Team:Wageningen UR/Safety

From 2012.igem.org

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== Introduction ==
== Introduction ==
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Our project is about viral coat proteins, produced in and extracted from ''E. coli'', that are fused to a coil for standardized attachment of ligands or structures to Virus-Like Particles (VLPs). One of the main reasons for our team to choose this project over some of our other brainstorm ideas is the relative safety of the end product. We envision an end product that is completely DNA-free and non-replicative. We think that such a product, once well purified, could be used in all kinds of processes without possessing any of the hazards and risks that are usually associated with Genetically Modified Organisms.
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Within the realm of synthetic biology, a lot of effort is put towards controlling GMOs after their release in a natural environment. Kill-switches and substrate dependencies are developed with increasing effectivity. Especially in iGEMs medical track, ‘safety of application’ considerations often involve double or even triple safety mechanisms that have to be inserted into the organism of choice. However, as was discussed in the [https://2012.igem.org/Regions/Europe/MeetingofYoungMinds Meeting of Young Minds] and various other platforms, these systems can never guarantee a complete Certainty of Containment.
<br><br>
<br><br>
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However, no matter how safe we envision our end product to be, the road towards it is a synthetic biology one. Synthetic Biology is a fun, interesting and above all promising scientific field. Nonetheless, it is also subject to inherent hazards which can affect both researchers, the public and the environment. It is therefore of crucial importance that anyone working in this field is thoroughly aware of these dangers and takes the necessary precautions to minimize any risks that might occur.
+
Our observations so far strongly suggest that through mutations and gene transfer, life will eventually find a way to bypass double, triple or even hundredfold safety mechanisms. Moreover, there is no way of foretelling how this will happen or what adverse effects may arise from it.
 +
<br>
 +
Current regulations for novel medicines require extensive testing and a thorough understanding and control of the substances to be delivered. It seems to us that the complicated, self-replicating and unpredictable nature that is inherent to living organisms excludes them from ever meeting these criteria.
 +
<br>
 +
With these considerations in mind, we believe that inserting GMO directly into a patient can hardly be considered a viable application of synthetic biology.  
<br><br>
<br><br>
-
This page will provide an overview of the issues related to biological safety and security that are relevant to our project, as well as answer the key safety questions provided by iGEM 2012. A review on the safety issues related to our use of Virus-Like Particles and their genes is included as a [[Team:Wageningen_UR/Virus-related issues|Virus-related safety]] page.
+
However, this should of course not exclude applications within the medical field from the realm of synthetic biology as a whole. Apart from relatively straightforward examples of using Genetically Engineered Machines to produce medicines, we believe that the power of synthetic biology can also be used in a more versatile, standardized medical approach.
 +
<br><br>
 +
We envision here the VLP-based Plug ‘n Apply System: A standardized universal packaging cage with a versatile modular attachment system on its exterior which allows it to become a target-specific medical delivery system.
 +
Virus-Like Particles aren’t self-replicating organisms and their relatively low level of complexity makes it possible to characterise them up to a point where they are predictable and safe enough to withstand clinical trials and be approved for use as medicines. [1-4]
 +
<br><br>
 +
However safe we envision our end product to be though, the road towards it is a synthetic biology one. Synthetic Biology is a fun, interesting and above all promising scientific field. Nonetheless, it is also subject to inherent hazards which can affect both researchers, the public and the environment. It is therefore of crucial importance that anyone working in this field is thoroughly aware of these dangers and takes the necessary precautions to minimize any risks that might occur.
 +
<br><br>
 +
These pages will provide an overview of the issues related to biological safety and security that are relevant to our project, as well as answer the key safety questions provided by iGEM 2012. A review on the safety issues related to our use of Virus-Like Particles and their genes is included as a [[Team:Wageningen_UR/Virus-related issues|Virus-related safety]] page. A brief literature study on the use of our Hepatitis B VLPs, armed with the PnA System, to treat colon cancer in human patients is included as a [[Team:Wageningen_UR/Application_safety|fifth focus]].
</p>
</p>
== Key Questions (Summary) ==
== Key Questions (Summary) ==
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''1. Would any of your project ideas raise safety issues in terms of:''
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===== 1. Would any of your project ideas raise safety issues in terms of: =====
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<br><br>
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''' • researcher safety, '''
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''• researcher safety, ''
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''' • public safety, or '''
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''• public safety, or ''
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''' • environmental safety '''
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''• environmental safety''
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For as far as we can see, our project poses no substantial risk to either researchers, the public or the environment.
For as far as we can see, our project poses no substantial risk to either researchers, the public or the environment.
All members of our team have been trained in both Good Microbiological Techniques and general and specific lab safety. The only organisms we use are non-pathogenic, commercially available lab-safe ''E. coli'' strains classified as Bio-Safety level 1. The existing biological [[Team:Wageningen_UR/Parts#Parts_we_used|parts we used]] don’t raise any foreseeable safety issues. The parts we introduced ourselves were derived from virus genes, but viral hazards were avoided at all times (see [[Team:Wageningen_UR/Virus-related_issues|Virus-related safety]]).  
All members of our team have been trained in both Good Microbiological Techniques and general and specific lab safety. The only organisms we use are non-pathogenic, commercially available lab-safe ''E. coli'' strains classified as Bio-Safety level 1. The existing biological [[Team:Wageningen_UR/Parts#Parts_we_used|parts we used]] don’t raise any foreseeable safety issues. The parts we introduced ourselves were derived from virus genes, but viral hazards were avoided at all times (see [[Team:Wageningen_UR/Virus-related_issues|Virus-related safety]]).  
-
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[[Team:Wageningen_UR/General_safety|More about General safety...]]
[[Team:Wageningen_UR/General_safety|More about General safety...]]
<br><br>
<br><br>
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''2. Do any of the new BioBrick parts (or devices) that you made this year raise safety issues? If yes,''
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===== 2. Do any of the new BioBrick parts (or devices) that you made this year raise safety issues? If yes, =====
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<br><br>
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''' • Did you document these issues in the Registry? '''
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''• Did you document these issues in the Registry? ''
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-
<br><br>
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''' • How did you manage to handle the safety issue? '''
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''• How did you manage to handle the safety issue? ''
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<br><br>
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''' • How could other teams learn from your experience? '''
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''• How could other teams learn from your experience?''
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<br><br>
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We made biological cages with an attachment system, derived from virus genes. By themselves, these cages are harmless. Malicious misuse can be harmful, but this seems like an acceptable risk considering the benefits of the system. No viral hazards are involved.  
We made biological cages with an attachment system, derived from virus genes. By themselves, these cages are harmless. Malicious misuse can be harmful, but this seems like an acceptable risk considering the benefits of the system. No viral hazards are involved.  
-
<br><br>
+
<br>
[[Team:Wageningen_UR/Virus-related_issues|More about Virus-related safety...]]
[[Team:Wageningen_UR/Virus-related_issues|More about Virus-related safety...]]
<br><br>
<br><br>
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''3. Is there a local biosafety group, committee, or review board at your institution?''
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===== 3. Is there a local biosafety group, committee, or review board at your institution? =====
-
<br><br>
+
 
