Team:Wageningen UR/Safety/Twelve

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Revision as of 21:31, 21 September 2011

Building a Synchronized Oscillatory System

Biosafety and biosecurity considerations

How could parts, devices and systems be made even safer through biosafety engineering?

In the Registry of Standard Biological Parts (RSBP) catalog already Biosafety applications can be found ([http://partsregistry.org/Cell_death Cell death]). Before this year’s iGEM competition, functional, BioBrick parts and composites are solely directed towards cell lysis (composite part [http://partsregistry.org/wiki/index.php?title=Part:BBa_K112808 example], constructed by iGEM 2008 UC Berkely team). Tackling the environmental impact problem by apoptosis (or induced cell death) is headed towards the right direction in our opinion. However, by damaging the cell chassis and stopping its activity, the BioBrick part information, its DNA, is still likely to be intact. By horizontal gene transfer, other micro-organisms in the environment might cause unwanted effects on an ecosystem. We would like to stress new iGEM teams should challenge themselves in improving the self-destructing mode by regulating DNA degradation. This process is performed by Deoxyribonucleases (nucleases) [http://en.wikipedia.org/wiki/Deoxyribonuclease Deoxyribonucleases]. Applicable probably are the Endodeoxyribonucleases, found in originally the prokaryote Staphylococcus aureus: [http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease]. Eukaryotes use these nucleases during apoptosis: [http://en.wikipedia.org/wiki/Deoxyribonuclease_I DNAse I] or DNAse II; they might have to be used in combination with enzymes that increase the permeability of the nuclear envelope for proper DNA degradation. The micrococcal nuclease gene, nuc, has already been cloned into an E. coli strain. Unfortunately the nuclease is an extracellular enzyme; possibly by creating a hybrid gene a functional intracellular micrococcal nuclease hybrid can be engineered. As self-destructing mechanisms cause a halt to the activation of the system itself at a certain point, it would be necessary to implement a way of storing the nuclease (for example: by a number of nuc gene hybrid copies that upon follow each other). Also important is to engineer the conditional activation of an intracellular nuclease. Some options will be given, but there should always be looked carefully if these are different from the ones that would be used in the BioBrick system that needs to be made safe. The options (or combinations of these) are for example:

a [http://partsregistry.org/wiki/index.php?title=Part:BBa_K112402 membrane damage interacting promoter];
a [http://partsregistry.org/wiki/index.php?title=Part:BBa_S03385 cold-sensing promoter] and
a [http://partsregistry.org/Help:Promoters/Regulation multi-regulated promoter] that is negatively controlled by two molecules that are rarely seen together in environmental niches.

A list of such promoters can be found below ‘Browse by regulation and RNA polymerase’ on http://partsregistry.org/Promoters/Catalog. It's up to future iGEM teams to see if or how the biosafety BioBrick system can be realized.

After cell damage, an "emergency button" would be used by the described biosafety BioBrick system.

