Our country uses a four-part „Safety Level“ rating system for laboratories. Level 4 is used for the most dangerous organisms.
This is equivalent to the WHO system. The Safety Level of our lab is Level 1 (low risk).

About our lab

Material used:
We use open benches and Laminar flow hood / biosafety cabinet with open front to handle biological materials.
We handle carcinogenic materials such as ethidium bromide or polyacrylamide under separate closable hoods. Also acidic and basic solutions are handled behind closable hoods. All radioactive materials or methods are located in a separate laboratory in the basement.
We also have a separate room for RNA work.

For protecting ourselves while doing lab chores, we use full face shields during cutting out gels or any work that involves longer exposure to UV radiation. We certainly use nitril gloves for handling any ethidium bromide and polyacrylamide contaminated materials. Safety glasses are frequently worn, especially if dangerous materials like acids, bases and liquid nitrogen are used or if there is anything that can splash like at the AKTA. Fur using -80°C freezers we use isolated gloves.
The laboratory safety training requirements of the Technical University Berlin can be found here or here (BG RCI).

All Team members received a safety training.

We collect biological waste in big containers within the lab and autoclave it later. The autoclaved waste is then taken care of by the institute. Contaminated and non-contaminated broken glas are collected separately. There is also a separate waste for carcinogenic and environmental hazardous waste like ethidium bromide gels etc.

Biosafety guidelines of the Technical University Berlin:
The Institutional Biosafety Officer (BSO) is responsible for ensuring that laboratories are working safely with biohazardous materials. This includes the periodic inspection of laboratories, developing emergency plans for handling spills and accidents and investigating laboratory accidents involving biohazardous materials. The BSO also provides technical consultation for researchers on conducting risk assessments, safety practices, and security. Environmental Health and Safety provides services necessary for biological research. These services include biomedical waste disposal, autoclave quality assurance, biosafety cabinet certification, biosafety inspections, training and emergency response. Know the hazards associated with the biological materials and procedures used in the laboratory. Follow approved lab procedures and safety guidelines. Know the emergency procedures. Complete all required training before conducting any lab activity. Utilize all required Personal Protective Equipment. Do not work alone in the laboratory.

German regulations that govern biosafety in research laboratories:

Identified possible risks
of our project

At this point we want to show that we have dealt with the possible risks of our project.
Risks to the safety and health of team members, or other people working in the lab:
We are working with E.coli, the strains we are using are characterized as non-pathogenic, BSL 1. However, we try to modify E.coli by knocking out genes - therefore, every person who is working in the lab has to take care of the possible risks. Consequently, it is mandatory to wear lab coats and gloves to minimize any risk of contamination. Also for other lab work e.g. dealing with chemicals such as Ethidium bromide, team members have to use the Personal Protective Equipment (PPE) and have to be personally instructed.
Risks to the safety and health of the general public (if any biological materials escaped from our lab):
We are using non-pathogenic E. coli strains and even our genetically modified E.coli strains are not changing the risk of pathogenic influences on human beings. Nevertheless, we are taking care to avoid any possibility of contaminating the environment with our E.coli strain or any kind of non-natural agents.
Risks to the environment (from waste disposal, or from materials escaping from our lab):
Material which was in contact with any organisms is autoclaved by normal BSL-1 procedures. Organic solvents, solutions as well as agarose gels and gloves containing Ethidium bromide are separately disposed according to the guidelines of our institution. We are strictly trying to reduce the amount of contaminated material and also the amount of consumables which are made of plastic.
Risks to security through malicious misuse by individuals, groups, or countries:
None. The entry of the BSL-1 are of our building is restricted and continuously controlled by security personnel. As our project does not create any E. coli strains or BioBricks with harmful or toxic properties, malicious misuse by other individuals is ruled out.
What new risks might arise from our project's growth?
If all of our dreams became true, one possible application of our project would be gut cancer treatment. The strains we are using are E.coli. This microorganism is ubiquitous in the human gut-system. Nobody is capable to say what would happen when our modified strains are in fact applied to a human being. It could for instance occur that the applied strain is interacting with the natural bacterial strains in the gut-system - this might provoke irritations and lead to stomach/intestinal problems. However, every developed system will change through evolution - so, nobody is capable to say what exactly will happen by application of the genetically modified E.coli. Any application should be under strict supervision and only be done by professional medical personnel.
For our possible application one could use inducible promoters. When you apply the modified E.coli strain the desired effects from BioBrick gene expression are then only induced in presence of a special non-harming chemical substance (e.g. IPTG).

