http://2012.igem.org/wiki/index.php?title=Special:Contributions/CharlotteBG&feed=atom&limit=50&target=CharlotteBG&year=&month=2012.igem.org - User contributions [en]2024-03-29T02:00:14ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Team:Cambridge/Safety/MSDSTeam:Cambridge/Safety/MSDS2012-09-24T14:52:13Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
==Materials Safety Data Sheets==<br />
<br />
<br />
We consider it good lab practice to keep MSDSs for the reagents we use in our experiments. Below are the MSDSs (where availbale) for the reagents used in the protocols listed on this wiki.<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M7154&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsigma%2Fm7154%3Flang%3Den 2-Mercaptoethanol]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsB0518.pdf 5x Phusion HF]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=320099&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dacetic%2Bacid%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Acetic Acid]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A3553&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DAcrylamide%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Acrylamide]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A1296&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dagar%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Agar]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A9539&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dagarose%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Agarose]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=33582&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dammonium%2520buffer%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286 Ammonium Buffer]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A3678&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsigma%2FA3678%3Flang%3Den Ammonium Persulphate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A4418&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DAmmonium%2Bsulfate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Ammonium Sulphate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A9393&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DAmpicillin%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Ampicillin]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A3256&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Darabinose%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Arabinose]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=B0126&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsial%2Fb0126%3Flang%3Den Bromophenol Blue]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_n3_uk5.pdf Buffer N3]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_p2_uk6.pdf Buffer P2]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_pb_uk6.pdf Buffer PB]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_pb_uk6.pdf Buffer QG]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=C1016&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dcalcium%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax CaCl<sub>2</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=C0378&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dchloramphenicol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Chloramphenicol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=W1754&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Ddeionized%2Bwater%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax DI water]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=DNTP100A&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DdNTP%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax dNTPs]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=E7023&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dethanol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Ethanol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G8270&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglucose%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Glucose]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G1251&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglutamic%2Bacid%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax L-Glutamic Acid]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G5516&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglycerol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Glycerol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G8898&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglycine%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Glycine]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=38280&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dhydrochloric%2Bacid%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax HCl]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=95304&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dhplc%2Bwater%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax HPLC Water]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=236489&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DIron%2528III%2529%2Bchloride%2Bhexahydrate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax FeCl<sub>3</sub>.6H<sub>2</sub>O]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=I9516&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Disopropanol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Isopropanol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=P3786&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Ddipotassium%2Bphosphate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax K<sub>2</sub>HPO<sub>4</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=B5264&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dkanamycin%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Kanamycin]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=P9791&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dpotassium%2Bphosphate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax KH<sub>2</sub>PO<sub>4</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=L1750&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dlactic%2Bacid%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax L-Lactic acid]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=L7275&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dliquid%2Bbroth%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax LB]<br />
<br />
[http://www.qiagen.com/support/msds/uk/gelpilot_5x_loading_dye_uk4.pdf 5x Loading Dye]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M8266&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dmagnesium%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax MgCl<sub>2</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M7506&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dmagnesium%2520sulphate%26lang%3Den%26region%3DGB%26N%3D0%2B219853121%2B219853286%2B220003048%26focus%3Dproduct%26mode%3Dmatch%2Bpartialmax%26cm_re%3DDid%2520You%2520Mean-_-magnesium%2520sulphate-_-mangesium%2520sulphate Magnesium Sulphate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=HT8028&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DMalachite%2BGreen%2Bsolution%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Malachite Green]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=203734&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DManganese%2528II%2529%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax MnCl<sub>2</sub>.4H<sub>2</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=146072&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DAcrylamide%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Methylenebis(acrylamide)]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M1254&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsigma%2Fm1254%3Flang%3Den MOPS]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsM0530.pdf Phusion DNA polymerase]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=03564&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Ffluka%2F03564%3Flang%3Den Potassium Hydroxide Solution]<br />
<br />
[http://www.qiagen.com/support/msds/uk/rnase_a_solution_uk5.pdf RNase A solution]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=HT90432&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dsafranin%26lang%3Den%26region%3DGB%26N%3D0%2B219853121%2B219853286%2B220003048%26focus%3Dproduct%26mode%3Dmatch%2Bpartialmax%26cm_re%3DDid%2520You%2520Mean-_-safranin-_-safronin Safranin O]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=L3771&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DSDS%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax SDS]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=201154&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3D201154%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Sodium Fluoride]<br />
<br />
[https://tools.invitrogen.com/content/sfs/msds/2012/S33102_MTR-EULT_BE.pdf SYBR safe]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsM0363.pdf T5 exonuclease]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T6025&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DTAE%2Bbuffer%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax TAE Buffer]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsM0208.pdf Taq DNA Ligase]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=D4545&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dtaq%2Bpolymerase%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Taq DNA Polymerase]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T9281&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DTetramethylethylenediamine%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax TEMED]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T4625&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DThiamine%2Bhydrochloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Thiamine Hydrochloride]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=93349&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Ffluka%2F93349%3Flang%3Den Tris Base]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=S1804&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dtrisodium%2Bcitrate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Trisodium Citrate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T7293&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dtryptone%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Tryptone]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T0254&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DTryptophan%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Tryptophan]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=92144&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dyeast%2Bextract%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Yeast extract]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=229997&brand=ALDRICH&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dzinc%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax ZnCl<sub>2</sub>]<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Project/BiosensorsTeam:Cambridge/Project/Biosensors2012-09-24T14:37:46Z<p>CharlotteBG: /* Other Biosensors */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_PROJECT}}<br />
<br />
=Ribosense=<br />
<br />
[[File:Magnesium riboswitch image.jpg|350px|right|thumb|The Magnesium Riboswitch we tested. The M-box on the left is the apamer, while the terminator on the left is the expression platform, active only when magnesium is bound. From Dann et al., Cell 2007.]]<br />
<br />
As the main crux of this project is a standardised output, we aimed to develop several biosensors, employing different mechanisms, to prove the extended functionality of the final product. To date, most of the biosensors in the registry use an inducible promoter to control expression of their reporter protein. We aim to use some of these as a proof of the compatability of our kit with a theoretical customers' sensors. However, we also explored another mechanism of biosensing in the form of riboswitches. These have several advantages over traditional inducible promotors: firstly, they are usually modular in design, typically containing an aptamer (ligand binding) domain and an expression platform domain, which alters expression of downstream genes. Such a structure may allow for abstraction of discrete parts of each riboswitch, and construction of new regulatory elements with engineered properties. Secondly, if the expression platform acts by altering translational rate after transcription has finished, such devices may allow for faster respone times than those seen for normal genetic devices, which can only alter transcriptional rates.<br />
<br />
==Our sensors==<br />
<br />
[[Team:Cambridge/Project/MagnesiumRiboswitch|Magnesium Riboswitch]]<br />
<br />
[[Team:Cambridge/Project/FluorideRiboswitch|Fluoride Riboswitch]]<br />
<br />
==Other Biosensors==<br />
<br />
We also aimed to use other biosensing parts that were pertinent to the topic of groundwater contamination and which were already available in the registry. Early thoughts of mercury and arsenic testing proved to be unfeasible within the time constraints as our laboratory does not usually handle these materials and so was not already equipped for their use. <br />
<br />
Copper [http://partsregistry.org/Part:BBa_K190024 BBa_K190024] and Zinc [http://partsregistry.org/Part:BBa_K190022 BBa_K190022] inducible promoters were selected from the registry, as they seemed promising, with our focus on the copper part as this was labelled as 'working' by the original team [https://2009.igem.org/Team:Groningen Groningen_09]. We have sadly been unable to replicate this result through our work over the summer. The capacity of metal ions to induce these promoters is highly dependent on the Heavy metal transporter protein [http://partsregistry.org/Part:BBa_K190018 BBa_K190018], also used by Groningen_09.<br />
<br />
One of our initial concerns was that the system may not be compatible in ''B.subtilis'' as it was designed in ''E.coli''. Tests in both species were unfavourable however. After several weeks with little success we sent these biobricks to [http://www.lifesciences.sourcebioscience.com/genomic-services/sanger-sequencing-service.aspx Source Bioscience Ltd] for sequencing. While we can now confirm the sequences of the inducible promoters, we found sequencing inconsistencies in the transport protein. This experience has been added to the parts registry. <br />
<br />
These inconsistencies seem to have rendered the protein non-functional or sufficiently less functional and time shortages prevented us from looking for an alternative. As such we have been unable to test the capacities of these biobricks in relation to our system. <br />
<br />
===References===<br />
<br />
*Nyan Win M. and Smolke C., A modular and extensible RNA-based gene-regulatory platform for engineering cellular function, Proc Natl Acad Sci USA (2007) vol. 104 (36) pp. 14283-8.<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Project/BiosensorsTeam:Cambridge/Project/Biosensors2012-09-24T14:36:07Z<p>CharlotteBG: /* Other Biosensors */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_PROJECT}}<br />
<br />
=Ribosense=<br />
<br />
[[File:Magnesium riboswitch image.jpg|350px|right|thumb|The Magnesium Riboswitch we tested. The M-box on the left is the apamer, while the terminator on the left is the expression platform, active only when magnesium is bound. From Dann et al., Cell 2007.]]<br />
<br />
As the main crux of this project is a standardised output, we aimed to develop several biosensors, employing different mechanisms, to prove the extended functionality of the final product. To date, most of the biosensors in the registry use an inducible promoter to control expression of their reporter protein. We aim to use some of these as a proof of the compatability of our kit with a theoretical customers' sensors. However, we also explored another mechanism of biosensing in the form of riboswitches. These have several advantages over traditional inducible promotors: firstly, they are usually modular in design, typically containing an aptamer (ligand binding) domain and an expression platform domain, which alters expression of downstream genes. Such a structure may allow for abstraction of discrete parts of each riboswitch, and construction of new regulatory elements with engineered properties. Secondly, if the expression platform acts by altering translational rate after transcription has finished, such devices may allow for faster respone times than those seen for normal genetic devices, which can only alter transcriptional rates.<br />
<br />
==Our sensors==<br />
<br />
[[Team:Cambridge/Project/MagnesiumRiboswitch|Magnesium Riboswitch]]<br />
<br />
[[Team:Cambridge/Project/FluorideRiboswitch|Fluoride Riboswitch]]<br />
<br />
==Other Biosensors==<br />
<br />
We also aimed to use other biosensing parts that were pertinent to the topic of groundwater contamination and which were already available in the registry. Early thoughts of mercury and arsenic testing proved to be unfeasible within the time constraints as our laboratory does not usually handle these materials and so was not already equipped for their use. <br />
<br />
Copper [http://partsregistry.org/Part:BBa_K190024 BBa_K190024] and Zinc [http://partsregistry.org/Part:BBa_K190022 BBa_K190022] inducible promoters were selected from the registry, as they seemed promising, with our focus on the copper part as this was labelled as 'working' by the original team [https://2009.igem.org/Team:Groningen Groningen_09]. We have sadly been unable to replicate this result through our work over the summer. The capacity of metal ions to induce these promoters is highly dependent on the Heavy metal transporter protein [http://partsregistry.org/Part:BBa_K190018 BBa_K190018], also used by Groningen_09.<br />
<br />
After several weeks with little success we sent these biobricks to [http://www.lifesciences.sourcebioscience.com/genomic-services/sanger-sequencing-service.aspx Source Bioscience Ltd] for sequencing. While we can now confirm the sequences of the inducible promoters, we found sequencing inconsistencies in the transport protein. This experience has been added to the parts registry. <br />
<br />
These inconsistencies seem to have rendered the protein non-functional or sufficiently less functional and time shortages prevented us from looking for an alternative. As such we have been unable to test the capacities of these biobricks in relation to our system. <br />
<br />
===References===<br />
<br />
*Nyan Win M. and Smolke C., A modular and extensible RNA-based gene-regulatory platform for engineering cellular function, Proc Natl Acad Sci USA (2007) vol. 104 (36) pp. 14283-8.<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Project/BiosensorsTeam:Cambridge/Project/Biosensors2012-09-24T14:35:32Z<p>CharlotteBG: /* Other Biosensors */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_PROJECT}}<br />
<br />
=Ribosense=<br />
<br />
[[File:Magnesium riboswitch image.jpg|350px|right|thumb|The Magnesium Riboswitch we tested. The M-box on the left is the apamer, while the terminator on the left is the expression platform, active only when magnesium is bound. From Dann et al., Cell 2007.]]<br />
<br />
As the main crux of this project is a standardised output, we aimed to develop several biosensors, employing different mechanisms, to prove the extended functionality of the final product. To date, most of the biosensors in the registry use an inducible promoter to control expression of their reporter protein. We aim to use some of these as a proof of the compatability of our kit with a theoretical customers' sensors. However, we also explored another mechanism of biosensing in the form of riboswitches. These have several advantages over traditional inducible promotors: firstly, they are usually modular in design, typically containing an aptamer (ligand binding) domain and an expression platform domain, which alters expression of downstream genes. Such a structure may allow for abstraction of discrete parts of each riboswitch, and construction of new regulatory elements with engineered properties. Secondly, if the expression platform acts by altering translational rate after transcription has finished, such devices may allow for faster respone times than those seen for normal genetic devices, which can only alter transcriptional rates.<br />
<br />
==Our sensors==<br />
<br />
[[Team:Cambridge/Project/MagnesiumRiboswitch|Magnesium Riboswitch]]<br />
<br />
[[Team:Cambridge/Project/FluorideRiboswitch|Fluoride Riboswitch]]<br />
<br />
==Other Biosensors==<br />
<br />
We also aimed to use other biosensing parts that were pertinent to the topic of groundwater contamination and which were already available in the registry. Early thoughts of mercury and arsenic testing proved to be unfeasible within the time constraints as our laboratory does not usually handle these materials and so was not already equipped for their use. <br />
<br />
Copper [http://partsregistry.org/Part:BBa_K190024 BBa_K190024] and Zinc [http://partsregistry.org/Part:BBa_K190022 BBa_K190022] inducible promoters were selected from the registry, as they seemed promising, with our focus on the copper part as this was labelled as 'working' by the original team [https://2009.igem.org/Team:Groningen | Groningen_09]. We have sadly been unable to replicate this result through our work over the summer. The capacity of metal ions to induce these promoters is highly dependent on the Heavy metal transporter protein [http://partsregistry.org/Part:BBa_K190018 BBa_K190018], also used by Groningen_09.<br />
<br />
After several weeks with little success we sent these biobricks to [http://www.lifesciences.sourcebioscience.com/genomic-services/sanger-sequencing-service.aspx Source Bioscience Ltd] for sequencing. While we can now confirm the sequences of the inducible promoters, we found sequencing inconsistencies in the transport protein. This experience has been added to the parts registry. <br />
<br />
These inconsistencies seem to have rendered the protein non-functional or sufficiently less functional and time shortages prevented us from looking for an alternative. As such we have been unable to test the capacities of these biobricks in relation to our system. <br />
<br />
===References===<br />
<br />
*Nyan Win M. and Smolke C., A modular and extensible RNA-based gene-regulatory platform for engineering cellular function, Proc Natl Acad Sci USA (2007) vol. 104 (36) pp. 14283-8.<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Project/BiosensorsTeam:Cambridge/Project/Biosensors2012-09-24T14:35:07Z<p>CharlotteBG: /* Other Biosensors */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_PROJECT}}<br />
<br />
=Ribosense=<br />
<br />
[[File:Magnesium riboswitch image.jpg|350px|right|thumb|The Magnesium Riboswitch we tested. The M-box on the left is the apamer, while the terminator on the left is the expression platform, active only when magnesium is bound. From Dann et al., Cell 2007.]]<br />
<br />
As the main crux of this project is a standardised output, we aimed to develop several biosensors, employing different mechanisms, to prove the extended functionality of the final product. To date, most of the biosensors in the registry use an inducible promoter to control expression of their reporter protein. We aim to use some of these as a proof of the compatability of our kit with a theoretical customers' sensors. However, we also explored another mechanism of biosensing in the form of riboswitches. These have several advantages over traditional inducible promotors: firstly, they are usually modular in design, typically containing an aptamer (ligand binding) domain and an expression platform domain, which alters expression of downstream genes. Such a structure may allow for abstraction of discrete parts of each riboswitch, and construction of new regulatory elements with engineered properties. Secondly, if the expression platform acts by altering translational rate after transcription has finished, such devices may allow for faster respone times than those seen for normal genetic devices, which can only alter transcriptional rates.<br />
<br />
==Our sensors==<br />
<br />
[[Team:Cambridge/Project/MagnesiumRiboswitch|Magnesium Riboswitch]]<br />
<br />
[[Team:Cambridge/Project/FluorideRiboswitch|Fluoride Riboswitch]]<br />
<br />
==Other Biosensors==<br />
<br />
We also aimed to use other biosensing parts that were pertinent to the topic of groundwater contamination and which were already available in the registry. Early thoughts of mercury and arsenic testing proved to be unfeasible within the time constraints as our laboratory does not usually handle these materials and so was not already equipped for their use. <br />
<br />
Copper [http://partsregistry.org/Part:BBa_K190024 BBa_K190024] and Zinc [http://partsregistry.org/Part:BBa_K190022 BBa_K190022] inducible promoters were selected from the registry, as they seemed promising, with our focus on the copper part as this was labelled as 'working' by the original team [https://2009.igem.org/Team:Groningen|Groningen_09]. We have sadly been unable to replicate this result through our work over the summer. The capacity of metal ions to induce these promoters is highly dependent on the Heavy metal transporter protein [http://partsregistry.org/Part:BBa_K190018 BBa_K190018], also used by Groningen_09.<br />
<br />
After several weeks with little success we sent these biobricks to [http://www.lifesciences.sourcebioscience.com/genomic-services/sanger-sequencing-service.aspx Source Bioscience Ltd] for sequencing. While we can now confirm the sequences of the inducible promoters, we found sequencing inconsistencies in the transport protein. This experience has been added to the parts registry. <br />
<br />
These inconsistencies seem to have rendered the protein non-functional or sufficiently less functional and time shortages prevented us from looking for an alternative. As such we have been unable to test the capacities of these biobricks in relation to our system. <br />
<br />
===References===<br />
<br />
*Nyan Win M. and Smolke C., A modular and extensible RNA-based gene-regulatory platform for engineering cellular function, Proc Natl Acad Sci USA (2007) vol. 104 (36) pp. 14283-8.<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Project/BiosensorsTeam:Cambridge/Project/Biosensors2012-09-24T14:34:15Z<p>CharlotteBG: /* Other Biosensors */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_PROJECT}}<br />
<br />
=Ribosense=<br />
<br />
[[File:Magnesium riboswitch image.jpg|350px|right|thumb|The Magnesium Riboswitch we tested. The M-box on the left is the apamer, while the terminator on the left is the expression platform, active only when magnesium is bound. From Dann et al., Cell 2007.]]<br />
<br />
As the main crux of this project is a standardised output, we aimed to develop several biosensors, employing different mechanisms, to prove the extended functionality of the final product. To date, most of the biosensors in the registry use an inducible promoter to control expression of their reporter protein. We aim to use some of these as a proof of the compatability of our kit with a theoretical customers' sensors. However, we also explored another mechanism of biosensing in the form of riboswitches. These have several advantages over traditional inducible promotors: firstly, they are usually modular in design, typically containing an aptamer (ligand binding) domain and an expression platform domain, which alters expression of downstream genes. Such a structure may allow for abstraction of discrete parts of each riboswitch, and construction of new regulatory elements with engineered properties. Secondly, if the expression platform acts by altering translational rate after transcription has finished, such devices may allow for faster respone times than those seen for normal genetic devices, which can only alter transcriptional rates.<br />
<br />
==Our sensors==<br />
<br />
[[Team:Cambridge/Project/MagnesiumRiboswitch|Magnesium Riboswitch]]<br />
<br />
[[Team:Cambridge/Project/FluorideRiboswitch|Fluoride Riboswitch]]<br />
<br />
==Other Biosensors==<br />
<br />
We also aimed to use other biosensing parts that were pertinent to the topic of groundwater contamination and which were already available in the registry. Early thoughts of mercury and arsenic testing proved to be unfeasible within the time constraints as our laboratory does not usually handle these materials and so was not already equipped for their use. <br />
<br />
Copper [http://partsregistry.org/Part:BBa_K190024 BBa_K190024] and Zinc [http://partsregistry.org/Part:BBa_K190022 BBa_K190022] inducible promoters were selected from the registry, as they seemed promising, with our focus on the copper part as this was labelled as 'working' by the original team ([[https://2009.igem.org/Team:Groningen|Groningen_09]]). We have sadly been unable to replicate this result through our work over the summer. The capacity of metal ions to induce these promoters is highly dependent on the Heavy metal transporter protein [http://partsregistry.org/Part:BBa_K190018 BBa_K190018], also used by Groningen_09.<br />
<br />
After several weeks with little success we sent these biobricks to [http://www.lifesciences.sourcebioscience.com/genomic-services/sanger-sequencing-service.aspx Source Bioscience Ltd] for sequencing. While we can now confirm the sequences of the inducible promoters, we found sequencing inconsistencies in the transport protein. This experience has been added to the parts registry. <br />
<br />
These inconsistencies seem to have rendered the protein non-functional or sufficiently less functional and time shortages prevented us from looking for an alternative. As such we have been unable to test the capacities of these biobricks in relation to our system. <br />
<br />
===References===<br />
<br />
*Nyan Win M. and Smolke C., A modular and extensible RNA-based gene-regulatory platform for engineering cellular function, Proc Natl Acad Sci USA (2007) vol. 104 (36) pp. 14283-8.<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/ProtocolsTeam:Cambridge/Protocols2012-09-24T10:48:01Z<p>CharlotteBG: /* Miscellaneous */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
<br />
=Protocols=<br />
<br />
==Safety==<br />
See our [[Team:Cambridge/Safety|<u>Safety Page</u>]] for [[Team:Cambridge/Safety/RiskAssessments|<u>Associated risk assessments</u>]] for the protocols below and [[Team:Cambridge/Safety/MSDS|<u>MSDS sheets </u>]] for the reagents we have used.<br />
<br />
==Methods==<br />
<br />
===Construct production===<br />
<br />
* [[Team:Cambridge/Protocols/GelElectrophoresis|<u><span style="color:#00000CD">Gel Electrophoresis</span></u>]] A technique for separating DNA strands of different lengths.<br />
* [[Team:Cambridge/Protocols/GelExtractionofDNA|<u><span style="color:#00000CD">Gel Extraction of DNA</span></u>]] A technique used to isolate a desired fragment of intact DNA from an agarose gel following agarose gel electrophoresis.<br />
* [[Team:Cambridge/Protocols/Gibsonassembly|<u><span style="color:#00000CD">Gibson Assembly</span></u>]] A technique for ligating multiple DNA fragments in one step, compatible with standard assembly.<br />
* [[Team:Cambridge/Protocols/PCRProtocol|<u><span style="color:#00000CD">PCR using a high temperature DNA polymerase</span></u>]] A method for amplifying a section of DNA.<br />
* [[Team:Cambridge/Protocols/DigestionLigation|<u><span style="color:#00000CD">Making a Biobrick</span></u>]] A final step to put your construct into the standard biobrick format to be submitted to the registry.<br />
<br />
===Transformation protocols===<br />
<br />
* [[Team:Cambridge/Protocols/Chemicallycompetentcells|<u><span style="color:#00000CD">Chemically competent cells generation</span></u>]] A technique to produce e.coli cellsreceptive to chemical transformation.<br />
