Team:WITS-South Africa/Safety

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= Safety =
= Safety =
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'''1.Would any of your project ideas raise safety issues in terms of:'''
 
-
'''* Researcher safety'''
 
-
'''* Public safety'''
 
-
'''* Environmental safety?'''
 
 +
'''1. Would any of your project ideas raise safety issues in terms of:'''
 +
*'''Researcher safety'''
 +
*'''Public safety'''
 +
*'''Environmental safety?'''
-
'''2.Do any of the new BioBrick parts (or devices) that you made this year raise any 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?'''
 
 +
'''There were several safety considerations that related to our project:'''
-
'''3.Is there a local biosafety group, committee, or review board at your institution?'''
+
'''General laboratory safety (Researcher safety)
-
'''* 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?'''
+
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[[ Image:Wits_Greg_at_work.jpg|150px|right]]
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Given that any laboratory can be a hazardous environment if the correct safety protocols are not adhered to, all team members who worked in the wetlab were briefed on laboratory safety. A departmental laboratory safety manual was provided and each person was expected to familiarise themselves with the contents of the manual as well as any specific safety rules pertaining to the laboratory which they were working in.
-
'''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?'''
 
 +
'''Working with bacteria (Researcher safety)'''
 +
The initial cloning steps used construct the machine were all conducted using laboratory adapted strains of ''E.coli'' such as DH5α and XL1-Blue, which when handled, stored and disposed of in the correct pose no safety risks.
 +
The final constructs were electroporated into a model Gram-positive organism (''Bacillus subtilis''). Some work was also done on the final intended chassis (''L.gasseri'' ADH). Both of these organisms are considered safe to handle and pose no risk to the researcher, although care was taken to handle, store and dispose of the bacteria in a safe and sterile way.
-
Would any of your project ideas raise safety issues in terms of:
 
-
* Researcher safety
 
-
* Public safety
 
-
* Environmental safety?
 
-
T'''here were several safety considerations that related to our project'''
+
'''Manipulating gene expression using quorum sensing (Environmental and public safety)'''
-
== 1. General laboratory safety (Researcher safety) ==
+
Our project deals with quorum sensing mechanisms in Gram-positive organisms. We have designed a fusion peptide which directly upregulates gene expression when it binds to its cognate promoter. It has been suggested that our peptide can activate expression of 20 different genes. The synthetic fusion peptide is also expected to be much more effective at increasing gene expression than the natural quorum peptides it is derived from. There are several safety issues regarding this Biobrick:
-
Given that any laboratory can be a hazardous environment if the correct safety protocols are not adhered to, all team members who worked in the wetlab were briefed on laboratory safety. A departmental laboratory safety manual was provided and each person was expected to familiarise themselves with the contents of the manual as well as any specific safety rules pertaining to the laboratory which they were working in.  
+
Firstly the quorum peptide we have selected activates virulence in ''Bacillus thuriengiensis'' and ''Bacillus anthracis''. ''B.thuriengiensis'' is a soil bacterium which is pathogenic to insects and ''B.anthracis'' is a human pathogen. It is possible that unintended exposure to our enhanced quorum peptide could increase virulence in these organisms.  
-
A copy of the Departmental Safety Manual can be found here.
 
-
== 2. Working with bacteria (Researcher safety) ==
+
It is also possible that the peptide could activate gene expression by binding to promoters other than the one we intended it to, causing off target effects in ''L. gasseri'' or other gram positives in the vaginal mucosa.  
-
The initial cloning steps used construct the machine were all conducted using laboratory adapted strains of E.coli such as DH5α and XL1-Blue, which when handled, stored and disposed of in the correct pose no safety risks.  
+
Although the work done to test this mechanism thus far has not posed a safety risk, as no ''in vivo'' work was conducted, and there was no possibility of the quorum peptide encountering any bacteria any than those we exposed it to in a sterile ''in vitro'' environment.  
-
The final constructs were electroporated into a model Gram-positive organism (Bacillus subtilis). Some work was also done on the final intended chassis (L.gasseri ADH). Both of these organisms are considered safe to handle and pose no risk to the researcher, although care was taken to handle, store and dispose of the bacteria in a safe and sterile way.  
+
-
== 3. Manipulating gene expression using quorum sensing (Environmental and public safety) ==
 
