- Overview -
In our project, the core goal of Human Practices is to ensure that our designed genetic
information transmission and encryption system is not only technically feasible but also adheres
to ethical and safety standards. Through expert interviews, social research, and exchanges with
other academic institutions, we have consistently focused on societal concerns such as
information security, privacy protection, and biosafety throughout the project design process.
Our research aims to develop a biological encryption and information transmission system
controlled by caffeine using synthetic biology methods, and Human Practices has helped us ensure
that this technology is safe, reliable, and aligned with the expectations and needs of the
public and relevant stakeholders in real-world applications. Through collaboration with
educational institutions, research centers, and industry, we have further validated the
practical effectiveness of this system in encryption, selective growth, and self-destruction
mechanisms, paving the way for future applications.
- Research -
· Questionnaire
Background: Our team constructed a social survey to visit a broader group of
individuals in a mall located at Shen Zhen Guang Ming and at the same time publish this survey
online for more people to access.
Purpose: We are collecting all the different results from various groups of people to organize data showing the degree to which information is readable after DNA mutations.
Results:
· Research on Model
A model to simulate the mutation sites in our constructed plasmid was developed. It predicted
what random genetic changes would do to the readability of the coding region. Conception Our
model will calculate the number of mutations, insertions, and deletions that could take place
overtime. It also provides a mechanism for redundancy in the model in order for information
integrity to be maintained even when such mutations take place. The analysis of different
scenarios-up to 10 mutations within a DNA sequence-keeps the information readable, which implies
that information can safely be stored in E. coli for tens of years with no significant
loss of
readability. Using the simulation of all different mutation scenarios, we saw that through
using
redundancy, a system's resistance to mutations significantly enhances so that over more
extended
periods, readability is ensured in stability.
- Interview -
· JHU Professor interview
Background: Farah Qureshi, ScD- Assistant Professor, Department of Population,
Family & Reproductive Health, Johns Hopkins Bloomberg School of Public Health)
Purpose: In this interview, we aimed to clarify our background and link our project to the range of society and the world.
Main Point: During this conversation with my professor, she explained the role of genomics in public health and how this field can benefit society. Before this discussion, I was unsure how our experiment could have societal applications or be relevant to various professions but her answer gave me a great inspiration of our goal. The class focused on the fundamentals of public health and all the factors that could influence individuals as a whole. My professor's insights encouraged me to explore how research in genomics and the transmission of genetic information can influence health and disease. This understanding leads to advancements in prevention, diagnosis, and treatment strategies, as more information can be effectively utilized for medical purposes.
· Sequencing Engineer Interview
Purpose: We want to have a better understanding of the current prices of DNA
sequencers and understand the future trends in DNA sequencer prices. DNA sequencer is a big part
of our project since it’s the basic need to read the message being transfered in bacteria’s DNA
sequence.
Key Highlights:
- Sanger sequencing history; The key point of Sanger sequencing is that ddNTP is added to extend DNA for termination signal; The sequencer can detect the fluorescent substance contained in ddNTP; CCD optical system increases readability; The fluorescent substance will remain at the end; The chain length is different (the fluorescent label is different)
- The working principle of the Sanger sequencer: fluorescent signal - electrical signal - DC data processing software - result peak graph.
- NGS can sequence millions of fragments simultaneously; the mechanism of NGS: high power supply
- Second-generation sequencing:The read length is relatively short, requiring linkage of segments. The read length is relatively short, requiring linkage of segments. The price for low-throughput sequencing is 2 million, while high-throughput is over 6 million. Sequencer price is around several hundred thousand. Sequencers are very large and inconvenient to move. Second-generation sequencers can test all 20,000 genes
-
Differencial section of second generation:
- Second-generation sequencing-- Library construction: DNA fragmentation (using the Covaris220 ultrasonic disruptor, genomic DNA is fragmented to between 100-2000bp by setting different parameters), end repair to make ends uniform (using reagents), addition of A-tails, ligation, and PCR. Library preparation is the key to sequencing.
