Team:Pasteur Paris/Safety




A major concern of our project is to prevent any risk for the environment and the human body. The genetically modified Escherichia coli must not leave the biofilm because they could have unintended environmental or health consequences. In order to avoid collateral damage, we implemented two barriers to prevent the genetically modified bacteria to spread outside the biofilm.

The first barrier is a physical one: the biofilm is contained inside a membrane having small pores that the bacteria cannot pass because of its size. The biocompatible membrane, made of aluminum oxide and covered by a polymer, has a porosity of 0.2 micrometers which is smaller than the size of the bacteria composing the biofilm. The second barrier is a biological one, that we integrated into the genetically modified E. coli forming the biofilm. Indeed, we worked on a kill switch that is cryo-sensitive. The bacteria will die when they leave the prosthesis and go in an environment that has a temperature lower than 37°C. In practice, the kill switch is fully effective when the temperature is lower than 22°C. The membrane and the kill switch confine the bacteria inside our device, so they won’t spread inside the human body or the environment.

This video explains in simple terms how the kill switch works. It was made with an educational intent and is dedicated mainly to children. We featured two bacteria in the biofilm that explain the objective of this biological barrier.


General reglementation

During one day as a lab worker, you may have to work in laboratories with different biosafety levels. There is a classification which takes into consideration the organism used, the equipment needed and the procedures you have to follow. Mainly, BSL-1 and BSL-2 are used for research and are allowed for iGEM. An important point is that rules are cumulative, it means that in BSL-2 you have to apply BSL-1 rules and BSL-2 rules.

BSL-1: a basic laboratory with a biosafety level 1

This laboratory is used for basic teaching and research. In this lab, you have to use good microbiological techniques (GMT). GMT rules should be applied every time you work with any microorganism, regardless the biosafety level. No safety equipment is required except an open bench work, proper personal equipment as lab coat, gloves and googles, and proper waste disposal. No isolation of laboratory is required.

BSL-2: a basic laboratory with a biosafety level 2

This laboratory is used for primary health services, diagnostic services and research. As a BSL-1 lab, you have to adopt GMT practices and wear protective clothing. In this lab, you will see the biohazard sign. Along with the bench work, you must have a class II BSC: a biological safety cabinet and a protection against potential aerosols. No isolation of laboratory is required. Closed doors are required.

BSL-3: the containment laboratory with a biosafety level 3

This laboratory is used for special diagnostic services and research. You must wear special clothing. This lab is controlled for its access, and has a directional airflow. As BSL-2 lab, this lab requires a class III BSC and other primary devices for special activities. Thus, isolation of laboratory is required.

BSL-4: the maximum containment laboratory with a biosafety level 4

This laboratory is a dangerous pathogen unit. In this lab, you have an airlock entry, a shower exit, and special waste disposal. Safety equipment is composed of a class III BSC with a double-ended autoclave. Moreover, the air is always filtered. Thus, isolation of laboratory is required.
In this lab, you must pay attention to personal safety monitoring capability: indeed, you must have a closed-circuit television and a two-way communication for example.

Safety in our lab

Working in a laboratory implies following many rules to ensure maximal safety, both for the workers and for the environment. To make the best out of our iGEM experience, we all followed a formation on Good Laboratory Practices at the beginning of the summer. Then, we made sure that each and every rule was followed properly.

To ensure workers protection, adequate equipment was worn for all manipulations. Glasses, lab coat, and gloves are the standard in a biology laboratory (Figure 2). Specific rules also apply to everyone. People with long hair must attach them, and everybody must wear clothes that cover all part of their body. Open shoes are not authorized in order to make sure no accidents happen. If any accident happens whatsoever, the laboratory is equipped with a shower and an emergency eye wash (Figure 1).

Figure 2: Our laboratory equipment

To preserve the environment from the sometimes-dangerous products used in the laboratory, every waste has to be taken care of depending on its nature. Six types of bins were at our disposition: biohazard, chemical and CMR (Carcinogenic, Mutagenic, Reprotoxic), one large bin for solids and one jerrycan for liquids, for each type of waste Figure 3). Waste is sorted in each category following an important hierarchy. If a waste contains any CMR product, it must go to the CMR bin, independently of the nature of its other compounds. Then, if a waste is both of biological and chemical nature, it must be treated as biological.

Once full, these different containers are sealed and brought to a place called “îlot-déchêts” in French. This place is a restricted area in which wastes are stored until they are taken in charge by companies specialized in their treatment (Figures 4 and 5). It also serves as a reserve to take a new empty bin once the sealed one is left there.

Figures 4 and 5 : Waste storage, restricted area


Ethics in the NeuronArch Project

When speaking about ethics, we generally think about the branch of philosophy that studies the concept of good and evil. Indeed, it is a general way to describe ethics, which is gaining in importance in the scientific field. It is important to note that ethics and law do not totally overlap. Something can be illegal and ethical, while something else can be legal but unethical. It is also important to note that ethical rules can have different sources such as State, committees, scientific panel, etc. As our project aims to enhance the living conditions of amputees, it is closely linked to human health. Research on human beings includes the use of biological samples, psychological studies, personal data, interviews, observations, etc. As we wanted to know more about the living conditions of amputees, we decided to meet the committee of the Institut Pasteur in charge of helping scientists concerning ethical questions.

