Overview
A scientist’s job and responsibility are not restricted to new discoveries and inventions but also expand to the safety, security, and etiquette of the laboratory in which they work. As he/she sets out on a quest for knowledge and thirst for new discoveries, ensuring safety along this journey is equally essential. This will ultimately impact the nation and contribute to research and development. By understanding and integrating safety protocols, risk management, and preventive measures, scientists protect themselves, their colleagues and the environment, leading to fruitful research.
Classification of Microorganisms
For our project, we selected our strains based on their potential to synthesise our required metabolites and the risks they pose to humans and the environment.
As per the Department of Biotechnology of India, microorganisms are classified into four categories based on their ability to cause diseases in humans/animals/plants.
Risk Group | Description |
---|---|
RG1 | It is unlikely to cause any human/animal/plant diseases |
RG2 | It can cause disease in humans/animals/plants, but exposure in the laboratory may not cause severe infection to individuals, and the risk of spread of infection is limited. |
RG3 | It can usually cause serious/lethal human/ animal/ plant disease but does not usually spread from one infected individual to another |
RG4 | It can usually cause severe/lethal human/ animal/ plant diseases that can be easily transmitted from one individual to another, directly or indirectly. |
Pseudomonas putida KT2440
The chassis organism that we will be using in our project is Pseudomonas putida KT2440 and two of its derivatives, Pseudomonas putida TA7 and Pseudomonas putida TA7-EG which were engineered by Dr Oliver Brandenberg, by incorporating the genes phA1II, tphA2II, tphA3II and tphBII under constitutive promoter PEM7 [1]. As per the FDA guidelines, the strain, P. putida KT2440, is HV1 certified, indicating it is safe to use in a P1 or ML1 environment [2]. It is a non-virulent strain, and hence, its potential to cause harm to humans is minimal.
Introduction
As researchers, maintaining proper safety conduct within the lab is a top priority. As per the Guidelines for the Establishment of Containment Facilities: Biosafety Level 2 (BSL-2) & 3 (BSL-3) and Certification of BSL-3 facility, 2020, our laboratory falls under Biosafety Level-II. For more information, please visit: https://ibkp.dbtindia.gov.in/
Before starting our project, we were given Biosafety level-II training by our laboratory technician, Mrs. Nithya Rani, wherein she provided extensive courses on safe work in the laboratory. We were given prior training on the proper and safe use of autoclave sterilisers, bio-safety cabinets and the usage of ethidium bromide and UV for visualising electrophoresis results.
Safety training conducted by Mrs.Nithya Rani
Laboratory Safety Equipments
All our experiments were conducted in the Advanced Biology Laboratory at IISER TVM. It is equipped with fire-retardant workbenches, biosafety cabinets, autoclave sterilisers, appropriately labelled chemicals and reagents and other required equipment. All chemicals and equipment were handled with necessary precautions.
In the case of a fire emergency, fire-safety equipment, such as fire hose and fire extinguishers are located in the vicinity of the laboratory. All were given the necessary training required for the handling of fire equipment. The laboratory is also equipped with shower and eyewash.
Disposal System
Standard decontamination and disposal protocols are followed according to Biomedical Waste Management Rules. The following procedures are strictly followed in the lab:
- Blue Bucket - General waste
- Yellow Bucket: Cytotoxic waste, Agarose gel (containing EtBr), Acrylamide gel (PAGE), Pathological Waste, Solid media, Body fluid/cytotoxic contaminated paper, cotton, swabs, and cloth, Tissue, and wipes contaminated with cytotoxic waste, Face masks
- Red Bucket: Gloves, tips and tubes, Syringe without needles, Culture plates without media, Pipettes, and Plasticware. Serological pipette without cover
- Transparent Bucket - Needles, syringes with fixed needles, blades, scalpels, forceps, burning scissors
INTRODUCTION
Our project will be engineering Pseudomonas putida TA7-EG to synthesise sandalwood oil components, santalol and santalene. To achieve this, we’ve incorporated several genes obtained from the Santalum album. None of these genes are known to have any virulent factors.