- Second-generation sequencing--Library capture: Probes labeled with biotin hybridize with library DNA under certain conditions, forming double strands through complementary base pairing with the target fragments.
- Second-generation --Illumina sequencing process: Clusters are generated on the flow cell using bridge PCR. Read 1 is sequenced for 150bp, followed by index sequencing, cluster flipping, and then Read 2 is sequenced for 150bp. Finally, washing is done on the NextSeq500.
- Third-generation sequencing: The read lengths are much longer, allows for distinguishing between true and false genes, but the cost is very high; the mainstream is still second-generation sequencing
Summarize :In this interview, we know about the kinds of sequencers and the mainstream sequencers in the market. We also know about the price of the sequencers and the prospect of these DNA sequencing machines. Because of this prediction of the sequencer future’s price, it would be more convenience to test DNA sequences and provide a easier platform for our technique to be use in future.
· Peking University 2018iGEM Leader (Doctoral students of Chinese Academy of Sciences)
Background: The person we interviewed is a PhD student in Chinese Academy of
Sciences. He was also the iGEM leader of Beijing University’s 2018 team and had
accumulated rich experiences in leading high school iGEM team.
Purpose: This project aims to develop a cost-effective, time-efficient method for DNA data storage and encryption, independent of sequencing methods. The information will be read continuously using green or red fluorescence as a key.
Highlights:
-
Reading Process:
Use fluorescence signals to continuously read encoded DNA, enhancing efficiency. -
Re-encryption and Key Changes:
Inspired by quantum communication, explore re-encryption methods and quick password changes using a key barcode and fixed codon system. This hides the encrypted protein sequence, making it indistinguishable from natural sequences.The fixed codon system ensures encrypted sequences are secure and hard to detect, appearing artificially generated and easy to distinguish from true information. -
Future Applications:
This method holds potential for secure, efficient data storage and transfer across various industries, including healthcare, data storage, and secure communications. -
Safety:
He also reminded us of keeping the safety of this experiment with using bacterias as a form of transmitter. He recommended us of applying saccharomycetes which has high safety level and can be physically touched, providing us a second choice for the use of bacteria. (But the bacteria that we used,escherichia coli, is also been proved as high safety level)
The system ensures encoded DNA sequences are secure and indistinguishable from natural ones. With a focus on biosafety, it uses safe enzyme bacteria for direct data transfer. The goal is to provide a highly secure, efficient solution for data storage and secure communications across various industries. Quantum communications is new as of this year it was finally accomplished our hope is to further this discovery and to integrate it with our own to create a quantum biological wonder of communication.
- Education -
· BISZ Science Fair
Purpose: We aimed to introduce synthetic biology to our students and popularize
how synthetic biology is already all around our lives. We choose to use an example of an
environmental problem that could influence human life and introduce the solution of synthetic
biology, to explain how synthetic biology could change human life.
Key Highlights:
- Students came and started discussions with us about the details of our solution based on synthetic biology.
- We introduced the basics of synthetic biology during our presentation.
- We shared opinions with other stations in the science fair and received advises form different teachers.
· Media
Purpose: Our aim is to popularize knowledge related to both biology and
information transmission. We have already written the article that explores ancient and modern
methods of information transmission, including introduction and comparison between these
transmission methods, description of the information transmission method of our group.
Additionally, we plan to further expand our content to cover various aspects of biological
knowledge and how it intersects with the field of information transmission and enhance public
understanding.
Key highlights:
- introduced the ancient and modern information transmission methods
- pros and cons of these methods
- presented our method of information transmission--DNA storage
Through official accounts, we presented our program and disseminated knowledge about biology. We also aimed to further extend the content to explore the intersections between biology and information transmission. We hope our articles will enhance people’s understand of synthetic biology as well as our project--transmitting information through DNA.
· Education Video
Purpose: Our group created multiple educational videos and published them on
Youtube to publicity the basic knowledge about synthetic biology and some intro videos to
introduce items in laboratory and concepts about basic experiments. At the same time, we
concluded our experimental design into different blocs and filmed them in to these educational
videos.