* [[Team:Cambridge/Protocols/Electrocompetentcells|<u><span style="color:#00000CD">Electocompetent cells generation</span></u>]] A technique to produce e.coli cells receptive to transformation by electroporation<br />
* [[Team:Cambridge/Protocols/ElectricalTransformation|<u><span style="color:#00000CD">Electroporation</span></u>]] A method for transforming appropriately competent cells with plasmid DNA using electricity. <br />
* [[Team:Cambridge/Protocols/GlycerolStocks|<u><span style="color:#00000CD">Glycerol stocks</span></u>]] A technique for long term storage of cells at -80 degrees without losing cell vitality.<br />
* [[Team:Cambridge/Protocols/TransformationofB.subtilis|<u><span style="color:#00000CD">Transformation of ''Bacillus subtilis''</span></u>]] A technique used to introduce foreign DNA into competent Bacillus cells. <br />
* [[Team:Cambridge/Protocols/TransformationofE.coli|<u><span style="color:#00000CD">Transformation of ''Escherichia coli''</span></u> ]] A method for transforming competent ''E.coli'' with DNA<br />
<br />
===Construct verification===<br />
<br />
* [[Team:Cambridge/Protocols/PCRcolony|<u><span style="color:#00000CD">Colony PCR</span></u>]] PCR with cells as a template. Useful for checking the length of an insert in an introduced plasmid.<br />
* [[Team:Cambridge/Protocols/RestrictionDigest|<u><span style="color:#00000CD">Restriction Enzyme Digest</span></u>]] A method for creating a restriction map of a plasmid. <br />
* [[Team:Cambridge/Protocols/MiniPrep|<u><span style="color:#00000CD">MiniPrep - DNA extraction</span></u>]] A method used to extract DNA from bacterial cells.<br />
<br />
===Ribosense testing===<br />
<br />
* [[Team:Cambridge/Protocols/beta-galactosidaseassay|<u><span style="color:#00000CD">&beta;-galactosidase assay</span></u>]] Assay to qualitatively measure the amount of the enzyme &beta;-galactosidase being produced by a population of cells. Useful as a reporter system.<br />
* [[Team:Cambridge/Protocols/MillerAssay|<u><span style="color:#00000CD">Miller assay</span></u>]] Assay to quantify the amount of the enzyme &beta;-galactosidase being produced by a population of cells. Useful as a quantitative reporter system.<br />
* [[Team:Cambridge/Protocols/MgFreeCells|<u><span style="color:#00000CD">Production of magnesium free cells.</span></u>]] Technique to produce cells that contain little or no magnesium, to control for this variable in tests involving the magnesium riboswitch.<br />
<br />
===Ratiometrica testing===<br />
<br />
* [[Team:Cambridge/Protocols/IPTGInduction|<u><span style="color:#00000CD">IPTG induction</span></u>]] A technique for inducing the pSPANK promoter in E.coli cells.<br />
<br />
===Sporulation and Germination===<br />
<br />
* [[Team:Cambridge/Protocols/SporeImage|<u><span style="color:#00000CD">Imaging spores</span></u>]] A method for seeing vegetative cells and bacillus spores under the microscope.<br />
* [[Team:Cambridge/Protocols/GetSpores|<u><span style="color:#00000CD">Producing high yields of spores</span></u>]] A method for obtaining high yields of spores from B. Subtilis<br />
<br />
===Miscellaneous===<br />
<br />
* [[Team:Cambridge/Protocols/biobrick_protocols|<u><span style="color:#00000CD">BioBricks</span></u>]] Resources for manipulation of BioBricks and information regarding the distribution.<br />
* [[Team:Cambridge/Protocols/Plates|<u><span style="color:#00000CD">LB Agar Plates preparation</span></u>]] A method used to prepare agar plate to culture common bacteria.<br />
* [[Team:Cambridge/Protocols/AntibioticStocks| Use of Antibiotic Stocks]] The production of Antibiotic LB agar plates and liquid medium to discriminate bacterial lineages.<br />
<br />
==Recipes==<br />
* [[Team:Cambridge/Protocols/M9Medium|<u><span style="color:#00000CD">M9 minimal medium</span></u>]] A recipe for making M9 minimal medium for use when autofluorescence must be avoided.<br />
* [[Team:Cambridge/Protocols/MediumB|<u><span style="color:#00000CD">Medium B</span></u>]] A recipe for making medium B.<br />
* [[Team:Cambridge/Protocols/CCMB80|<u><span style="color:#00000CD">CCMB80 for chemically competent cells generation</span></u>]] A recipe for making CCMB80<br />
* [[Team:Cambridge/Protocols/TAEBuffer|<u><span style="color:#00000CD">TAE buffer for gel electrophoresis</span></u>]] A recipe for making 10xTAE buffer<br />
* [[Team:Cambridge/Protocols/SOB|<u><span style="color:#00000CD">SOB growth medium</span></u>]] A recipe for making SOB growth medium<br />
* [[Team:Cambridge/Protocols/SporeMedia|<u><span style="color:#00000CD">CDSM</span></u>]] A Chemically Defined Media to induce sporulation in B. Subtilis<br />
* [[Team:Cambridge/Protocols/GermMedia|<u><span style="color:#00000CD">Germination Media</span></u>]] A Chemically Defined Media to induce Germination in B. Subtilis<br />
<br />
==Lab supplies== <br />
*[http://www.bioc.cam.ac.uk/stores/ <span style="color:#0000CD"><u>BioPath Stores</u></span>]<br />
*[http://www.plantsci.cam.ac.uk/camonly/stores/stock.xls <span style="color:#0000CD"><u>Plant Department Stores Catalogue xls (Updated 2nd July 2012)</u></span>]<br />
<br />
<br />
==Other resources==<br />
<br />
<u>[[File:Concentration calculator for lazy scientists.xls]]</u><br />
<br />
[http://meta.wikimedia.org/wiki/Help:Contents <u>Media wiki editing</u>]<br />
<br />
[http://blast.ncbi.nlm.nih.gov/Blast.cgi <u>BLAST at NCBI</u>]<br />
<br />
[http://www.finnzymes.fi/tm_determination.html <u>finnzymes Tm calculator</u>]<br />
<br />
[http://mfold.rna.albany.edu/?q=mfold <u>mfold</u>], DNA or RNA folding forms on the left hand side<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/RiskAssessments/AntibioticStocksTeam:Cambridge/RiskAssessments/AntibioticStocks2012-09-23T15:00:00Z<p>CharlotteBG: Created page with "{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}} ==Use of Antibiotic Stocks== The protocol for this technique can be found [[Team:Cambridge/Protocols/AntibioticStocks|..."</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
==Use of Antibiotic Stocks==<br />
<br />
The protocol for this technique can be found [[Team:Cambridge/Protocols/AntibioticStocks|here]] and MSDS for reagents used can be found [[Team:Cambridge/Protocols/beta-galactosidaseassay|here]].<br />
<br />
===Risks===<br />
<br />
'''Antibiotics''' - Good laboratory practice should always be observed but this is exceptionally important in the case of antibiotics, which should be treated as a hazardous chemical. Handle with care and never touch the face before washing hands having handled them. This is especially important if any member of the team has an allergy to the antibiotics used, most common are allergies to ampicillin (as a penicillin derivative) and kanamycin.<br />
<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Protocols/AntibioticStocksTeam:Cambridge/Protocols/AntibioticStocks2012-09-23T14:48:17Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
<br />
==Use of Antibiotic Stocks==<br />
<br />
[[Team:Cambridge/RiskAssessments/AntibioticStocks| Risk Assessment]]<br />
<br />
Stocks are to be kept in a -20<sup>o</sup>c freezer, clearly labelled. <br />
<br />
Available stocks in the lab are:<br />
*Ampicillin 100mg/ml , 1ml in each eppendorf<br />
*Chloramphenicol 25mg/ml , 200µl in each eppendorf<br />
*Kanamycin 50mg/ml , 1ml in each eppendorf<br />
*Erythromycin 10mg/ml , 1ml in each eppendorf<br />
<br />
===To make plates:===<br />
<br />
Put one entire tube into 1 litre of LB AGAR - This should be done in the flow hood. <br />
<br />
This will make the ''standard plates''<br />
*Ampicillin 100µg/ml<br />
*Chloramphenicol 5µg/ml<br />
*Kanamycin 50µg/ml<br />
*Erythromycin 5µg/ml<br />
<br />
To make these concentrations in the standard 250ml bottle LB Agar, add:<br />
*250µl ampicillin stock<br />
*50µl chloramphenicol stock<br />
*250µl kanamycin stock<br />
*125µl erythromycin stock<br />
<br />
===Common plate concentrations for backbones:===<br />
<br />
*pSB1C3 (''E.coli'') : 25µg/ml Chloramphenicol<br />
*pSJ150 (''E.coli'') : 100µg/ml Ampicillin <br />
*pSJ150 (''B.subtilis'') : 5µg/ml Chloramphenicol<br />
*pSB1K3 (''E.coli'') : 50µg/ml Kanamycin<br />
*PSB4K5 (''E.coli'') : 50µg/ml Kanamycin<br />
<br />
===To make liquid cultures===<br />
<br />
Check for specific concentrations, this is usually lower than the ones you use for plates, and add the required amount to sterile LB.<br />
<br />
<br />
<center>'''[[Team:Cambridge/Protocols|Back to Protocols]]'''</center><br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Protocols/AntibioticStocksTeam:Cambridge/Protocols/AntibioticStocks2012-09-23T14:44:35Z<p>CharlotteBG: Created page with "{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}} ==Use of Antibiotic Stocks== Stocks are to be kept in a -20<sup>o</sup>c freezer, clearly labelled. Available stocks ..."</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
<br />
==Use of Antibiotic Stocks==<br />
<br />
Stocks are to be kept in a -20<sup>o</sup>c freezer, clearly labelled. <br />
<br />
Available stocks in the lab are:<br />
*Ampicillin 100mg/ml , 1ml in each eppendorf<br />
*Chloramphenicol 25mg/ml , 200µl in each eppendorf<br />
*Kanamycin 50mg/ml , 1ml in each eppendorf<br />
*Erythromycin 10mg/ml , 1ml in each eppendorf<br />
<br />
===To make plates:===<br />
<br />
Put one entire tube into 1 litre of LB AGAR - This should be done in the flow hood. <br />
<br />
This will make the ''standard plates''<br />
*Ampicillin 100µg/ml<br />
*Chloramphenicol 5µg/ml<br />
*Kanamycin 50µg/ml<br />
*Erythromycin 5µg/ml<br />
<br />
To make these concentrations in the standard 250ml bottle LB Agar, add:<br />
*250µl ampicillin stock<br />
*50µl chloramphenicol stock<br />
*250µl kanamycin stock<br />
*125µl erythromycin stock<br />
<br />
===Common plate concentrations for backbones:===<br />
<br />
*pSB1C3 (''E.coli'') : 25µg/ml Chloramphenicol<br />
*pSJ150 (''E.coli'') : 100µg/ml Ampicillin <br />
*pSJ150 (''B.subtilis'') : 5µg/ml Chloramphenicol<br />
*pSB1K3 (''E.coli'') : 50µg/ml Kanamycin<br />
*PSB4K5 (''E.coli'') : 50µg/ml Kanamycin<br />
<br />
===To make liquid cultures===<br />
<br />
Check for specific concentrations, this is usually lower than the ones you use for plates, and add the required amount to sterile LB.<br />
<br />
<br />
<center>'''[[Team:Cambridge/Protocols|Back to Protocols]]'''</center><br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/User:CharlotteBGUser:CharlotteBG2012-09-23T14:44:20Z<p>CharlotteBG: Blanked the page</p>
<hr />
<div></div>CharlotteBGhttp://2012.igem.org/User:CharlotteBGUser:CharlotteBG2012-09-23T14:43:53Z<p>CharlotteBG: Created page with "{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}} ==Use of Antibiotic Stocks== Stocks are to be kept in a -20<sup>o</sup>c freezer, clearly labelled. Available stocks ..."</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
<br />
==Use of Antibiotic Stocks==<br />
<br />
Stocks are to be kept in a -20<sup>o</sup>c freezer, clearly labelled. <br />
<br />
Available stocks in the lab are:<br />
*Ampicillin 100mg/ml , 1ml in each eppendorf<br />
*Chloramphenicol 25mg/ml , 200µl in each eppendorf<br />
*Kanamycin 50mg/ml , 1ml in each eppendorf<br />
*Erythromycin 10mg/ml , 1ml in each eppendorf<br />
<br />
===To make plates:===<br />
<br />
Put one entire tube into 1 litre of LB AGAR - This should be done in the flow hood. <br />
<br />
This will make the ''standard plates''<br />
*Ampicillin 100µg/ml<br />
*Chloramphenicol 5µg/ml<br />
*Kanamycin 50µg/ml<br />
*Erythromycin 5µg/ml<br />
<br />
To make these concentrations in the standard 250ml bottle LB Agar, add:<br />
*250µl ampicillin stock<br />
*50µl chloramphenicol stock<br />
*250µl kanamycin stock<br />
*125µl erythromycin stock<br />
<br />
===Common plate concentrations for backbones:===<br />
<br />
*pSB1C3 (''E.coli'') : 25µg/ml Chloramphenicol<br />
*pSJ150 (''E.coli'') : 100µg/ml Ampicillin <br />
*pSJ150 (''B.subtilis'') : 5µg/ml Chloramphenicol<br />
*pSB1K3 (''E.coli'') : 50µg/ml Kanamycin<br />
*PSB4K5 (''E.coli'') : 50µg/ml Kanamycin<br />
<br />
===To make liquid cultures===<br />
<br />
Check for specific concentrations, this is usually lower than the ones you use for plates, and add the required amount to sterile LB.<br />
<br />
<br />
<center>'''[[Team:Cambridge/Protocols|Back to Protocols]]'''</center><br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Outreach/TripleHelixTeam:Cambridge/Outreach/TripleHelix2012-09-21T16:52:38Z<p>CharlotteBG: /* Triple Helix */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}}<br />
<br />
<br />
==Triple Helix==<br />
<br />
<br />
'''The Triple Helix is a global forum for science in society run by students at over 25 of the world's leading universities. Their journal 'Science in Society' is printed termly and Cambridge iGEM was asked to provide a short article for the Michaelmas 2012 (autumn) edition. Below is a copy of the article submitted:'''<br />
<br />
''The iGEM (international genetically engineered machines) competition began at MIT in 2003 and the Cambridge team has competed every year since 2005 when it first became international, winning the globally in 2009. Students work in teams over the summer and then present their research at international conferences; the university team will be going to Amsterdam for this purpose in early October. Though the competition is primarily for undergraduates, many teams benefit from graduate mentors who are often themselves previous iGEMers, who provide invaluable advice and guidance over the course of the project.<br />
<br />
''Central to the competition is the teams’ production and use of biobricks (standard biological parts) though synthetic biology. When put together the biobricks can be constructed into ‘devices’ within bacterial systems which can do anything from making E.coli smell of bananas to glow bright red in the presence of arsenic. <br />
<br />
''The team’s project this year has been focussed on producing a standardised output with instrumentation for biosensor experiments, such as are often used in within the iGEM competition. To do this we have created ratiometric light emitting constructs using fluorescent proteins and luciferases - bioluminescent proteins found in fireflies and some bacteria. <br />
<br />
''Many people are familiar with the idea of coupling light emmitance to the production of a substance within cells to estimate its concentration, but this system has inherent problems. Does a low reading indicate low production in a lot of cells or that most of the cells are dead and very high production exists among the survivors?<br />
<br />
''The ratiometric construct helps by using two colours. One colour is produced constantly while the cell is undergoing protein synthesis, the other induced under set circumstances. Taking the ratio of these outputs allows for calculations of production per cell. Through quantification experiments, plotting output per cell against known concentrations, it is possible to characterise biological parts – effectively, producing a data sheet. <br />
<br />
''Students must be in the intermediate years of their first degree to compete in the undergraduate division of iGEM and this year’s team features 6 biologists and 2 engineers. Many students choose to spend these summers on laboratory research placements or scientific internships and opportunities like these are intensely important to the students who take them, providing valuable laboratory experience and extremely interesting summers. <br />
<br />
''The great advantage of the iGEM competition however is that, while supervised (primarily by Dr Jim Haseloff); it is the students’ project from their interests. And though it can occasionally feel like being thrown in at the deep end – once you start climbing the rather steep learning curve, it’s more than worth it.''<br />
<br />
<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Outreach/TripleHelixTeam:Cambridge/Outreach/TripleHelix2012-09-21T16:43:16Z<p>CharlotteBG: /* Triple Helix */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}}<br />
<br />
<br />
==Triple Helix==<br />
<br />
<br />
'''The Triple Helix is a global forum for science in society run by students at over 25 of the world's leading universities. Their journal 'Science in Society' is printed termly and Cambridge iGEM was asked to provide a short article for the Michaelmas 2012 (autumn) edition. Below is a copy of the article submitted:'''<br />
<br />
''The iGEM (international genetically engineered machines) competition began at MIT in 2003 and the Cambridge team has competed every year since 2005 when it first became international, winning the globally in 2009. Students work in teams over the summer and then present their research at international conferences; the university team will be going to Amsterdam for this purpose in early October. Though the competition is primarily for undergraduates, many teams benefit from graduate mentors who are often themselves previous iGEMers, who provide invaluable advice and guidance over the course of the project.<br />
<br />
''Central to the competition is the teams’ production and use of biobricks (standard biological parts) though synthetic biology. When put together the biobricks can be constructed into ‘devices’ within bacterial systems which can do anything from making E.coli smell of bananas to glow bright red in the presence of arsenic. <br />
The team’s project this year has been focussed on producing a standardised output with instrumentation for biosensor experiments, such as are often used in within the iGEM competition. To do this we have created ratiometric light emitting constructs using fluorescent proteins and luciferases - bioluminescent proteins found in fireflies and some bacteria. <br />
<br />
''Many people are familiar with the idea of coupling light emmitance to the production of a substance within cells to estimate its concentration, but this system has inherent problems. Does a low reading indicate low production in a lot of cells or that most of the cells are dead and very high production exists among the survivors?<br />
<br />
''The ratiometric construct helps by using two colours. One colour is produced constantly while the cell is undergoing protein synthesis, the other induced under set circumstances. Taking the ratio of these outputs allows for calculations of production per cell. Through quantification experiments, plotting output per cell against known concentrations, it is possible to characterise biological parts – effectively, producing a data sheet. <br />
<br />
''Students must be in the intermediate years of their first degree to compete in the undergraduate division of iGEM and this year’s team features 6 biologists and 2 engineers. Many students choose to spend these summers on laboratory research placements or scientific internships and opportunities like these are intensely important to the students who take them, providing valuable laboratory experience and extremely interesting summers. <br />
<br />
''The great advantage of the iGEM competition however is that, while supervised (primarily by Dr Jim Haseloff); it is the students’ project from their interests. And though it can occasionally feel like being thrown in at the deep end – once you start climbing the rather steep learning curve, it’s more than worth it.''<br />
<br />
<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Outreach/OverviewTeam:Cambridge/Outreach/Overview2012-09-21T16:43:13Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}}<br />
<br />
==Human Practices:==<br />
<br />
'''iGEM criterion:''' Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.<br />
<br />
<br />
Our human practices this year has been a driving force of our project from the start, defining many of its key features. This part of our project has drawn on the safety, sharing and innovation criteria in a three part sub-project as well as incorporating outreach. In the safety category, we go beyond the iGEM requirement of the safety questions to present our idea of the standard of obvious safety consciousness that teams should provide. In sharing, we explain how the desire to produce a system that would encourage sharing between iGEM teams and allow collaborative projects with greater ease was one of the factors that helped define our project from the start and how the necessity for this became increasingly obvious as the project continued and we faced problems trying to build on the research of other teams.<br />
<br />
===Innovation:===<br />
<br />
We took the idea of considering our project as a product. Clearly in its current state it is not a product ready to go to market, but could be considered as a prototype for one that might be. Our system is designed to be used in a huge variety of circumstances, but for the sake of this exercise we have used just one.<br />
<br />
The idea was to consider the process of taking our ‘product’ and putting it in a ‘market. We have considered a suitable market for the product – in this case groundwater contamination in rural India, weighed up the strengths and weaknesses of currently available systems that cater for this market and how our system differs.<br />
<br />
We then consider the likely problems that would be faced were we attempting to attempt this now, ranging from mistrust of GMOs to bacterial disposal.<br />
<br />
'''Why is this relevant?'''<br />
<br />
The majority of us, whether we pursue careers in research or industry will probably at some point be involved with the production or release of a product. We have tried to use this as a trial run, to show teams what they might expect to come up against. We hope that this might inspire teams to consider human practices as a foundation for their projects as we did. Fluoride contamination was a major factor in the decision to design a system from start to finish that could quantifiably test for fluoride. We hope that this might encourage teams to think innovatively about their project when in the design phase, to consider a real world problem to which their project could be a solution and to consider the problems they might encounter in the course of applying that solution so that they can be tackled in the course of the project.<br />
<br />
Our innovation project can be found [[Team:Cambridge/Outreach/innovation|here]].<br />
<br />
===Safety:===<br />
<br />
Safety is core to the iGEM competition and all teams must complete a series of safety questions on their wiki to qualify for a medal to prove that they have considered the safety implications of their project as a whole and have set about working in compliance with good laboratory practice. In addition to this criterion we have also produced protocols for reference for all of the techniques we use in the lab. These also have risk assessments for the major risks associated with them and precaution suggestion where appropriate as well as MSDS sheets for all reagents used available in the safety section of our wiki.<br />
<br />
We assume that, like us, most iGEMers do not relish the thought of vast quantities of paperwork to accompany their projects. Our safety criteria do not impose this, but do demand further proof of safety consciousness than current requirements. <br />
<br />
'''Why is this relevant?'''<br />
<br />
The current team has found having this information readily accessible on the wiki (where it cannot be lost or tidied away) to be extremely useful and we consider it the duty of iGEM teams to leave their project in a sufficiently well documented state that future teams could pick up more or less where the previous team stopped. <br />
<br />
Where teams choose to modularise their project into several sub-projects, different teams may be working with different experiments at any given time. It may be weeks before certain teams use techniques that others utilised on their first day. This is where having reliably accessible information comes into its own. Which reagent comes next? It’s on the wiki. Waste disposal? On the wiki. Do I need a mask for this? On the wiki. Is it supposed to go that colour? It’s on the wiki.<br />
<br />
Perhaps more importantly, we have found that constantly updating and adding to the safety element of our project prevented it from slipping to the back of mind. We have found that we spent more time than anticipated considering the safety implications of experiments as we were planning and doing them, in the knowledge that we would be written up formally. <br />
<br />
The provision of detailed protocols, MSDS and at least basic risk assessments can be hugely helpful to future teams, especially students coming to the iGEM competition from non-biological disciplines. Even those of us thoroughly familiar with techniques like PCR found the last team’s notes useful for reference in the early weeks of our project. Many excellent projects have been stopped short because of time constraints. If another team wanted to build on it, they might be able to ask the previous team if it is the next year and at the same institution, but if it is several years before the project catches the imagination of another team, then the wiki is probably all they’ll have to work with. <br />
<br />
===Sharing:===<br />
<br />
Early in the summer, when we were trying to define our project, we started thinking about what we wanted it to do. We eventually settled on one of the key principles of synthetic biology – standardisation (strongly promoted by the engineers on the team). Biological research is currently a highly bespoke process with predominantly non-standardised biosensors – a multitude of output systems with a plethora of sensitivity curves exist. This renders individual sets of results amost meaningless as research from different teams is not directly comparable. This limits the capacity for sharing and collaboration as teams are effectively working on their own and this in turn limits the rate of progress.<br />
<br />
To this end our project was focussed on producing a standardised output system with instrumentation for biosensor experiments to promote facilitate sharing and collaboration between iGEM teams, with a myriad of possible applications. A ratiometric system was chosen to provide a reliable quantification system, it was decided that the system should be portable so that it could be used for field research as well as laboratory based research and relatively cheap, to make it accessible to other iGEM teams. We felt it important that the code used in the instrumentation be open source like the rest of the project, so that it could be tweaked by future users to match their needs.<br />
<br />
'''Why is this relevant?'''<br />
<br />
iGEM is open source and high value is placed on sharing, collaboration and building on the work of previous teams. Where there is a lack of standardisation however, it is hard for teams to know what they can expect when working with another team’s project. We have attributed at least some of the problems we have experienced when trying to work with previous teams’ biobricks this summer to this problem.<br />
<br />
We believe that a standardised output for biosensor experiments would be of enormous help to teams, giving them the tools to compare results, share and collaborate more effectively.<br />
<br />
===Outreach:===<br />
<br />
The Triple Helix is a global forum for science in society run by students at over 25 of the world's leading universities. Their journal 'Science in Society' is printed termly and Cambridge iGEM was asked to provide a short article for the Michaelmas 2012 (autumn) edition.<br />
<br />
A copy of this article can be found [[Team:Cambridge/Outreach/TripleHelix|here]]. <br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Outreach/TripleHelixTeam:Cambridge/Outreach/TripleHelix2012-09-21T16:29:09Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}}<br />
<br />
<br />
==Triple Helix==<br />
<br />
<br />
'''The Triple Helix is a global forum for science in society run by students at over 25 of the world's leading universities. Their journal 'Science in Society' is printed termly and Cambridge iGEM was asked to provide a short article for the Michaelmas 2012 (autumn) edition. Below is a copy of the article submitted:'''<br />
<br />
''The iGEM (international genetically engineered machines) competition began at MIT in 2003 and the Cambridge team has competed every year since 2005 when it first became international, winning the globally in 2009. Students work in teams over the summer and then present their research at international conferences; the university team will be going to Amsterdam for this purpose in early October. Though the competition is primarily for undergraduates, many teams benefit from graduate mentors who are often themselves previous iGEMers, who provide invaluable advice and guidance over the course of the project.<br />
Central to the competition is the teams’ production and use of biobricks (standard biological parts) though synthetic biology. When put together the biobricks can be constructed into ‘devices’ within bacterial systems which can do anything from making E.coli smell of bananas to glow bright red in the presence of arsenic. <br />
The team’s project this year has been focussed on producing a standardised output with instrumentation for biosensor experiments, such as are often used in within the iGEM competition. To do this we have created ratiometric light emitting constructs using fluorescent proteins and luciferases - bioluminescent proteins found in fireflies and some bacteria. <br />
Many people are familiar with the idea of coupling light emmitance to the production of a substance within cells to estimate its concentration, but this system has inherent problems. Does a low reading indicate low production in a lot of cells or that most of the cells are dead and very high production exists among the survivors?<br />
The ratiometric construct helps by using two colours. One colour is produced constantly while the cell is undergoing protein synthesis, the other induced under set circumstances. Taking the ratio of these outputs allows for calculations of production per cell. Through quantification experiments, plotting output per cell against known concentrations, it is possible to characterise biological parts – effectively, producing a data sheet. <br />
Students must be in the intermediate years of their first degree to compete in the undergraduate division of iGEM and this year’s team features 6 biologists and 2 engineers. Many students choose to spend these summers on laboratory research placements or scientific internships and opportunities like these are intensely important to the students who take them, providing valuable laboratory experience and extremely interesting summers. <br />
The great advantage of the iGEM competition however is that, while supervised (primarily by Dr Jim Haseloff); it is the students’ project from their interests. And though it can occasionally feel like being thrown in at the deep end – once you start climbing the rather steep learning curve, it’s more than worth it.''<br />
<br />
<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Outreach/TripleHelixTeam:Cambridge/Outreach/TripleHelix2012-09-21T16:27:30Z<p>CharlotteBG: /* Triple Helix */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}}<br />
<br />
<br />
==Triple Helix==<br />
<br />
<br />
'''The Triple Helix is a global forum for science in society run by students at over 25 of the world's leading universities. Their journal 'Science in Society' is printed termly and Cambridge iGEM was asked to provide a short article for the Michaelmas 2012 (autumn) edition. Below is a copy of the article submitted:'''<br />
<br />
''The iGEM (international genetically engineered machines) competition began at MIT in 2003 and the Cambridge team has competed every year since 2005 when it first became international, winning the globally in 2009. Students work in teams over the summer and then present their research at international conferences; the university team will be going to Amsterdam for this purpose in early October. Though the competition is primarily for undergraduates, many teams benefit from graduate mentors who are often themselves previous iGEMers, who provide invaluable advice and guidance over the course of the project.<br />