Addressing the safety of free accessible probiotic E. coli Nissle Strain 1917

E. coli Nissle 1917 is a probiotic strain used for medical treatment of gastroenterological diseases. The genome structure of the probiotic strain was analyzed by Grozdanov et al. (2004) with three different approaches. While the core gene pool of organisms such as E. coli is conserved and required for basic cellular functions the flexible gene pool allows for instance for variation to enable adaptation to special growth conditions. This variability offers a potential of gaining pathogenicity within nonpathogenic (also called commensal) strains as E. coli Nissle. Grozdanov et al. claim that E. coli strain Nissle 1917 is a typical example of a nonpathogenic, commensal E. coli isolate. However, commensal E. coli strains may develop into pathogenic variants and vice versa under certain environmental conditions. Therefore, the evolutionary aspects of the development of traits of colonization and commensalism in particular strains were also studied. Nonpathogenic and pathogenic E. coli strains differ in the presence of genetic information that may contribute to specific virulence traits (virulence factors) or to successful survival and fitness of the bacteria in the host. Both nonpathogenic and pathogenic E. coli strains are able to colonize the gut and are well adapted to the conditions found in the large intestine. Most of the determinants coding for such factors are thought to be acquired by horizontal gene transfer and are often clustered on the chromosome on genomic islands. A genomic island (GEI) is part of a genome that has evidence of horizontal origins.[1]
The results of Grozdanov et al. demonstrate that factors as adhesins, iron uptake systems, and proteases do not necessarily have to be considered virulence-associated factors but can also contribute to the fitness and adaptability of nonpathogenic bacteria.[1]

Thus, many of these gained features by gene transfer can be considered rather as contributing to fitness (e.g., iron uptake systems, bacteriocins, proteases, fimbriae, and other adhesins), thereby generally increasing adaptability, competitiveness, and the ability to efficiently colonize the human body, in contrast to typical virulence factors which are directly involved in infection. This finding is supported by the findings of Grozdanov et al., indicating that DNA regions of GEI INissle 1917 to GEI IVNissle 1917 can also be detected in nonpathogenic E. coli isolates. In addition, GEIs contain multiple copies of highly homologous functional and nonfunctional ORFs of mobile genetic elements which do not directly contribute to virulence.[1]

The specific combination of characteristic features might mirror the process of evolutionary withdrawal from the pathogenic E. coli serotype O6 lineages, indicating that horizontal gene transfer, subsequent loss of horizontally acquired genetic information, and point mutations have been involved in the evolution of strain Nissle 1917.[1]

In comparing the genome content of one nonpathogenic, probiotic E. coli O6 strain with that of two UPEC (urinary pathogenic E. coli) O6 isolates, it becomes clear that it is difficult to define true virulence factors. Taken together, it depends on the niche or growth conditions (a nonpathogenic milieu such as the gastrointestinal tract versus a pathogenic milieu such as the urinary tract) to show whether certain fitness factors can also promote virulence.[1]

Bacteria of the microflora like EcN interact with the lumen of the intestine by adhering factors and biofilm formation. These organisms facilitate the exchange of nutrients and induction of the host's immunity. The interaction between intestinal flora and the host’s epithelial cells can besides genetic predisposition along with a modern diet lead to increased energy storage causing pathogenic implications for the host. Since the cause of pathogenic E. coli strains are virulence factors, these factors can promote adaptability of the strain and hence provide a broad array of diseases.[2]

In experiments of Dr. Schmidt, EcN itself appeared to be invasive in the chosen cell culture model. The propagated safety of the strain is therefore not ensured. Dr. Schmidt concluded that it is necessary to investigate the traits of EcN closer to minimize the risk for patients consuming EcN. Simultaneously a genetic modification of EcN by deletion of the mobile genetic elements can contribute to the genomes stability. This way the safety of the strain with respect to modifications of its genome, thus leading to an increase in probiotic traits, can be provided so that employment of transport vehicles for in situ expression of therapeutic molecules is also made possible for seriously ill patients. Furthermore it was shown that EcN in artificial systems such as cell cultures or gnotobiotic mice exhibit a pathogenic potential.[2]

All in all, Whether a commensal E. coli will develop into a pathogen depends not only on the acquisition of fitness-conferring genetic information enabling successful colonization of the host, but also on the presence of functional genes directly contributing to pathogenesis. [1]

[1] L. Grozdanov, C. Raasch, J. Schulze, U. Sonnenborn, G. Gottschalk, J. Hacker, U. Dobrindt, Analysis of the Genome Structure of the Nonpathogenic Probiotic Escherichia coli Strain Nissle 1917, ASM, 2004, 186, 5432-5441.

