Team NCSU created the education drive, ‘Synthetic Biology in Space’ in collaboration with Genes in Space (GiS) and minipcr bio. We created a six week mentorship program for students at the local middle and high school levels who were interested in participating in the Genes in space competition or were interested in starting an iGEM team.
In this drive, we have partnered with ‘Genes in Space’ and ‘minipcr’ to provide an interactive and hands-on learning experience. Genes in Space runs an annual contest challenging students to design DNA experiments that can be performed in space. minipcr produces portable tools for molecular biology, enabling genetic experimentation outside traditional lab settings. With their expertise, we equip participants with practical skills in synthetic biology techniques and imagine real-world space applications.
Through informative sessions, hands-on activities using minipcr's portable lab equipment, and discussions, this drive aimed to provide participants with a basic understanding of synthetic biology and spark ideas for how it could aid future space missions.
We had a hard time finding comprehensive material to begin framing the course, and have created the below primer on Synbio and its applications in Space travel:
What is Synthetic biology?
Synthetic biology (SynBio) involves redesigning or building novel biological systems from scratch to perform specific functions, relying on engineering principles like standardization, modularity, and design-build-test cycles (Wang et. al, 2012). Biological parts encompass all the molecular tools that nature has made: from single-stranded RNA to DNA polymerases and entire organs. The engineering principles are methodologies and general goals to strive for when designing practical solutions to a problem.
Synthetic Biology (Synbio) is the practice of solving a problem using engineering principles and biological parts. Synbio requires us to combine both of these concepts to reverse engineer natural systems or build something from scratch (Wang et. al, 2012).
Synbio engineering principles are listed below:
▪ Problem-first: Tailor all approaches for the unique biology of the problem at hand.
▪ Modular parts: Biology is structurally made of functional parts (protein domains, receptors, adapters, transducers, etc.). How can you separate how these functional parts are naturally put together and recombine them into something new?
▪ Orthogonality: Stand alone engineering systems should not intervene with natural functions of the cell.
▪ Logical control: Predictable systems with specific outputs for specific inputs . Mathematical modeling for the intended system should be considered.
▪ Design for scale: Engineered solutions should be robust enough to be manufacturable and distributable on a large scale.
▪ Simplicity: A lower number of predictable parts can reduce complexity and engineering of the overall system.
▪ Test and iterate: A good design has to be readjusted a couple of times with the necessary variables in mind.
Keeping the central dogma of biology in mind, the basic units
Potential applications include microbial production of chemicals, pharmaceuticals, biofuels,
bioremediation, biosensors, and aiding regeneration and tissue engineering.
How can Synthetic Biology be utilized in Space?
Space agencies and private companies have ambitious goals of establishing permanent settlements on the Moon and sending crewed missions to Mars in the coming decades. To achieve the dream of sustained human presence beyond Earth's orbit, it is pivotal to develop technologies that enable independence from terrestrial resources and closed-loop utilization of materials. This is where synthetic biology can play a transformational role.
((Figure reproduced with permission from Koehle et. al, 2023 using the Creative Commons International license 4.0))
By reprogramming microbes at the genetic level, synthetic biology tools can be customized (Santomartino et. al, 2023) to perform functions from recycling air and waste to producing food, energy and medicines on demand. Some key applications and challenges include:
((Figure reproduced with permission from Santomartino et. al, 2023 using the Creative Commons International license 4.0))
Space medicine and human health are critical issues. Preventing disease and maintaining microbiome balance is difficult away from Earth's biosphere. Manufacturing synthetic drugs through synthetic biology can help combat illness, radiation damage from space travel, and effects of reduced gravity (Menezes et. al, 2015). For example, drugs that stimulate white blood cell production may counteract radiation exposure. Developing self-healing, radiation-resistant materials using synthetic biology can provide protective clothing and shielding to keep astronauts safe (Santomartino et. al, 2023).
((Figure reproduced with permission from Turroni et. al, 2020 using the Creative Commons International license 4.0))
Life support systems are essential for survival in space. Synthetic biology can improve biological waste management, especially for wastewater treatment. Incorporating engineered microbes into habitat walls could recycle carbon dioxide into oxygen while providing radiation shielding. Synthetic biology can also produce nutritious, flavorful biomass from inedible feedstocks to supplement astronaut nutrition (Santomartino et. al, 2023). Microbial fuel cells fed by wastewater could generate electricity while removing organics and nutrients (Menezes et. al, 2015).
Resource utilization is a key challenge on long missions. Synthetic microbes adapted to extreme environments can harness waste, volatiles, and minerals unavailable to humans. Wastes like metabolic, packaging, and trash materials can be digested to produce feedstocks. Volatiles like carbon dioxide and nitrogen extracted from life support systems and planetary atmospheres provide raw materials for manufacturing (Santomartino et. al, 2023). Biomining techniques can extract minerals and metals from extraterrestrial soils and rocks. The resulting feedstocks enable manufacturing of goods needed in space (Santomartino et. al, 2023).
Manufacturing food, fuel, building materials and more in situ reduces payload mass and cost. Synthetic biology can produce adhesives to bind regolith into bricks, biocement to build habitats, and biopolymer feedstocks for 3D printing (Menezes et. al, 2015). Metabolic engineering of microbes can yield fuels for energy and propulsion systems. Synthetic organisms can also produce materials needed for abiotic manufacturing approaches on site, lowering launch mass (Tesei et. al, 2015).
If terraforming is pursued to engineer habitable worlds, synthetic biology can help create enclosed habitats. Carefully designed microbes could establish a self-contained biosphere completing carbon, nitrogen and other cycles (Menezes et. al, 2015). This mimics Earth's global ecosystem within settlements protected from harsh exterior environments. Robust symbiotic communities are needed that thrive on available resources.