Central to the competition is the teams’ production and use of biobricks (standard biological parts) though synthetic biology. When put together the biobricks can be constructed into ‘devices’ within bacterial systems which can do anything from making E.coli smell of bananas to glow bright red in the presence of arsenic. <br />
The team’s project this year has been focussed on producing a standardised output with instrumentation for biosensor experiments, such as are often used in within the iGEM competition. To do this we have created ratiometric light emitting constructs using fluorescent proteins and luciferases - bioluminescent proteins found in fireflies and some bacteria. <br />
Many people are familiar with the idea of coupling light emmitance to the production of a substance within cells to estimate its concentration, but this system has inherent problems. Does a low reading indicate low production in a lot of cells or that most of the cells are dead and very high production exists among the survivors?<br />
The ratiometric construct helps by using two colours. One colour is produced constantly while the cell is undergoing protein synthesis, the other induced under set circumstances. Taking the ratio of these outputs allows for calculations of production per cell. Through quantification experiments, plotting output per cell against known concentrations, it is possible to characterise biological parts – effectively, producing a data sheet. <br />
Students must be in the intermediate years of their first degree to compete in the undergraduate division of iGEM and this year’s team features 6 biologists and 2 engineers. Many students choose to spend these summers on laboratory research placements or scientific internships and opportunities like these are intensely important to the students who take them, providing valuable laboratory experience and extremely interesting summers. <br />
The great advantage of the iGEM competition however is that, while supervised (primarily by Dr Jim Haseloff); it is the students’ project from their interests. And though it can occasionally feel like being thrown in at the deep end – once you start climbing the rather steep learning curve, it’s more than worth it.''<br />
<br />
<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Outreach/TripleHelixTeam:Cambridge/Outreach/TripleHelix2012-09-21T16:26:32Z<p>CharlotteBG: Created page with "{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}} ==Triple Helix== '''The Triple Helix is a global forum for science in society run by students at over 25 of the wo..."</p>
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==Triple Helix==<br />
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<br />
'''The Triple Helix is a global forum for science in society run by students at over 25 of the world's leading universities. Their journal 'Science in Society' is printed termly and Cambridge iGEM was asked to provide a short article for the Michaelmas 2012 (autumn) edition. Below is a copy of the article submitted:'''<br />
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''The iGEM (international genetically engineered machines) competition began at MIT in 2003 and the Cambridge team has competed every year since 2005 when it first became international, winning the globally in 2009. Students work in teams over the summer and then present their research at international conferences; the university team will be going to Amsterdam for this purpose in early October. Though the competition is primarily for undergraduates, many teams benefit from graduate mentors who are often themselves previous iGEMers, who provide invaluable advice and guidance over the course of the project.<br />
<br />
Central to the competition is the teams’ production and use of biobricks (standard biological parts) though synthetic biology. When put together the biobricks can be constructed into ‘devices’ within bacterial systems which can do anything from making E.coli smell of bananas to glow bright red in the presence of arsenic. <br />
<br />
The team’s project this year has been focussed on producing a standardised output with instrumentation for biosensor experiments, such as are often used in within the iGEM competition. To do this we have created ratiometric light emitting constructs using fluorescent proteins and luciferases - bioluminescent proteins found in fireflies and some bacteria. <br />
<br />
Many people are familiar with the idea of coupling light emmitance to the production of a substance within cells to estimate its concentration, but this system has inherent problems. Does a low reading indicate low production in a lot of cells or that most of the cells are dead and very high production exists among the survivors?<br />
<br />
The ratiometric construct helps by using two colours. One colour is produced constantly while the cell is undergoing protein synthesis, the other induced under set circumstances. Taking the ratio of these outputs allows for calculations of production per cell. Through quantification experiments, plotting output per cell against known concentrations, it is possible to characterise biological parts – effectively, producing a data sheet. <br />
<br />
Students must be in the intermediate years of their first degree to compete in the undergraduate division of iGEM and this year’s team features 6 biologists and 2 engineers. Many students choose to spend these summers on laboratory research placements or scientific internships and opportunities like these are intensely important to the students who take them, providing valuable laboratory experience and extremely interesting summers. <br />
<br />
The great advantage of the iGEM competition however is that, while supervised (primarily by Dr Jim Haseloff); it is the students’ project from their interests. And though it can occasionally feel like being thrown in at the deep end – once you start climbing the rather steep learning curve, it’s more than worth it. ''<br />
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{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Outreach/OverviewTeam:Cambridge/Outreach/Overview2012-09-21T15:57:26Z<p>CharlotteBG: /* Outreach: */</p>
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==Human Practices:==<br />
<br />
'''iGEM criterion:''' Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.<br />
<br />
<br />
Our human practices this year has been a driving force of our project from the start, defining many of its key features. This part of our project has drawn on the safety, sharing and innovation criteria in a three part sub-project as well as incorporating outreach. In the safety category, we go beyond the iGEM requirement of the safety questions to present our idea of the standard of obvious safety consciousness that teams should provide. In sharing, we explain how the desire to produce a system that would encourage sharing between iGEM teams and allow collaborative projects with greater ease was one of the factors that helped define our project from the start and how the necessity for this became increasingly obvious as the project continued and we faced problems trying to build on the research of other teams.<br />
<br />
===Innovation:===<br />
<br />
We took the idea of considering our project as a product. Clearly in its current state it is not a product ready to go to market, but could be considered as a prototype for one that might be. Our system is designed to be used in a huge variety of circumstances, but for the sake of this exercise we have used just one.<br />
<br />
The idea was to consider the process of taking our ‘product’ and putting it in a ‘market. We have considered a suitable market for the product – in this case groundwater contamination in rural India, weighed up the strengths and weaknesses of currently available systems that cater for this market and how our system differs.<br />
<br />
We then consider the likely problems that would be faced were we attempting to attempt this now, ranging from mistrust of GMOs to bacterial disposal.<br />
<br />
'''Why is this relevant?'''<br />
<br />
The majority of us, whether we pursue careers in research or industry will probably at some point be involved with the production or release of a product. We have tried to use this as a trial run, to show teams what they might expect to come up against. We hope that this might inspire teams to consider human practices as a foundation for their projects as we did. Fluoride contamination was a major factor in the decision to design a system from start to finish that could quantifiably test for fluoride. We hope that this might encourage teams to think innovatively about their project when in the design phase, to consider a real world problem to which their project could be a solution and to consider the problems they might encounter in the course of applying that solution so that they can be tackled in the course of the project.<br />
<br />
Our innovation project can be found [[Team:Cambridge/Outreach/innovation|here]].<br />
<br />
===Safety:===<br />
<br />
Safety is core to the iGEM competition and all teams must complete a series of safety questions on their wiki to qualify for a medal to prove that they have considered the safety implications of their project as a whole and have set about working in compliance with good laboratory practice. In addition to this criterion we have also produced protocols for reference for all of the techniques we use in the lab. These also have risk assessments for the major risks associated with them and precaution suggestion where appropriate as well as MSDS sheets for all reagents used available in the safety section of our wiki.<br />
<br />
We assume that, like us, most iGEMers do not relish the thought of vast quantities of paperwork to accompany their projects. Our safety criteria do not impose this, but do demand further proof of safety consciousness than current requirements. <br />
<br />
'''Why is this relevant?'''<br />
<br />
The current team has found having this information readily accessible on the wiki (where it cannot be lost or tidied away) to be extremely useful and we consider it the duty of iGEM teams to leave their project in a sufficiently well documented state that future teams could pick up more or less where the previous team stopped. <br />
<br />
Where teams choose to modularise their project into several sub-projects, different teams may be working with different experiments at any given time. It may be weeks before certain teams use techniques that others utilised on their first day. This is where having reliably accessible information comes into its own. Which reagent comes next? It’s on the wiki. Waste disposal? On the wiki. Do I need a mask for this? On the wiki. Is it supposed to go that colour? It’s on the wiki.<br />
<br />
Perhaps more importantly, we have found that constantly updating and adding to the safety element of our project prevented it from slipping to the back of mind. We have found that we spent more time than anticipated considering the safety implications of experiments as we were planning and doing them, in the knowledge that we would be written up formally. <br />
<br />
The provision of detailed protocols, MSDS and at least basic risk assessments can be hugely helpful to future teams, especially students coming to the iGEM competition from non-biological disciplines. Even those of us thoroughly familiar with techniques like PCR found the last team’s notes useful for reference in the early weeks of our project. Many excellent projects have been stopped short because of time constraints. If another team wanted to build on it, they might be able to ask the previous team if it is the next year and at the same institution, but if it is several years before the project catches the imagination of another team, then the wiki is probably all they’ll have to work with. <br />
<br />
===Sharing:===<br />
<br />
Early in the summer, when we were trying to define our project, we started thinking about what we wanted it to do. We eventually settled on one of the key principles of synthetic biology – standardisation (strongly promoted by the engineers on the team). Biological research is currently a highly bespoke process with predominantly non-standardised biosensors – a multitude of output systems with a plethora of sensitivity curves exist. This renders individual sets of results amost meaningless as research from different teams is not directly comparable. This limits the capacity for sharing and collaboration as teams are effectively working on their own and this in turn limits the rate of progress.<br />
<br />
To this end our project was focussed on producing a standardised output system with instrumentation for biosensor experiments to promote facilitate sharing and collaboration between iGEM teams, with a myriad of possible applications. A ratiometric system was chosen to provide a reliable quantification system, it was decided that the system should be portable so that it could be used for field research as well as laboratory based research and relatively cheap, to make it accessible to other iGEM teams. We felt it important that the code used in the instrumentation be open source like the rest of the project, so that it could be tweaked by future users to match their needs.<br />
<br />
'''Why is this relevant?'''<br />
<br />
iGEM is open source and high value is placed on sharing, collaboration and building on the work of previous teams. Where there is a lack of standardisation however, it is hard for teams to know what they can expect when working with another team’s project. We have attributed at least some of the problems we have experienced when trying to work with previous teams’ biobricks this summer to this problem.<br />
<br />
We believe that a standardised output for biosensor experiments would be of enormous help to teams, giving them the tools to compare results, share and collaborate more effectively.<br />
<br />
===Outreach:===<br />
<br />
Traditionally, this section of a wiki is labelled outreach and features teams promoting the iGEM competition and trying to improve public understanding and perceptions of synthetic biology as a whole. We have not had the time to do this as the vast majority of our project has been lab based; we have however written an article for the Cambridge University Graduate <br />
<br />
A copy of this article can be found [[Team:Cambridge/Outreach/TripleHelix|here]]. <br />
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{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Outreach/HumanPracticesTeam:Cambridge/Outreach/HumanPractices2012-09-20T06:10:37Z<p>CharlotteBG: Created page with "{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}} ==Human Practices – Groundwater contamination in rural India== Below is a summary of our research into the suitabi..."</p>
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==Human Practices – Groundwater contamination in rural India==<br />
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Below is a summary of our research into the suitability of our system for use in the field. <br />
<br />
===Finding a Market:===<br />
<br />
The potential use of our system in this context first came to light when we became aware of WaterLifeIndia Ltd who won an award for inclusive business models at the G20 conference earlier this year for their work in providing clean, safe water in response to groundwater contamination for B.O.P. (economic base of the pyramid) customers in India.<br />
<br />
We then contacted the British Red Cross, often the first on the ground when disaster strikes, to ask about the human impact of water contamination. When first arriving, all water must be treated as contaminated until it has been tested and shown not to be. For people living in areas with chronic contamination problems, finding clean water is an incredibly time consuming process which can take many hours out of peoples (predominantly women’s) days. <br />
<br />
Further research showed that the problem is extensive and as of April 2011, Arsonic, Fluoride, Iron, Salinity and Nitrate groundwater contamination continued to be a problem in many states – especially in rural areas.<br />
<br />
'''Who is our market?'''<br />
<br />
Groundwater contamination can be caused by a variety of factors ranging from natural disasters to improper disposal of industrial waste. Within the topic of groundwater contamination therefore, there is still substantial variety among potential customers. We anticipate that these customers will be looking at levels of a variety of contaminants in different areas though we anticipate that they will need their testing system to provide reliable, accurate quantitative data about more than one contaminant and that testing will probably involve multiple tests over a prolonged time span. Customers may include researchers, charity workers, public health workers or from industrial backgrounds.<br />
<br />
'''What are the current options available?'''<br />
<br />
Because of the rural nature of many of the presumed testing sites, standard laboratory equipment is impractical. A portable system therefore, is a necessity.<br />
<br />
Currently, two main types of sensing system are readily available for purchase.<br />
<br />
The first is a strip test system. The great advantages of this system is that it is far cheaper than the alternative and highly portable – the strips are extremely light and can easily be carried in pockets if more than one site within a location is to be tested. It is also quick and easy to acquire. Searching the internet for ‘groundwater testing kit’ brings up dozens of websites from which these systems can be purchased instantly and in the possession of the customer within days.<br />
<br />
The downsides to this system are that:<br />
<br />
# the tests are disposable and suitable for a single use only meaning that many have to be used and the product continuously repurchased if long term testing is going to be considered.<br />
# each strip will only test for one contaminant. Where a groundwater source is contaminated, it is unlikely that only a single potential contaminant will be of interest. For highly focussed research this may be acceptable, but in the case of broader research more than one kind of test strip will almost certainly be needed, and as with the problem of disposability, this will push up the costs.<br />
# These tests are often not highly quantitative – quantitative to the extent of orders of magnitude but without providing precise information about contamination levels which makes them unsuitable for detailed examination of contamination levels at a source, especially if the study involves taking multiple readings over a period of time, when the change could be small.<br />
<br />
The other major option is an electronic water testing system. These have the advantages of being more highly quantitative, reusable and often considering more than one contaminant within the same system. As with the strip tests however, there are major disadvantages. <br />
<br />
# acquiring these systems is not as easy. Often, instead of prices being offered, a quote must be obtained. A level of customisation is sometimes possible with the technology but it is invariably by far the more expensive of the two options.<br />
# electronic systems tend to be bigger and heavier, with complete systems often coming in bulky cases that would be difficult to transport without a vehicle. These systems act more as a field lab, and as such portability is vastly reduced.<br />
<br />
The major disadvantages to these systems are on one side a lack of quantitative results and reusability and on the other high, often prohibitive, costs.<br />
<br />
'''How our system is different'''<br />
<br />
Our system has been designed to be relatively low cost and the prices we have paid in producing the project, while not high, would be dramatically reduced by mass production. The system is light and portable but, between the output system and the implementation system, provides highly quantitative data. While the cuvettes and bacteria are single use, the implementation system is reusable. <br />
<br />
We consider there to be a potential market for a reliable, accurate, precise, quantitative measuring system that without the price tag of current electronic systems. We also feel that our system could fill this niche.<br />
<br />
==Likely Problems==<br />
<br />
'''The law''' – India banned the use of a GM eggplant shortly before it was due to be planted in 2010 and has recently revoked Monsanto’s liscence to distribute GM Bt cotton for planting in India. While this product is not a GM crop, it does not suggest that the wide distribution of such a system would be welcomed. The law on GM products varies from country to country and this may limit the available markets for a product.<br />
<br />
'''Public perception''' – <br />
It has been very difficult to find unbiased sources when looking at public perceptions of GM. Organisations such as Greenpeace and Friends of the Earth remain predictably opposed and while we, as students of a prestigious academic institution studying sciences and engineering and producing GM bacteria through a synthetic biology completion, do not claim to be unbiased we have attempted to set out as balanced a view as possible of the common arguments for and against GMOs.<br />
<br />
Common arguments in support of GMOs:<br />
<br />
1. Increased crop yields<br />
<br />
2. Increased range of environmental conditions under which crops may be grown<br />
<br />
3. Potential for growing crops in places where they previously could not <br />
<br />
4. Pharming - the possibility of using GM crops to produce pharmaceuticals rather than food<br />
<br />
5. Increased yield for biofuel crops, or crops drastically engineered to produce hydrogen<br />
<br />
Major success story: Insulin. Most human insulin is now produced by genetically modified E.coli. This is the accepted norm and even anti GM NGOs are reluctant to attack it. The obvious difference between this and the potential use of our system is that the insulin is produced in a laboratory and then shipped out to the consumer. At no stage does the customer come into contact with the bacteria so there is no chance of contamination.<br />
<br />
Common arguments against the use of GMOs:<br />
<br />
1. Strong public apprehension over an unfamiliar technology – which may require mass education programs to conquer.<br />
<br />
2. Potential for unintended consequences – e.g. accidental activation or silencing of genes<br />
<br />
3. High susceptibility of monocultures to pathogens – the genetic diversity usually found in non-GM populations means that if any plant is susceptible to a novel pathogen, the entire crop can be destroyed. This is somewhat unfortunate given that GM crops are often created for the purpose of resistance to pathogens<br />
<br />
4.It has been argued that GMOs are merely a ‘quick fix’ to the global food problem when changes to human behaviour would be more appropriate<br />
<br />
5. Potential for the companies that produce them to excersise an undue amount of power over the producers, buyers and ultimately consumers of the GMOs. This is a problem more with the distribution end of the business, but a valid concern – Monsanto is often cited as a case of this.<br />
<br />
Major distress story: Monsanto’s Bt cotton in India. This has been linked to multiple instances of host resistance, ill treatment of farmers by Monsanto and has recently been banned in India.<br />
<br />
'''Public perceptions of GMOs in India:'''<br />
<br />
Public perceptions in India are varied. Scientists and highly educated professionals tend to be more open to the idea of using GM crops so long as they are properly regulated. Farmers however often show a suspicion of GM foods, which is unlikely to have been improved by the Monsanto scandal. <br />
<br />
While the product in question is not a crop, public attitudes to GM crops often extend to GMOs of all kinds and this may limit the capacity to market and sell the product in this culture. More research into public opinion would be needed. <br />
<br />
'''Concerns about the product'''<br />
<br />
- Infection – Probably a major concern of most consumers. The bacteria used in our project were biosafety level one, non-pathogenic and their pathogenicity has not been increased by the addition of our system. In their current state, they pose no threat to the consumer or the environment. We additionally would not support the sale of this system using anything more dangerous than biosafety level one.<br />
<br />
- Disposal – the bacteria are currently stored in open topped plastic cuvettes for testing. This is clearly unsuitable in the field and would need to be swapped for an enclosed system, possibly with a valve to add the water for testing. Additionally, while autoclaving is used in the laboratory to destroy leftover bacteria, this is impossible in the field and B.subtilis usually produces spores when confronted with chemicals like bleach and alcohol often used antibacterially. We propose therefore that a system would be investigated that would allow the bacteria to sporulate only once. Having sporulated to be stored and shipped to their destination and germinated for testing, the bacteria would then be unable to re-sporulate, making them sensitive to solvents and detergents. We suggest that a small pouch of this could be included in the bacteria container to be activated once testing has finished, destroying the bacteria.<br />
<br />
===References===<br />
<br />
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761794/ Validation of Two Portable Instruments to Measure Iron Concentration in Groundwater in Rural Bangladesh]<br />
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[http://www.env.gov.bc.ca/wsd/plan_protect_sustain/groundwater/library/ground_fact_sheets/pdfs/fe_mg%28020715%29_fin2.pdf Iron and Manganese in Groundwater]<br />
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[http://annauniv.academia.edu/Elango/Papers/153253/Fluoride_contamination_in_groundwater_in_parts_of_Nalgonda_district_Andhra_Pradesh_India Fluoride contamination in groundwater]<br />
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[http://www.genecampaign.org/Publication/Pressrelease/GMO%20perceptions%20study%20in%20India%20-Press%20release%2001.04.2010.html Perceptions about GM crops]<br />
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[http://bio.sophiapublisher.com/html-200-12-gmo Factors influencing public perception of GMOs]<br />
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[http://www.jnu.ac.in/Academics/Schools/SchoolOfInternationalStudies/CITD/DiscussionPapers/DP02_2010.pdf Aversions to GM foods in India]<br />
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[http://www.academicjournals.org/ajb/PDF/pdf2011/1JunConf/Kimenju%20et%20al.pdf Attitudes towards biotechnology]<br />
<br />
[http://www.genecampaign.org/Publication/Pressrelease/GMO%20perception%20study%20-Press%20release%2001.04.pdf Perceptions of GM crops in India]<br />
<br />
[http://www.greenpeace.org.uk/gm/clarification-of-the-greenpeace-policy-on-golden-rice Greenpeace on Golden Rice]<br />
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[http://www.foe.co.uk/resource/press_releases/india_gm_09022010.html Friends of the Earth on GM aubergine]<br />
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[http://www.foe.co.uk/resource/reports/who_benefits_from_gm_crops.pdf Friends of the Earth on GM and Monsanto]<br />
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[http://www.guardian.co.uk/environment/2011/oct/19/gm-crops-insecurity-superweeds-pesticides GM crops]<br />
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[http://taketheflourback.org/resistance-to-gm-around-the-world/ Resistance to GM around the world]<br />
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[http://www.foei.org/en/media/archive/2009/gm-crops-feed-biotech-giants-only Friends of the Earth on GM and biotech giants]<br />
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[http://www.indialawjournal.com/volume3/issue_4/article_by_ashish_aman.html GM foods in India]<br />
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[http://rawearthliving.wordpress.com/2010/02/25/legal-cases-laid-ground-for-gmo-bt-brinjal-ban-india/ India and Bt cotton]<br />
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[http://www.wakingtimes.com/2012/06/19/government-of-india-declares-that-all-genetically-modified-foods-be-labeled/ GM foods and India]<br />
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{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Outreach/OverviewTeam:Cambridge/Outreach/Overview2012-09-20T06:10:04Z<p>CharlotteBG: Created page with "{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}} ==Human Practices:== '''iGEM criterion:''' Outline and detail a new approach to an issue of Human Practice in synthe..."</p>
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<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}}<br />
<br />
==Human Practices:==<br />
<br />
'''iGEM criterion:''' Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.<br />
<br />
<br />
Our human practices this year has been a driving force of our project from the start, defining many of its key features. This part of our project has drawn on the safety, sharing and innovation criteria in a three part sub-project as well as incorporating outreach. In the safety category, we go beyond the iGEM requirement of the safety questions to present our idea of the standard of obvious safety consciousness that teams should provide. In sharing, we explain how the desire to produce a system that would encourage sharing between iGEM teams and allow collaborative projects with greater ease was one of the factors that helped define our project from the start and how the necessity for this became increasingly obvious as the project continued and we faced problems trying to build on the research of other teams.<br />
<br />
===Innovation:===<br />
<br />
We took the idea of considering our project as a product. Clearly in its current state it is not a product ready to go to market, but could be considered as a prototype for one that might be. Our system is designed to be used in a huge variety of circumstances, but for the sake of this exercise we have used just one.<br />
<br />
The idea was to consider the process of taking our ‘product’ and putting it in a ‘market. We have considered a suitable market for the product – in this case groundwater contamination in rural India, weighed up the strengths and weaknesses of currently available systems that cater for this market and how our system differs.<br />
<br />
We then consider the likely problems that would be faced were we attempting to attempt this now, ranging from mistrust of GMOs to bacterial disposal.<br />
<br />
'''Why is this relevant?'''<br />
<br />
The majority of us, whether we pursue careers in research or industry will probably at some point be involved with the production or release of a product. We have tried to use this as a trial run, to show teams what they might expect to come up against. We hope that this might inspire teams to consider human practices as a foundation for their projects as we did. Fluoride contamination was a major factor in the decision to design a system from start to finish that could quantifiably test for fluoride. We hope that this might encourage teams to think innovatively about their project when in the design phase, to consider a real world problem to which their project could be a solution and to consider the problems they might encounter in the course of applying that solution so that they can be tackled in the course of the project.<br />
<br />