-
''• If yes, what does your local biosafety group think about your project? ''
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''' • If yes, what does your local biosafety group think about your project? '''
-
<br><br>
+
 
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''• If no, which specific biosafety rules or guidelines do you have to consider in your country?''
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''' • If no, which specific biosafety rules or guidelines do you have to consider in your country? '''
-
<br><br>
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Wageningen UR has its own biosafety rules next to the national biosafety regulations. Its rules can be found on this [http://www.wageningenuniversity.nl/UK/informationfor/Current+students/Student+information/healthsafety/Laboratory+general/?wbc_purpose=basic#basic laboratory safety page]. We have discussed our project with the Biosafety officer for our project. The laboratory we used and our own techniques all comply to the European [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2009:125:0075:0097:EN:PDF Directive on the contained use of micro-organisms].
Wageningen UR has its own biosafety rules next to the national biosafety regulations. Its rules can be found on this [http://www.wageningenuniversity.nl/UK/informationfor/Current+students/Student+information/healthsafety/Laboratory+general/?wbc_purpose=basic#basic laboratory safety page]. We have discussed our project with the Biosafety officer for our project. The laboratory we used and our own techniques all comply to the European [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2009:125:0075:0097:EN:PDF Directive on the contained use of micro-organisms].
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[[Team:Wageningen_UR/Regulations|More about Regulations...]]
[[Team:Wageningen_UR/Regulations|More about Regulations...]]
<br><br>
<br><br>
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''4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?''
+
 
