Team:IISER-Tirupati India/Safety
The Youth Declaration for Biosecurity: Mobilizing Youth to Strengthen the Biological Weapons Convention
After our nomination for the Safety & Security award, we were invited to the Meeting of States Parties to the Biological Weapons Convention to highlight the 'Safety & Security' aspects of our project on 22nd November 2021.
Safety Of OviCloak
Choice of Commensal
Millions of commensals colonise the upper female reproductive tract. In our project, we plan to engineer a commensal, i.e. Lactobacillus acidophilus. The use of commensal avoids the chances of harmful effects by using foreign cells in the human body. We chose our commensal, which would primarily reside in the desired region; in our case, it’s the fallopian tube. The points which favour commensal’s inhabitance in the fallopian tube are-
pH variation
Direction of ciliary movement
The variation of the pH in the female reproductive tract is that vagina has the lowest pH of 4.42, increasing with the pH of nearly 7.94 in the fallopian tube, and then the pH of the ovarian fluid is maintained at 8.5. Our commensal (Lactobacillus acidophilus) mostly stays in the fallopian tube, i.e. at a pH of nearly 7.94 [1]. And as we know, the bacterial cell primarily resides in a particular pH, which mostly restricts their release in some other region of the body.
The luminal cells in the fallopian tube have cilia on their surface, and its movement is from the ovary to the uterus [2]. And as our commensal bacteria Lactobacillus acidophilus is inmotile, it will move mostly in the direction of ciliary movement. Hence, decreasing the possibility of it going towards the ovary.
Ovastacin- A native protein
We are engineering our commensal bacteria to produce an Astacin-like metalloendopeptidase named Ovastacin. Ovastacin is a cortical protease produced naturally in humans for the post-fertilisation cleavage of ZP2. Hence there will be less possibility for this protein to cause any problem in the human system.
Horizontal Gene Transfer
One of the associated concerns with our proposed contraceptive OviCloak is Horizontal Gene Transfer (HGT). After the delivery of the bacteria to the site of fertilisation, i.e. the ampulla region of the fallopian tube, there are chances for the transfer of artificially constructed plasmid to the natural bacteria present in the fallopian tube. Considering this, we propose integrating our desired genetic circuit with the genome of our bacteria, Lactobacillus acidophilus with the help of cloning. This process is known as genome integration. This method will lessen the possibility of horizontal gene transfer as genome size is quite long, which will take time to get entirely transferred in the other bacteria. But for the horizontal gene transfer, the pilus is not stable for a long time. Hence, there happens to be less probability for the genome to transfer.
Biosafety Kill Switch (Biocontamination control)
We have engineered our bacteria with a kill switch to avoid their escape from the reproductive tract and prevent biocontamination. For more information about biosafety kill switch, see Blueprint.
Dual Use
- Due to the involvement/enforcement of other people, women might not be able to use xylose for the induction of the kill switch. Hence, women using this contraceptive might not be able to induce the kill switch for reversibility.
- On the other hand, someone can use Ovastacin and inject it into the ovary, which will cleave the ZP2 of the oocytes forming in the ovary and making the women sterile completely.
Lab Safety
Safety and Security plays a vital role in performing responsible research and hence, our team strived to practice safe and secure lab practices.
We initiated our safety practices with risk assessment to find the risk involved in doing the intended experiments and to strategize how to manage them. This was followed by the filling of the preliminary safety form.
We underwent a safety training program facilitated by IISER Tirupati during the initial days of research activity in our lab. This helped us understand the potential sources of risk and the management/disposal of biohazards, chemicals and physical hazards.
During our project experimentation, we worked mainly in the undergraduate lab of IISER Tirupati.
We strictly adhered to the general safety guidelines and, in particular, the biology department safety guidelines. iGEM safety rules and policies were also followed while doing research activity in our lab. While working in the lab we used appropriate personal protective equipment like lab coats, long pants, nitrile gloves, and shoes.
