Difference between revisions of "Team:Paris Saclay/Safety"

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<html><style>header{background-image: url("https://static.igem.org/mediawiki/2016/4/4c/T--Paris_Saclay--banniere_safety.jpg");}</style></html>
  
 
=Introduction=
 
=Introduction=
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Safety is a crucial issue in iGEM projects. As students imagine their own project, they have to make sure that their idea is not hazardous. Likewise, realization of the project in the lab is a second challenge for young students in terms of security. Working on living organisms and biological parts requires good laboratory practices in order to prevent spreading, contamination, or physical injuries.  
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Safety is a crucial issue for the iGEM projects. As students imagine their own project, they have to make sure that their idea is not hazardous. Likewise, the project's development in the lab is a second challenge for young students in terms of security. Working on living organisms and biological parts requires good laboratory practices to prevent spreading, contamination or physical injuries.
  
 
=A good laboratory practice=
 
=A good laboratory practice=
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To prevent disorder and accidents, the lab was divided in two parts: a wet laboratory for experiments and a dry laboratory for personal and computer work. Students who were performing experiments were always wearing lab coats and kept experiment materials in the wet part of the laboratory.
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To prevent disorder and accidents, the lab was divided in two parts : a wet laboratory for experiments and a dry laboratory for personal working. Students who were performing experiments were always wearing lab coats and kept experiment materials in the wet laboratory.  
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==Chemical product handling==
 
==Chemical product handling==
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Students who were experimenting sometimes had to use dangerous chemical products. Extra precautions were taken to handle them:
  
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Students who were experimenting sometimes had to use dangerous chemical products. Extra precautions were taken to handle them :
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{| class="wikitable"
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|-
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!Products
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!Dangers
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!Precautions
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!Usages
 +
|-
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|EtBr (Ethidium Bromide)
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|Mutagenic agent and cancer-causing agent
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|Always manipulate EtBr wearing gloves - Add EtBR in cool solution only to prevent inhalation - Set up a special place and gather material to manipulate EtBr only
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|DNA visualization in agarose gel
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|-
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|Phenol / Chloroform
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|Mutagenic agent, toxic agent, irritating agent and cancer-causing agent
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|Always manipulate Phenol / Chloroform wearing gloves under a hood
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|DNA extraction
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|}
  
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[[File:T--Paris_Saclay--120916_tableau_safety_1.png|500px|thumb|right]]
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Contaminated waste was placed in a special trash, and safely packaged to be treated in another facility.
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Contaminated waste was put in special trash, and packaged to be treated elsewhere in a safe manner.
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==Organisms and Biological parts used in experiments==
 
==Organisms and Biological parts used in experiments==
  
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[[File:T--Paris_Saclay--120916_tableau_safety_2.png|500px|thumb|right]]
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{| class="wikitable"
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|-
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<p>Our project was designed to use two different strains of E. coli. These organisms are non-pathogenic chassis ranked in class 1. They do not induce any effects on humans and we could manipulate them safely without any special equipment in BLS 1 ( Biosafety Level 1) laboratory.
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!Organism
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!Strain
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<p>Biological parts:
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!Risk group
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[[File:T--Paris_Saclay--120916_tableau_safety_3.png|300px|thumb|right]]
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|-
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<p>Biological parts we engineered were integrated in E.Coli. New activities of these engineered bacteria are not dangerous for human health. Especially dcas9 do not have nuclease activity. Besides RNA guide do not target human genes.
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|''Escherichia coli''
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|DH5a
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<p>Since we generated genetically modified organisms, we had to make sure it was not spread in the environment. We put biological waste in special trashes which were heated at high temperature to kill microorganisms. Then it was treated as usual waste. Moreover dcas9 proteins were not integrated  into the genome of sexually reproducing organisms. By this way, we prevent new genes transfert to other organisms than E.Coli.
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|1
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|-
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<p>Our project in the future
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|''Escherichia coli''
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|BL21
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<p>Our project aims to develop a new molecular tool to bring closer DNA strands in bacterial cells. If we manage to achieve our project, this new biological tool could only be used by scientists interested in DNA conformation study.
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|1
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They will be able to target any DNA sequences by designing their own guide RNAs. In order to prevent physical injuries and genetically modified organisms spreading, they will have to take the same precautions we took during the internship listed above.
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|-
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|''Escherichia coli''
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<p>Conclusion:
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|PhB1040 strain 594
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|1
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<p>To conclude our new tool will provide new possibilities in biology research. Scientists will be able to change DNA 3D organization and thus study links between DNA organization and cellular functions in bacteria. As our new tool will used only by scientists  it do not really pose new safety issues.
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|}
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<p>On this page of your wiki, you should write about how you are addressing any safety issues in your project. The wiki is a place where you can <strong>go beyond the questions on the safety forms</strong>, and write about whatever safety topics are most interesting in your project. (You do not need to copy your safety forms onto this wiki page.)</p>
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</div>
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Our project was designed to use two different strains of ''E. coli''. These organisms are non-pathogenic chassis ranked in class 1. They do not induce any effects on humans and we could manipulate them safely without any special equipment in BLS 1 (Biosafety Level 1) laboratory.
  