-
<br><br>
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===== 4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering? =====
 +
 
A kill-switch should be implemented in all standard ''E. coli'' lab strains. This shouldn't be too hard to accomplish on a short term basis, yet it would improve the safety of all experiments that are performed in ''E. coli'' worldwide.  
A kill-switch should be implemented in all standard ''E. coli'' lab strains. This shouldn't be too hard to accomplish on a short term basis, yet it would improve the safety of all experiments that are performed in ''E. coli'' worldwide.  
-
<br><br>
+
<br>
On the long term, we should work towards a Certainty of Containment. One way to do this seems to be the expansion of the genetic code by incorporation of new bases in the DNA. Eventually, this should lead to a situation where synthetic biology constructs are always encoded on unnatural DNA, unreadable to natural organisms.
On the long term, we should work towards a Certainty of Containment. One way to do this seems to be the expansion of the genetic code by incorporation of new bases in the DNA. Eventually, this should lead to a situation where synthetic biology constructs are always encoded on unnatural DNA, unreadable to natural organisms.
-
<br><br>
+
<br>
[[Team:Wageningen_UR/Possible_Improvements|More about our Suggestions...]]
[[Team:Wageningen_UR/Possible_Improvements|More about our Suggestions...]]
<br><br>
<br><br>
-
----
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===== 5. [Bonus Question] Have you thought about safety issues related to possible end applications of your product? =====
 +
 
 +
Our end product is non-replicative and contains no genetic material. Nevertheless, anything that is going to be inserted in a human body will first have to undergo rigorous clinical trials. We are not capable of doing this ourselves, so we performed a brief literature study towards the viability of our [[Team:Wageningen_UR/HumanBody#Case_study:_colorectal_cancer|case-study]]: Human colon cancer treatment using HepB VLPs.
 +
<br>
 +
[[Team:Wageningen_UR/Application_safety|More about Safety of Application...]]
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<br><br>
 +
 
 +
== References ==
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1. Harro, C.D., et al., ''Safety and Immunogenicity Trial in Adult Volunteers of a Human Papillomavirus 16 L1 Virus-Like Particle Vaccine''. Journal of the National Cancer Institute, 2001. 93(4): p. 284-292.
 +
 
 +
2. Roy, P. and R. Noad, ''Virus-like particles as a vaccine delivery system - Myths and facts''. Human Vaccines, 2008. 4(1): p. 5-12.
 +
 
 +
3. Ma, Y., R.J.M. Nolte, and J.J.L.M. Cornelissen, ''Virus-based nanocarriers for drug delivery''. Advanced Drug Delivery Reviews, 2012. 64(9): p. 811-825.
 +
 
 +
4. Garcea, R.L. and L. Gissmann, ''Virus-like particles as vaccines and vessels for the delivery of small molecules''. Current Opinion in Biotechnology, 2004. 15(6): p. 513-517.
 +
 
 +
----
=== Safety ===
=== Safety ===
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[[Team:Wageningen_UR/Possible_Improvements|4. Suggestions]]
[[Team:Wageningen_UR/Possible_Improvements|4. Suggestions]]
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[[Team:Wageningen_UR/Safety_references|References]]
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[[Team:Wageningen_UR/Application_safety|5. Safety of application]]
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----
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=== References ===
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1. Final risk assessment of Escherichia coli K-12 Derivatives
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2. Chart, H., et al., An investigation into the pathogenic properties of Escherichia coli strains BLR, BL21, DH5alpha and EQ1. J Appl Microbiol, 2000. 89(6): p. 1048-58.
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3. Studier, F.W., et al., Understanding the Differences between Genome Sequences of Escherichia coli B Strains REL606 and BL21(DE3) and Comparison of the E. coli B and K-12 Genomes. J Mol Biol, 2009. 394(4): p. 653-680.
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-
 