Waste Disposal
We segregate the waste produced in the lab as Sharps, biological solid/plastic waste, biological liquid material waste, and other solid waste. Sharps were collected in a puncture-proof sharp container. Biological solid/plastic wastes are collected in the red-biohazard bag and autoclaved for decontamination and picked by the specified agency of the institute for incineration. While the liquid biological waste was contained in a container and treated with 10% bleach and kept overnight before discarding. Other solid wastes are collected and discarded off with other waste.
Waste containing hazardous chemicals like Ethidium bromide containing agarose gel, SDS gels were discarded separately and picked by the specified agency of the institute for incineration.Organic solvents are disposed separately from other liquid solvents, so as the plastic wares contaminated with organic solvents.
Organisms, Parts and Activities
During our research activities, we used Escherichia coli DH5Alpha, Escherichia coli BL21, Escherichia coli NEB 10-beta, Bacillus subtilis 168, Saccharomyces cerevisiae S288C strains which were risk group 1 organisms.
Moreover, All the parts and activities were in the white list.
Lab safety under the context of COVID-19
To avoid contributing to the spread of COVID-19, we worked considering our local conditions and followed local and national public health guidelines. We were quarantined after our return from local states to the institute as per institute guidelines. Thereafter, we maintained social distancing and responsible interaction during our lab work including wearing masks and frequent sanitizing. We made sure that we are strictly adhering to the COVID-19 protocols followed in the institute.
Safety and Security - Human Practices
Safety and Security are crucial when it comes to human practices, especially during this pandemic scenario. We ensured to carry out our Social Science Research responsibly.
Safety and Security
We thought of safety of conducting in-person interactions from the planning of our activities. We decided:
- To engage with people virtually
All the public engagement and communication events were held online. We thought of utilising social media as a platform for outreach and education.
- Practice Social distancing during in-person interviews
When the Covid cases went down in number, we thought of meeting experts in-person. But we strictly adhered to COVID guidelines such as wearing masks, sanitising, and social distancing.
- Engage with family-members
We planned to do In-depth interviews to reflect the needs and necessity of people. Under the Covid scenario, this was not possible. Hence we thought to start our IDI from our homes, with our family members.
Responsible Research
For a responsible conduction of our Human practices, we made sure the following :
- Follow Social Science Research ethics and it’s regulations
We observed UNESCO’s Code of conduct for Social Science Research, while carrying out surveys and IDIs. We also got sanction from the ethics committee of our institution for carrying out our surveys.
- Collect Informed Consent
We made sure to collect written informed consent from individuals participating in our surveys and In-Depth Interviews. We made sure that the informed consent contains:
- Information about the data we are collecting and the purpose and most importantly, we informed them that the participation is voluntary and they have the right to discontinue their participation at any point of the data collection process without any consequences.
- A checklist to confirm:
- They have had the chance to ask any questions regarding the project.
- They understand that their participation is voluntary and that they could terminate their contribution at any time without consequences.
- They agree to participate in the study and (if applicable) they agree to be recorded.
We also checked with our institute on the format of informed consent and got approved.
- Anonymising data
We assured our participants of the survey that the data collected will be anonymous. We collected written permission for publishing the data collected from experts during in-depth interviews for integrated human practices. We also paid attention whether our any of expert is an EU Citizen, so that we could follow General Data Protection Regulation (GDPR).
References:
- Patiño, R., Bolamba, D., Thomas, P., & Kumakura, N. (2005). Effects of external pH on hormonally regulated ovarian follicle maturation and ovulation in Atlantic croaker. General and comparative endocrinology, 141(2), 126-134.
- Shi, D., Komatsu, K., Hirao, M., Toyooka, Y., Koyama, H., Tissir, F., ... & Fujimori, T. (2014). Celsr1 is required for the generation of polarity at multiple levels of the mouse oviduct. Development, 141(23), 4558-4568
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