-
Our project deals with quorum sensing mechanisms in Gram-positive organisms. We have designed a fusion peptide which directly upregulates gene expression when it binds to its cognate promoter. It has been suggested that our peptide can activate expression of 20 different genes. The synthetic fusion peptide is also expected to be much more effective at increasing gene expression than the natural quorum peptides it is derived from. There are several safety issues regarding this Biobrick:
 
-
Firstly the quorum peptide we have selected activates virulence in Bacillus thuriengiensis and Bacillus anthracis. B.t is a soil bacterium which is pathogenic to insects and b,a is a human pathogen. It is possible that unintended exposure to our enhanced quorum peptide could increase virulence in these organisms.
 
-
It is also possible that the peptide could activate gene expression by binding to promoters other than the one we intended it to, causing off target effects in lgasseri or other gram positives in the vaginal mucosa.
 
-
Although the work done to test this mechanism thus far has not posed a safety risk, as no invivo work was conducted, and there was no possibility of the quorum peptide encountering any bacteria any than those we exposed it to in a sterile in vitro environment.
 
However, if this work was to be developed further, the implications of this Biobrick part and how to ensure that it acts only on its intended target need to be carefully considered.  
However, if this work was to be developed further, the implications of this Biobrick part and how to ensure that it acts only on its intended target need to be carefully considered.  
-
Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,
 
-
o did you document these issues in the Registry?
 
-
o how did you manage to handle the safety issue?
 
-
o How could other teams learn from your experience?
 
-
The plCR-PapR quorum peptide is the only part which could raise a potential safety risk. It only poses a safety risk if it comes into contact with other Gram-positive organisms. The full potential risks were documented on this part’s page on the Registry.  
+
'''2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues?'''
-
This safety risk was only theoretical due to the fact that we only worked with it in a very contained lab environment thus no special precautions needed to be taken.  
+
 
 +
'''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?'''
 +
 
 +
 
 +
The plCR-PapR quorum peptide is the only part which could raise a potential safety risk. It only poses a safety risk if it comes into contact with other Gram-positive organisms. The full potential risks were documented on this part’s page on the Registry. This safety risk was only theoretical due to the fact that we only worked with it in a very contained lab environment thus no special precautions needed to be taken.  
 +
 
It is important to consider all the possible effects of a Biobrick part. Many transcriptional activators or regulators have off-target effects. It is important to build in regulatory mechanisms that can limit or control such effects, or to keep these possibilities in mind if any testing is to be undertaken outside of a controlled and sterile setting.  
It is important to consider all the possible effects of a Biobrick part. Many transcriptional activators or regulators have off-target effects. It is important to build in regulatory mechanisms that can limit or control such effects, or to keep these possibilities in mind if any testing is to be undertaken outside of a controlled and sterile setting.  
-
Is there a local biosafety group, committee, or review board at your institution?
 
-
Yes. We informed them of our project in its current form as well as the possible next steps that could be undertaken and they responded thus:
 
-
The safety aspects pertaining to an engineered commensal bacterium would depend on what is being inserted into the bacterium (as the commensals themselves are safe for use) – presumably in this case a expression casette producing a colour reagent upon stimulus.
 
-
One would question the possible toxicity of such a colour product if it is not one that has been tested for human use (many dyes of often used in patients to detect various disorders etc – so many are considered safe for in vivo use). Some dyes may perhaps cause allergic reactions in some individuals.
 
-
I would hardly think mere manipulation of the commensal would turn the “good guy” into a pathogenic organism – there are many published articles that show very positive use of genetically engineered commensals so would support that this would be a highly unlikely event.
 
-
 
-
This project is a proof-of-principle design therefore would need to be demonstrated as a workable in an in vitro system. If promising as a concept then issues pertaining to safety would become relevant. Then either further preclinical work could be done in an animal model to test for safety and efficacy in a cervical cancer/HPV challenge model; phase 1 safety trial in humans and so on.
 
-
 
-
I think this is a great concept that should not to my mind present any major hurdles w.r.t. safety considerations; certainly at this early stage general safety rules of any basic laboratory would apply. 
 