NAME OF GENE | DESCRIPTION | SOURCE OF GENE |
---|---|---|
FPPS (Farnesyl Pyrophosphate Synthase) | Catalyses the condensation of DMAPP with IPP to produce FPP | Santalum album |
SaSSy (Santalene Synthase) | Converts FPP to santalene | Santalum album |
Cytochrome P450 monooxygenase(CYP450) | Further oxidises the santalene to santalol | Santalum album |
Cytochrome P450 reductase(CPR) | Transfers electrons from NADPH to CYP450 monooxygenase | Santalum album |
DXS (DXP Synthase) | Converts GAP and pyruvate to DXP | Present in P. putida KT2440 |
DXR (DXP reductoisomerase) | Reduction of DXP to MEP | Present in P. putida KT2440 |
We chose suitable pSEVA backbones of low copy number to avoid burdening our bacteria and attain stable gene expression within our chassis.
Santalum album oil has been used to make small quantities of traditional medicines and personal care products. Santalum album oil has been previously tested on humans, and it has not caused any irritation or discomfort. In the case of oil from Western Australia (Santalum spicatum) or Hawaiian sandalwood (Santalum paniculatum), significant amounts of farnesol, which is known to cause allergic reactions, are present. However, Santalum album oil does not contain farnesol; hence, it does not cause any allergic reaction and is a safer option [3].
REAGENTS
We followed all the instructions on properly using and handling common reagents used in procedures such as gel electrophoresis, Western Blotting, Coomassie, SDS-PAGE, etc.
Antibiotics were used for selection procedures. We used ampicillin, spectinomycin, streptomycin, gentamicin, kanamycin, and anhydrotetracycline and the safety hazards regarding each reagent were verified using the National Center for Biotechnology Information. Ampicillin, gentamicin, kanamycin, and anhydrotetracycline were already prepared at appropriate concentrations provided by our supervisors, whereas spectinomycin and streptomycin were obtained as powders. The powders were weighed and solubilized. All antibiotics were handled with proper care, and special instructions given by our lab instructor were followed.
INTRODUCTION
As part of our project, we conducted several interviews, surveys and competitions to spread awareness and gain more insight regarding the project. As we had to interact with various groups of people, we had to ensure that all relevant laws and regulations were strictly followed. Permission from legal authorities was acquired before conducting any activities involving the public.
PROJECT APPROVAL
According to theb Regulations and Guidelines on Biosafety of Recombinant DNA Research & Biocontainment, our experiments fall under Category II, and hence, prior authorisation from the Institutional Biosafety Committee (IBSC) was given before the commencement of the experiments. We filled out all necessary applications required for the authorisation to handle GMOs and our work was approved by the Review Committee on Genetic Manipulation (RCGM) under the Department of Biotechnology.
SURVEY
Multiple surveys were released by the Human Practices, Outreach and Proposed Implementation sub-teams. Prior consent was sought from the participants at the beginning of the forms, and they were clearly informed that all data collected would only be used for the purpose of the research.
WEBINARS
Prior consent to use any video recordings and images of webinars and interviews conducted as part of our project was given. A consent form regarding the use of any necessary content on online platforms was signed and given to us by the participants.
PROPOSED IMPLEMENTATION SAFETY
Since the beginning of PETal we ensured that we followed safe practices in all aspects of our project by identifying all the potential risks we may face in the future, from synthesising our product within the laboratory to manufacturing it in bioreactors for making consumer-based products. We talked to relevant producers and start-up companies and studied relevant literature regarding the same. More information regarding future safety measures is explained in the Proposed Implementation page.
- Brandenberg OF, Schubert OT, Kruglyak L. Towards synthetic PETtrophy: Engineering Pseudomonas putida for concurrent polyethylene terephthalate (PET) monomer metabolism and PET hydrolase expression. Microb Cell Fact. 2022 Jun 18;21(1):119. doi: 10.1186/s12934-022-01849-7. PMID: 35717313; PMCID: PMC9206389.
- Kampers LFC, Volkers RJM, Martins Dos Santos VAP. Pseudomonas putida KT2440 is HV1 certified, not GRAS. Microb Biotechnol. 2019 Sep;12(5):845-848. doi:
10.1111/1751-7915.13443. Epub 2019 Jun 14. PMID: 31199068; PMCID: PMC6680625. - Moy RL, Levenson C. Sandalwood Album Oil as a Botanical Therapeutic in Dermatology. J Clin Aesthet Dermatol. 2017 Oct;10(10):34-39. Epub 2017 Oct 1. PMID: 29344319; PMCID: PMC5749697.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5749697/