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4. Park, J.H., et al., Escherichia coli W as a new platform strain for the enhanced production of L-Valine by systems metabolic engineering. Biotechnology and Bioengineering, 2011. 108(5): p. 1140-1147.
+
-
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5. Roy, P. and R. Noad, Virus-like particles as a vaccine delivery system - Myths and facts. Human Vaccines, 2008. 4(1): p. 5-12.
+
-
+
-
6. Ma, Y., R.J.M. Nolte, and J.J.L.M. Cornelissen, Virus-based nanocarriers for drug delivery. Advanced Drug Delivery Reviews, 2012. 64(9): p. 811-825.
+
-
+
-
7. Yang, X.-Y., H. Bo, and Y.-L. Shu, Hepatitis B virus core antigen as a carrier for virus-like partical vaccine: a review. Bing du xue bao = Chinese journal of virology / [bian ji, Bing du xue bao bian ji wei yuan hui], 2012. 28(3): p. 311-6.
+
-
+
-
8. Mayo, M., et al., Mechanical transmission of Potato leafroll virus. Journal of General Virology, 2000. 81(11): p. 2791-2795.
+
-
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-
9. Directive 200118EC of the European Parliament and of the Council of 12 March 2001 on the deliberate release into the environment of genetically modified organisms and repealing Council Directive 90220EEC - Commission Declaration.
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-
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-
10. Schmidt, M. and V. de Lorenzo, Synthetic constructs in/for the environment: Managing the interplay between natural and engineered Biology. FEBS Letters, 2012. 586(15): p. 2199-2206.
+
-
+
-
11. Yang, Z., et al., Amplification, Mutation, and Sequencing of a Six-Letter Synthetic Genetic System. Journal of the American Chemical Society, 2011. 133(38): p. 15105-15112.
+

Latest revision as of 16:17, 26 October 2012

Contents

Safety

Introduction

Within the realm of synthetic biology, a lot of effort is put towards controlling GMOs after their release in a natural environment. Kill-switches and substrate dependencies are developed with increasing effectivity. Especially in iGEMs medical track, ‘safety of application’ considerations often involve double or even triple safety mechanisms that have to be inserted into the organism of choice. However, as was discussed in the Meeting of Young Minds and various other platforms, these systems can never guarantee a complete Certainty of Containment.

Our observations so far strongly suggest that through mutations and gene transfer, life will eventually find a way to bypass double, triple or even hundredfold safety mechanisms. Moreover, there is no way of foretelling how this will happen or what adverse effects may arise from it.
Current regulations for novel medicines require extensive testing and a thorough understanding and control of the substances to be delivered. It seems to us that the complicated, self-replicating and unpredictable nature that is inherent to living organisms excludes them from ever meeting these criteria.
With these considerations in mind, we believe that inserting GMO directly into a patient can hardly be considered a viable application of synthetic biology.

However, this should of course not exclude applications within the medical field from the realm of synthetic biology as a whole. Apart from relatively straightforward examples of using Genetically Engineered Machines to produce medicines, we believe that the power of synthetic biology can also be used in a more versatile, standardized medical approach.

We envision here the VLP-based Plug ‘n Apply System: A standardized universal packaging cage with a versatile modular attachment system on its exterior which allows it to become a target-specific medical delivery system. Virus-Like Particles aren’t self-replicating organisms and their relatively low level of complexity makes it possible to characterise them up to a point where they are predictable and safe enough to withstand clinical trials and be approved for use as medicines. [1-4]

However safe we envision our end product to be though, the road towards it is a synthetic biology one. Synthetic Biology is a fun, interesting and above all promising scientific field. Nonetheless, it is also subject to inherent hazards which can affect both researchers, the public and the environment. It is therefore of crucial importance that anyone working in this field is thoroughly aware of these dangers and takes the necessary precautions to minimize any risks that might occur.

