Description

Our amazing journey for iGEM 2022 started with the deep enthusiasm which roots in our instinct since the canopy of stars firstly shining in the eyes of H.sapiens. Throughout the long history, people are always in quest for things beyond, beyond life, nature, and beyond our dear cradle named Earth.

When time moves on to the 21th century, people are blessed with the unprecedented capability and ambition to launch deep space explorations and vast interstellar operations. Aerospace engineering agencies and private companies in many countries and regions are planning related missions. Therefore, it's not a surprise why our team this year is also attracted by this topic.

Among the many technologies which pave the road to outer space, we discover that data storage and transportation is still in a blank. Maybe it's hard to feel, but data and information plays an important role in our day-to-day life. Every morning we wake up to check our work list, listen to the radio and read the edible method on a new package of cereal. Our team, inspired by this trivial details of daily routines, realize that despite the great improvement of fantastic technologies which enable human to travel in space, what also matters is the information storage system. An expedition or even an interstellar migration can never be a reality if the vast amount of information, accumulated throughout history, can't find a right place to be stored along the way, or the pioneers heading beyond will finally propagate into a civilization only with future but not past.

This year, iGEMers from SJTU-BioX-Shanghai decided to make some improvements to address this problem since it is a gradually urgent one because the wildest dream of mankind seems now just around the corner. We decided to use the DNA data storage system to keep the information. Besides, we realized there must be many challenges along the way of transporting, so we give our stored information a spacesuit, which is the engineered spores of B.subtilis, to protect it from the harsh environment of outer space. All these efforts remind us of the human hero 2000 years ago, Odyssey, with his great spirit of resistance and preservation, he struggled against the nature, god and monsters before ultimately becoming a symbolic character standing by the Aegean Sea.

In the process of DNA data storage, information exists in the form of double helix chain of nucleotides. Therefore, how to keep the security and stability of this significant polymer named Deoxyribonucleic acid (DNA) is what counts indeed.

Generally, scientists are concerning storing DNA in vivo as a promising methods. This is a natural idea since life is just the original container of DNA. Storing heterogeneous DNA sequence in vivo can be realized by well-developed bioengineering approaches such as gene transfer with plasmid vectors or DNA recombination. Apart from in vivo storage, on the other hand, scientists are also exploring the possibility of maintaining DNA with inorganic materials such as salt, silicon or in the form of solvent.

However, after reading papers and consulting experts, our team decided to store information in vivo. Storing in vivo may not be the method with biggest density, compared to solid inorganic materials, but it is now widely used when researchers trying to test the stability and fidelity of their DNA information. This is partly due to the ease of later manipulations, such as inserting, transforming and sequencing the DNAs. Also, storing in vivo take the advantage of organisms' repair system, which shall keep the DNA in a stable manner with much less mutations or other damages.

Cosmic environment is always harsh with lots of challenges: microgravity, extreme temperatures, strong radiations and low pressure. Each one of these conditions fatally threaten the existence of life or macromolecular substances such as DNA in the universe. According to NASA, Galactic Cosmic Radiation (GCR)is one of the most dangerous factors defecting lives in the space for it can cause DNA damage especially double strands break (DSB) in the body of any organism, including our astronauts and impair their self-repair mechanisms which finally leads to potential health risk. Other damages caused by radiations maybe the synthesis of photoproducts and the byproduct of ROS, which can both hinder the stability of DNA or even result in the negative mutations inside cells.

A eukaryote named water bear is famous for its viability
in the space. Experiments carried out indicate that this tiny
animal can survive under conditions without oxygen and heat for more
than 100 days [3]. Their astonishing resistances have attracted many scientists to unravel the mechanisms underlying. And one of the findings is a group of species-specific proteins, TSP(Taedigrade Specific Protein), which includes Dsup (damage suppressor), allows the animal to survive many abiotic factors like freezing and heat. Studies on human cell line and E.coli have proved that, when expressed in transgenic organisms, dsup proteins could still paly a significant role in protecting the genome against radiations, though the detailed mechanisms are still unclear.

On the other hand, if we dismiss the special water bear and pay attention to various organisms around us, even ourselves, we shall discover a very common mechanism for creatures on earth use to protect themselves from ultraviolet or absorb electromagnetic radiation to catch heat. And that is melanin. Melanin is a bio-pigment and responsible for radiation-consuming. Different organisms produce different kinds of melanin from substrate with the help of different tyrosinases. For example, RelA is the gene responsible for coding tyrosinase in Bacillus megaterium.

In addition to the radiation-resistant modifications mentioned above, we also look for the possible organisms to serve as a potential spacesuit to our information DNAs. Organisms once be assessed were pollen of the famous lily named Paris japonica which is reckoned to contain the biggest genome. And the diatom, an adorable little creature belonging to photosynthesising algae and owning a siliceous skeleton, gaining insprations from some work that attempted to encapsulate DNA into silicon dioxide.

However, B.subtilis and its amazing endospores were finally be chosen, and the following tells the reasons for their standing out.

Firstly, B.subtilis is the only bacterium-based host able to clone giant DNA above 1000 kbp, which guarantees the insertion of large information content into its genome as we manage to carry about large pieces of information encoded in DNA along the journey in space.

Secondly, as one of the well-characterized model organism, B.subtilis is safe for us operate and easy to handle. Abundant protocols for some major operations based on B.subtilis, including bacterial culture, electrotransfermation, sporulation and purification, can be found in others' articles or previous iGEM teams' protocols, which provide us with lots of convenience in our work.

Most importantly, B.subtilis produce endospores. An endospore is a dormant, tough, and non-reproductive structure produced by some bacteria. They can be reckoned as the seed of bacteria produced in negative environment to tolerate the damage factors and germinate when conditions allow. Spores are famous for their resistance to harsh environment and strong vitality, which is also the reason why iGEM committee ask for a check-in form for the spore-producing fungi! (visit our safety page to see how we address it!). From the description above, it’s easily to draw a conclusion that spores, if being used as our container, shall naturally offer a protective function, distinguishing it from other forms of organisms.

In the era of mankind striding towards the deep space, 18 iGEMers from 2022 SJTU-BioX-Shanghai are exploring the intriguing combination of DNA data storage technology and the novel application scenario of interstellar communication with the help of synthetic biology!

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