- Wet Lab
- Dry Lab
- Human Practices
Safety isn't expensive, it's priceless... We at iGEM Athens 2019, as a multidisciplinary team consisting of students from the fields of medicine, biology and engineering, realized this from the start. When we ultimately presented our finalized project and our ambitious timeline to our PIs & to our instructors, they confessed that it would be a race against time. Therefore we had one additional excuse to be extra careful these past months, since safety breaches such as contaminations would have costed us, apart from money: time, a commodity that was rare to us.
The first lab that hosted us was the Molecular Microbiology Lab of the Biology Department in Athens. It was a period when we were:
- putting the finishing touches to our project design,
- deciding which DNA sequences to order and
- formulating a strategy to create the mighty Morbidostat.
Therefore we were mostly occupied with:
- observing the experiments of the teams carried out there and
- receiving important tutorials on a daily basis regarding lab safety, protocols and the use and handling of various equipments (laminars, centrifuges, thermocyclers etc).
However since this lab was dealing with Aspergillus nidulans, it was a Biosafety Level 2 lab. Therefore it was suitable for our initial experiments with our E.coli chassis, a Biosafety Level 1 organism.
During our stay there we strictly abided by the lab safety manual that is followed by the department
Ever since August, iGEM Athens 2019 relocated to the Physiology Lab of the Medical School of Athens, the lab that turned into our measurement hub for the remainder of the season, and the place where MEDEA became alive. Upon our arrival, we received once again proper training on the use of the facilities and the new equipment. The guidance we received from our lab technician and instructor Dr. Lempessis, in this lab, was critical for the smooth and safe lab experience that ensued.
In the following section you can find supplementary information regarding lab safety
Our project is in full compliance with the safety regulations of the competition. As we wanted to improve our project while simultaneously adhering to safety principles:
- we sought the opinion of multiple specialists in the field of Synthetic Biology and
- we additionally consulted the Bioethics Committee of Greece regarding the safety and ethics of our project (and Synthetic Biology in general) -(see our Integarted Human Practices page)-.
Upon reflection, they couldn’t pinpoint to any specific direct risks associated with our project, other than, possibly, the growing problem with antibiotic resistance. The latter was a matter that we attended to carefully.
Aptamers are widely considered as safer molecules in comparison to antibodies, as they have no antigenicity and pose no threat to humans and other organisms. They can also be very easily degraded by RNAses, which may be a problem when considering possible applications, but, on the other hand, contributes further to their low risk. In addition, we chose as a chassis organism the DH5a strain of E-coli which is a white-list organism according to the iGEM Safety committee.
Our proof-of-concept project, is by definition a very safe experiment to conduct with regards to biosafety. However, prior to beginning our wet lab work, we did identify a few potential hazards, that one could come across while running MEDEA. Below we have categorized these hazards into 3 distinct categories (Design - Experiments - Hardware) and we have coupled them with our solution strategy.
MEDEA is a groundbreaking foundational method of producing aptamers in a swift and cheap manner. As a method widely available to anyone, it was important that we consider the various applications it could have and their potential hazards. With a single literature search, thousands of applications turned up, from the improvement of laboratory techniques to diagnostics, therapeutics, industry, the environment and many more. Therefore, it was important, as a part of “Responsible Science”, that we provide as much safety and security information in our wiki as possible, so prospective users can work with a safe protocol.
In every application, the process of testing is of uttermost importance. Before any aptamer is utilized, extended measurement of its properties must take place. These should follow this order:
1. In-silico and in-vitro testing of the aptamer. Computational methods can compare the sequence against other sequences using BLAST software to exclude the possibility of unwanted effects. In-vitro testing such as voltometry can aid in the characterization of the aptamer.
2. In-vivo testing in microorganisms and/or animals, after the necessary bioethic permission has been obtained.
3. In the case of therapeutics and diagnostics, clinical trials are necessary, which have to be carefully designed and executed.
For instance: MEDEA could be used to aid in the creation of a new class of drugs, that would be thermally stable, potent and with a long shelf-life. That is why antivenoms were on the table, as we initially considered to run MEDEA on a toxin (or venom in that case), in order to produce an effective and cheap antitoxin. This reasoning led us to communicate with Piers Millett of the iGEM Safety Board, who proceeded in elaborating the processes and the precautions we would have to take, were we to work with toxins (such as consulting toxicologists and conducting these experiments in a proper environment under professional supervision).
His input is of importance not only for our team, or for this particular adaptation of MEDEA, but can rather be applied to many potential applications involving the use of toxic agents.
Ultimately, we, as iGEM Athens, decided that such side-project on venoms would be beyond the scope of our 2019 project considering the demanding iGEM timeline. However we do stress the potential it has and it’s very likely applicability.
P.S: You can read more on prospective applications (link to applications) and on the market model of MEDEA
Our Safety Checklist was inspired from our Human Practices. Read more here!
As stated in the previous section, our project aims to provide an accessible platform for aptamer production, which is safe and secure. Subsequently, even novice scientific groups can possibly use it without any risk involved. As our team supports access to science as the main axis of its human practices work, it is important that we also foresee the needs of people new to science, and particularly to synthetic biology, especially when it comes to issues such as safety.
The idea came to us during our attendance of the 25th Scientific Congress of Hellenic Medical Students, where Professor Richard R. Schulick presented an intervention his team had implemented in the Surgical Inpatient Unit, which comprised of a safety checklist for self assessment before and during each procedure. Apparently, this is a common best practice in surgical departments, as it has been shown to decrease errors and adverse events, while increasing teamwork and communication, so that it is even proposed by WHO.  Therefore, we realized it could make a great contribution to synthetic biology and iGEM, because:
1. For many participants, this is the first team research project they take part in
2. As a multidisciplinary scientific field, the proper communication between people from different backgrounds is essential
3. Safety may be sometimes undermined amidst all the different aspects of the competition
After a quick literature search we found that some institutions do provide their laboratories with safety checklists. We did review some of them and decided to adapt the Georgia Tech template, since it was the most complete one in consideration of the lab safety part. We furthermore added a second section, implementing the project safety guidelines provided by the iGEM Safety Committee, so that, after every project design modification, all the possible hazards are considered.
During the development of our checklist we came to realize that iGEM Thessaloniki was working on a checklist which could be of great use when evaluating safety standards in accordance to national and international ones. Therefore we decided to collaborate and offer recommendations to each other.
You can find our self-assessment safety form below: