Talk:Pushing the P1

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Keep in mind that for storing competent bacteria, skim milk is superior to glycerol. See the numbers of recoveries after hurricane Katrina here http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2551311/

We can start without -80 °C. In old times, the postdoc would grow bacteria overnight, make them competent in the morning, transform them in the evening.

Old Hackpad Page

Wanna go P1 ? Introduction: Ultimately one of our fixed goal is to be able to work in a P1 environment. This would open the doors to a vast range of experimental possibilities and a important value added to a space like ours. But like Stanley Martin Lieber said: "With great power comes great responsibilities". This quote in my opinion reflects with exactitude what working with a P1 is. On one hand greater experimentation freedom could come out of a space like this, most probably wider impact results, the scientific thrill of getting access to advanced biotechnological tools & a bigger ponderation among the scientific community be it corporative & academic. On the other hand, the risks of environmental bacteriological releases, a stricter working condition, the need of righteous, self disciplined collaborators and neatly defined boundaries and follow up procedures are a counterpart that should not be overlooked. I strongly believe achieving such performances is in our reach and working towards it is, per se, a goal worth investing energy and capitals in.

A word on micro-organisms safety denomination: You can find a decent summary on wiki: http://en.wikipedia.org/wiki/Biosafety_level

Requirements: Legal & Ethics: Defining boundaries is a first step towards such achievement. What better guidelines is there than the Federal Act on Non-Human Gene Technology (LGG), The Ordinance on Handling Organisms in Contained Systems (OUC) and the WHO's manuel de sécurité en laboratoire (MSBL). Note that any legal act is studied in french since it has no legal power in English. Here I try to answer several questions using those two base texts and my day-to-day life in a P1 lab as a chemical biology PhD student but first a small summary on the main ideas and intentions contained in both texts:

LGG: The LGG has as main goal to protect and to serve welfare of all living beings against abuses in genetical engineering (GE). The aim of LGG is to protect the health and safety, conserve the biological diversity & to ensure respect to all living beings. It also precludes hazards and harms caused by GE. MSBL: The MSBL is focused on good laboratory practices, security means to avoid hazards and harms & takes on the topic of international regimentation on GE and GMO transport. The MSBL gives extensive guidelines on the the good microbiology techniques (GMT). This document is the milestone in the ethics and GMO management and most of its items go far beyond what is the scope of our goal. The take home message: Safety, standardized procedures & professionalism! The following document is a good summary of what is asked to get a P1 and the general legislative implications http://www.cusstr.ch/repository/133.pdf

What requirements / equipment is needed for a lab to be a P1 lab ? What formation is needed for the coworkers to work in a P1 lab ? What is the range of activities allowed in a P1 lab ? How should the waste be treated ? How should the incoming and outgoing accesses to the lab be limited & controlled ? What personal protective equipment is required in a P1 lab ? Working zone behavior: what is the good behavior and how should the work bench be treated ? To whom should we announce our will to work with GMOs and to whom should we notify our activities ? other obligations

a: What requirements / equipment is needed for a lab to be a P1 lab ? from MSBL: People should have a standardized, basic microbiology formation and strictly follow good laboratory practice. Material wise the safety is limited and work can be done in the open. Any apparatus can be operated in the same room no separated room for certain operations is needed. ref: page 1 to 4

b: What formation is needed for the coworkers to work in a P1 lab ? from MSBL: GMT are a must! They increase the safety of all occupants and the operator. Every lab has to be equipped with manuals describing the operation of each tool, microbiology operation and safety measures. All security means necessary have to be taken into account and organized such that every member working in the P1 area knows how to react and operate the safety means and procedures. ref: page 9 - 10 Continuous "on the fly " formation and safety sensitization of the collaborators has to be a day-to-day task. ref: page 18

c: What is the range of activities allowed in a P1 lab ? from MSBL: If a lab is doing biological analysis, Biological Safety 2 (BS2) is to be observed since the samples are not always known. (Item needs to be studied in greater detail / it is not in the scope of our goal) ref: page 9 from experience: Organisms modification can be made, iGEM style, through building blocks or standardized procedures.

d: How should the waste be treated ? from MSBL: Contaminated fluids and solids have to be decontaminated by chemical or physical means. Different compartments have to exist in order to store separately non contaminated wastes, cutting or sharp objects (syringes), contaminated solids & contaminated liquids. ref: page 19-21 from experience: Liquids are neutralized with 20% bleach. Solids are autoclaved in a double layer of plastic bags before being thrown away. (Question: do we need a special waste service ? ) . Usually needles are not used in microbiology and molecular biology. A document describing the process has to be available. from cusstr: All wastes contaminated by GMO have to be inactivated (autoclave) before being eliminated by a normal waste treatment.