The Open Desk at Institut Pasteur

In order to better understand the functioning of the committee in charge of ethics at Institut Pasteur concerning research on human beings, we interviewed Dr. Odile Gelpi, Director of medical affairs and public health at the Institut Pasteur.

A committee has been created within the Institut Pasteur, in charge of advising researchers on ethical questions concerning human research. This committee meets during sessions called “Open Desk”, which have been set up since the end of 2016. The aim of the Open Desk is to facilitate exchanges concerning ethics and to guide researchers. The advantage of the Open Desk is that everyone is gathered in one session, which permits a more in-depth discussion with a confluence of different points of view and an overview of all ethical questions the researcher has to pay attention to.

The Open Desk is mainly directed by the translational research department. However, the Open desk committee’s composition is diverse, with persons coming from different departments. Moreover, the composition of the committee is adapted as much as possible to the subject presented.

It is important to note that the goal of the Open Desk is to help researchers to be conscious of all the ethical aspects their research are related to. The Open Desk we presented in front of was related to human research, however, other Open Desks exist such as the Open Desk concerning research on animals.

Presentation of the NeuronArch project at the Open Desk

As Human practices are an integral part of the iGEM competition, and as we must think about the impact of our project as a whole on the society, we wanted to create a survey in order to have a better understanding of people’s opinion about our project. As we also wanted to better understand the everyday life of amputees and people wearing prostheses, we thought about interviewing volunteers. However, as those type of information are personal and medical data, we thought we should talk about our plans to the committee.

We decided to present our project in front of the committee for them to give us an outside perspective of our work. They took the time to explain to us that interviewing amputees and people wearing prostheses was, indeed, human research and that the people we were interviewing had to be seen as patients. They pointed out the fact that, as students, we did not have the qualifications to talk about such subjects, and that we would need the help of a psychiatrist.

However, they suggested that we could talk to health professionals and association representatives instead, so we would be able to collect information about patients.

Inclusion of GDPR concerns in our survey

In the context of the human practices we also wanted to study how people perceive synthetic biology, GMOs and our project. We decided to create a survey using the Google Form Platform. However, we had to pay close attention to the General Data Protection Regulation (GDPR), which is applicable since May 25th, 2018. To conform to the GDPR, we made sure that:

  • Those polled were informed about the aim of our study and the use of the data they would give.
  • Those polled accepted or refused the use of their answers in the context of the survey and of the iGEM competition. They had two options: they could agree to the data collection and analysis or refuse. In the case of a refusal, they would not be able to answer the survey. These boxes were the way we chose to attract their attention to the data collection.
  • We only asked for data that were significant and genuinely useful to our study.

Indeed, article 4 of the GDPR defines personal data as “any information relating to an identified or identifiable natural person (‘data subject’); an identifiable natural person is one who can be identified, directly or indirectly, in particular by reference to an identifier such as a name, an identification number, location data, an online identifier or to one or more factors specific to the physical, physiological, genetic, mental, economic, cultural or social identity of that natural person”. We then tried to ask for pieces of information that were relevant to our study and we made sure that those polled were not identifiable through collected information. We asked for gender, age and scientific background for the French survey (and the nationality for the international survey). Those pieces of information, as they do not allow us to identify a person, are not considered as personal data.

Ethical reflections concerning lab experiments

Apart from ethical questions surrounding personal data and human research, questions have also been raised concerning our lab experiments using neuronal cells. Indeed, one important component of our experimental part included the establishment of a model for the interface of our biofilm with neurons. We initially planned to perform dissection of dorsal root ganglia from E18 rats to obtain primary neuronal cells which would be placed in culture. The impact of our biofilm would then be studied in providing growth factors. However, within our team, we raised the question of whether there was a better way to have access to neuronal cells. This led to a discussion about dissection in general.

We decided to include this theme in the Parisian Meetup we organized. The Parisian Meetup of 7th July 2018 was composed of two parts, one was dedicated to a rehearsal session of all teams, and the second part was dedicated to roundtables about ethics in biology. Each roundtable was composed of 1 speaker and around 10 team members. We invited people from the National animal well-being committee, law, ethics education, and human evolution forecasters, allowing each team members to discuss and exchange their opinions about ethics in biology and general science.

After a discussion within our team, we tried to find another way to make our experiment using primary neuronal cells, without taking them directly from a rat. Even though our experiment necessarily implies the use of rat’s neuronal cells, we finally decided to order E18 rat cortexes from the company Brainbits, instead of taking them directly from rats. Our reasoning was the following: as we were only taking the part we needed, other parts of the rat would be used by other customers.

What is the role of ethics in research?

As simple as it might appear, this question is in reality, a very wide and tricky one. We asked Dr. Odile Gelpi about this question. One big role of Ethics in the field of science is the question of the balance between risks and interests. Indeed, as noted by Mrs. Gelpi, “scientific knowledge cannot be acquired at any cost”. It is also important to note that ethics is closely related to culture. Although international ethical principles are applied almost everywhere, some rules or point of views can differ. For example, when talking about the balance of interest between risks and interests, the issue of this balance can differ according to whether you analyze the interest from the point of view of the patient as an individual or from the point of view of the society, who could benefit from this research. The topic of ethics is a tricky subject, which needs the gathering of different points of view to be analyzed in the best way.