English Version

Many people know those movies: an accident at a laboratory of a ruthless multinational company and soon almost whole mankind mutates to all sorts of strange creatures. In the majority of these cases muscled armed forces march up and shoot at everything that comes across their ways. Thus it's not astonishing that some people I was talking to had exactly this pictures from movies and computer games on their minds during our conversation about synthetic biology and biosafety. But can this myth from Hollywood bear reality?

During my commitment at the firefighters I already got to knew some courses of action to ensure ABC-safety and experienced such an effort myself (fortunately just a false alarm – as it turned out afterwards). Now the opportunity arouse to visit the open day at the ABC-defense regiment of the German military forces to receive an impression of the alleged “Rambos”.

After arrival at the barracks we were welcome by some friendly men in uniforms who gave us a tour and patiently answered our questions about their jobs. Numerous demonstrations and stands informed about the wide range of duties. We gained deep insights into a world beyond our cuddly lab. For instance, the armoured reconnaissance vehicle „Fuchs“ as a „mobile laboratory“ offers the opportunity to detect radioactive and chemical contamination directly on-site. In cases of biological weapons or compounds sample taking for analysis in an facility assigned for this purpose is also possible. Sophisticated filtering systems, mobile mass spectrometers and numerous other assistive equipment enable missions at locations where most people would usually rather reluctantly go for a drive at.

After Missions within safety zones around contaminated areas, of course materials and persons have to be decontaminated. Impressively the forces demonstrated this multi-step process. At this the whole procedure from sample taking by the tank Fuchs to decontamination of the rubber boots of the ABC-protection suits with decontaminating agents were shown. Finally persons enter the decontamination tent, which works therefore as a lock-like passage between the safety area and surroundings. There potentially contaminated persons have to wash themselves according to orders and put on new clothes. Efforts and throughput were remarkable and, of course, of an other dimension as our hand disinfection in the laboratory. Further materials for detoxification and decontamination were available on trucks after detection.

The scope of duties of the ABC-defense regiment proved to be more diverse than expected. Even water conditioning, hygiene measures, weather observations or actions to rescue or fire fighting belong to range of tasks.

Not only military conflicts belong to the operational area of the ABC-defense regiment, but also humanitarian emergencies, support at huge events (e.g. G8 conference or the football world championship in Germany) or containment of pathogens (for example the Influenza A/H5N1 pandemia in Germany 2006).

Beside all kinds of other exciting experiences, as an dark obstacle course which had to be passed with a nightscope, we were able to talk to several people about biosafety and synthetic biology. Unfortunately, we cannot present an official statement here, but recommend the books “Biologische Gefahren I” and “Biologische Gefahren II” of the Bundesamt für Bevölkerungsschutz und Katastrophenhilfe together with the Robert-Koch-Institut referring to biological threats.

The day at the barracks has been a very exciting change and attracted many visitors of the non-military population. The German military forces presented themselves as a team of specialists endeavored to avert damage at the hazard of their lives. Wannabe lone fighters couldn't be found.

German Version

Viele Menschen kennen diese Filme: ein Laborunfall in einem skrupellosen multinationalen Konzern und schon mutiert, bis auf wenige Ausnahmen, die gesamte Menschheit zu allerhand seltsamer Kreaturen. Meistens rücken in diesen Fällen mit Muskeln bepackte Streitkräfte an und beschießen alles was in ihren Weg kommt. Wenig verwunderlich, dass einige Menschen mit denen ich gesprochen habe genau dieses Bild aus Filmen oder Computerspielen vor Augen haben, wenn ich mit ihnen über synthetische Biologie und Biosicherheit spreche. Aber kann der Hollywood-Mythos der Realität standhalten?

Über mein Engagement bei der Feuerwehr kenne ich bereits einige Abläufe zur Gewährleistung der ABC-Sicherheit und konnte schon an einem derartigen Einsatz teilnehmen (glücklicherweise Fehlalarm – wie sich hinterher herausstellte). Nun bot sich die Gelegenheit beim Tag der offenen Tür des ABC-Abwehrregiments der deutschen Bundeswehr ein Mal selbst einen Eindruck von den vermeintlichen Rambos zu gewinnen.

In der Kaserne angekommen wurden wir von einigen freundlichen uniformierten Herren begrüßt, die uns herumführten und uns geduldig Fragen zu ihrem Beruf beantworteten. Zahlreiche Vorführungen und Stände informierten über das Einsatzspektrum und verschafften tiefere Einblicke in eine Welt fern ab von unserem kuscheligen Labor. Der Spürpanzer „Fuchs“ als „mobiles Labor“ bietet dabei die Möglichkeit radioaktive und chemische Kontamination direkt vor Ort in einer Erstanalyse zu detektieren. Im Falle biologischer Waffen ist eine Probennahme zur Analyse in einer dafür bestimmten Einrichtung möglich. Ausgefeilte Filtersysteme, mobile Massenspektrometer und zahlreiche andere technische Hilfsmittel ermöglichen den Einsatz an Orten, an denen man normalerweise eher ungern spazieren fahren würde.

Nach Einsätzen innerhalb von Sicherheitszonen um entsprechende Kontaminationsstellen müssen natürlich Materialien und Personen dekontaminiert werden. Eindrucksvoll wurde uns dieser mehrstufige Prozess demonstriert. Hierbei wurde der gesamte Vorgang von der Probennahme durch den Panzer Fuchs bis hin zur Behandlung des Gummistiefel des ABC-Anzuges mit Dekontaminationsmittel gezeigt. Der schleusen-artige Übergang durch das Dekontaminationszelt, in dem sich potentiell kontaminierte Personen nach Anweisungen duschen und umziehen mussten stellte hierbei den letzten Schritt dar. Der Aufwand und Durchsatz waren beachtlich und natürlich in einer ganz anderen Größenordnung angesetzt als unserer Händedesinfektion im Labor. Auf LKWs wurde weiteres Material zur Entgiftung, Entstrahlung und Entseuchung nach der Detektion vorgehalten.