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<div class="column full_size">
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==Biological parts==
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<h5>Safe Project Design</h5>
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<p>Does your project include any safety features? Have you made certain decisions about the design to reduce risks? Write about them here! For example:</p>
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{| class="wikitable"
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|-
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!Biological part name
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!Origin
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!Use
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|-
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|dCas9 NM
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|DNA synthesis
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|Fused to FRB/FKBP12 system, this part wil allow us to change DNA conformation
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|-
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|dCas9 ST
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|DNA synthesis
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|Fused to FRB/FKBP12 system, this part wil allow us to change DNA conformation
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|-
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|FRB/FKBP12 system
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|
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|Fused to dCas9 NM and dCas9 ST, this part wil allow us to change DNA conformation
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|-
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|Tripartite GFP
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|
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|Fused to dCas9 NM ans dCas9 ST, this part will confirm that two DNA strands are closed
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|-
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|K1372001
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|Registry part
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|This part produces a tRNA supressor when salicylate is added to the medium
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|}
  
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<ul>
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Biological parts we engineered were integrated in ''E. coli''. New activities of these engineered bacteria are not dangerous for human health. Especially dcas9 do not have nuclease activity. Besides RNA guide do not target human genes.
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<li>Choosing a non-pathogenic chassis</li>
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<li>Choosing parts that will not harm humans / animals / plants</li>
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<li>Substituting safer materials for dangerous materials in a proof-of-concept experiment</li>
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<li>Including an "induced lethality" or "kill-switch" device</li>
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</ul>
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</div>
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Since we generated genetically modified organisms, we had to make sure it was not spread in the environment. We placed biological wastes in special trashes which were heated at high temperatures to kill the microorganisms. Then, it was treated as usual waste. Moreover dcas9 proteins were not integrated into the genome of sexually reproducing organisms. By this way, we prevented the transfer of new genes to other organisms than ''E. coli''.
  
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<div class="column half_size">
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=Perspectives of our project and safety issues=
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<h5>Safe Lab Work</h5>
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Our project aims to develop a new molecular tool to bring closer DNA strands in bacterial cells. If we manage to achieve our goal, this new biological tool could only be used by scientists interested in DNA conformation studies.
  
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<p>What safety procedures do you use every day in the lab? Did you perform any unusual experiments, or face any unusual safety issues? Write about them here!</p>
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They will be able to target any DNA sequence by designing their own RNA guides. To prevent physical injuries and genetically modified organisms spreading, they will have to take the same precautions we took during the experiments, listed above.
  