Main Points:
- Introduced the basic experiment in laboratory which is the PCR procedures
- Basic theories about DNA and Synthetic biology
- Explain our accomplishment and experiment designs on our project
We wish these videos could help all the students that are interested in synthetic biology and wanting to join iGEM. Furthermore, we want to share our experimental design to all the iGEMers and share ideas with each other.
- Collaboration -
· CCIC
Purpose: This is our first collaboration with multiple iGEMers around the world
in different fields and different levels, we wish we could achieve a better design and
performance of our project through the conversations and advice we received from various
professors and iGEM teams in both high school fields and University fields.
Main Points:
Professor Zhang emphasized the importance of the security protection of biological information. While advocating for new developments, innovators are invited to re-examine the negative impacts and potential limitations of technology. For example, the misuse of AI, the control of illegal drugs (e.g. poppies), etc. It’s related to our project since we use E. coli, which has a very low potential of acting as a pathogen, but it’s worthwhile to note that yeast might be a potent candidate in the future instead of sticking with E. coli.
After the lecture prof, Zhang and Dr.Bao stressed the idea of critically reassessing our project designs. He pointed out that:” it’s fine for a student to include downsides of their project, and I personally encourage it.” We could include this in our human practice section.
Pieces of Advice we got to improve our design:
-
A suitable approach for the translation between the combination of bps and Mandarin.
- avoid multiple recurrences of some letters----bps
- More enigmatic
- A compelling background& introduction part-demonstration of the novelty and importance
Anywhere the facilities are new and delicate. The big screens in the lecture hall look great. Nexus X XJTLU logo is plastered all over the room, you can tell that the organizer have put a lot of effort into it. There were a lot of new technology companies and they had their own booths where scholars could interact with others in front of their posters. These multiple booths provided us a lot of study chances and opportunities to conduct more in depth communications that can help on our design of project.
Meet up with iGEM Team of Imperial College London
Imperial College team: a short conversation with Edward Wu. He generally supports our project and raised a concern about the limitation of bacterial survival on hands. Edward suggested that we should use Bacillus instead of Escherichia coli to achieve better bacterial survival on hands. However, it is worth noting that the strong odor of Bacillus is easily detectable by people, which contradicts our "stealth" theme. Through further research, we found that bacteria can exist in a dormant state on hands and do not completely die. His question has been constructive in helping us understand the topic better. At the same time, I learned that they are working on a bacterial regeneration rubber project, and I also made him aware of the efficiency and cost issues.
Shanghai Technology university Their delegate proposed the RSA encryption method, which is a public-key encryption algorithm based on the factorization of large prime numbers, used to ensure the security of data transmission. However, after our discussion, we found that such an encryption algorithm is too complex for high school students and requires specialized equipment. It does not align with our theme of "agents" and rapid decoding. Therefore, we created a method of converting Chinese Wubi input into binary as an additional feature.
· Visit to Zhenhe Manufacturing
Purpose: This laboratory visit aims to deepen our understanding of synthetic
biology by observing cutting-edge techniques in gene transfer, automated production, and
advanced technologies. We will explore how synthetic biology principles combine with automation
and interdisciplinary collaboration, showcasing how such innovations can revolutionize the
production of artemisinin and other bioactive compounds.
Key Highlights:
-
Synthetic Biology Principles:
Design: Creating DNA assembly schematics, including parts and systems design.
Construction and Testing: Automated processes for cell transformation, colony extraction, and fluorescence sorting, alongside transcription, protein, and metabolic analyses.
Hardware and Software Integration: Development of automated equipment integrated with software for experimental control.
-
Automation Solutions:
DNA Synthesis: Utilizing chemical synthesis, DNA chip synthesis, and optical synthesis methods.
DNA Assembly: Employing techniques such as Golden Gate assembly and whole-gene synthesis.
Nucleic Acid Extraction: Implementing mature, standardized automated processes.
DNA Transformation: Full automation of the DNA transformation process.
-
Automated Synthetic Biology Platforms:
iBioFAB System & EGF Facility: Advanced platforms for automated synthesis and testing.
Amyris BOT Platform: Specializes in splicing reaction modules.
