Team:SYSU-Software/Safety

SYSU-Software:Project

OVERVIEW

To eliminate potential safety problem in our software, we consulted the professors about the safety
regulations on such software. We also found Catalogue of Hazardous Chemicals and forbid users to
synthesis products in this catalogue.

BIOSAFETY CONSULTING DRY-LAB BIOSAFETY WET-LAB BIOSAFETY

BIOSAFETY CONSULTING

Since our project can auto-generate and select circuit from the target products given by the users, and databases sup-
port our software also record all chemical reactions in nearly 7600 species of bacteria, potential safety problems could
be serious if we perform no restriction to the users.
Some users might use our software to derive the circuit synthesizing dangerous chemicals or their precursors, such as
drugs. Theoretically, this situation is very likely to happen because substrates and products in cognizant bacterium are
all weaved as a large network, and some dangerous chemicals surely connect with the network inside, with a series of
feasible circuits output.
Some users might face other kinds of safety problems when their origin targets are harmless, but the selected circuit
will produce deleterious intermediate products. However, users are unlikely to know what exactly produce except his
targets in circuits when experiment because details are hidden behind the user interface.

DRY-LAB BIOSAFETY

Since our project can auto-generate and select circuit from the target products given by the users, and databases
support our software also record all chemical reactions in nearly 7600 species of bacteria, potential safety problems
could be serious if we perform no restriction to the users.
Some users might use our software to derive the circuit synthesizing dangerous chemicals or their precursors, such
as drugs. Theoretically, this situation is very likely to happen because substrates and products in cognizant bacterium
are all weaved as a large network, and some dangerous chemicals surely connect with the network inside, with a series
of feasible circuits output.
Some users might face other kinds of safety problems when their origin targets are harmless, but the selected cir-
cuit will produce deleterious intermediate products. However, users are unlikely to know what exactly produce except
his targets in circuits when experiment because details are hidden behind the user interface.
To solve the problems above, we tried to add a recognition system in our software and set a ban list. This system
will work when it detect the users have input the products in our ban list, or the circuits producing intermediate prod-
ucts. It will interrupt the users and give warnings, or eliminate the alternative circuits with safety problems.

The ban list originally came from the Catalogue of Hazardous Chemicals (2015 version), issued by China State Ad-
ministration of Work Safety, formulated following Globally Harmonized System of Classification and Labeling of Chemi-
cals (GHS). However, this catalogue covers 3012 chemicals, and some of them is necessary for life events (They are
dangerous because flammability or explosive, but not harmful to life or environment), thus we selected 148 chemicals
labeled with toxic as our ban list.
Every chemical in this list has an unique CAS number, same as those in our software, and our system can work
through these pairs.

Our software will provide the results with their suitable chassis species, which is selected from software data, so it
is likely to give the users the species with high risk. Thus we should filter the 7000 species according to the Risk Group
List, ensuring that the results will only give the users species in Risk Group 1 or 2.
To solve this problem, we made a list of species in Risk Group 3 and 4, originally coming from Appendix B in NIH
Guidelines (April 2016), and then we deleted the chassis species belonging to the list.

Our results combine CDS sequences with promoters and RBSs meeting the requirements from users, which come
from iGEM Registry, and form complete circuits. Although unlike the CDSs, promoters and RBSs won’t express pro-
teins that might have potential safety problems to the environment or organisms, we are not sure if some of them are
also labeled with red flags. Considering this, we search the whole database for promoters and RBSs in Registry and find
that all promoter and RBS parts are freed of Red Flags, thus we can use nearly all promoter and RBSs parts if they are
still available.

WET-LAB BIOSAFETY

We conducted our wet lab 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.

We received bio safety training from multiple people. Post doctor Dongni Chen in Prof. Lu’s team taught us how to
operating our experiment correctly including inoculating, transduction and the operation of ELIASA, avoiding the dam-
ages to the environment.

We learned about the basic safety protocols concerning cultivating bacteria, conduction of a plasmid and so on.
Also, to reduce risks, we have been educated about working in properly equipped facilities and using standard lab
safety techniques. The safety instructions about organisms, parts are educated in our lab meeting.