-
The normal flora of the vaginal mucosa would present no problem. However, under conditions of altered flora such as in sexually transmitted diseases, bacterial species can be very altered. I don’t think the species you mention are generally around even under pathogenic conditions, but can’t be sure.  
+
 
-
It should also be kept in mind that there are some very unusual sexual practices (herbal, additives to dry the vagina etc)  where some unusual “creatures” may be introduced (and I don’t mean the sexual partner – although that may be another story).
+
'''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?'''
 +
 
 +
 
 +
Yes. We informed them of our project in its current form as well as the possible next steps that could be undertaken and they responded that the following safety concerns needed to be considered:
 +
 
   
   
-
Again, in terms of safety testing at a time of being introduced one would ideally first test in a normal healthy non-pathogenic setting; once safety shown this could then be tested in individuals with STDs or HIV-1 etc as these patient groups would be associated with distorted bacterial floras.  
+
*The possible toxicity/allergenicity of the colour products produced by the bacteria if it is not one that has been tested for human use (bearing in mind that many dyes are often used in patients to detect various disorders – so many are considered safe for ''in vivo'' use). Some dyes may perhaps cause allergic reactions in some individuals.
-
+
 
-
http://web.wits.ac.za/Academic/Research/Biosafety.htm
+
*How the microbial flora may be altered in the vaginal mucosa of a person with an infection (Sexually transmitted or otherwise). In a South African context HIV-1 is the most significant and likely possible infection. In terms of safety testing at a time of being introduced they would recommend first testing in a normal healthy non-pathogenic setting; once safety was shown this could then be tested in individuals with STDs or HIV-1 as these patient groups would be associated with distorted bacterial floras.  
-
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?  
+
 
-
Although
+
*Unusual sexual practices with cultural origins (such as herbal additives to dry the vagina) may impact on our device.
 +
 
 +
*Overall, the committee commented that as this project is a proof-of-principle design, at this stage "it is a great concept that should not present any major hurdles with respect to safety considerations; certainly at this early stage general safety rules of any basic laboratory would apply."
 +
 
 +
*They further went on to state that it would need to be demonstrated as a workable in an ''in vitro'' system, and if promising as a concept then issues pertaining to safety would become relevant. Then either further preclinical work could be done in an animal model to test for safety and efficacy in a cervical cancer/HPV challenge model and phase 1 safety trials in humans.
 +
 
 +
 
 +
More information about the Wits Biosafety Committee can be found at http://web.wits.ac.za/Academic/Research/Biosafety.htm
 +
 
 +
 
 +
 
 +
'''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?'''
 +
 
 +
 
 +
Our final construct (Lacto-report) had a negative regulator built into it - It was intended that once gene expression was positively activated, a system to switch it off again after a time-delay would be activated as well. All genetic machines should have regulatory mechanisms in place, both to control the system and as an emergency failsafe. One future version of our device had a "kill switch" built into it - a genetically engineered susceptibility to a certain antibiotic or compound that could be administered to destroy the machine by killing the bacterial chassis. This type of regulatory mechanism could be useful to ensure that the part's behaviour is carefully controlled.
 +
 
 +
 
 +
We feel that it is important to research beforehand, as thoroughly as possible, the possible impacts that using a certain part or system would have on its intended target or in its intended environment. The use of mathematical models here is also important to attempt to predict how a part will behave within a specific context.
 +
 
 +
</div>

Latest revision as of 21:46, 27 October 2010


Safety

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

  • Researcher safety
  • Public safety
  • Environmental safety?


There were several safety considerations that related to our project:

General laboratory safety (Researcher safety)

Wits Greg at work.jpg

Given that any laboratory can be a hazardous environment if the correct safety protocols are not adhered to, all team members who worked in the wetlab were briefed on laboratory safety. A departmental laboratory safety manual was provided and each person was expected to familiarise themselves with the contents of the manual as well as any specific safety rules pertaining to the laboratory which they were working in.


Working with bacteria (Researcher safety)

The initial cloning steps used construct the machine were all conducted using laboratory adapted strains of E.coli such as DH5α and XL1-Blue, which when handled, stored and disposed of in the correct pose no safety risks. The final constructs were electroporated into a model Gram-positive organism (Bacillus subtilis). Some work was also done on the final intended chassis (L.gasseri ADH). Both of these organisms are considered safe to handle and pose no risk to the researcher, although care was taken to handle, store and dispose of the bacteria in a safe and sterile way.