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-In the Registry of Standard Biological Parts’ (RSBP’) catalog already Biosafety applications can be found ([http://partsregistry.org/Cell_death Cell death]). Before this year’s iGEM competition, functional, BioBrick parts and composites are solely directed towards cell lysis (composite part [http://partsregistry.org/wiki/index.php?title=Part:BBa_K112808  example], constructed by iGEM 2008 UC Berkely team). Tackling the environmental impact problem by apoptosis (or induced cell death) is headed towards the right direction in our opinion. However, by damaging the cell chassis and stopping its activity, the BioBrick part information, its DNA, is still likely to be intact. By horizontal gene transfer, other micro-organisms in the environment might cause unwanted effects on an ecosystem. We would like to stress new iGEM teams should challenge themselves in improving the self-destructing mode by regulating DNA degradation. This process is performed by Deoxyribonucleases (nucleases) [http://en.wikipedia.org/wiki/Deoxyribonuclease Deoxyribonucleases]. Applicable probably are the Endodeoxyribonucleases, found in originally the prokaryote Staphylococcus aureus: [http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease]. Eukaryotes use these nucleases during apoptosis: [http://en.wikipedia.org/wiki/Deoxyribonuclease_I DNAse I] or DNAse II; they might have to be used in combination with enzymes that increase the permeability of the nuclear envelope for proper DNA degradation. The micrococcal nuclease gene, nuc, has already been cloned into an E. coli strain. Unfortunately the nuclease is an extracellular enzyme; possibly by creating a hybrid gene a functional intracellular micrococcal nuclease hybrid can be engineered. As self-destructing mechanisms cause a halt to the activation of the system itself at a certain point, it would be necessary to implement a way of storing the nuclease (for example: by a number of nuc gene hybrid copies that follow each other up). Also important is to engineer the conditional activation of an intracellular nuclease. Some options will be given, but there should always be looked carefully if these are different from the ones that would be used in the BioBrick system that needs to be made safe. The options (or combinations of these) are for example:
+In the Registry of Standard Biological Parts (RSBP) catalog already Biosafety applications can be found ([http://partsregistry.org/Cell_death Cell death]). Before this year’s iGEM competition, functional, BioBrick parts and composites are solely directed towards cell lysis (composite part [http://partsregistry.org/wiki/index.php?title=Part:BBa_K112808  example], constructed by iGEM 2008 UC Berkely team). Tackling the environmental impact problem by apoptosis (or induced cell death) is headed towards the right direction in our opinion. However, by damaging the cell chassis and stopping its activity, the BioBrick part information, its DNA, is still likely to be intact. By horizontal gene transfer, other micro-organisms in the environment might cause unwanted effects on an ecosystem. We would like to stress new iGEM teams should challenge themselves in improving the self-destructing mode by regulating DNA degradation. This process is performed by Deoxyribonucleases (nucleases) [http://en.wikipedia.org/wiki/Deoxyribonuclease Deoxyribonucleases]. Applicable probably are the Endodeoxyribonucleases, found in originally the prokaryote ''Staphylococcus aureus'': [http://en.wikipedia.org/wiki/Micrococcal_nuclease Micrococcal nuclease]. Eukaryotes use these nucleases during apoptosis: [http://en.wikipedia.org/wiki/Deoxyribonuclease_I DNAse I] or DNAse II; they might have to be used in combination with enzymes that increase the permeability of the nuclear envelope for proper DNA degradation. The micrococcal nuclease gene, nuc, has already been cloned into an ''E. coli'' strain. Unfortunately the nuclease is an extracellular enzyme; possibly by creating a hybrid gene a functional intracellular micrococcal nuclease hybrid can be engineered. As self-destructing mechanisms cause a halt to the activation of the system itself at a certain point, it would be necessary to implement a way of storing the nuclease (for example: by a number of nuc gene hybrid copies that upon follow each other). Also important is to engineer the conditional activation of an intracellular nuclease. Some options will be given, but there should always be looked carefully if these are different from the ones that would be used in the BioBrick system that needs to be made safe. The options (or combinations of these) are for example:
 :*a [http://partsregistry.org/wiki/index.php?title=Part:BBa_K112402 membrane damage interacting promoter];
 :*a [http://partsregistry.org/wiki/index.php?title=Part:BBa_S03385 cold-sensing promoter] and
 :*a [http://partsregistry.org/Help:Promoters/Regulation multi-regulated promoter] that is negatively controlled by two molecules that are rarely seen together in environmental niches.
-A list of such promoters can be found below ‘Browse by regulation and RNA polymerase’ on  http://partsregistry.org/Promoters/Catalog. It's up to future iGEM teams to see if or how the biosafety BioBrick system can be realized now.
+A list of such promoters can be found below ‘Browse by regulation and RNA polymerase’ on  http://partsregistry.org/Promoters/Catalog. It's up to future iGEM teams to see if or how the biosafety BioBrick system can be realized.
 [[File:The_self-destructing_mode.jpg|350px|center|thumb|After cell damage, an "emergency button" would be used by the described biosafety BioBrick system.]]
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