Our innovation project can be found [[Team:Cambridge/Outreach/innovation|here]].<br />
<br />
===Safety:===<br />
<br />
Safety is core to the iGEM competition and all teams must complete a series of safety questions on their wiki to qualify for a medal to prove that they have considered the safety implications of their project as a whole and have set about working in compliance with good laboratory practice. In addition to this criterion we have also produced protocols for reference for all of the techniques we use in the lab. These also have risk assessments for the major risks associated with them and precaution suggestion where appropriate as well as MSDS sheets for all reagents used available in the safety section of our wiki.<br />
<br />
We assume that, like us, most iGEMers do not relish the thought of vast quantities of paperwork to accompany their projects. Our safety criteria do not impose this, but do demand further proof of safety consciousness than current requirements. <br />
<br />
'''Why is this relevant?'''<br />
<br />
The current team has found having this information readily accessible on the wiki (where it cannot be lost or tidied away) to be extremely useful and we consider it the duty of iGEM teams to leave their project in a sufficiently well documented state that future teams could pick up more or less where the previous team stopped. <br />
<br />
Where teams choose to modularise their project into several sub-projects, different teams may be working with different experiments at any given time. It may be weeks before certain teams use techniques that others utilised on their first day. This is where having reliably accessible information comes into its own. Which reagent comes next? It’s on the wiki. Waste disposal? On the wiki. Do I need a mask for this? On the wiki. Is it supposed to go that colour? It’s on the wiki.<br />
<br />
Perhaps more importantly, we have found that constantly updating and adding to the safety element of our project prevented it from slipping to the back of mind. We have found that we spent more time than anticipated considering the safety implications of experiments as we were planning and doing them, in the knowledge that we would be written up formally. <br />
<br />
The provision of detailed protocols, MSDS and at least basic risk assessments can be hugely helpful to future teams, especially students coming to the iGEM competition from non-biological disciplines. Even those of us thoroughly familiar with techniques like PCR found the last team’s notes useful for reference in the early weeks of our project. Many excellent projects have been stopped short because of time constraints. If another team wanted to build on it, they might be able to ask the previous team if it is the next year and at the same institution, but if it is several years before the project catches the imagination of another team, then the wiki is probably all they’ll have to work with. <br />
<br />
===Sharing:===<br />
<br />
Early in the summer, when we were trying to define our project, we started thinking about what we wanted it to do. We eventually settled on one of the key principles of synthetic biology – standardisation (strongly promoted by the engineers on the team). Biological research is currently a highly bespoke process with predominantly non-standardised biosensors – a multitude of output systems with a plethora of sensitivity curves exist. This renders individual sets of results amost meaningless as research from different teams is not directly comparable. This limits the capacity for sharing and collaboration as teams are effectively working on their own and this in turn limits the rate of progress.<br />
<br />
To this end our project was focussed on producing a standardised output system with instrumentation for biosensor experiments to promote facilitate sharing and collaboration between iGEM teams, with a myriad of possible applications. A ratiometric system was chosen to provide a reliable quantification system, it was decided that the system should be portable so that it could be used for field research as well as laboratory based research and relatively cheap, to make it accessible to other iGEM teams. We felt it important that the code used in the instrumentation be open source like the rest of the project, so that it could be tweaked by future users to match their needs.<br />
<br />
'''Why is this relevant?'''<br />
<br />
iGEM is open source and high value is placed on sharing, collaboration and building on the work of previous teams. Where there is a lack of standardisation however, it is hard for teams to know what they can expect when working with another team’s project. We have attributed at least some of the problems we have experienced when trying to work with previous teams’ biobricks this summer to this problem.<br />
<br />
We believe that a standardised output for biosensor experiments would be of enormous help to teams, giving them the tools to compare results, share and collaborate more effectively.<br />
<br />
===Outreach:===<br />
<br />
Traditionally, this section of a wiki is labelled outreach and features teams promoting the iGEM competition and trying to improve public understanding and perceptions of synthetic biology as a whole. We have not had the time to do this as the vast majority of our project has been lab based; we have however written an article for the Cambridge University Graduate <br />
<br />
A copy of this article can be found here. <br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Outreach/innovationTeam:Cambridge/Outreach/innovation2012-09-20T06:08:48Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}}<br />
<br />
==Human Practices – Groundwater contamination in rural India==<br />
<br />
Below is a summary of our research into the suitability of our system for use in the field. <br />
<br />
===Finding a Market:===<br />
<br />
The potential use of our system in this context first came to light when we became aware of WaterLifeIndia Ltd who won an award for inclusive business models at the G20 conference earlier this year for their work in providing clean, safe water in response to groundwater contamination for B.O.P. (economic base of the pyramid) customers in India.<br />
<br />
We then contacted the British Red Cross, often the first on the ground when disaster strikes, to ask about the human impact of water contamination. When first arriving, all water must be treated as contaminated until it has been tested and shown not to be. For people living in areas with chronic contamination problems, finding clean water is an incredibly time consuming process which can take many hours out of peoples (predominantly women’s) days. <br />
<br />
Further research showed that the problem is extensive and as of April 2011, Arsonic, Fluoride, Iron, Salinity and Nitrate groundwater contamination continued to be a problem in many states – especially in rural areas.<br />
<br />
'''Who is our market?'''<br />
<br />
Groundwater contamination can be caused by a variety of factors ranging from natural disasters to improper disposal of industrial waste. Within the topic of groundwater contamination therefore, there is still substantial variety among potential customers. We anticipate that these customers will be looking at levels of a variety of contaminants in different areas though we anticipate that they will need their testing system to provide reliable, accurate quantitative data about more than one contaminant and that testing will probably involve multiple tests over a prolonged time span. Customers may include researchers, charity workers, public health workers or from industrial backgrounds.<br />
<br />
'''What are the current options available?'''<br />
<br />
Because of the rural nature of many of the presumed testing sites, standard laboratory equipment is impractical. A portable system therefore, is a necessity.<br />
<br />
Currently, two main types of sensing system are readily available for purchase.<br />
<br />
The first is a strip test system. The great advantages of this system is that it is far cheaper than the alternative and highly portable – the strips are extremely light and can easily be carried in pockets if more than one site within a location is to be tested. It is also quick and easy to acquire. Searching the internet for ‘groundwater testing kit’ brings up dozens of websites from which these systems can be purchased instantly and in the possession of the customer within days.<br />
<br />
The downsides to this system are that:<br />
<br />
# the tests are disposable and suitable for a single use only meaning that many have to be used and the product continuously repurchased if long term testing is going to be considered.<br />
# each strip will only test for one contaminant. Where a groundwater source is contaminated, it is unlikely that only a single potential contaminant will be of interest. For highly focussed research this may be acceptable, but in the case of broader research more than one kind of test strip will almost certainly be needed, and as with the problem of disposability, this will push up the costs.<br />
# These tests are often not highly quantitative – quantitative to the extent of orders of magnitude but without providing precise information about contamination levels which makes them unsuitable for detailed examination of contamination levels at a source, especially if the study involves taking multiple readings over a period of time, when the change could be small.<br />
<br />
The other major option is an electronic water testing system. These have the advantages of being more highly quantitative, reusable and often considering more than one contaminant within the same system. As with the strip tests however, there are major disadvantages. <br />
<br />
# acquiring these systems is not as easy. Often, instead of prices being offered, a quote must be obtained. A level of customisation is sometimes possible with the technology but it is invariably by far the more expensive of the two options.<br />
# electronic systems tend to be bigger and heavier, with complete systems often coming in bulky cases that would be difficult to transport without a vehicle. These systems act more as a field lab, and as such portability is vastly reduced.<br />
<br />
The major disadvantages to these systems are on one side a lack of quantitative results and reusability and on the other high, often prohibitive, costs.<br />
<br />
'''How our system is different'''<br />
<br />
Our system has been designed to be relatively low cost and the prices we have paid in producing the project, while not high, would be dramatically reduced by mass production. The system is light and portable but, between the output system and the implementation system, provides highly quantitative data. While the cuvettes and bacteria are single use, the implementation system is reusable. <br />
<br />
We consider there to be a potential market for a reliable, accurate, precise, quantitative measuring system that without the price tag of current electronic systems. We also feel that our system could fill this niche.<br />
<br />
==Likely Problems==<br />
<br />
'''The law''' – India banned the use of a GM eggplant shortly before it was due to be planted in 2010 and has recently revoked Monsanto’s liscence to distribute GM Bt cotton for planting in India. While this product is not a GM crop, it does not suggest that the wide distribution of such a system would be welcomed. The law on GM products varies from country to country and this may limit the available markets for a product.<br />
<br />
'''Public perception''' – <br />
It has been very difficult to find unbiased sources when looking at public perceptions of GM. Organisations such as Greenpeace and Friends of the Earth remain predictably opposed and while we, as students of a prestigious academic institution studying sciences and engineering and producing GM bacteria through a synthetic biology completion, do not claim to be unbiased we have attempted to set out as balanced a view as possible of the common arguments for and against GMOs.<br />
<br />
Common arguments in support of GMOs:<br />
<br />
1. Increased crop yields<br />
<br />
2. Increased range of environmental conditions under which crops may be grown<br />
<br />
3. Potential for growing crops in places where they previously could not <br />
<br />
4. Pharming - the possibility of using GM crops to produce pharmaceuticals rather than food<br />
<br />
5. Increased yield for biofuel crops, or crops drastically engineered to produce hydrogen<br />
<br />
Major success story: Insulin. Most human insulin is now produced by genetically modified E.coli. This is the accepted norm and even anti GM NGOs are reluctant to attack it. The obvious difference between this and the potential use of our system is that the insulin is produced in a laboratory and then shipped out to the consumer. At no stage does the customer come into contact with the bacteria so there is no chance of contamination.<br />
<br />
Common arguments against the use of GMOs:<br />
<br />
1. Strong public apprehension over an unfamiliar technology – which may require mass education programs to conquer.<br />
<br />
2. Potential for unintended consequences – e.g. accidental activation or silencing of genes<br />
<br />
3. High susceptibility of monocultures to pathogens – the genetic diversity usually found in non-GM populations means that if any plant is susceptible to a novel pathogen, the entire crop can be destroyed. This is somewhat unfortunate given that GM crops are often created for the purpose of resistance to pathogens<br />
<br />
4.It has been argued that GMOs are merely a ‘quick fix’ to the global food problem when changes to human behaviour would be more appropriate<br />
<br />
5. Potential for the companies that produce them to excersise an undue amount of power over the producers, buyers and ultimately consumers of the GMOs. This is a problem more with the distribution end of the business, but a valid concern – Monsanto is often cited as a case of this.<br />
<br />
Major distress story: Monsanto’s Bt cotton in India. This has been linked to multiple instances of host resistance, ill treatment of farmers by Monsanto and has recently been banned in India.<br />
<br />
'''Public perceptions of GMOs in India:'''<br />
<br />
Public perceptions in India are varied. Scientists and highly educated professionals tend to be more open to the idea of using GM crops so long as they are properly regulated. Farmers however often show a suspicion of GM foods, which is unlikely to have been improved by the Monsanto scandal. <br />
<br />
While the product in question is not a crop, public attitudes to GM crops often extend to GMOs of all kinds and this may limit the capacity to market and sell the product in this culture. More research into public opinion would be needed. <br />
<br />
'''Concerns about the product'''<br />
<br />
- Infection – Probably a major concern of most consumers. The bacteria used in our project were biosafety level one, non-pathogenic and their pathogenicity has not been increased by the addition of our system. In their current state, they pose no threat to the consumer or the environment. We additionally would not support the sale of this system using anything more dangerous than biosafety level one.<br />
<br />
- Disposal – the bacteria are currently stored in open topped plastic cuvettes for testing. This is clearly unsuitable in the field and would need to be swapped for an enclosed system, possibly with a valve to add the water for testing. Additionally, while autoclaving is used in the laboratory to destroy leftover bacteria, this is impossible in the field and B.subtilis usually produces spores when confronted with chemicals like bleach and alcohol often used antibacterially. We propose therefore that a system would be investigated that would allow the bacteria to sporulate only once. Having sporulated to be stored and shipped to their destination and germinated for testing, the bacteria would then be unable to re-sporulate, making them sensitive to solvents and detergents. We suggest that a small pouch of this could be included in the bacteria container to be activated once testing has finished, destroying the bacteria.<br />
<br />
===References===<br />
<br />
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761794/ Validation of Two Portable Instruments to Measure Iron Concentration in Groundwater in Rural Bangladesh]<br />
<br />
[http://www.env.gov.bc.ca/wsd/plan_protect_sustain/groundwater/library/ground_fact_sheets/pdfs/fe_mg%28020715%29_fin2.pdf Iron and Manganese in Groundwater]<br />
<br />
[http://annauniv.academia.edu/Elango/Papers/153253/Fluoride_contamination_in_groundwater_in_parts_of_Nalgonda_district_Andhra_Pradesh_India Fluoride contamination in groundwater]<br />
<br />
[http://www.genecampaign.org/Publication/Pressrelease/GMO%20perceptions%20study%20in%20India%20-Press%20release%2001.04.2010.html Perceptions about GM crops]<br />
<br />
[http://bio.sophiapublisher.com/html-200-12-gmo Factors influencing public perception of GMOs]<br />
<br />
[http://www.jnu.ac.in/Academics/Schools/SchoolOfInternationalStudies/CITD/DiscussionPapers/DP02_2010.pdf Aversions to GM foods in India]<br />
<br />
[http://www.academicjournals.org/ajb/PDF/pdf2011/1JunConf/Kimenju%20et%20al.pdf Attitudes towards biotechnology]<br />
<br />
[http://www.genecampaign.org/Publication/Pressrelease/GMO%20perception%20study%20-Press%20release%2001.04.pdf Perceptions of GM crops in India]<br />
<br />
[http://www.greenpeace.org.uk/gm/clarification-of-the-greenpeace-policy-on-golden-rice Greenpeace on Golden Rice]<br />
<br />
[http://www.foe.co.uk/resource/press_releases/india_gm_09022010.html Friends of the Earth on GM aubergine]<br />
<br />
[http://www.foe.co.uk/resource/reports/who_benefits_from_gm_crops.pdf Friends of the Earth on GM and Monsanto]<br />
<br />
[http://www.guardian.co.uk/environment/2011/oct/19/gm-crops-insecurity-superweeds-pesticides GM crops]<br />
<br />
[http://taketheflourback.org/resistance-to-gm-around-the-world/ Resistance to GM around the world]<br />
<br />
[http://www.foei.org/en/media/archive/2009/gm-crops-feed-biotech-giants-only Friends of the Earth on GM and biotech giants]<br />
<br />
[http://www.indialawjournal.com/volume3/issue_4/article_by_ashish_aman.html GM foods in India]<br />
<br />
[http://rawearthliving.wordpress.com/2010/02/25/legal-cases-laid-ground-for-gmo-bt-brinjal-ban-india/ India and Bt cotton]<br />
<br />
[http://www.wakingtimes.com/2012/06/19/government-of-india-declares-that-all-genetically-modified-foods-be-labeled/ GM foods and India]<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Outreach/innovationTeam:Cambridge/Outreach/innovation2012-09-20T06:08:23Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}}<br />
<br />
==Human Practices – Groundwater contamination in rural India==<br />
<br />
Below is a summary of our research into the suitability of our system for use in the field. <br />
<br />
===Finding a Market:===<br />
<br />
The potential use of our system in this context first came to light when we became aware of WaterLifeIndia Ltd who won an award for inclusive business models at the G20 conference earlier this year for their work in providing clean, safe water in response to groundwater contamination for B.O.P. (economic base of the pyramid) customers in India.<br />
<br />
We then contacted the British Red Cross, often the first on the ground when disaster strikes, to ask about the human impact of water contamination. When first arriving, all water must be treated as contaminated until it has been tested and shown not to be. For people living in areas with chronic contamination problems, finding clean water is an incredibly time consuming process which can take many hours out of peoples (predominantly women’s) days. <br />
<br />
Further research showed that the problem is extensive and as of April 2011, Arsonic, Fluoride, Iron, Salinity and Nitrate groundwater contamination continued to be a problem in many states – especially in rural areas.<br />
<br />
'''Who is our market?'''<br />
<br />
Groundwater contamination can be caused by a variety of factors ranging from natural disasters to improper disposal of industrial waste. Within the topic of groundwater contamination therefore, there is still substantial variety among potential customers. We anticipate that these customers will be looking at levels of a variety of contaminants in different areas though we anticipate that they will need their testing system to provide reliable, accurate quantitative data about more than one contaminant and that testing will probably involve multiple tests over a prolonged time span. Customers may include researchers, charity workers, public health workers or from industrial backgrounds.<br />
<br />
'''What are the current options available?'''<br />
<br />
Because of the rural nature of many of the presumed testing sites, standard laboratory equipment is impractical. A portable system therefore, is a necessity.<br />
<br />
Currently, two main types of sensing system are readily available for purchase.<br />
<br />
The first is a strip test system. The great advantages of this system is that it is far cheaper than the alternative and highly portable – the strips are extremely light and can easily be carried in pockets if more than one site within a location is to be tested. It is also quick and easy to acquire. Searching the internet for ‘groundwater testing kit’ brings up dozens of websites from which these systems can be purchased instantly and in the possession of the customer within days.<br />
<br />
The downsides to this system are that:<br />
<br />
# the tests are disposable and suitable for a single use only meaning that many have to be used and the product continuously repurchased if long term testing is going to be considered.<br />
# each strip will only test for one contaminant. Where a groundwater source is contaminated, it is unlikely that only a single potential contaminant will be of interest. For highly focussed research this may be acceptable, but in the case of broader research more than one kind of test strip will almost certainly be needed, and as with the problem of disposability, this will push up the costs.<br />
# These tests are often not highly quantitative – quantitative to the extent of orders of magnitude but without providing precise information about contamination levels which makes them unsuitable for detailed examination of contamination levels at a source, especially if the study involves taking multiple readings over a period of time, when the change could be small.<br />
<br />
The other major option is an electronic water testing system. These have the advantages of being more highly quantitative, reusable and often considering more than one contaminant within the same system. As with the strip tests however, there are major disadvantages. <br />
<br />
# acquiring these systems is not as easy. Often, instead of prices being offered, a quote must be obtained. A level of customisation is sometimes possible with the technology but it is invariably by far the more expensive of the two options.<br />
# electronic systems tend to be bigger and heavier, with complete systems often coming in bulky cases that would be difficult to transport without a vehicle. These systems act more as a field lab, and as such portability is vastly reduced.<br />
<br />
The major disadvantages to these systems are on one side a lack of quantitative results and reusability and on the other high, often prohibitive, costs.<br />
<br />
'''How our system is different'''<br />
<br />
Our system has been designed to be relatively low cost and the prices we have paid in producing the project, while not high, would be dramatically reduced by mass production. The system is light and portable but, between the output system and the implementation system, provides highly quantitative data. While the cuvettes and bacteria are single use, the implementation system is reusable. <br />
<br />
We consider there to be a potential market for a reliable, accurate, precise, quantitative measuring system that without the price tag of current electronic systems. We also feel that our system could fill this niche.<br />
<br />
==Likely Problems==<br />
<br />
'''The law''' – India banned the use of a GM eggplant shortly before it was due to be planted in 2010 and has recently revoked Monsanto’s liscence to distribute GM Bt cotton for planting in India. While this product is not a GM crop, it does not suggest that the wide distribution of such a system would be welcomed. The law on GM products varies from country to country and this may limit the available markets for a product.<br />
<br />
'''Public perception''' – <br />
It has been very difficult to find unbiased sources when looking at public perceptions of GM. Organisations such as Greenpeace and Friends of the Earth remain predictably opposed and while we, as students of a prestigious academic institution studying sciences and engineering and producing GM bacteria through a synthetic biology completion, do not claim to be unbiased we have attempted to set out as balanced a view as possible of the common arguments for and against GMOs.<br />
<br />
Common arguments in support of GMOs:<br />
<br />
1. Increased crop yields<br />
<br />
2. Increased range of environmental conditions under which crops may be grown<br />
<br />
3. Potential for growing crops in places where they previously could not <br />
<br />
4. Pharming - the possibility of using GM crops to produce pharmaceuticals rather than food<br />
<br />
5. Increased yield for biofuel crops, or crops drastically engineered to produce hydrogen<br />
<br />
Major success story: Insulin. Most human insulin is now produced by genetically modified E.coli. This is the accepted norm and even anti GM NGOs are reluctant to attack it. The obvious difference between this and the potential use of our system is that the insulin is produced in a laboratory and then shipped out to the consumer. At no stage does the customer come into contact with the bacteria so there is no chance of contamination.<br />
<br />
Common arguments against the use of GMOs:<br />
<br />
1. Strong public apprehension over an unfamiliar technology – which may require mass education programs to conquer.<br />
<br />
2. Potential for unintended consequences – e.g. accidental activation or silencing of genes<br />
<br />
3. High susceptibility of monocultures to pathogens – the genetic diversity usually found in non-GM populations means that if any plant is susceptible to a novel pathogen, the entire crop can be destroyed. This is somewhat unfortunate given that GM crops are often created for the purpose of resistance to pathogens<br />
<br />
4.It has been argued that GMOs are merely a ‘quick fix’ to the global food problem when changes to human behaviour would be more appropriate<br />
<br />
5. Potential for the companies that produce them to excersise an undue amount of power over the producers, buyers and ultimately consumers of the GMOs. This is a problem more with the distribution end of the business, but a valid concern – Monsanto is often cited as a case of this.<br />
<br />
Major distress story: Monsanto’s Bt cotton in India. This has been linked to multiple instances of host resistance, ill treatment of farmers by Monsanto and has recently been banned in India.<br />
<br />
'''Public perceptions of GMOs in India:'''<br />
<br />
Public perceptions in India are varied. Scientists and highly educated professionals tend to be more open to the idea of using GM crops so long as they are properly regulated. Farmers however often show a suspicion of GM foods, which is unlikely to have been improved by the Monsanto scandal. <br />
<br />
While the product in question is not a crop, public attitudes to GM crops often extend to GMOs of all kinds and this may limit the capacity to market and sell the product in this culture. More research into public opinion would be needed. <br />
<br />
'''Concerns about the product'''<br />
<br />
- Infection – Probably a major concern of most consumers. The bacteria used in our project were biosafety level one, non-pathogenic and their pathogenicity has not been increased by the addition of our system. In their current state, they pose no threat to the consumer or the environment. We additionally would not support the sale of this system using anything more dangerous than biosafety level one.<br />
<br />
- Disposal – the bacteria are currently stored in open topped plastic cuvettes for testing. This is clearly unsuitable in the field and would need to be swapped for an enclosed system, possibly with a valve to add the water for testing. Additionally, while autoclaving is used in the laboratory to destroy leftover bacteria, this is impossible in the field and B.subtilis usually produces spores when confronted with chemicals like bleach and alcohol often used antibacterially. We propose therefore that a system would be investigated that would allow the bacteria to sporulate only once. Having sporulated to be stored and shipped to their destination and germinated for testing, the bacteria would then be unable to re-sporulate, making them sensitive to solvents and detergents. We suggest that a small pouch of this could be included in the bacteria container to be activated once testing has finished, destroying the bacteria.<br />
<br />
===References===<br />
<br />
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761794/ Validation of Two Portable Instruments to Measure Iron Concentration in Groundwater in Rural Bangladesh]<br />
<br />
[http://www.env.gov.bc.ca/wsd/plan_protect_sustain/groundwater/library/ground_fact_sheets/pdfs/fe_mg%28020715%29_fin2.pdf Iron and Manganese in Groundwater]<br />
<br />
[http://annauniv.academia.edu/Elango/Papers/153253/Fluoride_contamination_in_groundwater_in_parts_of_Nalgonda_district_Andhra_Pradesh_India Fluoride contamination in groundwater]<br />
<br />
[http://www.genecampaign.org/Publication/Pressrelease/GMO%20perceptions%20study%20in%20India%20-Press%20release%2001.04.2010.html Perceptions about GM crops]<br />
<br />
[http://bio.sophiapublisher.com/html-200-12-gmo Factors influencing public perception of GMOs]<br />
<br />
[http://www.jnu.ac.in/Academics/Schools/SchoolOfInternationalStudies/CITD/DiscussionPapers/DP02_2010.pdf Aversions to GM foods in India]<br />
<br />
[http://www.academicjournals.org/ajb/PDF/pdf2011/1JunConf/Kimenju%20et%20al.pdf Attitudes towards biotechnology]<br />
<br />
[http://www.genecampaign.org/Publication/Pressrelease/GMO%20perception%20study%20-Press%20release%2001.04.pdf Perceptions of GM crops in India]<br />
<br />
[http://www.greenpeace.org.uk/gm/clarification-of-the-greenpeace-policy-on-golden-rice Greenpeace on Golden Rice]<br />
<br />
[http://www.foe.co.uk/resource/press_releases/india_gm_09022010.html Friends of the Earth on GM aubergine]<br />
<br />
[http://www.foe.co.uk/resource/reports/who_benefits_from_gm_crops.pdf Friends of the Earth on GM and Monsanto]<br />
<br />
[http://www.guardian.co.uk/environment/2011/oct/19/gm-crops-insecurity-superweeds-pesticides GM crops]<br />
<br />
[http://taketheflourback.org/resistance-to-gm-around-the-world/ Resistance to GM around the world]<br />
<br />
[http://www.foei.org/en/media/archive/2009/gm-crops-feed-biotech-giants-only Friends of the Earth on GM and biotech giants]<br />
<br />
[http://www.indialawjournal.com/volume3/issue_4/article_by_ashish_aman.html GM foods in India]<br />
<br />
[http://rawearthliving.wordpress.com/2010/02/25/legal-cases-laid-ground-for-gmo-bt-brinjal-ban-india/ India and Bt cotton]<br />
<br />
[http://www.wakingtimes.com/2012/06/19/government-of-india-declares-that-all-genetically-modified-foods-be-labeled/ GM foods and India]<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Outreach/innovationTeam:Cambridge/Outreach/innovation2012-09-20T06:07:39Z<p>CharlotteBG: Created page with "{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}} ==Human Practices – Groundwater contamination in rural India== Below is a summary of our research into the suitabi..."</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}}<br />