((Figure reproduced with permission from Santomartino et. al, 2023. TRL 6 and above are advanced technologies.Using the Creative Commons International license 4.0))
How can this engineering be achieved?
By building layers of complexity with logical systems (genetic circuits):
((Figure reproduced with permission from Wang et. al, 2012. Using the Creative Commons International license 4.0))
As described in the above diagram,inputs can range from light to antigens and the engineered logic gate will determine outputs. We can engineer logical checks and balances into our plasmids by placing small segments of DNA that act as sensors, which will control how and when our plasmid genes will get expressed.
Some elements can boost gene expression (promoters), while others repress gene expression (repressors). Other sensors do the same boosting (enhancers) and repressing (insulators) but at further distances from our gene of interest.
((Figure reproduced with permission from Ciu et. al, 2021. Using the Creative Commons International license 4.0))
Logical OR gate: this circuit will transcribe its controlled gene product in the presence of signal A or B
The OR gate is a series connection with two or more activators, and only one input is required to activate the transcription of the output (Ciu et. al, 2021).
((Figure reproduced with permission from Ciu et. al, 2021. Using the Creative Commons International license 4.0))
Logical AND gate: this circuit will only express its controlled gene and produce the desired gene product when signals A and B are both present
The AND gate requires all input to form a protein complex, which activates the transcription of the output (Ciu et. al, 2021). Transcription factors that have to form a heterodimer in order to activate the next stage of the circuit.
((Figure reproduced with permission from Ciu et. al, 2021. Using the Creative Commons International license 4.0))
Logical NOT gate: A function that outputs an OFF state when the input is ON
The signal molecule forms a complex with the repressor, inhibits the transcription of the output protein, and converts the signal (Ciu et.al, 2021).
Combination of genetic circuits for required output:
((Figure reproduced with permission from Ciu et. al, 2021. Using the Creative Commons International license 4.0))
The inputs are glucose, oxygen, and acetate. PgluA7 promoter responds to glucose. PfnrF8 responds to oxygen but is inhibited by it. PglnAP2s respond to acetate. Maximal output occurs when glucose and acetate are present while oxygen is absent (Ciu et. al, 2021). This is one of the more complicated genetic circuit layers synthetic biologists use today.
Examples of metabolic engineering using combination gates (Ciu et. al, 2021):
Host
Sensing signal
Target pathways
Genetic circuit layers
Breast cancer cells
miniVPR,dCas12a,
crRNA
GFP
AND,NOT gate
B. subtilis
GlcN6P
GlcNAc
NOT Gate
E. coli
Glu,Oxygen,Ace
Acetate
AND,NAND gates
Expert talks
The Duke iGEM team explained the basics of gene delivery and genomics.
Dr. Jesse Boehm. Intellia therapeutics and Locus Biosciences complementing information on CRISPR technology and current use cases.
Dr. Vandana Shashi explaining good research practices in rare diseases. Space acquired health disorders have been considered a subset of rare diseases. We had an exhilarating discussion about framing scientific questions in this context (Puscas et. al, 2022). In partnership with the NORD chapter at NCSU.
Pristine and V Senthil are finalists at the 2022 GiS competition and an iGEMer, they were invited to share insights about success in the two competitions and transitioning from GiS to iGEM.
We conducted a mock UN session in partnership with the CRISPR Hub at NCSU to explore the international partnerships required to use Synbio in Space at the proposed scale.
Student proposals
Within our internal cohort, the following abstract was selected:
GiS abstract-
We will evaluate if spaceflight decreases vitamin K-producing gut microbes and contributes to bone deterioration. Using 16S rRNA sequencing and qRT-PCR, we will analyze the gut microbiome and vitamin K levels pre/during/post-flight and relate changes to bone density. Results could enable probiotic interventions to mitigate bone loss in astronauts and osteoporosis patients.
We worked with the chosen cohort to design iGEM parts for their hypothesis. Through these efforts, we hope to inspire students to participate in competitions like GiS and iGEM empowering the next generation of Synthetic biologists.
iGEM part designed-
BBa_K4943507: Quorum sensing(QS) for probiotic Menaquinone 7 (Vitamin K) synthesis in Bacillus subtilis 168
Some design considerations:
▪ Bacillus subtilis is a common bacterium that can survive in space for up to six years. It holds the record for the longest survival in space, which was six years on a NASA satellite (Madigan et. al, 1991).
▪ QS is utilized by extremophiles for processes like cold adaptation, biofilm formation, oxidative stress resistance and persister cell formation.A QS system controls cell density-dependent processes and does not depend on a metabolic pathway or require inducers or other interventions.
This can be used to engineer biosafety measures as the next optimization step.
Future directions: Development of specific precision probiotics tailored per astronaut’s microbiome, novel strategies to improve gut-organ axis. Understanding the microbiome dysbiosis in response to simulated microgravity.
Gut microbiome library
As part of the synthetic biology education drive, high school students got creative and made informative Instagram posts about various gut microbes and how they relate to human health and disease. Students researched probiotics like Lactobacillus and Bifidobacterium, which support digestion and immunity when in balance, versus harmful bacteria that can cause infections and inflammation when overgrown. Their posts used graphics and captions to explain concepts like microbial balance versus dysbiosis, the gut-barrier function, short-chain fatty acids, and inflammation.
Creating this microbiome content for social media enabled the students to engage their peers and spread awareness about gut health in a fun, relatable way. The Instagram project made learning synthetic biology and microbiology very applied and accessible to young students.
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