[2] D. S. Schmidt, Dissertation, Technischen Universität Dresden, 2009.

Further Literature:

The WHO website:

Show Papers dealing with different aspects of synthetic biology  

- Zheng-jun Guan, Markus Schmidt, Lei Pei, Wei Wei, and Ke-ping Ma, 2013:
- Biosafety Considerations of Synthetic Biology in the International Genetically Engineered Machine (iGEM) Competition. BioScience 63(1): 25-34 ( , online 17.08.2014)
- Acevedo-Rocha CG, Fang G, Schmidt M, Ussery DW, Danchin A, 2012: From essential to persistent genes: a functional approach to constructing synthetic life. Trends in Genetics.
- Guan Z, Pei L, Schmidt M, Wei W, 2012: Assessment and management of biosafety in synthetic biology. Biodiversity Science 20(2): 138-150.
- Schmidt M, de Lorenzo V, 2012: Synthetic constructs in/for the environment: Managing the interplay between natural and engineered Biology. FEBSLetters. Vol. 586: 2199-2206.
- Schmidt M, 2012: Synthetic Biology: Industrial and Environmental Applications. Wiley-VCH.
- Pei L, Gaisser S, Schmidt M, 2011: Synthetic Biology in the view of European public funding organisation. Public Understanding of Sciences 1: 1–14.
- Schmidt M, Pei L, 2011: Synthetic Toxicology: Where engineering meets biology and toxicology.Toxicological Sciences 120(1): 204–24.
- Schmidt M, Giersch G, 2011: DNA Synthesis and Security, in: Campbell M J, 2011: DNA Microarrays, Synthesis and Synthetic DNA.
- Schmidt M, 2011: Synthetic biology: planning for a secure future. American Institute for the Biological Sciences.
- Schmidt M, Dando M, Deplazes A, 2010: Dealing with the outer reaches of synthetic biology. Biosafety, biosecurity, IPR and ethical challenges of chemical synthetic biology. In: Luisi PL, 2011: Chemical Synthetic Biology.
- Schmidt M, Torgersen H, Schneider-Voss S, Gaszo A, 2010: Perception of Complexity, Trust, Knowledge, and Communication Skills in Gene Science: A Survey among Different Stakeholders in Austria. In Lavino J, Neumann R, 2010: Psychology of Risk Perception.
- Schmidt M, 2010: Xenobiology: A new form of life as the ultimate biosafety tool. BioEssays 32(4): 322-331.
- Schmidt M, 2009: Special issue: societal aspects of synthetic biology. Systems and Synthetic Biology 3(1-4): 1-2.
- Schmidt et al., 2009: A priority paper for the societal and ethical aspects of synthetic biology. Systems and Synthetic Biology 3(1-4): 3-7.
- Schmidt M, 2009: Do I understand what I can create? Biosafety issues in synthetic biology. Chapter 6, in: Schmidt M, Kelle A, Ganguli A, de Vriend H, 2009: Synthetic Biology. The Technoscience and its Societal Consequences.
- Schmidt M, Kelle A, Ganguli A, de Vriend H, 2009: Synthetic Biology. The Technoscience and its Societal Consequences.
- Torgersen H, 2009: Synthetic biology in society: learning from past experience? Systems and Synthetic Biology 3(1-4): 9-17.
- Kelle A, 2009: Ensuring the security of synthetic biology—towards a 5P governance strategy. Systems and Synthetic Biology 3(1-4): 85-90.
- Marliere P, 2009: The farther, the safer: a manifesto for securely navigating synthetic species away from the old living world. Systems and Synthetic Biology 3(1-4): 77-84.
- Deplazes A, Huppenbauer M, 2009: Synthetic organisms and living machines: Positioning the products of synthetic biology at the borderline between living and non-living matter. Systems and Synthetic Biology 3(1-4): 55-63.
- Kelle A, 2009: Synthetic biology and biosecurity. From low levels of awareness to a comprehensive strategy. EMBO Reports 10: 1; 23–7.
- Deplazes A, 2009: Piecing together a puzzle. An exposition of synthetic biology. EMBO Reports 10: 428-432.
- Ganguli-Mitra A, Schmidt M, Torgersen H, Deplazes A, Biller-Andorno N, 2009: Of Newtons and heretics. Nature Biotechnology 27(4): 321– 2.
- Schmidt M, Torgersen H, Ganguli-Mitra A, Kelle A, Deplazes A, Biller-Andorno N, 2008: SYNBIOSAFE e-conference: online community discussion on the societal aspects of synthetic biology. Systems and Synthetic Biology 2(1-2): 7-17.
- Schmidt M, Biller-Andorno N, Deplazes A, Ganguli-Mitra A, Kelle A, Torgersen H, 2008: Background document for the SYNBIOSAFE e-conference. Organisation for International Dialogue and Conflict Management.
- SYNBIOSAFE, 2008: Compilation of all SYNBIOSAFE e-conference contributions.
- Schmidt M, 2008: Diffusion of synthetic biology: a challenge to biosafety. Systems and Synthetic Biology 2(1-2): 1-6.
- Schmidt M, 2008: Microbesoft? Biomaschinen und ihre Auswirkungen. 14(7).
- Kelle A, 2007: Synthetic Biology and Biosecurity Awareness In Europe. Bradford Science and Technology Report 9.
- Meinhart C, Schmidt M, 2007: Interviews with 15 key synthetic biology experts.
- Schmidt M, 2006: Public will fear biological accidents, not just attacks. Nature 441(7097): 1048.