Manipulating gene expression using quorum sensing (Environmental and public safety)

Our project deals with quorum sensing mechanisms in Gram-positive organisms. We have designed a fusion peptide which directly upregulates gene expression when it binds to its cognate promoter. It has been suggested that our peptide can activate expression of 20 different genes. The synthetic fusion peptide is also expected to be much more effective at increasing gene expression than the natural quorum peptides it is derived from. There are several safety issues regarding this Biobrick:

Firstly the quorum peptide we have selected activates virulence in Bacillus thuriengiensis and Bacillus anthracis. B.thuriengiensis is a soil bacterium which is pathogenic to insects and B.anthracis is a human pathogen. It is possible that unintended exposure to our enhanced quorum peptide could increase virulence in these organisms.


It is also possible that the peptide could activate gene expression by binding to promoters other than the one we intended it to, causing off target effects in L. gasseri or other gram positives in the vaginal mucosa. Although the work done to test this mechanism thus far has not posed a safety risk, as no in vivo work was conducted, and there was no possibility of the quorum peptide encountering any bacteria any than those we exposed it to in a sterile in vitro environment.


However, if this work was to be developed further, the implications of this Biobrick part and how to ensure that it acts only on its intended target need to be carefully considered.


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


The plCR-PapR quorum peptide is the only part which could raise a potential safety risk. It only poses a safety risk if it comes into contact with other Gram-positive organisms. The full potential risks were documented on this part’s page on the Registry. This safety risk was only theoretical due to the fact that we only worked with it in a very contained lab environment thus no special precautions needed to be taken.


It is important to consider all the possible effects of a Biobrick part. Many transcriptional activators or regulators have off-target effects. It is important to build in regulatory mechanisms that can limit or control such effects, or to keep these possibilities in mind if any testing is to be undertaken outside of a controlled and sterile setting.


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?


Yes. We informed them of our project in its current form as well as the possible next steps that could be undertaken and they responded that the following safety concerns needed to be considered:


  • The possible toxicity/allergenicity of the colour products produced by the bacteria if it is not one that has been tested for human use (bearing in mind that many dyes are often used in patients to detect various disorders – so many are considered safe for in vivo use). Some dyes may perhaps cause allergic reactions in some individuals.
  • How the microbial flora may be altered in the vaginal mucosa of a person with an infection (Sexually transmitted or otherwise). In a South African context HIV-1 is the most significant and likely possible infection. In terms of safety testing at a time of being introduced they would recommend first testing in a normal healthy non-pathogenic setting; once safety was shown this could then be tested in individuals with STDs or HIV-1 as these patient groups would be associated with distorted bacterial floras.
  • Unusual sexual practices with cultural origins (such as herbal additives to dry the vagina) may impact on our device.
  • Overall, the committee commented that as this project is a proof-of-principle design, at this stage "it is a great concept that should not present any major hurdles with respect to safety considerations; certainly at this early stage general safety rules of any basic laboratory would apply."
  • They further went on to state that it would need to be demonstrated as a workable in an in vitro system, and if promising as a concept then issues pertaining to safety would become relevant. Then either further preclinical work could be done in an animal model to test for safety and efficacy in a cervical cancer/HPV challenge model and phase 1 safety trials in humans.


More information about the Wits Biosafety Committee can be found at http://web.wits.ac.za/Academic/Research/Biosafety.htm


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?


Our final construct (Lacto-report) had a negative regulator built into it - It was intended that once gene expression was positively activated, a system to switch it off again after a time-delay would be activated as well. All genetic machines should have regulatory mechanisms in place, both to control the system and as an emergency failsafe. One future version of our device had a "kill switch" built into it - a genetically engineered susceptibility to a certain antibiotic or compound that could be administered to destroy the machine by killing the bacterial chassis. This type of regulatory mechanism could be useful to ensure that the part's behaviour is carefully controlled.


We feel that it is important to research beforehand, as thoroughly as possible, the possible impacts that using a certain part or system would have on its intended target or in its intended environment. The use of mathematical models here is also important to attempt to predict how a part will behave within a specific context.

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