e: How should the incoming and outgoing accesses to the lab be limited & controlled ? from MSBL: No person foreign to the working area is allowed to penetrate the working zone. Lab doors have to be closed and have a log and locking system. No kids and pets are allowed in the working zone. ref page 10-11

f: What personal protective equipment is required in a P1 lab / What are the security requirements? from MSBL: (non exhaustive list - removed common sense articles...) The standard "chemistry blouse" is to be worn. Appropriate gloves have to be worn when manipulating biological material and hands must be disinfected afterwards. No food is allowed in the lab. No open shoes are allowed in the lab. ref: page 10 to 15 from OUC: Art 12. safety measures: The general safety measures listed in Annex 4 and the special safety measures required according to the type and class of activity must be taken, and an operational safety concept must be devised. The safety measures taken must take account of the risk determined in the individual case and the state of the art of safety technology.

g: Working zone behavior: what is the good behavior and how should the work bench be treated ? from MSBL: The bench has to be clean of work unrelated objects and disinfected at the end of the day. Every piece of material has to be decontaminated before being thrown away or cleaned if reused. from experience: Cluttering is quite common. Anyhow you still have lots of space to work and nothing unrelated is on the benches.

h: To whom should we announce our will to work with GMOs and to whom should we notify our activities ? from OUC: Art 8: Any person who wishes to carry out Class 1 activities with genetically modified organisms must notify this globally, at the latest when beginning the activities.

Art. 11: Submission to the authorities Notifications and authorisation applications must be submitted to the Federal Coordination Centre for Biotechnology. (BAFU) Notifications and authorisation applications must include the information listed in Annex 3. In the information, procedures and methods related in their nature, extent and purpose may be summarised. The information may be entered directly into the electronic database provided by the Federal Coordination Centre for Biotechnology. i: other obligations: from OUC:

Documents World Health Organisation (MSBL): WHO's manuel de sécurité en laboratoire Loi sur le Genie Genetique (LGG):

Federal Act on Non-Human Gene Technology 

Loi fédérale sur la protection de l'environnement (LPE): http://www.admin.ch/opc/fr/classified-compilation/19830267/index.html Loi fédérale sur la lutte contre les maladies transmissibles de l'homme (Loi sur les épidémies) http://www.admin.ch/opc/fr/classified-compilation/19700277/index.html Loi du 1er juillet 1966 sur les épizooties (LFE) http://www.admin.ch/opc/fr/classified-compilation/19660145/index.html Ordonnance sur l’utilisation d’organismes dans l’environnement (ODE) http://www.admin.ch/opc/fr/classified-compilation/20062651/index.html Ordonnance sur la protection des travailleurs contre les risques liés aux microorganismes (OPTM) http://www.admin.ch/opc/fr/classified-compilation/19994946/index.html

Ordonnance sur l’utilisation des organismes en milieu confiné (OUC)

http://www.admin.ch/opc/fr/classified-compilation/20100803/index.html

Autorities Bureau de biotechnologie de la Confédération (BAFU) http://www.bafu.admin.ch/biotechnologie/01744/01745/index.html?lang=fr http://www.efbs.admin.ch/fr/themes/index.html

Waste treatment According to the following document and from the EPFL and UNIL directives, elimination of wastes in a P1 environment is pretty straightforward. Both liquid wastes and solid wastes can be autoclaved. Autoclaved liquid wastes can be the poored down the drain, solid wastes have to be transferred to a white and red thick plastic bag and be eliminated according to the procedure 18 01 03 ds on the OMoD website. Usually the town seems to be able to proceed to such wastes evacuation.

refs: general : http://www.cusstr.ch/repository/133.pdf EPFL : http://www.cusstr.ch/repository/175.pdf UNIL : http://www.unil.ch/files/live//sites/fbm/files/shared/securite/Pro_032_traitement_dechet_01.pdf OMoD : https://www.veva-online.admin.ch/

Therefore, we can expect to generate little amount of solid wastes and the only real problem now is to set fixed rules on the usage of the lab as a P1 Lab.


What's next then ? Honestly I think we are not prepared for that yet. Material and organisation wise much needs to be done. The lab should be more clearly defined in terms of space enclosures, meaning the access to Hackuarium should not directly communicate with the green space and the outside but people should enter FROM the green space and the though the conference room and afterwards if part of the team or coming for a visit (and therefore escorted) be allowed inside. In terms of instruments, a clear operation booklet is to be put close to it, people should have a formation by a member. Instrument usage should be monitored to make sure they are functional and not getting used in a incorrect way. In terms of manipulation, none should be allowed without a proper formation. And the documentation should be much more thorough! The project follow up have to be thorough, nobody should be allowed to do a project without the accordance of the board and without a clear project file explaining what will be done, trough which modifications, using which bio-tool or transformation. There should be common stocks, like electricians have a rack with components, we biologist should have a freezer with common competent cells, common base plasmids, common stock solutions. The need of a -80°C freezer.