<br />
==Human Practices – Groundwater contamination in rural India==<br />
<br />
Below is a summary of our research into the suitability of our system for use in the field. <br />
<br />
===Finding a Market:===<br />
<br />
The potential use of our system in this context first came to light when we became aware of WaterLifeIndia Ltd who won an award for inclusive business models at the G20 conference earlier this year for their work in providing clean, safe water in response to groundwater contamination for B.O.P. (economic base of the pyramid) customers in India.<br />
<br />
We then contacted the British Red Cross, often the first on the ground when disaster strikes, to ask about the human impact of water contamination. When first arriving, all water must be treated as contaminated until it has been tested and shown not to be. For people living in areas with chronic contamination problems, finding clean water is an incredibly time consuming process which can take many hours out of peoples (predominantly women’s) days. <br />
<br />
Further research showed that the problem is extensive and as of April 2011, Arsonic, Fluoride, Iron, Salinity and Nitrate groundwater contamination continued to be a problem in many states – especially in rural areas.<br />
<br />
'''Who is our market?'''<br />
<br />
Groundwater contamination can be caused by a variety of factors ranging from natural disasters to improper disposal of industrial waste. Within the topic of groundwater contamination therefore, there is still substantial variety among potential customers. We anticipate that these customers will be looking at levels of a variety of contaminants in different areas though we anticipate that they will need their testing system to provide reliable, accurate quantitative data about more than one contaminant and that testing will probably involve multiple tests over a prolonged time span. Customers may include researchers, charity workers, public health workers or from industrial backgrounds.<br />
<br />
'''What are the current options available?'''<br />
<br />
Because of the rural nature of many of the presumed testing sites, standard laboratory equipment is impractical. A portable system therefore, is a necessity.<br />
<br />
Currently, two main types of sensing system are readily available for purchase.<br />
<br />
The first is a strip test system. The great advantages of this system is that it is far cheaper than the alternative and highly portable – the strips are extremely light and can easily be carried in pockets if more than one site within a location is to be tested. It is also quick and easy to acquire. Searching the internet for ‘groundwater testing kit’ brings up dozens of websites from which these systems can be purchased instantly and in the possession of the customer within days.<br />
<br />
The downsides to this system are that:<br />
<br />
# the tests are disposable and suitable for a single use only meaning that many have to be used and the product continuously repurchased if long term testing is going to be considered.<br />
# each strip will only test for one contaminant. Where a groundwater source is contaminated, it is unlikely that only a single potential contaminant will be of interest. For highly focussed research this may be acceptable, but in the case of broader research more than one kind of test strip will almost certainly be needed, and as with the problem of disposability, this will push up the costs.<br />
# These tests are often not highly quantitative – quantitative to the extent of orders of magnitude but without providing precise information about contamination levels which makes them unsuitable for detailed examination of contamination levels at a source, especially if the study involves taking multiple readings over a period of time, when the change could be small.<br />
<br />
The other major option is an electronic water testing system. These have the advantages of being more highly quantitative, reusable and often considering more than one contaminant within the same system. As with the strip tests however, there are major disadvantages. <br />
<br />
# acquiring these systems is not as easy. Often, instead of prices being offered, a quote must be obtained. A level of customisation is sometimes possible with the technology but it is invariably by far the more expensive of the two options.<br />
# electronic systems tend to be bigger and heavier, with complete systems often coming in bulky cases that would be difficult to transport without a vehicle. These systems act more as a field lab, and as such portability is vastly reduced.<br />
<br />
The major disadvantages to these systems are on one side a lack of quantitative results and reusability and on the other high, often prohibitive, costs.<br />
<br />
'''How our system is different'''<br />
<br />
Our system has been designed to be relatively low cost and the prices we have paid in producing the project, while not high, would be dramatically reduced by mass production. The system is light and portable but, between the output system and the implementation system, provides highly quantitative data. While the cuvettes and bacteria are single use, the implementation system is reusable. <br />
<br />
We consider there to be a potential market for a reliable, accurate, precise, quantitative measuring system that without the price tag of current electronic systems. We also feel that our system could fill this niche.<br />
<br />
==Likely Problems==<br />
<br />
'''The law''' – India banned the use of a GM eggplant shortly before it was due to be planted in 2010 and has recently revoked Monsanto’s liscence to distribute GM Bt cotton for planting in India. While this product is not a GM crop, it does not suggest that the wide distribution of such a system would be welcomed. The law on GM products varies from country to country and this may limit the available markets for a product.<br />
<br />
'''Public perception''' – <br />
It has been very difficult to find unbiased sources when looking at public perceptions of GM. Organisations such as Greenpeace and Friends of the Earth remain predictably opposed and while we, as students of a prestigious academic institution studying sciences and engineering and producing GM bacteria through a synthetic biology completion, do not claim to be unbiased we have attempted to set out as balanced a view as possible of the common arguments for and against GMOs.<br />
<br />
Common arguments in support of GMOs:<br />
<br />
1. Increased crop yields<br />
<br />
2. Increased range of environmental conditions under which crops may be grown<br />
<br />
3. Potential for growing crops in places where they previously could not <br />
<br />
4. Pharming - the possibility of using GM crops to produce pharmaceuticals rather than food<br />
<br />
5. Increased yield for biofuel crops, or crops drastically engineered to produce hydrogen<br />
<br />
Major success story: Insulin. Most human insulin is now produced by genetically modified E.coli. This is the accepted norm and even anti GM NGOs are reluctant to attack it. The obvious difference between this and the potential use of our system is that the insulin is produced in a laboratory and then shipped out to the consumer. At no stage does the customer come into contact with the bacteria so there is no chance of contamination.<br />
<br />
Common arguments against the use of GMOs:<br />
<br />
1. Strong public apprehension over an unfamiliar technology – which may require mass education programs to conquer.<br />
<br />
2. Potential for unintended consequences – e.g. accidental activation or silencing of genes<br />
<br />
3. High susceptibility of monocultures to pathogens – the genetic diversity usually found in non-GM populations means that if any plant is susceptible to a novel pathogen, the entire crop can be destroyed. This is somewhat unfortunate given that GM crops are often created for the purpose of resistance to pathogens<br />
<br />
4.It has been argued that GMOs are merely a ‘quick fix’ to the global food problem when changes to human behaviour would be more appropriate<br />
<br />
5. Potential for the companies that produce them to excersise an undue amount of power over the producers, buyers and ultimately consumers of the GMOs. This is a problem more with the distribution end of the business, but a valid concern – Monsanto is often cited as a case of this.<br />
<br />
Major distress story: Monsanto’s Bt cotton in India. This has been linked to multiple instances of host resistance, ill treatment of farmers by Monsanto and has recently been banned in India.<br />
<br />
'''Public perceptions of GMOs in India:'''<br />
<br />
Public perceptions in India are varied. Scientists and highly educated professionals tend to be more open to the idea of using GM crops so long as they are properly regulated. Farmers however often show a suspicion of GM foods, which is unlikely to have been improved by the Monsanto scandal. <br />
<br />
While the product in question is not a crop, public attitudes to GM crops often extend to GMOs of all kinds and this may limit the capacity to market and sell the product in this culture. More research into public opinion would be needed. <br />
<br />
'''Concerns about the product'''<br />
<br />
- Infection – Probably a major concern of most consumers. The bacteria used in our project were biosafety level one, non-pathogenic and their pathogenicity has not been increased by the addition of our system. In their current state, they pose no threat to the consumer or the environment. We additionally would not support the sale of this system using anything more dangerous than biosafety level one.<br />
<br />
- Disposal – the bacteria are currently stored in open topped plastic cuvettes for testing. This is clearly unsuitable in the field and would need to be swapped for an enclosed system, possibly with a valve to add the water for testing. Additionally, while autoclaving is used in the laboratory to destroy leftover bacteria, this is impossible in the field and B.subtilis usually produces spores when confronted with chemicals like bleach and alcohol often used antibacterially. We propose therefore that a system would be investigated that would allow the bacteria to sporulate only once. Having sporulated to be stored and shipped to their destination and germinated for testing, the bacteria would then be unable to re-sporulate, making them sensitive to solvents and detergents. We suggest that a small pouch of this could be included in the bacteria container to be activated once testing has finished, destroying the bacteria.<br />
<br />
===References===<br />
<br />
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761794/ Validation of Two Portable Instruments to Measure Iron Concentration in Groundwater in Rural Bangladesh]<br />
<br />
[http://www.env.gov.bc.ca/wsd/plan_protect_sustain/groundwater/library/ground_fact_sheets/pdfs/fe_mg%28020715%29_fin2.pdf Iron and Manganese in Groundwater]<br />
<br />
[http://annauniv.academia.edu/Elango/Papers/153253/Fluoride_contamination_in_groundwater_in_parts_of_Nalgonda_district_Andhra_Pradesh_India Fluoride contamination in groundwater]<br />
<br />
[http://www.genecampaign.org/Publication/Pressrelease/GMO%20perceptions%20study%20in%20India%20-Press%20release%2001.04.2010.html Perceptions about GM crops]<br />
<br />
[http://bio.sophiapublisher.com/html-200-12-gmo Factors influencing public perception of GMOs]<br />
<br />
[http://www.jnu.ac.in/Academics/Schools/SchoolOfInternationalStudies/CITD/DiscussionPapers/DP02_2010.pdf Aversions to GM foods in India]<br />
<br />
[http://www.academicjournals.org/ajb/PDF/pdf2011/1JunConf/Kimenju%20et%20al.pdf Attitudes towards biotechnology]<br />
<br />
[http://www.genecampaign.org/Publication/Pressrelease/GMO%20perception%20study%20-Press%20release%2001.04.pdf Perceptions of GM crops in India]<br />
<br />
[http://www.greenpeace.org.uk/gm/clarification-of-the-greenpeace-policy-on-golden-rice Greenpeace on Golden Rice]<br />
<br />
[http://www.foe.co.uk/resource/press_releases/india_gm_09022010.html Friends of the Earth on GM aubergine]<br />
<br />
[http://www.foe.co.uk/resource/reports/who_benefits_from_gm_crops.pdf Friends of the Earth on GM and Monsanto]<br />
<br />
[http://www.guardian.co.uk/environment/2011/oct/19/gm-crops-insecurity-superweeds-pesticides GM crops]<br />
<br />
[http://taketheflourback.org/resistance-to-gm-around-the-world/ Resistance to GM around the world]<br />
<br />
[http://www.foei.org/en/media/archive/2009/gm-crops-feed-biotech-giants-only Friends of the Earth on GM and biotech giants]<br />
<br />
[http://www.indialawjournal.com/volume3/issue_4/article_by_ashish_aman.html GM foods in India]<br />
<br />
[http://rawearthliving.wordpress.com/2010/02/25/legal-cases-laid-ground-for-gmo-bt-brinjal-ban-india/ India and Bt cotton]<br />
<br />
[http://www.wakingtimes.com/2012/06/19/government-of-india-declares-that-all-genetically-modified-foods-be-labeled/ GM foods and India]</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/OutreachTeam:Cambridge/Outreach2012-09-20T05:50:52Z<p>CharlotteBG: /* Innovation: */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}}<br />
<br />
==Human Practices:==<br />
<br />
'''iGEM criterion:''' Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.<br />
<br />
<br />
Our human practices this year has been a driving force of our project from the start, defining many of its key features. This part of our project has drawn on the safety, sharing and innovation criteria in a three part sub-project as well as incorporating outreach. In the safety category, we go beyond the iGEM requirement of the safety questions to present our idea of the standard of obvious safety consciousness that teams should provide. In sharing, we explain how the desire to produce a system that would encourage sharing between iGEM teams and allow collaborative projects with greater ease was one of the factors that helped define our project from the start and how the necessity for this became increasingly obvious as the project continued and we faced problems trying to build on the research of other teams.<br />
<br />
===Innovation:===<br />
<br />
We took the idea of considering our project as a product. Clearly in its current state it is not a product ready to go to market, but could be considered as a prototype for one that might be. Our system is designed to be used in a huge variety of circumstances, but for the sake of this exercise we have used just one.<br />
<br />
The idea was to consider the process of taking our ‘product’ and putting it in a ‘market. We have considered a suitable market for the product – in this case groundwater contamination in rural India, weighed up the strengths and weaknesses of currently available systems that cater for this market and how our system differs.<br />
<br />
We then consider the likely problems that would be faced were we attempting to attempt this now, ranging from mistrust of GMOs to bacterial disposal.<br />
<br />
'''Why is this relevant?'''<br />
<br />
The majority of us, whether we pursue careers in research or industry will probably at some point be involved with the production or release of a product. We have tried to use this as a trial run, to show teams what they might expect to come up against. We hope that this might inspire teams to consider human practices as a foundation for their projects as we did. Fluoride contamination was a major factor in the decision to design a system from start to finish that could quantifiably test for fluoride. We hope that this might encourage teams to think innovatively about their project when in the design phase, to consider a real world problem to which their project could be a solution and to consider the problems they might encounter in the course of applying that solution so that they can be tackled in the course of the project.<br />
<br />
Our innovation project can be found [[Team:Cambridge/Outreach/innovation|here]].<br />
<br />
===Safety:===<br />
<br />
Safety is core to the iGEM competition and all teams must complete a series of safety questions on their wiki to qualify for a medal to prove that they have considered the safety implications of their project as a whole and have set about working in compliance with good laboratory practice. In addition to this criterion we have also produced protocols for reference for all of the techniques we use in the lab. These also have risk assessments for the major risks associated with them and precaution suggestion where appropriate as well as MSDS sheets for all reagents used available in the safety section of our wiki.<br />
<br />
We assume that, like us, most iGEMers do not relish the thought of vast quantities of paperwork to accompany their projects. Our safety criteria do not impose this, but do demand further proof of safety consciousness than current requirements. <br />
<br />
'''Why is this relevant?'''<br />
<br />
The current team has found having this information readily accessible on the wiki (where it cannot be lost or tidied away) to be extremely useful and we consider it the duty of iGEM teams to leave their project in a sufficiently well documented state that future teams could pick up more or less where the previous team stopped. <br />
<br />
Where teams choose to modularise their project into several sub-projects, different teams may be working with different experiments at any given time. It may be weeks before certain teams use techniques that others utilised on their first day. This is where having reliably accessible information comes into its own. Which reagent comes next? It’s on the wiki. Waste disposal? On the wiki. Do I need a mask for this? On the wiki. Is it supposed to go that colour? It’s on the wiki.<br />
<br />
Perhaps more importantly, we have found that constantly updating and adding to the safety element of our project prevented it from slipping to the back of mind. We have found that we spent more time than anticipated considering the safety implications of experiments as we were planning and doing them, in the knowledge that we would be written up formally. <br />
<br />
The provision of detailed protocols, MSDS and at least basic risk assessments can be hugely helpful to future teams, especially students coming to the iGEM competition from non-biological disciplines. Even those of us thoroughly familiar with techniques like PCR found the last team’s notes useful for reference in the early weeks of our project. Many excellent projects have been stopped short because of time constraints. If another team wanted to build on it, they might be able to ask the previous team if it is the next year and at the same institution, but if it is several years before the project catches the imagination of another team, then the wiki is probably all they’ll have to work with. <br />
<br />
===Sharing:===<br />
<br />
Early in the summer, when we were trying to define our project, we started thinking about what we wanted it to do. We eventually settled on one of the key principles of synthetic biology – standardisation (strongly promoted by the engineers on the team). Biological research is currently a highly bespoke process with predominantly non-standardised biosensors – a multitude of output systems with a plethora of sensitivity curves exist. This renders individual sets of results amost meaningless as research from different teams is not directly comparable. This limits the capacity for sharing and collaboration as teams are effectively working on their own and this in turn limits the rate of progress.<br />
<br />
To this end our project was focussed on producing a standardised output system with instrumentation for biosensor experiments to promote facilitate sharing and collaboration between iGEM teams, with a myriad of possible applications. A ratiometric system was chosen to provide a reliable quantification system, it was decided that the system should be portable so that it could be used for field research as well as laboratory based research and relatively cheap, to make it accessible to other iGEM teams. We felt it important that the code used in the instrumentation be open source like the rest of the project, so that it could be tweaked by future users to match their needs.<br />
<br />
'''Why is this relevant?'''<br />
<br />
iGEM is open source and high value is placed on sharing, collaboration and building on the work of previous teams. Where there is a lack of standardisation however, it is hard for teams to know what they can expect when working with another team’s project. We have attributed at least some of the problems we have experienced when trying to work with previous teams’ biobricks this summer to this problem.<br />
<br />
We believe that a standardised output for biosensor experiments would be of enormous help to teams, giving them the tools to compare results, share and collaborate more effectively.<br />
<br />
===Outreach:===<br />
<br />
Traditionally, this section of a wiki is labelled outreach and features teams promoting the iGEM competition and trying to improve public understanding and perceptions of synthetic biology as a whole. We have not had the time to do this as the vast majority of our project has been lab based; we have however written an article for the Cambridge University Graduate <br />
<br />
A copy of this article can be found here. <br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/OutreachTeam:Cambridge/Outreach2012-09-20T05:50:22Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}}<br />
<br />
==Human Practices:==<br />
<br />
'''iGEM criterion:''' Outline and detail a new approach to an issue of Human Practice in synthetic biology as it relates to your project, such as safety, security, ethics, or ownership, sharing, and innovation.<br />
<br />
<br />
Our human practices this year has been a driving force of our project from the start, defining many of its key features. This part of our project has drawn on the safety, sharing and innovation criteria in a three part sub-project as well as incorporating outreach. In the safety category, we go beyond the iGEM requirement of the safety questions to present our idea of the standard of obvious safety consciousness that teams should provide. In sharing, we explain how the desire to produce a system that would encourage sharing between iGEM teams and allow collaborative projects with greater ease was one of the factors that helped define our project from the start and how the necessity for this became increasingly obvious as the project continued and we faced problems trying to build on the research of other teams.<br />
<br />
===Innovation:===<br />
<br />
We took the idea of considering our project as a product. Clearly in its current state it is not a product ready to go to market, but could be considered as a prototype for one that might be. Our system is designed to be used in a huge variety of circumstances, but for the sake of this exercise we have used just one.<br />
<br />
The idea was to consider the process of taking our ‘product’ and putting it in a ‘market. We have considered a suitable market for the product – in this case groundwater contamination in rural India, weighed up the strengths and weaknesses of currently available systems that cater for this market and how our system differs.<br />
<br />
We then consider the likely problems that would be faced were we attempting to attempt this now, ranging from mistrust of GMOs to bacterial disposal.<br />
<br />
'''Why is this relevant?'''<br />
<br />
The majority of us, whether we pursue careers in research or industry will probably at some point be involved with the production or release of a product. We have tried to use this as a trial run, to show teams what they might expect to come up against. We hope that this might inspire teams to consider human practices as a foundation for their projects as we did. Fluoride contamination was a major factor in the decision to design a system from start to finish that could quantifiably test for fluoride. We hope that this might encourage teams to think innovatively about their project when in the design phase, to consider a real world problem to which their project could be a solution and to consider the problems they might encounter in the course of applying that solution so that they can be tackled in the course of the project.<br />
<br />
Our innovation project can be found [Team:Cambridge/Outreach/innovation|here].<br />
<br />
===Safety:===<br />
<br />
Safety is core to the iGEM competition and all teams must complete a series of safety questions on their wiki to qualify for a medal to prove that they have considered the safety implications of their project as a whole and have set about working in compliance with good laboratory practice. In addition to this criterion we have also produced protocols for reference for all of the techniques we use in the lab. These also have risk assessments for the major risks associated with them and precaution suggestion where appropriate as well as MSDS sheets for all reagents used available in the safety section of our wiki.<br />
<br />
We assume that, like us, most iGEMers do not relish the thought of vast quantities of paperwork to accompany their projects. Our safety criteria do not impose this, but do demand further proof of safety consciousness than current requirements. <br />
<br />
'''Why is this relevant?'''<br />
<br />
The current team has found having this information readily accessible on the wiki (where it cannot be lost or tidied away) to be extremely useful and we consider it the duty of iGEM teams to leave their project in a sufficiently well documented state that future teams could pick up more or less where the previous team stopped. <br />
<br />
Where teams choose to modularise their project into several sub-projects, different teams may be working with different experiments at any given time. It may be weeks before certain teams use techniques that others utilised on their first day. This is where having reliably accessible information comes into its own. Which reagent comes next? It’s on the wiki. Waste disposal? On the wiki. Do I need a mask for this? On the wiki. Is it supposed to go that colour? It’s on the wiki.<br />
<br />
Perhaps more importantly, we have found that constantly updating and adding to the safety element of our project prevented it from slipping to the back of mind. We have found that we spent more time than anticipated considering the safety implications of experiments as we were planning and doing them, in the knowledge that we would be written up formally. <br />
<br />
The provision of detailed protocols, MSDS and at least basic risk assessments can be hugely helpful to future teams, especially students coming to the iGEM competition from non-biological disciplines. Even those of us thoroughly familiar with techniques like PCR found the last team’s notes useful for reference in the early weeks of our project. Many excellent projects have been stopped short because of time constraints. If another team wanted to build on it, they might be able to ask the previous team if it is the next year and at the same institution, but if it is several years before the project catches the imagination of another team, then the wiki is probably all they’ll have to work with. <br />
<br />
===Sharing:===<br />
<br />
Early in the summer, when we were trying to define our project, we started thinking about what we wanted it to do. We eventually settled on one of the key principles of synthetic biology – standardisation (strongly promoted by the engineers on the team). Biological research is currently a highly bespoke process with predominantly non-standardised biosensors – a multitude of output systems with a plethora of sensitivity curves exist. This renders individual sets of results amost meaningless as research from different teams is not directly comparable. This limits the capacity for sharing and collaboration as teams are effectively working on their own and this in turn limits the rate of progress.<br />
<br />
To this end our project was focussed on producing a standardised output system with instrumentation for biosensor experiments to promote facilitate sharing and collaboration between iGEM teams, with a myriad of possible applications. A ratiometric system was chosen to provide a reliable quantification system, it was decided that the system should be portable so that it could be used for field research as well as laboratory based research and relatively cheap, to make it accessible to other iGEM teams. We felt it important that the code used in the instrumentation be open source like the rest of the project, so that it could be tweaked by future users to match their needs.<br />
<br />
'''Why is this relevant?'''<br />
<br />
iGEM is open source and high value is placed on sharing, collaboration and building on the work of previous teams. Where there is a lack of standardisation however, it is hard for teams to know what they can expect when working with another team’s project. We have attributed at least some of the problems we have experienced when trying to work with previous teams’ biobricks this summer to this problem.<br />
<br />
We believe that a standardised output for biosensor experiments would be of enormous help to teams, giving them the tools to compare results, share and collaborate more effectively.<br />
<br />
===Outreach:===<br />
<br />
Traditionally, this section of a wiki is labelled outreach and features teams promoting the iGEM competition and trying to improve public understanding and perceptions of synthetic biology as a whole. We have not had the time to do this as the vast majority of our project has been lab based; we have however written an article for the Cambridge University Graduate <br />
<br />
A copy of this article can be found here. <br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Safety/MSDSTeam:Cambridge/Safety/MSDS2012-08-24T10:56:19Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
==Materials Safety Data Sheets==<br />
<br />
<br />