Automated Cell Chassis Cultivation: High-throughput engineering of Aspergillus niger genomes.
Rapid Natural Product Biosynthesis: Using Auto-HTP for high-throughput gene cluster characterization.
Metabolic Pathway Optimization: Streamlined experimental workflows for efficiency.
-
Laboratory Operations:
Cross-disciplinary Collaboration: Integration of digital and automated technologies across life sciences and other fields.
International Collaboration: Partnerships with global factories for the production of automated machinery.
Workflow Improvements: Optimizing life science laboratory workflows and providing machinery, alongside after-sales services.
-
Single-Molecule Digital Immunoassay Analyzer:
Enhanced Sensitivity: Achieving detection levels down to femtograms or lower.
Liquid Handling Module: Automated liquid processing systems.
Vacuum Suction: Utilized for plate movements within automated systems.
This laboratory visit was an inspiring opportunity to witness the forefront of synthetic biology and its applications in artemisinin and bioactive compound production. We gained valuable insights into DNA design, automation in construction and testing, and the integration of hardware and software. Automated platforms like iBioFAB, EGF, and Amyris BOT are leading the way in synthetic biology, optimizing gene cluster characterization and metabolic pathway refinement with incredible efficiency. The advancements in automated DNA synthesis, assembly, and transformation, combined with cutting-edge laboratory workflows and equipment, highlight the potential to transform life science research. This visit has truly showcased the future of synthetic biology, where innovation and expertise are set to redefine bioactive compound production and propel scientific research to new heights.
· Shenzhen Institute of Brain Science, Shenzhen Technology University
Purpose: Our team’s trip to the Institute of Brain Science, Shenzhen University
of Technology aided us in a deeper understanding of our experiments with the connectivity and
linkage of DNA. We also found this trip very useful as it explained to us how scientists use the
functions of our brains to further science and medicine.
Key highlights:
- The connection between smell and memory
- We get introduced to how many techniques had been already invented to be used in public with the inspiration of synthetic biology
This tour showed us how important science is and how it delves into a bit of everything. We also learned a wide array of information on solving many problems and theories. This tour not only aided us in our understanding of our research but many others as well including mental health. It was inspiring to see the bright scientists of Brain Science at work and the high-tech machines we saw left us in awe. It was a truly mesmerizing and educational experience that we would recommend to anyone not just people interested in biology.
· Shenzhen engineering biology industry innovation center
Purpose: By organizing this visit, we aimed to explore and advance synthetic
biology, new methods of information transfer through innovative technologies and applications
that will realize the cross boundary integration of biology and information technology and
create a new field of biological information transfer.
Key highlights:
- Genome assembly: Dividing the genome into cassettes, 100 times larger than the viral. The inspiration of this invention is for developing new techniques to assemble more than 100 cassettes into complete genomes for encoding and conveying complex information
- Cell oscillator: the use of the cell cycle oscillation to control cell division cycle, occurred by using only three genes rhythm control, make the synthetic cells can accurately mimic the behavior of natural cells, thus control information transmission time node.
- Yeast genome programming: programming the yeast genome, show progress in the microbial genome project and the possibility of information coding.
- Protein expression: the expression of two proteins in series or parallel to perform a specific function Inspired which is a shift from qualitative to quantitative characterization of these functions, providing more precise control of information transfer
- Artemisinin acid synthesis: the path of the refactoring artemisinin acid synthesis in e. coli, demonstrate the ability of the synthesis of complex molecules 6 in bacteria.
