing solutions to real world problems such as pollution and global warming......

Figure 1: six commercially-available products that are changing our world by Chris Voigt (MIT)[1].

There is no doubt that innovations in this field will continue to surge, but for microorganisms engineered to function beyond laboratories, some obstacles are holding them back.

What is and what could be

Through reviewing related background research that have previously been conducted by scientists working to tackle highly relevant aspects of the problem as well as taking our thoughts into further discussion with experts in the field (For more details please click the button below), a more thorough analysis of the situation came into being.

Current setbacks

We have now identified three main setbacks of synthetic biology applications targeted beyond labs:

1. Social and technical constraints regarding biosafety;

2. Highly fluctuative environments outside of labs negatively affect the performance of engineered living machines;

3. Lack of effective tracing and control in the occurrence of an escape.

A more detailed explanation is as follows:

Biosafety related constraints

It is inevitable that advances in technologies will raise safety concerns. Yet, in the field of biological sciences, this may be especially prominent due to the relative uncontrollability of engineered life forms coupled with the highly interconnected nature of ecosystems. For example, strains designed to sense heavy metal ions could have enormous benefits, both environmental and economical. However, should they be unintentionally released and directly contact water bodies, such strains could be challenging to control and potentially lead to cascading consequences. In the case of using E.coli strains as chassis, infections or more severe conditions could result in populations after accidental consumption of polluted water. Concerns about similar events becoming a reality have planted strong opposition against the deliberate release of genetically modified microorganisms into the wild, though under good intentions.

Adding on to social constraints, meeting the demand for a platform enabling the containment of the strains while encouraging their robust function is far from being sufficiently met.

Fluctuative environmental factors

Functioning in the wild has been no easy task for the strains compared with the "safe and cozy" lab environment in petri dishes or test-tubes.

Taking E.coli designed for drug delivery as an example, oral intake unavoidably involves passage through the stomach, which is highly acidic. Without external protection, it would be nearly impossible for their viability to be retained, posing challenges for successful probiotic delivery.

In general, when in harsh conditions such as heat, and extreme pH, even the survival of engineered strains has become challenging, let alone being able to carry out their synthetic function.

Tracing and control

As we all have experienced during the recent COVID-19 outbreak, biology "respects" no boundaries. Likewise, without appropriate elimination methods, once unleashed to the environment, engineered microorganisms would likely proliferate out of control. Current strategies often involve the design of genetic kill switches. While guaranteeing an acceptable level of control, it lacks measures in tracing the origin of the escape and records of its development. Without appropriate circumvention, this may even potentially cause difficulties in jurisdictional issues. (as we have discovered during our human practice)

Our solution

The complexity of the situation inspired NDNF_China on taking a more combinative approach.

The scientific side

Figure 2: A diagram showing design of Hidro system.

In addressing the problem of biocontainment and providing a robust environment, we have adopted physical measures. Hydrogel materials emerged as a suitable selection due to their considerably "innovative" properties and existing applications across many fields.

The outer shell of Hidro is a hybrid hydrogel consisting of ionically crosslinked alginate and covalently cross-linked acrylamide. During stretching, the polyacrylamide network remains intact, whereas the ionic linking in the alginate network unzips progressively and provides the basis for later reformation. The combination of the two networks confers mechanical toughness for the entire bead. In addition, with pores no larger than 50 nanometers, containment of microbes is guaranteed, whereas high permeability towards analytes that are being sensed and molecules secreted is still retained.

The inner core of Hidro is alginate-based and also contains nutrients supporting microbial growth and survival. Not only is it highly biocompatible, it is also able to remain relatively stable and robust under a certain range of external pressure. By working in unison with the external layer mentioned above, the chemical and mechanical properties of the Hidro system can be significantly improved, offering a suitable environment for the strains even under extreme pH levels, high temperatures and drought.

Further, to build a Tracing and Control system, we have integrated a customizable DNA barcode into our strains, as well as a customizable genetic kill switch. The escaped bacteria can be tracked using CRISPR-Cas12a nucleic acid detection technology, and could be killed by user-defined chemical molecules.

[To see how to make Hidro and its performance, please see: Protocols and Proof-Of-Concept]

Also, feel free to explore our Proposed Implementation webpage for more details on how Hidro can be used.

The social side

Figure 3: A complete feedbacks-based human practices loop in NDNF_China.

We have also involved ourselves in the social aspect of taking engineered organisms beyond labs. In fact, human practice activities have been an integral propellant in achieving our aims. From surveys collected during initial stages, we discovered that there still is a knowledge gap among non-scientific members of public on the significance of biosafety, but that they were willing to learn more; through reaching out to other iGEM teams and contacting experts in the field helped us to further grasp the current situation of implementing synbio beyond laboratories; sharing our ideas with related industries and our peers, as well as to even broader groups also brought unexpected rewards. During the course of the project, we have also realised that a more proactive approach should be taken in regulating biotechnologies and related products, which led to our law proposals on improving the current biosafety regulations of China.

Click here to learn more

It was through these activities that we gradually understood: resolving technical constraints is just a starting point, and despite the road ahead being long and somewhat challenging, effective engagement with different communities could pave the way.

Future perspectives

Though Hidro will not be able to turn back the hands of time and retract biosafety accidents as in fictitious scenes presented in our promotion video, we believe it is promising that in future, engineered organisms will be able to function in real world scenarios in a safe, robust and traceable manner. And with more emphasis put not on "what is" but "what could be", their potential could possibly be further enhanced.

We sincerely hope that with Hidro and other similar platforms, the path of synbio saying hi to the world will be a widely celebrated one!!!

References

1. Voigt, C. A. Synthetic biology 2020–2030: six commercially-available products that are changing our world. Nat Commun 11, 6379 (2020).

2. Kwok, R. Five hard truths for synthetic biology. Nature 463, 288–290 (2010).

3. Li, J., Zhao, H., Zheng, L. & An, W. Advances in Synthetic Biology and Biosafety Governance. Frontiers Bioeng Biotechnology 9, 598087 (2021).

4. Bernhardt, J. R., O’Connor, M. I., Sunday, J. M. & Gonzalez, A. Life in fluctuating environments. Philosophical Transactions Royal Soc B 375, 20190454 (2020).

5. Hu, B., Guo, H., Zhou, P. & Shi, Z.-L. Characteristics of SARS-CoV-2 and COVID-19. Nat Rev Microbiol 19, 141–154 (2021).

6. Tang, T.-C. et al. Hydrogel-based biocontainment of bacteria for continuous sensing and computation. Nat Chem Biol 1–8 (2021) doi:10.1038/s41589-021-00779-6.