We consider it good lab practice to keep MSDSs for the reagents we use in our experiments. Below are the MSDSs (where availbale) for the reagents used in the protocols listed on this wiki.<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M7154&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsigma%2Fm7154%3Flang%3Den 2-Mercaptoethanol]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsB0518.pdf 5x Phusion HF]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=320099&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dacetic%2Bacid%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Acetic Acid]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A3553&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DAcrylamide%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Acrylamide]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A1296&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dagar%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Agar]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A9539&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dagarose%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Agarose]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=33582&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dammonium%2520buffer%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286 Ammonium Buffer]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A3678&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsigma%2FA3678%3Flang%3Den Ammonium Persulphate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A4418&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DAmmonium%2Bsulfate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Ammonium Sulphate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A9393&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DAmpicillin%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Ampicillin]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A3256&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Darabinose%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Arabinose]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=B0126&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsial%2Fb0126%3Flang%3Den Bromophenol Blue]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_n3_uk5.pdf Buffer N3]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_p2_uk6.pdf Buffer P2]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_pb_uk6.pdf Buffer PB]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_pb_uk6.pdf Buffer QG]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=C1016&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dcalcium%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax CaCl<sub>2</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=C0378&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dchloramphenicol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Chloramphenicol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=W1754&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Ddeionized%2Bwater%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax DI water]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=DNTP100A&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DdNTP%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax dNTPs]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=E7023&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dethanol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Ethanol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G8270&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglucose%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Glucose]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G1251&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglutamic%2Bacid%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax L-Glutamic Acid]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G5516&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglycerol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Glycerol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G8898&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglycine%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Glycine]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=38280&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dhydrochloric%2Bacid%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax HCl]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=95304&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dhplc%2Bwater%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax HPLC Water]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=236489&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DIron%2528III%2529%2Bchloride%2Bhexahydrate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax FeCl<sub>3</sub>.6H<sub>2</sub>O]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=I9516&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Disopropanol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Isopropanol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=P3786&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Ddipotassium%2Bphosphate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax K<sub>2</sub>HPO<sub>4</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=B5264&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dkanamycin%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Kanamycin]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=P9791&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dpotassium%2Bphosphate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax KH<sub>2</sub>PO<sub>4</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=L1750&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dlactic%2Bacid%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax L-Lactic acid]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=L7275&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dliquid%2Bbroth%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax LB]<br />
<br />
[http://www.qiagen.com/support/msds/uk/gelpilot_5x_loading_dye_uk4.pdf 5x Loading Dye]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M8266&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dmagnesium%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax MgCl<sub>2</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M7506&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dmagnesium%2520sulphate%26lang%3Den%26region%3DGB%26N%3D0%2B219853121%2B219853286%2B220003048%26focus%3Dproduct%26mode%3Dmatch%2Bpartialmax%26cm_re%3DDid%2520You%2520Mean-_-magnesium%2520sulphate-_-mangesium%2520sulphate Magnesium Sulphate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=203734&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DManganese%2528II%2529%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax MnCl<sub>2</sub>.4H<sub>2</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=146072&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DAcrylamide%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Methylenebis(acrylamide)]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M1254&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsigma%2Fm1254%3Flang%3Den MOPS]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsM0530.pdf Phusion DNA polymerase]<br />
<br />
[http://www.qiagen.com/support/msds/uk/rnase_a_solution_uk5.pdf RNase A solution]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=L3771&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DSDS%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax SDS]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=201154&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3D201154%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Sodium Fluoride]<br />
<br />
[https://tools.invitrogen.com/content/sfs/msds/2012/S33102_MTR-EULT_BE.pdf SYBR safe]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsM0363.pdf T5 exonuclease]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T6025&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DTAE%2Bbuffer%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax TAE Buffer]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsM0208.pdf Taq DNA Ligase]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=D4545&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dtaq%2Bpolymerase%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Taq DNA Polymerase]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T9281&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DTetramethylethylenediamine%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax TEMED]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T4625&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DThiamine%2Bhydrochloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Thiamine Hydrochloride]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=93349&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Ffluka%2F93349%3Flang%3Den Tris Base]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=S1804&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dtrisodium%2Bcitrate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Trisodium Citrate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T0254&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DTryptophan%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Tryptophan]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=92144&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dyeast%2Bextract%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Yeast extract]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=229997&brand=ALDRICH&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dzinc%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax ZnCl<sub>2</sub>]<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Safety/RiskAssessmentsTeam:Cambridge/Safety/RiskAssessments2012-08-23T13:41:14Z<p>CharlotteBG: /* Risk Assessments */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
=Risk Assessments=<br />
<br />
<br />
Here you can find guidelines for the most common risks assosiated with the protocols used in the course of our experiments and the specific risk assessments for each of the protocols listed on the wiki.<br />
<br />
<br />
===Risk Assessments===<br />
<br />
[[Team:Cambridge/RiskAssessments/beta-galactocidaseassay|&beta;-galactosidase Assay]]<br />
<br />
[[Team:Cambridge/Safety/RiskAssessments/biobrick|Using Biobricks from the distribution plates]]<br />
<br />
[[Team:Cambridge/RiskAssessments/ColonyPCR|Colony PCR]]<br />
<br />
[[Team:Cambridge/RiskAssessments/ChemicallyCompetentCellGeneration|Chemically competent cell - generation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/electrocompetentcellgeneration|Electrocompetent cell - generation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Electroporation|Electroporation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Gelelectrophoresis|Gel electrophoresis]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Gelextractionofdna|Gel extraction of DNA]]<br />
<br />
[[Team:Cambridge/RiskAssessments/GibsonAssembly|Gibson Assembly]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Glycerolstocks|Glycerol Stocks]]<br />
<br />
[[Team:Cambridge/Safety/RiskAssessments/IPTGindiction|IPTG Induction]]<br />
<br />
[[Team:Cambridge/RiskAssessments/LBplates|LB agar plates - preparation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Miniprep|Miniprep - DNA extraction]]<br />
<br />
[[Team:Cambridge/RiskAssessments/PCR|PCR using high temperature DNA polymerase]]<br />
<br />
[[Team:Cambridge/RiskAssessments/SDSpage|SDS PAGE protein analysis]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Restrictionenzymedigest|Restriction Enzyme Digest]]<br />
<br />
[[Team:Cambridge/RiskAssessments/TransformationofBsubtilis|Transformation of ''Bacillus subtilis'']]<br />
<br />
[[Team:Cambridge/RiskAssessments/TransformationofEcoli|Transformation of ''Escherichia coli'']]<br />
<br />
[[Team:Cambridge/RiskAssessments/NaF|Use of Sodium Fluoride for construct testing]]<br />
<br />
===General Risks===<br />
<br />
It is expected that good laboratory practice will be observed and that the correct PPE (personal protective equipment) will be worn at all times. Further precautions must be taken however in light of some hazards.<br />
<br />
'''Bacteria'''- Depending on the bacteria used in your experiments, the danger associated with exposure will vary. Our laboratory is only authorised to use Biosafety level 1 (non-pathogenic) bacteria and so in our experiments the risk to scientists is minimal. It is however the policy of the department to treat all bacteria as pathogens. This will be increasingly important if pathogenic strains of bacteria are used.<br />
<br />
:::'''Infection''' - the risk of infection in our experiment was not of great concern as non-pathogenic strains were used. Gloves and lab coats were still always worn when working with bacteria (this was also to help prevent contamination of samples). Where there is a greater risk masks should also be work to prevent access via the mouth or airways. Despite wearing gloves while working with bacteria, scientists must still wash their hands before leaving the lab to eliminate the chance of contaminating food. <br />
<br />
:::'''Disposal''' - Unused bacteria and any material that has come into contact with the bacteria (including gloves)should be disposed of in the biological waste vessels in the laboratory. When full, these materials are then autoclaved and disposed of in accordance with normal departmental procedures.<br />
<br />
'''Cold''' - The extreme cold used to store the competent cells until use is capable of causing freeze burns. If prolonged exposure to these temperatures is required the wearing of heat proof gloves is recommended.<br />
<br />
'''Gel preparation''' - the TAE buffer and agarose are not inherently dangerous but to be effectively mixed together they need to be heated, usually in a microwave. To fully dissolve the agarose, the mixture must be heated to a temperature too hot to touch. The container must therefore be handled with a heat proof glove. <br />
<br />
There is also a danger that the mixture could superheat and this is extremely dangerous. A mixture that does not appear to be boiling when taken out of the microwave can boil violently when swirled. The mixture should therefore be heated gradually, in small bursts and then swirled at arms length to heat to the minimum possible temperature to completely dissolve. The lid of the container must be on, but not screwed tight as tight as possible to allow for gas expansion as the mixture heats up.<br />
<br />
'''Glass''' - Glass is somewhat ubiquitous in laboratories and though it is expected that scientists will work safely, accidents still happen. All glassware in use should be labelled so that in the case of a breakage the carried substance can be identified. Broken glass is obviously a hazard through the liklihood of injury and it should be cleared away as soon as possible. The contents of the vessel will often be of greater concern however. Post breakage procedures will vary in accordance with what was in the container before the break and scientists should familiarise themselves with the disposal measures of their department. <br />
<br />
'''Hazardous Chemicals''' - some of the chemicals used in these protocols carry specific health risks. These will be listed on an individual basis in the relevant risk assessments below but in all cases it is worth noting that additional PPE may have to be worn and that normal waste disposal procedures may not be appropriate.<br />
<br />
'''Heat'''- While most PCR is now carried out using specialised machines, it is possible to perform PCR by hand using heat blocks and waterbaths. The high temperatures used in this technique are sufficient to burn the skin so care must be taken when using machinery and transferring samples. The use of tongs or heat proof gloves is recommended in this case. <br />
<br />
'''Voltage''' - The Genepulse device administers a very high voltage and therefore the electroporation cuvette should only be used with the device in the manner described by the manufacturer. This will normally involve the use of a plastic loading device which connects the cuvette to the electrodes prior to electroporation. If in doubt, seek advice before connecting the cuvette to the device. <br />
<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Safety/RiskAssessmentsTeam:Cambridge/Safety/RiskAssessments2012-08-23T13:39:52Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
=Risk Assessments=<br />
<br />
<br />
Here you can find guidelines for the most common risks assosiated with the protocols used in the course of our experiments and the specific risk assessments for each of the protocols listed on the wiki.<br />
<br />
<br />
===Risk Assessments===<br />
<br />
[[Team:Cambridge/RiskAssessments/beta-galactocidaseassay|&beta;-galactosidase Assay]]<br />
<br />
[[Team:Cambridge/RiskAssessments/biobrick|Using Biobricks from the distribution plates]]<br />
<br />
[[Team:Cambridge/RiskAssessments/ColonyPCR|Colony PCR]]<br />
<br />
[[Team:Cambridge/RiskAssessments/ChemicallyCompetentCellGeneration|Chemically competent cell - generation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/electrocompetentcellgeneration|Electrocompetent cell - generation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Electroporation|Electroporation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Gelelectrophoresis|Gel electrophoresis]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Gelextractionofdna|Gel extraction of DNA]]<br />
<br />
[[Team:Cambridge/RiskAssessments/GibsonAssembly|Gibson Assembly]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Glycerolstocks|Glycerol Stocks]]<br />
<br />
[[Team:Cambridge/Safety/RiskAssessments/IPTGindiction|IPTG Induction]]<br />
<br />
[[Team:Cambridge/RiskAssessments/LBplates|LB agar plates - preparation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Miniprep|Miniprep - DNA extraction]]<br />
<br />
[[Team:Cambridge/RiskAssessments/PCR|PCR using high temperature DNA polymerase]]<br />
<br />
[[Team:Cambridge/RiskAssessments/SDSpage|SDS PAGE protein analysis]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Restrictionenzymedigest|Restriction Enzyme Digest]]<br />
<br />
[[Team:Cambridge/RiskAssessments/TransformationofBsubtilis|Transformation of ''Bacillus subtilis'']]<br />
<br />
[[Team:Cambridge/RiskAssessments/TransformationofEcoli|Transformation of ''Escherichia coli'']]<br />
<br />
[[Team:Cambridge/RiskAssessments/NaF|Use of Sodium Fluoride for construct testing]]<br />
<br />
===General Risks===<br />
<br />
It is expected that good laboratory practice will be observed and that the correct PPE (personal protective equipment) will be worn at all times. Further precautions must be taken however in light of some hazards.<br />
<br />
'''Bacteria'''- Depending on the bacteria used in your experiments, the danger associated with exposure will vary. Our laboratory is only authorised to use Biosafety level 1 (non-pathogenic) bacteria and so in our experiments the risk to scientists is minimal. It is however the policy of the department to treat all bacteria as pathogens. This will be increasingly important if pathogenic strains of bacteria are used.<br />
<br />
:::'''Infection''' - the risk of infection in our experiment was not of great concern as non-pathogenic strains were used. Gloves and lab coats were still always worn when working with bacteria (this was also to help prevent contamination of samples). Where there is a greater risk masks should also be work to prevent access via the mouth or airways. Despite wearing gloves while working with bacteria, scientists must still wash their hands before leaving the lab to eliminate the chance of contaminating food. <br />
<br />
:::'''Disposal''' - Unused bacteria and any material that has come into contact with the bacteria (including gloves)should be disposed of in the biological waste vessels in the laboratory. When full, these materials are then autoclaved and disposed of in accordance with normal departmental procedures.<br />
<br />
'''Cold''' - The extreme cold used to store the competent cells until use is capable of causing freeze burns. If prolonged exposure to these temperatures is required the wearing of heat proof gloves is recommended.<br />
<br />
'''Gel preparation''' - the TAE buffer and agarose are not inherently dangerous but to be effectively mixed together they need to be heated, usually in a microwave. To fully dissolve the agarose, the mixture must be heated to a temperature too hot to touch. The container must therefore be handled with a heat proof glove. <br />
<br />
There is also a danger that the mixture could superheat and this is extremely dangerous. A mixture that does not appear to be boiling when taken out of the microwave can boil violently when swirled. The mixture should therefore be heated gradually, in small bursts and then swirled at arms length to heat to the minimum possible temperature to completely dissolve. The lid of the container must be on, but not screwed tight as tight as possible to allow for gas expansion as the mixture heats up.<br />
<br />
'''Glass''' - Glass is somewhat ubiquitous in laboratories and though it is expected that scientists will work safely, accidents still happen. All glassware in use should be labelled so that in the case of a breakage the carried substance can be identified. Broken glass is obviously a hazard through the liklihood of injury and it should be cleared away as soon as possible. The contents of the vessel will often be of greater concern however. Post breakage procedures will vary in accordance with what was in the container before the break and scientists should familiarise themselves with the disposal measures of their department. <br />
<br />
'''Hazardous Chemicals''' - some of the chemicals used in these protocols carry specific health risks. These will be listed on an individual basis in the relevant risk assessments below but in all cases it is worth noting that additional PPE may have to be worn and that normal waste disposal procedures may not be appropriate.<br />
<br />
'''Heat'''- While most PCR is now carried out using specialised machines, it is possible to perform PCR by hand using heat blocks and waterbaths. The high temperatures used in this technique are sufficient to burn the skin so care must be taken when using machinery and transferring samples. The use of tongs or heat proof gloves is recommended in this case. <br />
<br />
'''Voltage''' - The Genepulse device administers a very high voltage and therefore the electroporation cuvette should only be used with the device in the manner described by the manufacturer. This will normally involve the use of a plastic loading device which connects the cuvette to the electrodes prior to electroporation. If in doubt, seek advice before connecting the cuvette to the device. <br />
<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Safety/RiskAssessments/IPTGindictionTeam:Cambridge/Safety/RiskAssessments/IPTGindiction2012-08-23T13:39:16Z<p>CharlotteBG: Created page with "{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}} =IPTG Induction of Ratiometrica in E. coli= The protocol for this technique can be found [[Team:Cambridge/Protocols/IP..."</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
=IPTG Induction of Ratiometrica in E. coli=<br />
<br />
The protocol for this technique can be found [[Team:Cambridge/Protocols/IPTGInduction|here]] and the MSDS for the reagents used can be found [[Team:Cambridge/Safety/MSDS|here]].<br />
<br />
===Risks===<br />
<br />
'''Bacteria'''- Depending on the bacteria used in your experiments, the danger associated with exposure will vary. Our laboratory is only authorised to use Biosafety level 1 (non-pathogenic) bacteria and so in our experiments the risk to scientists is minimal. It is however the policy of the department to treat all bacteria as pathogens. This will be increasingly important if pathogenic strains of bacteria are used.<br />
<br />
:::'''Infection''' - the risk of infection in our experiment was not of great concern as non-pathogenic strains were used. Gloves and lab coats were still always worn when working with bacteria (this was also to help prevent contamination of samples). Where there is a greater risk masks should also be work to prevent access via the mouth or airways. Despite wearing gloves while working with bacteria, scientists must still wash their hands before leaving the lab to eliminate the chance of contaminating food. <br />
<br />
:::'''Disposal''' - Unused bacteria and any material that has come into contact with the bacteria (including gloves)should be disposed of in the biological waste vessels in the laboratory. When full, these materials are then autoclaved and disposed of in accordance with normal departmental procedures.<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Protocols/IPTGInductionTeam:Cambridge/Protocols/IPTGInduction2012-08-23T13:27:53Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
<br />
=IPTG Induction of Ratiometrica in E. coli=<br />
<br />
'''[[Team:Cambridge/Safety/RiskAssessments/IPTGindiction|Risk Assessment]]'''<br />
<br />
This protocol is an adaptation of this one: http://www.genetics.wustl.edu/tslab/?page_id=107<br />
and is used to test the induction of the pSPANK promoter with IPTG in E.coli<br />
<br />
===Preparation===<br />
<br />
Prepare LB/AMP/IPTG plates with 100ug/ml of Ampicillin and a final concentration of 0.5mM. Also have a couple of normal amp plates ready.<br />
<br />
===Protocol===<br />
<br />
1) Pick cultures and grow in 2ml LB/AMP (100ug/ml) in a 15ml snap cap tube overnight at 37<sup>0</sup>C at 160RPM.<br />
<br />
2)Dilute 1:100 and grow for 3-4 hours in 2ml LB/AMP (100ug/ml) in a 15ml snap cap tube <br />
<br />
3)Spread 250uL and 25uL onto you IPTG plates. Also spread some on normal amp plates as a control. Allow to grow in incubator.<br />
<br />
<br />
<center>'''[[Team:Cambridge/Protocols|Back to Protocols]]'''</center><br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Safety/RiskAssessments/biobrickTeam:Cambridge/Safety/RiskAssessments/biobrick2012-08-23T13:13:51Z<p>CharlotteBG: /* Biobricks */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
=Biobricks=<br />
<br />
The protocol for this technique can be found [[Team:Cambridge/Protocols/biobrick_protocols|here]] and the MSDS for the reagents used [[Team:Cambridge/Safety/MSDS|here]].<br />
<br />
===Risks===<br />
<br />
None of the reagents used in this practical have specific hazards associated with them but gloves must always be worn. Partly as this is good laboratory practice but mostly to prevent contamination with human DNA.<br />
<br />
'''Cold''' - The distribution plates are stored in a -20<sup>o</sup>c freezer and prolonged exposure to these temperatures can cause freezer burn. If working at these temperatures more than briefly, we recommend wearing heat proof gloves. <br />
<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Safety/RiskAssessments/biobrickTeam:Cambridge/Safety/RiskAssessments/biobrick2012-08-23T13:13:14Z<p>CharlotteBG: Created page with "{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}} =Biobricks= The protocol for this technique can be found here and the MSDS for t..."</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
=Biobricks=<br />
<br />
The protocol for this technique can be found [[Team:Cambridge/Protocols/biobrick|here]] and the MSDS for the reagents used [[Team:Cambridge/Safety/MSDS|here]].<br />
<br />
===Risks===<br />
<br />
None of the reagents used in this practical have specific hazards associated with them but gloves must always be worn. Partly as this is good laboratory practice but mostly to prevent contamination with human DNA.<br />
<br />
'''Cold''' - The distribution plates are stored in a -20<sup>o</sup>c freezer and prolonged exposure to these temperatures can cause freezer burn. If working at these temperatures more than briefly, we recommend wearing heat proof gloves. <br />
<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Protocols/biobrick_protocolsTeam:Cambridge/Protocols/biobrick protocols2012-08-23T13:02:25Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
=BioBricks=<br />
<br />
'''[[Team:Cambridge/Safety/RiskAssessments/biobrick|Risk Assessment]]'''<br />
<br />
[http://partsregistry.org/Help:Distribution_Kits Distribution Kit page] A link to the Registry of Standard Biological Parts<br />
<br />
==Resuspension of BioBricks from the distribution==<br />
<br />
see [http://partsregistry.org/Help:Distribution_Kits#Using_the_Spring_2012_DNA_Distribution Using the Spring 2012 DNA Distribution] for a more detailed protocol!<br />
<br />
#Locate your BioBrick of interest in the Distribution: [http://partsregistry.org/assembly/libraries.cgi?id=42 Spring 2012 Distribution, DNA Part Repositories] Make sure the plate is properly orientated! The two notched corners of the plate are oriented at the BOTTOM of the plate.<br />
#Pierce foil of required well and pipette 10µL dH<sub>2</sub>O (distilled water).<br />
#Pipette up and down several times to fully resuspend the DNA sample. Sit for 10 minutes.<br />
#The BioBrick is now ready for transformation.<br />
<br />
==Linearised Plasmid Backbones==<br />
<br />
[http://partsregistry.org/Help:Protocols/Linearized_Plasmid_Backbones Linearised Plasmid Backbone]<br />
<br />
<br />
<center>'''[[Team:Cambridge/Protocols|Back to Protocols]]'''</center><br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Protocols/biobrick_protocolsTeam:Cambridge/Protocols/biobrick protocols2012-08-23T13:02:08Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
=BioBricks=<br />
<br />
[[Team:Cambridge/Safety/RiskAssessments/biobrick|Risk Assessment]]<br />
<br />
[http://partsregistry.org/Help:Distribution_Kits Distribution Kit page] A link to the Registry of Standard Biological Parts<br />
<br />
==Resuspension of BioBricks from the distribution==<br />
<br />
see [http://partsregistry.org/Help:Distribution_Kits#Using_the_Spring_2012_DNA_Distribution Using the Spring 2012 DNA Distribution] for a more detailed protocol!<br />
<br />
#Locate your BioBrick of interest in the Distribution: [http://partsregistry.org/assembly/libraries.cgi?id=42 Spring 2012 Distribution, DNA Part Repositories] Make sure the plate is properly orientated! The two notched corners of the plate are oriented at the BOTTOM of the plate.<br />
#Pierce foil of required well and pipette 10µL dH<sub>2</sub>O (distilled water).<br />
#Pipette up and down several times to fully resuspend the DNA sample. Sit for 10 minutes.<br />
#The BioBrick is now ready for transformation.<br />
<br />
==Linearised Plasmid Backbones==<br />
<br />
[http://partsregistry.org/Help:Protocols/Linearized_Plasmid_Backbones Linearised Plasmid Backbone]<br />
<br />
<br />
<center>'''[[Team:Cambridge/Protocols|Back to Protocols]]'''</center><br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Protocols/beta-galactosidaseassayTeam:Cambridge/Protocols/beta-galactosidaseassay2012-08-23T12:58:09Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
<br />
==&beta;-galactosidase Assay==<br />
<br />
'''[[Team:Cambridge/RiskAssessments/beta-galactocidaseassay|Risk Assessment]]'''<br />
<br />
===Theory===<br />
<br />
[[File:x-galreaction.jpg|right|500px|thumb|Chemical reaction by which X-Gal produces a coloured solution in the presence of &beta;-galactosidase.]]<br />
<br />
* X-Gal itself is colourless and undetectable in the spectrophotometer.<br />
<br />
* X-Gal is cleaved by &beta;-galactosidase, forming 5-bromo-4-chloro-3-hydroxyindole.<br />
<br />
* This dimerises to form 5,5'-dibromo-4,4'-dichloro-indigo. This can be detected as a considerable change in the colour of the solution.<br />
<br />
* The precise shade of the resultant solution can therefore be used to quantify the amount of &beta;-galactosidase reporter being produced.<br />
<br />
===Protocol===<br />
<br />
*Take suspension of cells grown up overnight and dilute 200 times in appropriate growth medium (for example LB broth for e.coli). If genetic construct can be selected for by an antibiotic, include this in the growth medium according to needs - this prevents loss of the plasmid during growth.<br />
<br />
*Now add the following to each of your eppindorf tubes:<br />
<br />
{| class="wikitable" style="text-align: center;"<br />
||'''Reagent'''||'''Volume (µl)'''<br />
|-<br />
||X-Gal (10mg/ml)||20<br />
|-<br />
||Substance of interest (e.g. Fluoride) (0.5 M)||1 for each mM desired in final solution<br />
|-<br />
||Cell suspension||Make up to 500 &mu;l<br />
|}<br />
<br />
*Leave tubes overnight in 37 &deg;C incubator.<br />
<br />
*Tubes with greatest &beta;-galactosidase activity will have greatest blue colouration.<br />
<br />
<br />
<br />
<br />
<center>'''[[Team:Cambridge/Protocols|Back to Protocols]]'''</center><br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Protocols/beta-galactosidaseassayTeam:Cambridge/Protocols/beta-galactosidaseassay2012-08-23T12:57:49Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
<br />
==&beta;-galactosidase Assay==<br />
<br />
'''[[Team:Cambridge/RiskAssessments/beta-galactocidaseassay|Risk Assessment]]'''<br />
<br />
===Theory===<br />
<br />
[[File:x-galreaction.jpg|right|500px|thumb|Chemical reaction by which X-Gal produces a coloured solution in the presence of &beta;-galactosidase.]]<br />
<br />
* X-Gal itself is colourless and undetectable in the spectrophotometer.<br />
<br />
* X-Gal is cleaved by &beta;-galactosidase, forming 5-bromo-4-chloro-3-hydroxyindole.<br />
<br />
* This dimerises to form 5,5'-dibromo-4,4'-dichloro-indigo. This can be detected as a considerable change in the colour of the solution.<br />