These pages will provide an overview of the issues related to biological safety and security that are relevant to our project, as well as answer the key safety questions provided by iGEM 2012. A review on the safety issues related to our use of Virus-Like Particles and their genes is included as a Virus-related safety page. A brief literature study on the use of our Hepatitis B VLPs, armed with the PnA System, to treat colon cancer in human patients is included as a fifth focus.

Key Questions (Summary)

1. Would any of your project ideas raise safety issues in terms of:

• researcher safety,

• public safety, or

• environmental safety

For as far as we can see, our project poses no substantial risk to either researchers, the public or the environment. All members of our team have been trained in both Good Microbiological Techniques and general and specific lab safety. The only organisms we use are non-pathogenic, commercially available lab-safe E. coli strains classified as Bio-Safety level 1. The existing biological parts we used don’t raise any foreseeable safety issues. The parts we introduced ourselves were derived from virus genes, but viral hazards were avoided at all times (see Virus-related safety).
More about General safety...

2. Do any of the new BioBrick parts (or devices) that you made this year raise safety issues? If yes,

• Did you document these issues in the Registry?

• How did you manage to handle the safety issue?

• How could other teams learn from your experience?

We made biological cages with an attachment system, derived from virus genes. By themselves, these cages are harmless. Malicious misuse can be harmful, but this seems like an acceptable risk considering the benefits of the system. No viral hazards are involved.
More about Virus-related safety...

3. Is there a local biosafety group, committee, or review board at your institution?

• If yes, what does your local biosafety group think about your project?

• If no, which specific biosafety rules or guidelines do you have to consider in your country?

Wageningen UR has its own biosafety rules next to the national biosafety regulations. Its rules can be found on this [http://www.wageningenuniversity.nl/UK/informationfor/Current+students/Student+information/healthsafety/Laboratory+general/?wbc_purpose=basic#basic laboratory safety page]. We have discussed our project with the Biosafety officer for our project. The laboratory we used and our own techniques all comply to the European [http://eur-lex.europa.eu/LexUriServ/LexUriServ.do?uri=OJ:L:2009:125:0075:0097:EN:PDF Directive on the contained use of micro-organisms].
More about Regulations...

4. Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?

A kill-switch should be implemented in all standard E. coli lab strains. This shouldn't be too hard to accomplish on a short term basis, yet it would improve the safety of all experiments that are performed in E. coli worldwide.
On the long term, we should work towards a Certainty of Containment. One way to do this seems to be the expansion of the genetic code by incorporation of new bases in the DNA. Eventually, this should lead to a situation where synthetic biology constructs are always encoded on unnatural DNA, unreadable to natural organisms.
More about our Suggestions...

5. [Bonus Question] Have you thought about safety issues related to possible end applications of your product?

Our end product is non-replicative and contains no genetic material. Nevertheless, anything that is going to be inserted in a human body will first have to undergo rigorous clinical trials. We are not capable of doing this ourselves, so we performed a brief literature study towards the viability of our case-study: Human colon cancer treatment using HepB VLPs.
More about Safety of Application...

References

1. Harro, C.D., et al., Safety and Immunogenicity Trial in Adult Volunteers of a Human Papillomavirus 16 L1 Virus-Like Particle Vaccine. Journal of the National Cancer Institute, 2001. 93(4): p. 284-292.

2. Roy, P. and R. Noad, Virus-like particles as a vaccine delivery system - Myths and facts. Human Vaccines, 2008. 4(1): p. 5-12.

3. Ma, Y., R.J.M. Nolte, and J.J.L.M. Cornelissen, Virus-based nanocarriers for drug delivery. Advanced Drug Delivery Reviews, 2012. 64(9): p. 811-825.

4. Garcea, R.L. and L. Gissmann, Virus-like particles as vaccines and vessels for the delivery of small molecules. Current Opinion in Biotechnology, 2004. 15(6): p. 513-517.


Safety

Introduction

1. General safety

2. Virus-related safety

3. Regulations

4. Suggestions

5. Safety of application

Retrieved from "http://2012.igem.org/Team:Wageningen_UR/Safety"