Team:SYSU-Software/Safety
Biosafety in Dry-lab
Base our project on White List of 2015
Safety in iGEM includes safe choice of organisms to operate the genetic design in vivo, and safe choice of parts to construct the genetic circuits. For more detail, please see “White List” of 2015.
“Will the database of CORE consists of parts originating from Risk Group 3 or 4 organisms?”
In the Project Assessment of our Human Practices, we examined the database of CORE in order to find out the origins of the biological parts in the database of CORE (for the methods we adopted to do this examination, please click “Human Practices/Risk Assessment”).
Here we repeat the result we obtained.
It is obvious that most of the parts in the database have no information on origins. This is because in Registry information of most of these parts is NOT complete; from Registry we can know little about where these parts come from. However, after we confirm these parts in the Registry, all of them contain no Red Flags.
Fortunately, for parts which we could find the origins of, most of them come from Escherichia coli. (Unfortunately still, in Registry they do not tell us whether they come from E. coli strain K-12.) After we confirm the Risk Group of these organisms with the DSMZ database, we found that in the database of CORE no KNOWN Risk Group 3 and Risk Group 4 organisms involved.
It is obvious that most of the parts in the database have no information on origins. This is because in Registry information of most of these parts is NOT complete; from Registry we can know little about where these parts come from. However, after we confirm these parts in the Registry, all of them contain no Red Flags.
Fortunately, for parts which we could find the origins of, most of them come from Escherichia coli. (Unfortunately still, in Registry they do not tell us whether they come from E. coli strain K-12.) After we confirm the Risk Group of these organisms with the DSMZ database, we found that in the database of CORE no KNOWN Risk Group 3 and Risk Group 4 organisms involved.
Conclusion
All the parts with known origins come from Risk Group 1 and Risk Group 2 organisms, and they are relatively safe.
“Will the database of CORE consists of parts with Red Flags?”
The iGEM Safety Committee has placed a Red Flag on parts which present safety risks beyond what is normal for the Registry (For a complete list, please click here.We searched all these parts in our software and no such parts were found.
Conclusion
In CORE, users are NOT able to use the parts with Red Flag to design circuits.
Risk Level Warning in Design module
Design and simulation of genetic circuits are the functions of CORE. For some of the genetic circuits have been reported in previous journal papers, the safety of these well-known genetic circuits are well tested. And CORE adopts these circuits as raw materials for further design by users. When users utilize CORE to design new circuits or systems, they will be asked to consider about dangers of their designs. Our software provides a risk classified system which will give the Risk-Level Warning. There are four class in this system:
- Low risk (1)
- Moderate risk (2)
- High risk (3)
- Extreme risk (4)
Biosafety in CORE Bank & Co-development
As an open platform, CORE which allows every user to exchange and evaluate each other's ideas and design, subjects the biosafety issue of every design to everyone for evaluation. It is the potential use of Crowdsourcing in evaluating safety issues of the design.
Users can make a detail safety assessment of each circuit or system and then rate the design. These ratings can be used to decide whether the circuits should be moved to the public.
In addition to ratings, users can detail their remarks on safety in the Co-development module. Their remarks will help others to evaluate the safety issues of the design.
Users can make a detail safety assessment of each circuit or system and then rate the design. These ratings can be used to decide whether the circuits should be moved to the public.
In addition to ratings, users can detail their remarks on safety in the Co-development module. Their remarks will help others to evaluate the safety issues of the design.
Warning after finishing the design
Following the advice from our instructor, Prof. Yang, and the ideas from team member Xiaoran Yang, we added a warning into the CORE Design module so that we can remind the users of biosafety issue. Therefore, CORE can be responsible for its users and the users can be responsible for their design.
Biosafety in wet-lab
About the wet-lab for the validation of our software and the experiments for interlab study
Consideration of the circuit design
In the wet-lab part of our project, our circuit was designed with the help of our software. As all the parts in our software are in the white list, our circuit is 100 percent safe. Besides, we use the risk classified system in our software to assess our design. Photo.1 shows that our design is at a low risk level. Therefore, our circuit can be constructed.
In the interlab study, we followed the instruction of safety level 1 procedures and design our experiment in an appropriate way.
In the interlab study, we followed the instruction of safety level 1 procedures and design our experiment in an appropriate way.
Consideration of the experimental material before experiments
Which risk level was our project at?
We conducted our wetlab experiments and interlab study in Level 1 labs and used Risk Group 1 organisms (We used Escherichia coli DH5αas our organisms.). Meanwhile, our design, which does not have a real world application, is fundamental and will be only used in lab.
Who we consulted?
- Senior lab member
- Sa Xiao
- Zhenhuang Ge
- Biosafety officer
- laboratory manager
- Lei He
- iGEM team
- SYSU-China
What we have learnt?
- We had discussion with our senior lab member about the standard protocol in lab.
- We consulted the biosafety problem with professor
- We consulted the laboratory manager for the lab where we work. See more detail at our human & practice page:
What safety rule did we follow?
We followed the rules in the Sun Yat-sen university laboratorial safety book as well as the regular safety protocol in our lab.
Sun Yat-sen university laboratorial safety book
Consideration of biosafety problem during experiments
Our protection:
- Gloves
- Lab coats
- Long pants
- Mask
- PE gloves
Management of corrosive and volatilized laboratory reagents
When we use the laboratory reagents which are corrosive and are easy to volatilize, we conduct our experiment in the fuming cupboard and use specific instrument. If we accidentally pour over the volatilized reagents, we can wash ourselves immediately by the washing system in our lab.
Consideration of the lab supplies management after experiments
- EB agarose gel collecting box & EB area
- Sterilization of agar plates and test tubes
- Specific laboratorial waste bin