Show Papers dealing with sociotal issues of synthetic biology  

- Markus Schmidt, Agomoni Ganguli-Mitra, Helge Torgersen, Alexander Kelle, Anna Deplazes, Nikola Biller-Andorno, 2009: A priority paper for the societal and ethical aspects of synthetic biology. Systems and Synthetic Biology 3(1-4): 3-7.
- Calvert J, Martin P, 2009: The role of social scientists in synthetic biology. EMBO reports 10(3): 201–204.
- Bedau M, Parke, EC, 2008: The Ethics of Protocells. Moral and Social Implications of Creating Life in the Laboratory. MIT Press.
- Pauwels E, 2008: Trends in American and European Press Coverage of Synthetic Biology.Woodrow Wilson International Center for Scholars.
- Boldt J and Müller O, 2008: Newtons of the leaves of grass. Nature Biotechnology 4: 387-389.
- O’Malley M, Powell A, Davies JF, Calvert J, 2008: Knowledge-making distinctions in synthetic biology. BioEssays 30(1): 57.
- Bernauer H et al., 2008: Technical solutions for biosecurity in synthetic biology. IASB Industry Association Synthetic Biology.
- Garfinkel M, Endy D, Epstein GL, Friedman RM, 2007: Synthetic Genomics – Options for Governance.
- Selgelid M, 2007: The tale of two studies: Ethics, Bioterrorism, and the Censorship of Science. Hastings Center Report 37(3): 35-43.
- van Est R, de Vriend H, Walhout B, 2007: The world of synthetic biology. Rathenau Institute, The Hague Netherlands.
- Rai A, and Boyle J, 2007: Synthetic Biology: Caught between Property Rights, the Public Domain, and the Commons. PLoS Biol. 13;5(3): e58.
- ETC Group, 2007: Extreme Genetic Engineering: ETC Group Releases Report on Synthetic Biology.
- Tucker JB and Zilinska RA., 2006: The Promise and Perils of Synthetic Biology. The new Atlantis: 25-45.
- Check E, 2006: Synthetic biologists try to calm fears. Nature 441( 7092): 388-389.
- Bhutkar A, 2005: Synthetic Biology: Navigating the Challenges Ahead. J. BIOLAW & BUS 8(2): 19-29.
- Tumpej TM et al., 2005: Characterization of the Reconstructed 1918 Spanish Influenza Pandemic Virus. Science 310(5745): 77-80.
- Sharp P A, 2005: 1918 Flu and Responsible Science. Science 310(5745): 17.
- Church G, 2005: Let us go forth and safely multiply. Nature 438: 423.
- Balmer A, Martin P, 2008: Synthetic Biology. Social and Ethical Challenges. Institute for Science and Society. University of Nottingham
- IRGC, 2008: Concept note: Synthetic Biology. Risks and opportunities of an emerging field. International Risk Governance Council, Geneva:
- De Vriend, H, 2006: Constructing Life. Early social reflections on the emerging field of synthetic biology. The Hague: Rathenau Institute;Working Document 97.
- European Commission, 2005: Synthetic Biology: Applying Engineering to Biology ). Report 21796.