<br />
* The precise shade of the resultant solution can therefore be used to quantify the amount of &beta;-galactosidase reporter being produced.<br />
<br />
===Protocol===<br />
<br />
*Take suspension of cells grown up overnight and dilute 200 times in appropriate growth medium (for example LB broth for e.coli). If genetic construct can be selected for by an antibiotic, include this in the growth medium according to needs - this prevents loss of the plasmid during growth.<br />
<br />
*Now add the following to each of your eppindorf tubes:<br />
<br />
{| class="wikitable" style="text-align: center;"<br />
||'''Reagent'''||'''Volume (µl)'''<br />
|-<br />
||X-Gal (10mg/ml)||20<br />
|-<br />
||Substance of interest (e.g. Fluoride) (0.5 M)||1 for each mM desired in final solution<br />
|-<br />
||Cell suspension||Make up to 500 &mu;l<br />
|}<br />
<br />
*Leave tubes overnight in 37 &deg;C incubator.<br />
<br />
*Tubes with greatest &beta;-galactosidase activity will have greatest blue colouration.<br />
<br />
'''[[Team:Cambridge/Protocols|Back to Protocols]]'''<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Protocols/beta-galactosidaseassayTeam:Cambridge/Protocols/beta-galactosidaseassay2012-08-23T12:57:02Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
<br />
==&beta;-galactosidase Assay==<br />
<br />
[[Team:Cambridge/RiskAssessments/beta-galactocidaseassay|Risk Assessment]]<br />
<br />
===Theory===<br />
<br />
[[File:x-galreaction.jpg|right|500px|thumb|Chemical reaction by which X-Gal produces a coloured solution in the presence of &beta;-galactosidase.]]<br />
<br />
* X-Gal itself is colourless and undetectable in the spectrophotometer.<br />
<br />
* X-Gal is cleaved by &beta;-galactosidase, forming 5-bromo-4-chloro-3-hydroxyindole.<br />
<br />
* This dimerises to form 5,5'-dibromo-4,4'-dichloro-indigo. This can be detected as a considerable change in the colour of the solution.<br />
<br />
* The precise shade of the resultant solution can therefore be used to quantify the amount of &beta;-galactosidase reporter being produced.<br />
<br />
===Protocol===<br />
<br />
*Take suspension of cells grown up overnight and dilute 200 times in appropriate growth medium (for example LB broth for e.coli). If genetic construct can be selected for by an antibiotic, include this in the growth medium according to needs - this prevents loss of the plasmid during growth.<br />
<br />
*Now add the following to each of your eppindorf tubes:<br />
<br />
{| class="wikitable" style="text-align: center;"<br />
||'''Reagent'''||'''Volume (µl)'''<br />
|-<br />
||X-Gal (10mg/ml)||20<br />
|-<br />
||Substance of interest (e.g. Fluoride) (0.5 M)||1 for each mM desired in final solution<br />
|-<br />
||Cell suspension||Make up to 500 &mu;l<br />
|}<br />
<br />
*Leave tubes overnight in 37 &deg;C incubator.<br />
<br />
*Tubes with greatest &beta;-galactosidase activity will have greatest blue colouration.<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/RiskAssessments/beta-galactocidaseassayTeam:Cambridge/RiskAssessments/beta-galactocidaseassay2012-08-23T12:55:23Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
=&beta;-galactosidase Assay=<br />
<br />
The protocol for this technique can be found [[Team:Cambridge/Protocols/beta-galactosidaseassay|here]] and MSDS for reagents used can be found [[Team:Cambridge/Protocols/beta-galactosidaseassay|here]].<br />
<br />
===Risks===<br />
<br />
'''Bacteria'''- Depending on the bacteria used in your experiments, the danger associated with exposure will vary. Our laboratory is only authorised to use Biosafety level 1 (non-pathogenic) bacteria and so in our experiments the risk to scientists is minimal. It is however the policy of the department to treat all bacteria as pathogens. This will be increasingly important if pathogenic strains of bacteria are used.<br />
<br />
:::'''Infection''' - the risk of infection in our experiment was not of great concern as non-pathogenic strains were used. Gloves and lab coats were still always worn when working with bacteria (this was also to help prevent contamination of samples). Where there is a greater risk masks should also be work to prevent access via the mouth or airways. Despite wearing gloves while working with bacteria, scientists must still wash their hands before leaving the lab to eliminate the chance of contaminating food. <br />
<br />
:::'''Disposal''' - Unused bacteria and any material that has come into contact with the bacteria (including gloves)should be disposed of in the biological waste vessels in the laboratory. When full, these materials are then autoclaved and disposed of in accordance with normal departmental procedures.<br />
<br />
<br />
'''Hazardous Chemicals''' - There is potential for use of hazardous chemicals in this protocol depending on experimental design (e.g. fluoride). These will need to be considered on an individual basis and appropriate risk assessments produced but in all cases it is worth noting that additional PPE may have to be worn and that normal waste disposal procedures may not be appropriate.<br />
<br />
If in doubt, consult the departmental poster on our safety homepage for guidelines.<br />
<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/RiskAssessments/beta-galactocidaseassayTeam:Cambridge/RiskAssessments/beta-galactocidaseassay2012-08-23T12:54:59Z<p>CharlotteBG: Created page with "{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}} =&beta;-galactosidase Assay= The protocol for this technique can be found [[Team:Cambridge/Protocols/beta-galactosidas..."</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
=&beta;-galactosidase Assay=<br />
<br />
The protocol for this technique can be found [[Team:Cambridge/Protocols/beta-galactosidaseassay|here]] and MSDS for reagents used can be found [[Team:Cambridge/Protocols/beta-galactosidaseassay|here]].<br />
<br />
===Risks===<br />
<br />
'''Bacteria'''- Depending on the bacteria used in your experiments, the danger associated with exposure will vary. Our laboratory is only authorised to use Biosafety level 1 (non-pathogenic) bacteria and so in our experiments the risk to scientists is minimal. It is however the policy of the department to treat all bacteria as pathogens. This will be increasingly important if pathogenic strains of bacteria are used.<br />
<br />
:::'''Infection''' - the risk of infection in our experiment was not of great concern as non-pathogenic strains were used. Gloves and lab coats were still always worn when working with bacteria (this was also to help prevent contamination of samples). Where there is a greater risk masks should also be work to prevent access via the mouth or airways. Despite wearing gloves while working with bacteria, scientists must still wash their hands before leaving the lab to eliminate the chance of contaminating food. <br />
<br />
:::'''Disposal''' - Unused bacteria and any material that has come into contact with the bacteria (including gloves)should be disposed of in the biological waste vessels in the laboratory. When full, these materials are then autoclaved and disposed of in accordance with normal departmental procedures.<br />
<br />
<br />
'''Hazardous Chemicals''' - There is potential for use of hazardous chemicals in this protocol depending on experimental design (e.g. fluoride). These will need to be considered on an individual basis and appropriate risk assessments produced but in all cases it is worth noting that additional PPE may have to be worn and that normal waste disposal procedures may not be appropriate.<br />
<br />
If in doubt, consult the departmental poster on our safety homepage for guidelines.</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Safety/MSDSTeam:Cambridge/Safety/MSDS2012-08-23T11:42:37Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
==Materials Safety Data Sheets==<br />
<br />
<br />
We consider it good lab practice to keep MSDSs for the reagents we use in our experiments. Below are the MSDSs (where availbale) for the reagents used in the protocols listed on this wiki.<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M7154&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsigma%2Fm7154%3Flang%3Den 2-Mercaptoethanol]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsB0518.pdf 5x Phusion HF]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=320099&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dacetic%2Bacid%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Acetic Acid]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A3553&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DAcrylamide%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Acrylamide]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A1296&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dagar%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Agar]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A9539&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dagarose%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Agarose]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=33582&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dammonium%2520buffer%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286 Ammonium Buffer]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A3678&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsigma%2FA3678%3Flang%3Den Ammonium Persulphate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A4418&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DAmmonium%2Bsulfate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Ammonium Sulphate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A9393&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DAmpicillin%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Ampicillin]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A3256&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Darabinose%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Arabinose]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=B0126&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsial%2Fb0126%3Flang%3Den Bromophenol Blue]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_n3_uk5.pdf Buffer N3]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_p2_uk6.pdf Buffer P2]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_pb_uk6.pdf Buffer PB]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_pb_uk6.pdf Buffer QG]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=C1016&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dcalcium%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax CaCl<sub>2</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=C0378&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dchloramphenicol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Chloramphenicol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=W1754&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Ddeionized%2Bwater%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax DI water]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=DNTP100A&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DdNTP%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax dNTPs]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=E7023&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dethanol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Ethanol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G8270&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglucose%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Glucose]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G1251&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglutamic%2Bacid%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax L-Glutamic Acid]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G5516&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglycerol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Glycerol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G8898&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglycine%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Glycine]<br />
<br />
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<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=95304&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dhplc%2Bwater%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax HPLC Water]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=236489&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DIron%2528III%2529%2Bchloride%2Bhexahydrate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax FeCl<sub>3</sub>.6H<sub>2</sub>O]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=I9516&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Disopropanol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Isopropanol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=P3786&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Ddipotassium%2Bphosphate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax K<sub>2</sub>HPO<sub>4</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=B5264&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dkanamycin%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Kanamycin]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=P9791&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dpotassium%2Bphosphate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax KH<sub>2</sub>PO<sub>4</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=L1750&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dlactic%2Bacid%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax L-Lactic acid]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=L7275&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dliquid%2Bbroth%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax LB]<br />
<br />
[http://www.qiagen.com/support/msds/uk/gelpilot_5x_loading_dye_uk4.pdf 5x Loading Dye]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M8266&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dmagnesium%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax MgCl<sub>2</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M7506&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dmagnesium%2520sulphate%26lang%3Den%26region%3DGB%26N%3D0%2B219853121%2B219853286%2B220003048%26focus%3Dproduct%26mode%3Dmatch%2Bpartialmax%26cm_re%3DDid%2520You%2520Mean-_-magnesium%2520sulphate-_-mangesium%2520sulphate Magnesium Sulphate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=203734&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DManganese%2528II%2529%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax MnCl<sub>2</sub>.4H<sub>2</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=146072&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DAcrylamide%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Methylenebis(acrylamide)]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsM0530.pdf Phusion DNA polymerase]<br />
<br />
[http://www.qiagen.com/support/msds/uk/rnase_a_solution_uk5.pdf RNase A solution]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=L3771&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DSDS%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax SDS]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=201154&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3D201154%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Sodium Fluoride]<br />
<br />
[https://tools.invitrogen.com/content/sfs/msds/2012/S33102_MTR-EULT_BE.pdf SYBR safe]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsM0363.pdf T5 exonuclease]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T6025&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DTAE%2Bbuffer%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax TAE Buffer]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsM0208.pdf Taq DNA Ligase]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=D4545&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dtaq%2Bpolymerase%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Taq DNA Polymerase]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T9281&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DTetramethylethylenediamine%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax TEMED]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T4625&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DThiamine%2Bhydrochloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Thiamine Hydrochloride]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=93349&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Ffluka%2F93349%3Flang%3Den Tris Base]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=S1804&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dtrisodium%2Bcitrate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Trisodium Citrate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T0254&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DTryptophan%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Tryptophan]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=92144&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dyeast%2Bextract%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Yeast extract]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=229997&brand=ALDRICH&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dzinc%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax ZnCl<sub>2</sub>]<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Protocols/ChemicallycompetentcellsTeam:Cambridge/Protocols/Chemicallycompetentcells2012-08-23T11:19:52Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
<br />
=Generating Chemically Competent Cells=<br />
<br />
'''[[Team:Cambridge/RiskAssessments/ChemicallyCompetentCellGeneration|Risk Assessment]]'''<br />
<br />
The following protocol has been taken from [http://openwetware.org/index.php?title=TOP10_chemically_competent_cells&oldid=288222 Openwetware.org]<br />
<br />
==Overview==<br />
This protocol is a variant of the Hanahan protocol using CCMB80 buffer for DH10B, TOP10 and MachI strains. It builds on Example 2 of the Bloom05 patent as well. This protocol has been tested on TOP10, MachI and BL21(DE3) cells. See Bacterial Transformation for a more general discussion of other techniques. Jesse '464 patent describes using this buffer for DH5&alpha; cells. The Bloom04 patent describes the use of essentially the same protocol for the Invitrogen Mach 1 cells.<br />
<br />
'''This is the chemical transformation protocol used by Tom Knight and the [http://partsregistry.org Registry of Standard Biological Parts].<br />
<br />
==Materials==<br />
*Detergent-free, sterile glassware and plasticware (see procedure)<br />
*Table-top OD600nm spectrophotometer<br />
*SOB<br />
<br />
===SOB===<br />
*0.5% (w/v) yeast extract<br />
*2% (w/v) tryptone<br />
*10 mM NaCl<br />
*2.5 mM KCl<br />
*20 mM MgSO<sub>4</sub><br />
<br />
Per liter:<br />
*5 g yeast extract<br />
*20 g tryptone<br />
*0.584 g NaCl<br />
*0.186 g KCl<br />
*2.4 g MgSO<sub>4</sub><br />
<br />
*Some formulations of SOB use 10 mM MgCl<sub>2</sub> and 10 mM MgSO<sub>4</sub> instead of 20 mM MgSO<sub>4</sub>.<br />
*Adjust to pH 7.5 prior to use. This requires approximately 25 ml of 1M NaOH per liter.<br />
<br />
===CCMB80 buffer===<br />
* 10 mM KOAc pH 7.0 (10 ml of a 1M stock/L or 0.98g/L)<br />
* 80 mM CaCl<sub>2</sub>.2H<sub>2</sub>O (11.8 g/L)<br />
* 20 mM MnCl<sub>2</sub>.4H<sub>2</sub>O (4.0 g/L)<br />
* 10 mM MgCl<sub>2</sub>.6H<sub>2</sub>O (2.0 g/L or 5ml of 2M stock/L)<br />
* 10% glycerol (100 ml/L)<br />
* Fill up with DI water AFTER regulating pH<br />
<br />
* adjust pH DOWN to 6.4 with 0.1N HCl if necessary<br />
** adjusting pH up will precipitate manganese dioxide from Mn containing solutions.<br />
* sterile filter and store at 4&deg;C<br />
* slight dark precipitate appears not to affect its function<br />
<br />
==Procedure==<br />
===Preparing glassware and media===<br />
====Eliminating detergent====<br />
Detergent is a major inhibitor of competent cell growth and transformation. Glass and plastic<br />
must be detergent free for these protocols. The easiest way to do this is to avoid washing<br />
glassware, and simply rinse it out. Autoclaving glassware filled 3/4 with DI water is an effective<br />
way to remove most detergent residue. Media and buffers should be prepared in detergent free glassware and cultures grown up in detergent free glassware.<br />
<br />
====Prechill plasticware and glassware====<br />
Prechill 250mL centrifuge tubes and screw cap tubes before use.<br />
<br />
===Preparing seed stocks===<br />
# Streak TOP10 cells on an SOB plate and grow for single colonies at 23&deg;C<br />
#* room temperature works well<br />
# Pick single colonies into 2 ml of SOB medium and shake overnight at 23&deg;C<br />
#* room temperature works well<br />
# Add glycerol to 15%<br />
# Aliquot 1 ml samples to Nunc cryotubes<br />
# Place tubes into a zip lock bag, immerse bag into a dry ice/ethanol bath for 5 minutes<br />
#* This step may not be necessary<br />
# Place in -80&deg;C freezer indefinitely.<br />
<br />
===Preparing competent cells===<br />
# Inoculate 250 ml of SOB medium with 1 ml vial of seed stock and grow at 20&deg;C to an OD600nm of 0.3<br />
#* This takes approximately 16 hours.<br />
#* Controlling the temperature makes this a more reproducible process, but is not essential.<br />
#* Room temperature will work. You can adjust this temperature somewhat to fit your schedule<br />
#* Aim for lower, not higher OD if you can't hit this mark<br />
# Centrifuge at 3000g at 4&deg;C for 10 minutes in a flat bottom centrifuge bottle.<br />
#* Flat bottom centrifuge tubes make the fragile cells much easier to resuspend<br />
#* It is often easier to resuspend pellets by mixing ''before'' adding large amounts of buffer<br />
# Gently resuspend in 80 ml of ice cold CCMB80 buffer<br />
#* sometimes this is less than completely gentle. It still works.<br />
# Incubate on ice 20 minutes<br />
# Centrifuge again at 4&deg;C and resuspend in 10 ml of ice cold CCMB80 buffer.<br />
# Test OD of a mixture of 200 &mu;l SOC and 50 &mu;l of the resuspended cells.<br />
# Add chilled CCMB80 to yield a final OD of 1.0-1.5 in this test. <br />
# Incubate on ice for 20 minutes<br />
# Aliquot to chilled screw top 2 ml vials or 50 &mu;l into chilled microtiter plates<br />
# Store at -80&deg;C indefinitely.<br />
#* Flash freezing does not appear to be necessary<br />
# Test competence (see below)<br />
# Thawing and refreezing partially used cell aliquots dramatically reduces transformation efficiency by about 3x the first time, and about 6x total after several freeze/thaw cycles.<br />
<br />
===Measurement of competence===<br />
# Transform 50 &mu;l of cells with 1 &mu;l of standard pUC19 plasmid (Invitrogen)<br />
#* This is at 10 pg/&mu;l or 10<sup>-5</sup> &mu;g/&mu;l<br />
#* This can be made by diluting 1 &mu;l of NEB pUC19 plasmid (1 &mu;g/&mu;l, NEB part number N3401S) into 100 ml of TE<br />
# Hold on ice 0.5 hours<br />
# Heat shock 60 sec at 42C<br />
# Add 250 &mu;l SOC<br />
# Incubate at 37 C for 1 hour in 2 ml centrifuge tubes rotated<br />
#* using 2ml centrifuge tubes for transformation and regrowth works well because the small volumes flow well when rotated, increasing aeration.<br />
#* For our plasmids (pSB1AC3, pSB1AT3) which are chloramphenicol and tetracycline resistant, we find growing for 2 hours yields many more colonies<br />
#* Ampicillin and kanamycin appear to do fine with 1 hour growth<br />
# Plate 20 &mu;l on AMP plates using sterile 3.5 mm glass beads<br />
#* Good cells should yield around 100 - 400 colonies<br />
#* Transformation efficiency is (dilution factor=15) x colony count x 10<sup>5</sup>/µgDNA<br />
#*We expect that the transformation efficiency should be between 5x10<sup>8</sup> and 5x10<sup>9</sup> cfu/µgDNA<br />
<br />
==References==<br />
<Biblio><br />
# Hanahan91 pmid=1943786<br />
# Reusch86 pmid=3536850<br />
# Addison04 pmid=15470891<br />
# Bloom04 US Patent 6,709,852<br />
# Bloom05 US Patent 6,855,494<br />
# Jesse05 US Patent 6,960,464<br />
</Biblio><br />
<br />
<center>'''[[Team:Cambridge/Protocols|Back to Protocols]]'''</center><br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Protocols/PCRcolonyTeam:Cambridge/Protocols/PCRcolony2012-08-23T11:09:04Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
<br />
==Colony PCR:==<br />
<br />
'''[[Team:Cambridge/RiskAssessments/ColonyPCR|Risk Assessment]]'''<br />
<br />
<br />
Used to amplify DNA directly from cell culture, the reaction is the same as for normal PCR but with modified reaction composition and cycle settings, here shown for a 50 µl reaction using Taq polymerase.<br />
<br />
{| class="wikitable" style="text-align: center;"<br />
||Reagent||Volume (µl)||Final Concentration<br />
|-<br />
||Water||35.7|| <br />
|-<br />
||10 mM dNTPs||1||200 µM<br />
|-<br />
||10 x NH<sub>4</sub> buffer||5||1x<br />
|-<br />
||Forward Primer||2.5||0.5 µM<br />
|-<br />
||Reverse Primer||2.5||0.5 µM<br />
|-<br />
||Template Cells||1.3 (from liquid culture or picked colony)|| <br />
|-<br />
||Taq polymerase 5u/µl||1||0.1 u/ µl<br />
|}<br />
<br />
Please refer to the [[Team:Cambridge/Protocols/PCRProtocol|standard PCR protocol]] for the remainder of this protocol.<br />
<br />
<!--<br />
<br />
PCR machine settings:<br />
<br />
{|class="wikitable" style="text-align: center; color: purple;"<br />
|colspan="2"| ||Temperature (oc)||Time (s)<br />
|-<br />
|colspan="2"|Step 1 (cell breakage)||95||360<br />
|-<br />
|rowspan="3"|Step 2 (Cycle 30x)||Denaturing||98||10<br />
|-<br />
||Annealing||60||30<br />
|-<br />
||Elongation||72||120<br />
|-<br />
|colspan="2"|Step 3 (final extension)||72||300<br />
|}<br />
<br />
--><br />
<br />
'''Notes on colony PCR'''<br />
<br />
*This technique should only really be used for crude PCR assays, such as diagnostic PCR. If high quality DNA is desired, [[Team:Cambridge/Protocols/MiniPrep|Miniprep]] followed by [[Team:Cambridge/Protocols/PCRProtocol|standard PCR]] should be used.<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<center>'''[[Team:Cambridge/Protocols|Back to Protocols]]'''</center><br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Protocols/PCRcolonyTeam:Cambridge/Protocols/PCRcolony2012-08-23T11:07:30Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_DIARY}}<br />
<br />
==Colony PCR:==<br />
<br />
Used to amplify DNA directly from cell culture, the reaction is the same as for normal PCR but with modified reaction composition and cycle settings, here shown for a 50 µl reaction using Taq polymerase.<br />
<br />
{| class="wikitable" style="text-align: center;"<br />
||Reagent||Volume (µl)||Final Concentration<br />
|-<br />
||Water||35.7|| <br />
|-<br />
||10 mM dNTPs||1||200 µM<br />
|-<br />
||10 x NH<sub>4</sub> buffer||5||1x<br />
|-<br />
||Forward Primer||2.5||0.5 µM<br />
|-<br />
||Reverse Primer||2.5||0.5 µM<br />
|-<br />
||Template Cells||1.3 (from liquid culture or picked colony)|| <br />
|-<br />
||Taq polymerase 5u/µl||1||0.1 u/ µl<br />
|}<br />
<br />
Please refer to the [[Team:Cambridge/Protocols/PCRProtocol|standard PCR protocol]] for the remainder of this protocol.<br />
<br />
<!--<br />
<br />
PCR machine settings:<br />
<br />
{|class="wikitable" style="text-align: center; color: purple;"<br />
|colspan="2"| ||Temperature (oc)||Time (s)<br />
|-<br />
|colspan="2"|Step 1 (cell breakage)||95||360<br />
|-<br />
|rowspan="3"|Step 2 (Cycle 30x)||Denaturing||98||10<br />
|-<br />
||Annealing||60||30<br />
|-<br />
||Elongation||72||120<br />
|-<br />
|colspan="2"|Step 3 (final extension)||72||300<br />
|}<br />
<br />
--><br />
<br />
'''Notes on colony PCR'''<br />
<br />
*This technique should only really be used for crude PCR assays, such as diagnostic PCR. If high quality DNA is desired, [[Team:Cambridge/Protocols/MiniPrep|Miniprep]] followed by [[Team:Cambridge/Protocols/PCRProtocol|standard PCR]] should be used.<br />
<br />
<br />
<br />
<br />
<style="text-align: right;">'''[[Team:Cambridge/RiskAssessments/ColonyPCR|Risk Assessment]]<br />
<br />
<br />
<center>'''[[Team:Cambridge/Protocols|Back to Protocols]]'''</center><br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/OutreachTeam:Cambridge/Outreach2012-08-22T12:55:48Z<p>CharlotteBG: Created page with "{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}} {{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}"</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_OUTREACH}}<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Safety/MSDSTeam:Cambridge/Safety/MSDS2012-08-22T12:51:37Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
==Materials Safety Data Sheets==<br />
<br />
<br />
We consider it good lab practice to keep MSDSs for the reagents we use in our experiments. Below are the MSDSs (where availbale) for the reagents used in the protocols listed on this wiki.<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M7154&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsigma%2Fm7154%3Flang%3Den 2-Mercaptoethanol]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsB0518.pdf 5x Phusion HF]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A3553&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DAcrylamide%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Acrylamide]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A1296&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dagar%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Agar]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A9539&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dagarose%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Agarose]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=33582&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dammonium%2520buffer%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286 Ammonium Buffer]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A3678&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsigma%2FA3678%3Flang%3Den Ammonium Persulphate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A4418&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DAmmonium%2Bsulfate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Ammonium Sulphate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=A3256&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Darabinose%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Arabinose]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=B0126&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Fsial%2Fb0126%3Flang%3Den Bromophenol Blue]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_n3_uk5.pdf Buffer N3]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_p2_uk6.pdf Buffer P2]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_pb_uk6.pdf Buffer PB]<br />
<br />