Das Aufgabenfeld des ABC-Abwehrregiments erweist sich jedoch vielfältiger als gedacht, denn auch die Wasseraufbereitung, Hygienemaßnahmen, Wetterbeobachtung oder Maßnahmen zur Rettung, Bergung oder Brandbekämpfung fallen in das Aufgabenspektrum.

Zum Einsatzgebiet des Regiments zählen neben Einsätzen in militärischen Konflikten auch humanitäre Einsätze oder die Unterstützung bei Großereignissen (z.B. G8 oder Fußball-Weltmeisterschaft in Deutschland), oder der Eindämmung von Pathogenen (z.B. Influenza A/H5N1 (2006)).

Neben allerhand anderer spannender Erlebnisse, wie einem Hindernisparkour im Dunkeln mit Nachtsichtgeräten, kamen wir mit einigen Personen über Biosicherheit ins Gespräch. Leider können wir an dieser Stelle keine offizielle Stellungnahme präsentieren, empfehlen jedoch das Buch “Biologische Gefahren I” und “Biologische Gefahren II” des Bundesamts für Bevölkerungsschutz und Katastrophenhilfe sowie des Robert Koch-Instituts im Bezug auf biologische Gefahrenlagen.

Der Tag in der Kaserne war eine sehr spannende Abwechslung und zog reges Interesse der Bevölkerung auf sich. Die Bundeswehr präsentierte sich als ein Team von Spezialisten bemüht um Abwendung von Schaden unter Einsatz ihres Lebens. Möchtegern-Einzelkämpfer waren hier nicht zu finden.

Cybersafety

Our software team developed the NRPSDesigner, a web application capable of suggesting cloning strategies for the creation of artificial NRP-synthetases, which can synthesize a peptide of choice. The very nature of this project meant that we were confronted with safety issues all web developers face, as well as by issues specific to the biological underpinnings of our software. The latter overlapped in many cases with our considerations throughout the wetlab projects.

Any web application has to deal with diverse attacks of malicious intent. Dealing with these was simplified by using Django, a stable web framework. Such frameworks try to trivialize common tasks in the work of a web developer and of course safety issues fall into this category. For example, Django provides a mechanism for [https://docs.djangoproject.com/en/1.5/ref/contrib/csrf/ protection] against cross site request forgery attempts, in which a malicious site can cause actions in the server by using the credentials of a logged-in user. The Django development team also uses a very strict [https://docs.djangoproject.com/en/dev/internals/security/ process] for dealing with new security issues in a timely and safe fashion by initially fixing these through private, confidential channels. Once the patches have been applied, the security issue is publicly disclosed, so that server maintainers can update to the latest Django version. As an example, this September a set of [https://www.djangoproject.com/weblog/2013/sep/15/security/ security releases] were issued by the Django development team in order to remedy a problem with denial-of-service (DoS) attacks. Of course, after being informed of this release, we immediately updated the Django version running on our server to the latest one.

A second issue arising during web development, is the safety of a user's confidential data. Again Django provides an in-built authentication system which encrypts the password of all registered users using PBKDF2 (Password-Based Key Derivation Function 2). Beyond the Django security features, we also used a password protected storage server for the MySQL NRPSDesigner database.

In regards to the biological background of the NRPSDesigner software, we were particularly troubled about not leading a user astray with the organisms suggested for the cloning, especially in case they were not of the S1 safety level. This is particular important in the case of NRPS, because many interesting NRPS such as Pyoverdine, a fluorescent siderophore, are produced by pathogenic microorganisms (e.g. ''Pseudomonas aeruginosa''). As of the European wiki freeze, the NRPSDesigner database includes only S1 organisms. Nevertheless, as in the future the database may be expanded with S2 organisms, we intend to handle such cases by issuing appropriate alert messages to the end-user and also allowing him to filter the domains available to his constructs based on the safety level.

A second consideration arises from the extensibility of the NRPSDesigner database, which means that any user can enter new NRPS domain sequences. These in turn are fed into the algorithm for the design of synthetic NRPS constructs. Thus it is important to ensure that no malicious sequence can be entered, which could then be returned as the output of the NRPSDesigner to an unsuspecting user. This is achieved by ensuring the correct domains have been entered by use of the automated domain prediction pipeline using Hidden Markov Models. Additionally, a user that wants to be particularly safe, can filter the domains available to the NRPSDesigner algorithm according to curation status. (Curated domains have been entered or validated by an iGEM Heidelberg or Edinburgh 2013 team member or by another NRPS specialist in contrast to domains that have been entered by other end-users.) The other non-NRPS sequences, such as backbones, promoters etc., which can be added to the constructs after the domains have been determined by the software, are specific to the user that entered them (e.g. by the automated interface to the API of the Parts Registry) and hence pose no danger to other users.

Another important safety issue arising from the theoretical underpinnings of the NRPSDesigner is its use for the malicious synthesis of toxic peptides. Thus in a future version we want to integrate information from databases on toxins in order disable the design of NRPS domains for toxic peptides. We also searched for peptide toxicity prediction tools which could be integrated with the NRPSDesigner. One such tool, called ToxinPred , uses machine learning methods and a dataset of 1805 toxic peptides in order to accomplish this very task. Unfortunately, the current implementation only considers peptides consisting of proteinogenic amino acids and not the variety of modified or D-amino acids available to NRP-synthetases.