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</div>
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=Conclusion=
  
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<div class="column half_size">
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To conclude our new tool will provide new possibilities in biology research. Scientists will be able to change DNA 3D organization and thus study links between DNA organization and cellular functions in bacteria. As our new tool will be used only by scientists it doesn't pose new safety issues.
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<h5>Safe Shipment</h5>
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<p>Did you face any safety problems in sending your DNA parts to the Registry? How did you solve those problems?</p>
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{{Team:Paris_Saclay/project_footer}}
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</div>
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Latest revision as of 14:27, 19 October 2016

Safety

Introduction

Safety is a crucial issue for the iGEM projects. As students imagine their own project, they have to make sure that their idea is not hazardous. Likewise, the project's development in the lab is a second challenge for young students in terms of security. Working on living organisms and biological parts requires good laboratory practices to prevent spreading, contamination or physical injuries.

A good laboratory practice

To prevent disorder and accidents, the lab was divided in two parts: a wet laboratory for experiments and a dry laboratory for personal and computer work. Students who were performing experiments were always wearing lab coats and kept experiment materials in the wet part of the laboratory.

Chemical product handling

Students who were experimenting sometimes had to use dangerous chemical products. Extra precautions were taken to handle them:

Products Dangers Precautions Usages
EtBr (Ethidium Bromide) Mutagenic agent and cancer-causing agent Always manipulate EtBr wearing gloves - Add EtBR in cool solution only to prevent inhalation - Set up a special place and gather material to manipulate EtBr only DNA visualization in agarose gel
Phenol / Chloroform Mutagenic agent, toxic agent, irritating agent and cancer-causing agent Always manipulate Phenol / Chloroform wearing gloves under a hood DNA extraction

Contaminated waste was placed in a special trash, and safely packaged to be treated in another facility.

Organisms and Biological parts used in experiments

Organism Strain Risk group
Escherichia coli DH5a 1
Escherichia coli BL21 1
Escherichia coli PhB1040 strain 594 1

Our project was designed to use two different strains of E. coli. These organisms are non-pathogenic chassis ranked in class 1. They do not induce any effects on humans and we could manipulate them safely without any special equipment in BLS 1 (Biosafety Level 1) laboratory.

Biological parts

Biological part name Origin Use
dCas9 NM DNA synthesis Fused to FRB/FKBP12 system, this part wil allow us to change DNA conformation
dCas9 ST DNA synthesis Fused to FRB/FKBP12 system, this part wil allow us to change DNA conformation
FRB/FKBP12 system Fused to dCas9 NM and dCas9 ST, this part wil allow us to change DNA conformation
Tripartite GFP Fused to dCas9 NM ans dCas9 ST, this part will confirm that two DNA strands are closed
K1372001 Registry part This part produces a tRNA supressor when salicylate is added to the medium

Biological parts we engineered were integrated in E. coli. New activities of these engineered bacteria are not dangerous for human health. Especially dcas9 do not have nuclease activity. Besides RNA guide do not target human genes.

Since we generated genetically modified organisms, we had to make sure it was not spread in the environment. We placed biological wastes in special trashes which were heated at high temperatures to kill the microorganisms. Then, it was treated as usual waste. Moreover dcas9 proteins were not integrated into the genome of sexually reproducing organisms. By this way, we prevented the transfer of new genes to other organisms than E. coli.

Perspectives of our project and safety issues

Our project aims to develop a new molecular tool to bring closer DNA strands in bacterial cells. If we manage to achieve our goal, this new biological tool could only be used by scientists interested in DNA conformation studies.

They will be able to target any DNA sequence by designing their own RNA guides. To prevent physical injuries and genetically modified organisms spreading, they will have to take the same precautions we took during the experiments, listed above.

Conclusion

To conclude our new tool will provide new possibilities in biology research. Scientists will be able to change DNA 3D organization and thus study links between DNA organization and cellular functions in bacteria. As our new tool will be used only by scientists it doesn't pose new safety issues.





Université Paris Sud
91405 Orsay, France
Copyright © 2016 iGEM Paris Saclay. All rights reserved All inspirations encouraged.
*This wiki was conceived during long nights of work and a great coffee experience in the beautiful Orsay, France.