- Codon diversity: synthesis of different kinds of codes to encode different information that is combined with the wubi input method, by e. coli, transfer and expression in Chinese information, expand the genetic code, additional DNA codon (ATGCHX)
- Synthetic biology applications: develop products for daily life, including sports equipment medicine meat cosmetics animal feed, soap and perfume fuel to improve fruit quality and reduce the cost of corn to produce ethanol
-
Synthetic biology and human health:
- Synthetic bacteria therapy: treatment using engineered bacteria
- Synthetic virotherapy: development of synthetic viruses to combat drug-resistant pathogens
- Synthetic molecular therapies: advancing mRNA vaccines and other molecular therapies
- Synthetic microbial therapies: implementation of live bacterial therapies
- Synthetic cell therapies: Leveraging high biocompatibility and low immunogenicity Long cycle time without the risk of cancer treatment in synthesis of red blood cells
The human practice aims to use synthetic biology to create and control new life forms and information transfer method By advancing the genome assembly technology development cell oscillator and programming yeast genome, we paved the way for the innovation and application of various industries Specific to our topic, to realize the Chinese information transfer using biological coding, demonstrates the great potential of biological information technology The active method embodies the instead of looking forward to the future, is to create ideas.
· Meetup with Shenzhen University iGEM group
Purpose:
During this meetup, we look forward to more advice from a university iGEM group with their
experience and a more integrated experimental group. The reason for this meeting is to get an
out of box perspective of our work. Our team strongly believes that questions lead to solutions
and their comments and need for clarification can help us find holes in our project.
Furthermore, we looked forward to exchanging opinions and findings with the college branch of
the iGEM group to gain more knowledge and insight into the program. In conclusion, we will be
absorbing the wisdom of our seniors and discovering new innovative angles to approach our
project.
Main Points:
- We received questions on decoding the information form the bacteria and ways we could enhance our efficiency on reading message
- We understand our problem in explaining the process of decoding based on Chinese character and the points that we added in for concealment.
- The students in Shenzhen University also pointed out the problem in clarifying the DNA cellular transcription instructions.
· Visit to SIYOMICRO
Two representatives from our team visited SIYOMICRO. The company primarily focuses on synthetic
biology cosmetic ingredients, such as SOD honey, vanillin, and other chemical products. Their
equipment is very advanced, and we observed that each lab personnel adheres strictly to safety
measures. However, it is worth mentioning that the company's control over odors and ventilation
is inadequate. This might be due to the fermentation equipment producing a large amount of
organic gases. Although these gases are not very harmful to humans, they are quite unpleasant to
smell. Another area lacking is the wastewater treatment system. Improving waste management might
be something they need to focus on next. Additionally, while the working environment is sterile,
the lighting could be more vibrant to enhance the brand image.
· Campus Meetup-Beijing Huijia Private school
Purpose:
Soon, Team JIASHU-China will be participating in the Grand Jamboree. To meetup with like-minded
peers in school would be a great way for us to procure direct insights from other High school
team; reconfirm things that’s being missed throughout the working interim as well as practicing
our final presentation. Moreover, we strive for a accreditation of our delicate introductory
part, in order to corroborate our intriguing coding-decoding design.
Key highlights:
- Our team has received valuable insights and references on Modeling, which is related to YIYE-Academy’s unique R language programming.
- Garnered information on Cell-specimen vivo migration experiment, which is slightly different from our Bacterial colony culturing.
- We’ve also received invaluable information especially on RNA codons, which they presented their avenue of inhibiting protein expression.
- Conclusion -
Through a series of Human Practices activities, we have made significant progress in various
aspects of our project. In the research aspect, we collected public concerns about information
security through surveys and model studies, validating the feasibility and necessity of our
project in real-world applications. From expert interviews, we gained valuable feedback,
particularly in gene encoding, information transmission, and biosafety, which helped us optimize
the project design. In education, through science videos, exhibitions, and official accounts, we
successfully promoted the basic concepts of synthetic biology to the public and demonstrated how
our innovative technology addresses modern information security challenges. In collaboration, we
engaged with several universities and research institutions both domestically and
internationally, enhancing our experimental design and deepening our understanding of the
industrial applications of synthetic biology technologies.
Through these efforts, we ensured that our project is socially responsible, feasible, and safe. Ultimately, our Human Practices work not only supported the achievement of the project's technical goals but also laid a solid social and ethical foundation for its future applications.
Through these efforts, we ensured that our project is socially responsible, feasible, and safe. Ultimately, our Human Practices work not only supported the achievement of the project's technical goals but also laid a solid social and ethical foundation for its future applications.