[http://www.qiagen.com/support/msds/uk/buffer_pb_uk6.pdf Buffer QG]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=C1016&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dcalcium%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax CaCl<sub>2</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=C0378&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dchloramphenicol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Chloramphenicol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=W1754&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Ddeionized%2Bwater%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax DI water]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=DNTP100A&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DdNTP%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax dNTPs]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=E7023&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dethanol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Ethanol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G8270&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglucose%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Glucose]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G5516&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglycerol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Glycerol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=G8898&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dglycine%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Glycine]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=95304&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dhplc%2Bwater%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax HPLC Water]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=I9516&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Disopropanol%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Isopropanol]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=P3786&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Ddipotassium%2Bphosphate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax K<sub>2</sub>HPO<sub>4</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=B5264&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dkanamycin%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Kanamycin]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=P9791&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dpotassium%2Bphosphate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax KH<sub>2</sub>PO<sub>4</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=L7275&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dliquid%2Bbroth%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax LB]<br />
<br />
[http://www.qiagen.com/support/msds/uk/gelpilot_5x_loading_dye_uk4.pdf 5x Loading Dye]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M8266&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dmagnesium%2Bchloride%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax MgCl<sub>2</sub>]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=M7506&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dmagnesium%2520sulphate%26lang%3Den%26region%3DGB%26N%3D0%2B219853121%2B219853286%2B220003048%26focus%3Dproduct%26mode%3Dmatch%2Bpartialmax%26cm_re%3DDid%2520You%2520Mean-_-magnesium%2520sulphate-_-mangesium%2520sulphate Magnesium Sulphate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=146072&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DProduct%2520Name%26term%3DAcrylamide%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D220003048%2B219853121%2B219853286%26mode%3Dmode%2520matchpartialmax Methylenebis(acrylamide)]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsM0530.pdf Phusion DNA polymerase]<br />
<br />
[http://www.qiagen.com/support/msds/uk/rnase_a_solution_uk5.pdf RNase A solution]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=L3771&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DSDS%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax SDS]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=201154&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3D201154%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Sodium Fluoride]<br />
<br />
[https://tools.invitrogen.com/content/sfs/msds/2012/S33102_MTR-EULT_BE.pdf SYBR safe]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsM0363.pdf T5 exonuclease]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T6025&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DTAE%2Bbuffer%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax TAE Buffer]<br />
<br />
[http://www.neb.com/nebecomm/MSDSFiles/msdsM0208.pdf Taq DNA Ligase]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=D4545&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dtaq%2Bpolymerase%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Taq DNA Polymerase]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T9281&brand=SIGMA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DTetramethylethylenediamine%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax TEMED]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=93349&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fproduct%2Ffluka%2F93349%3Flang%3Den Tris Base]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=S1804&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dtrisodium%2Bcitrate%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Trisodium Citrate]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=T0254&brand=SIAL&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3DTryptophan%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Tryptophan]<br />
<br />
[http://www.sigmaaldrich.com/MSDS/MSDS/DisplayMSDSPage.do?country=GB&language=en&productNumber=92144&brand=FLUKA&PageToGoToURL=http%3A%2F%2Fwww.sigmaaldrich.com%2Fcatalog%2Fsearch%3Finterface%3DAll%26term%3Dyeast%2Bextract%26lang%3Den%26region%3DGB%26focus%3Dproduct%26N%3D0%2B220003048%2B219853121%2B219853286%26mode%3Dmatch%2520partialmax Yeast extract]<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Safety/RiskAssessmentsTeam:Cambridge/Safety/RiskAssessments2012-08-20T19:49:29Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
=Risk Assessments=<br />
<br />
<br />
Here you can find guidelines for the most common risks assosiated with the protocols used in the course of our experiments and the specific risk assessments for each of the protocols listed on the wiki.<br />
<br />
<br />
===Risk Assessments===<br />
<br />
[[Team:Cambridge/RiskAssessments/ColonyPCR|Colony PCR]]<br />
<br />
[[Team:Cambridge/RiskAssessments/ChemicallyCompetentCellGeneration|Chemically competent cell - generation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/electrocompetentcellgeneration|Electrocompetent cell - generation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Electroporation|Electroporation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Gelelectrophoresis|Gel electrophoresis]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Gelextractionofdna|Gel extraction of DNA]]<br />
<br />
[[Team:Cambridge/RiskAssessments/GibsonAssembly|Gibson Assembly]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Glycerolstocks|Glycerol Stocks]]<br />
<br />
[[Team:Cambridge/RiskAssessments/LBplates|LB agar plates - preparation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Miniprep|Miniprep - DNA extraction]]<br />
<br />
[[Team:Cambridge/RiskAssessments/PCR|PCR using high temperature DNA polymerase]]<br />
<br />
[[Team:Cambridge/RiskAssessments/SDSpage|SDS PAGE protein analysis]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Restrictionenzymedigest|Restriction Enzyme Digest]]<br />
<br />
[[Team:Cambridge/RiskAssessments/TransformationofBsubtilis|Transformation of ''Bacillus subtilis'']]<br />
<br />
[[Team:Cambridge/RiskAssessments/TransformationofEcoli|Transformation of ''Escherichia coli'']]<br />
<br />
[[Team:Cambridge/RiskAssessments/NaF|Use of Sodium Fluoride for construct testing]]<br />
<br />
===General Risks===<br />
<br />
It is expected that good laboratory practice will be observed and that the correct PPE (personal protective equipment) will be worn at all times. Further precautions must be taken however in light of some hazards.<br />
<br />
'''Bacteria'''- Depending on the bacteria used in your experiments, the danger associated with exposure will vary. Our laboratory is only authorised to use Biosafety level 1 (non-pathogenic) bacteria and so in our experiments the risk to scientists is minimal. It is however the policy of the department to treat all bacteria as pathogens. This will be increasingly important if pathogenic strains of bacteria are used.<br />
<br />
:::'''Infection''' - the risk of infection in our experiment was not of great concern as non-pathogenic strains were used. Gloves and lab coats were still always worn when working with bacteria (this was also to help prevent contamination of samples). Where there is a greater risk masks should also be work to prevent access via the mouth or airways. Despite wearing gloves while working with bacteria, scientists must still wash their hands before leaving the lab to eliminate the chance of contaminating food. <br />
<br />
:::'''Disposal''' - Unused bacteria and any material that has come into contact with the bacteria (including gloves)should be disposed of in the biological waste vessels in the laboratory. When full, these materials are then autoclaved and disposed of in accordance with normal departmental procedures.<br />
<br />
'''Cold''' - The extreme cold used to store the competent cells until use is capable of causing freeze burns. If prolonged exposure to these temperatures is required the wearing of heat proof gloves is recommended.<br />
<br />
'''Gel preparation''' - the TAE buffer and agarose are not inherently dangerous but to be effectively mixed together they need to be heated, usually in a microwave. To fully dissolve the agarose, the mixture must be heated to a temperature too hot to touch. The container must therefore be handled with a heat proof glove. <br />
<br />
There is also a danger that the mixture could superheat and this is extremely dangerous. A mixture that does not appear to be boiling when taken out of the microwave can boil violently when swirled. The mixture should therefore be heated gradually, in small bursts and then swirled at arms length to heat to the minimum possible temperature to completely dissolve. The lid of the container must be on, but not screwed tight as tight as possible to allow for gas expansion as the mixture heats up.<br />
<br />
'''Glass''' - Glass is somewhat ubiquitous in laboratories and though it is expected that scientists will work safely, accidents still happen. All glassware in use should be labelled so that in the case of a breakage the carried substance can be identified. Broken glass is obviously a hazard through the liklihood of injury and it should be cleared away as soon as possible. The contents of the vessel will often be of greater concern however. Post breakage procedures will vary in accordance with what was in the container before the break and scientists should familiarise themselves with the disposal measures of their department. <br />
<br />
'''Hazardous Chemicals''' - some of the chemicals used in these protocols carry specific health risks. These will be listed on an individual basis in the relevant risk assessments below but in all cases it is worth noting that additional PPE may have to be worn and that normal waste disposal procedures may not be appropriate.<br />
<br />
'''Heat'''- While most PCR is now carried out using specialised machines, it is possible to perform PCR by hand using heat blocks and waterbaths. The high temperatures used in this technique are sufficient to burn the skin so care must be taken when using machinery and transferring samples. The use of tongs or heat proof gloves is recommended in this case. <br />
<br />
'''Voltage''' - The Genepulse device administers a very high voltage and therefore the electroporation cuvette should only be used with the device in the manner described by the manufacturer. This will normally involve the use of a plastic loading device which connects the cuvette to the electrodes prior to electroporation. If in doubt, seek advice before connecting the cuvette to the device. <br />
<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/Safety/RiskAssessmentsTeam:Cambridge/Safety/RiskAssessments2012-08-20T19:46:02Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
=Risk Assessments=<br />
<br />
<br />
Here you can find guidelines for the most common risks assosiated with the protocols used in the course of our experiments and the specific risk assessments for each of the protocols listed on the wiki.<br />
<br />
===General Risks===<br />
<br />
It is expected that good laboratory practice will be observed and that the correct PPE (personal protective equipment) will be worn at all times. Further precautions must be taken however in light of some hazards.<br />
<br />
'''Bacteria'''- Depending on the bacteria used in your experiments, the danger associated with exposure will vary. Our laboratory is only authorised to use Biosafety level 1 (non-pathogenic) bacteria and so in our experiments the risk to scientists is minimal. It is however the policy of the department to treat all bacteria as pathogens. This will be increasingly important if pathogenic strains of bacteria are used.<br />
<br />
:::'''Infection''' - the risk of infection in our experiment was not of great concern as non-pathogenic strains were used. Gloves and lab coats were still always worn when working with bacteria (this was also to help prevent contamination of samples). Where there is a greater risk masks should also be work to prevent access via the mouth or airways. Despite wearing gloves while working with bacteria, scientists must still wash their hands before leaving the lab to eliminate the chance of contaminating food. <br />
<br />
:::'''Disposal''' - Unused bacteria and any material that has come into contact with the bacteria (including gloves)should be disposed of in the biological waste vessels in the laboratory. When full, these materials are then autoclaved and disposed of in accordance with normal departmental procedures.<br />
<br />
'''Cold''' - The extreme cold used to store the competent cells until use is capable of causing freeze burns. If prolonged exposure to these temperatures is required the wearing of heat proof gloves is recommended.<br />
<br />
'''Gel preparation''' - the TAE buffer and agarose are not inherently dangerous but to be effectively mixed together they need to be heated, usually in a microwave. To fully dissolve the agarose, the mixture must be heated to a temperature too hot to touch. The container must therefore be handled with a heat proof glove. <br />
<br />
There is also a danger that the mixture could superheat and this is extremely dangerous. A mixture that does not appear to be boiling when taken out of the microwave can boil violently when swirled. The mixture should therefore be heated gradually, in small bursts and then swirled at arms length to heat to the minimum possible temperature to completely dissolve. The lid of the container must be on, but not screwed tight as tight as possible to allow for gas expansion as the mixture heats up.<br />
<br />
'''Glass''' - Glass is somewhat ubiquitous in laboratories and though it is expected that scientists will work safely, accidents still happen. All glassware in use should be labelled so that in the case of a breakage the carried substance can be identified. Broken glass is obviously a hazard through the liklihood of injury and it should be cleared away as soon as possible. The contents of the vessel will often be of greater concern however. Post breakage procedures will vary in accordance with what was in the container before the break and scientists should familiarise themselves with the disposal measures of their department. <br />
<br />
'''Hazardous Chemicals''' - some of the chemicals used in these protocols carry specific health risks. These will be listed on an individual basis in the relevant risk assessments below but in all cases it is worth noting that additional PPE may have to be worn and that normal waste disposal procedures may not be appropriate.<br />
<br />
'''Heat'''- While most PCR is now carried out using specialised machines, it is possible to perform PCR by hand using heat blocks and waterbaths. The high temperatures used in this technique are sufficient to burn the skin so care must be taken when using machinery and transferring samples. The use of tongs or heat proof gloves is recommended in this case. <br />
<br />
'''Voltage''' - The Genepulse device administers a very high voltage and therefore the electroporation cuvette should only be used with the device in the manner described by the manufacturer. This will normally involve the use of a plastic loading device which connects the cuvette to the electrodes prior to electroporation. If in doubt, seek advice before connecting the cuvette to the device. <br />
<br />
<br />
===Risk Assessments===<br />
<br />
[[Team:Cambridge/RiskAssessments/ColonyPCR|Colony PCR]]<br />
<br />
[[Team:Cambridge/RiskAssessments/ChemicallyCompetentCellGeneration|Chemically competent cell - generation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/electrocompetentcellgeneration|Electrocompetent cell - generation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Electroporation|Electroporation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Gelelectrophoresis|Gel electrophoresis]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Gelextractionofdna|Gel extraction of DNA]]<br />
<br />
[[Team:Cambridge/RiskAssessments/GibsonAssembly|Gibson Assembly]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Glycerolstocks|Glycerol Stocks]]<br />
<br />
[[Team:Cambridge/RiskAssessments/LBplates|LB agar plates - preparation]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Miniprep|Miniprep - DNA extraction]]<br />
<br />
[[Team:Cambridge/RiskAssessments/PCR|PCR using high temperature DNA polymerase]]<br />
<br />
[[Team:Cambridge/RiskAssessments/SDSpage|SDS PAGE protein analysis]]<br />
<br />
[[Team:Cambridge/RiskAssessments/Restrictionenzymedigest|Restriction Enzyme Digest]]<br />
<br />
[[Team:Cambridge/RiskAssessments/TransformationofBsubtilis|Transformation of ''Bacillus subtilis'']]<br />
<br />
[[Team:Cambridge/RiskAssessments/TransformationofEcoli|Transformation of ''Escherichia coli'']]<br />
<br />
[[Team:Cambridge/RiskAssessments/NaF|Use of Sodium Fluoride for construct testing]]<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/SafetyTeam:Cambridge/Safety2012-08-14T13:26:06Z<p>CharlotteBG: </p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
=Safety=<br />
<br />
<br />
<br />
<br />
'''N.B.''' This page is a work in process and will be added to and improved over the course of the project.<br />
<br />
===iGEM safety questions===<br />
<br />
'''1. Would any of your project ideas raise safety issues in terms of:'''<br />
*researcher safety,<br />
<br />
Our laboratory is only authorised to use Biosafety level 1 (non-pathogenic) bacteria and we therefore consider our project to be '''harmless to researchers''' as none of our experiments have any known action in increasing the pathogenicity of the bacteria we use or the host range. It is departmental policy however to treat all bacteria as potential pathogens and to take suitable safety precautions. We understand that it is essential to wear suitable PPE (personal protective equipment) at all times, in our experiments this usually means labcoats and gloves. All laboratory equipment and bacterial cultures are to be decontaminated by autoclaving. A copy of the departmental regulations for waste disposal is available at the bottom of this page.<br />
<br />
Several techniques used in the course of this project call for the use of potentially hazardous substances which range from causing minor skin irritations to being toxic if ingested. For this reason we have created risk assessment pages for each of the protocols used in the course of our research. These are not intended to be used instead of departmental safety procedures, but outline the major concerns for each protocol for reference by future teams. MSDS sheets for reagents used in the course of our project are also available on this wiki.<br />
<br />
Sodium Fluoride is hazardous and was necessary for testing our fluoride riboswitch. Full departmental risk assessments were completed before working with this substance and a brief risk assessment outlining the main dangers can be found on this wiki ([[Team:Cambridge/RiskAssessments/NaF|here]]) as well as a MSDS.<br />
<br />
We anticipate that elements of our project could be used for a wide variety of purposes and these may include the use of potentially harmful substances. Any future teams would need to consider the safety implications of their project on a case by case basis, though our project should not raise any safety concerns. <br />
<br />
*public safety, <br />
<br />
We understand public apprehension surrounding the use of genetically modified bacteria, in the unlikely event that members of the public came into contact with the bacteria used in our project we anticipate that there would be '''no threat to public safety''' as we are using non-pathogenic strains. <br />
<br />
*environmental safety?<br />
<br />
While we appreciate that pathogenic strains of the species we are using exist, we are using disabled, non-pathogenic strains that should otherwise interact in an identical manner with the environment. We therefore anticipate that any released bacteria would be '''disadvantaged''' and are not expected to survive outside of the favorable conditions engineered in the lab.<br />
<br />
'''2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,'''<br />
*did you document these issues in the Registery?<br />
*how did you manage to handle the safety issue?<br />
*how could other teams learn from your experience<br />
<br />
Our biobricks are designed to create a biological system whereby a bacterial cell takes in metal ions and this induces a light output. None of our biobricks increase either the pathogenicity of the bacteria used or the range of usable hosts. <br />
<br />
'''Our biobricks do not raise any safety issues.'''<br />
<br />
'''3. Is there a local biosafety group, committee or review board at your institution?'''<br />
*If yes, what does your local biosafety group think about your project?<br />
<br />
Departmental Codes of Practice for GM organisms were also consulted before we began our project. We have thus been cleared to work with bacteria that have been classified as being "unlikely to cause human disease". <br />
<br />
Our project and protocols have been reviewed and accepted by our advisers and the departmental safety officer as suitable. <br />
<br />
As we are a UK team there are also national biosafety regulations ([http://www.hse.gov.uk/biosafety/gmo/law.htm here]) that we were made aware of before beginning our project. We have complied with all of these guidelines, and hence have worked well within the law. <br />
<br />
*If no, which specific biosafety rules or guidelines do you have to consider in your country<br />
<br />
'''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 />
Biosafety was a major consideration when planning our project and many (we feel) quite brilliant project ideas were discarded because they posed significant safety risks or the procedures it would be necessary to implement to work safely were unfeasible within the time scale of the project. We hope that future teams will make biosafety a major consideration when planning their projects.<br />
<br />
===Additional safety information===<br />
*'''[[Team:Cambridge/Safety/RiskAssessments|Risk Assessments]]''' Risk assessments for any experiments we do and safety information for carrying out any of the protocols listed on this wiki.<br />
<br />
*'''[[Team:Cambridge/Safety/MSDS|MSDS Sheets]]''' Materials Safety Data Sheets for the reagents used in the course of our project.<br />
<br />
*'''[[Team:Cambridge/Protocols|Protocols]]''' Protocols used in the course of our project.<br />
<br />
*'''Waste procedure summary''' A copy of several waste safety posters around the department:<br />
[[File:cam_waste_chart.jpg|centre|720px]]<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/SafetyTeam:Cambridge/Safety2012-08-14T13:25:15Z<p>CharlotteBG: /* iGEM safety questions */</p>
<hr />
<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
<br />
=Safety=<br />
<br />
<br />
<br />
<br />
'''N.B.''' This page is a work in process and will be added to and improved over the course of the project.<br />
<br />
===iGEM safety questions===<br />
<br />
'''1. Would any of your project ideas raise safety issues in terms of:'''<br />
*researcher safety,<br />
<br />
Our laboratory is only authorised to use Biosafety level 1 (non-pathogenic) bacteria and we therefore consider our project to be '''harmless to researchers''' as none of our experiments have any known action in increasing the pathogenicity of the bacteria we use or the host range. It is departmental policy however to treat all bacteria as potential pathogens and to take suitable safety precautions. We understand that it is essential to wear suitable PPE (personal protective equipment) at all times, in our experiments this usually means labcoats and gloves. All laboratory equipment and bacterial cultures are to be decontaminated by autoclaving. A copy of the departmental regulations for waste disposal is available at the bottom of this page.<br />
<br />
Several techniques used in the course of this project call for the use of potentially hazardous substances which range from causing minor skin irritations to being toxic if ingested. For this reason we have created risk assessment pages for each of the protocols used in the course of our research. These are not intended to be used instead of departmental safety procedures, but outline the major concerns for each protocol for reference by future teams. MSDS sheets for reagents used in the course of our project are also available on this wiki.<br />
<br />
Sodium Fluoride is hazardous and was necessary for testing our fluoride riboswitch. Full departmental risk assessments were completed before working with this substance and a brief risk assessment outlining the main dangers can be found on this wiki ([[Team:Cambridge/RiskAssessments/NaF|here]]) as well as a MSDS.<br />
<br />
We anticipate that elements of our project could be used for a wide variety of purposes and these may include the use of potentially harmful substances. Any future teams would need to consider the safety implications of their project on a case by case basis, though our project should not raise any safety concerns. <br />
<br />
*public safety, <br />
<br />
We understand public apprehension surrounding the use of genetically modified bacteria, in the unlikely event that members of the public came into contact with the bacteria used in our project we anticipate that there would be '''no threat to public safety''' as we are using non-pathogenic strains. <br />
<br />
*environmental safety?<br />
<br />
While we appreciate that pathogenic strains of the species we are using exist, we are using disabled, non-pathogenic strains that should otherwise interact in an identical manner with the environment. We therefore anticipate that any released bacteria would be '''disadvantaged''' and are not expected to survive outside of the favorable conditions engineered in the lab.<br />
<br />
'''2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,'''<br />
*did you document these issues in the Registery?<br />
*how did you manage to handle the safety issue?<br />
*how could other teams learn from your experience<br />
<br />
Our biobricks are designed to create a biological system whereby a bacterial cell takes in metal ions and this induces a light output. None of our biobricks increase either the pathogenicity of the bacteria used or the range of usable hosts. <br />
<br />
'''Our biobricks do not raise any safety issues.'''<br />
<br />
'''3. Is there a local biosafety group, committee or review board at your institution?'''<br />
*If yes, what does your local biosafety group think about your project?<br />
<br />
Departmental Codes of Practice for GM organisms were also consulted before we began our project. We have thus been cleared to work with bacteria that have been classified as being "unlikely to cause human disease". <br />
<br />
Our project and protocols have been reviewed and accepted by our advisers and the departmental safety officer as suitable. <br />
<br />
As we are a UK team there are also national biosafety regulations ([http://www.hse.gov.uk/biosafety/gmo/law.htm here]) that we were made aware of before beginning our project. We have complied with all of these guidelines, and hence have worked well within the law. <br />
<br />
*If no, which specific biosafety rules or guidelines do you have to consider in your country<br />
<br />
'''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 />
Biosafety was a major consideration when planning our project and many (we feel) quite brilliant project ideas were discarded because they posed significant safety risks or the procedures it would be necessary to implement to work safely were unfeasible within the time scale of the project.<br />
<br />
===Additional safety information===<br />
*'''[[Team:Cambridge/Safety/RiskAssessments|Risk Assessments]]''' Risk assessments for any experiments we do and safety information for carrying out any of the protocols listed on this wiki.<br />
<br />
*'''[[Team:Cambridge/Safety/MSDS|MSDS Sheets]]''' Materials Safety Data Sheets for the reagents used in the course of our project.<br />
<br />
*'''[[Team:Cambridge/Protocols|Protocols]]''' Protocols used in the course of our project.<br />
<br />
*'''Waste procedure summary''' A copy of several waste safety posters around the department:<br />
[[File:cam_waste_chart.jpg|centre|720px]]<br />
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{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBGhttp://2012.igem.org/Team:Cambridge/SafetyTeam:Cambridge/Safety2012-08-14T13:24:48Z<p>CharlotteBG: </p>
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<div>{{Template:Team:Cambridge/CAM_2012_TEMPLATE_HEAD_SAFETY}}<br />
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=Safety=<br />
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'''N.B.''' This page is a work in process and will be added to and improved over the course of the project.<br />
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===iGEM safety questions===<br />
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'''1. Would any of your project ideas raise safety issues in terms of:'''<br />
*researcher safety,<br />
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Our laboratory is only authorised to use Biosafety level 1 (non-pathogenic) bacteria and we therefore consider our project to be '''harmless to researchers''' as none of our experiments have any known action in increasing the pathogenicity of the bacteria we use or the host range. It is departmental policy however to treat all bacteria as potential pathogens and to take suitable safety precautions. We understand that it is essential to wear suitable PPE (personal protective equipment) at all times, in our experiments this usually means labcoats and gloves. All laboratory equipment and bacterial cultures are to be decontaminated by autoclaving. A copy of the departmental regulations for waste disposal is available at the bottom of this page.<br />
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Several techniques used in the course of this project call for the use of potentially hazardous substances which range from causing minor skin irritations to being toxic if ingested. For this reason we have created risk assessment pages for each of the protocols used in the course of our research. These are not intended to be used instead of departmental safety procedures, but outline the major concerns for each protocol for reference by future teams. MSDS sheets for reagents used in the course of our project are also available on this wiki.<br />
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Sodium Fluoride is hazardous and was necessary for testing our fluoride riboswitch. Full departmental risk assessments were completed before working with this substance and a brief risk assessment outlining the main dangers can be found on this wiki ([[Team:Cambridge/RiskAssessments/NaF|here]]) as well as a MSDS.<br />
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We anticipate that elements of our project could be used for a wide variety of purposes and these may include the use of potentially harmful substances. Any future teams would need to consider the safety implications of their project on a case by case basis, though our project should not raise any safety concerns. <br />
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*public safety, <br />
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We understand public apprehension surrounding the use of genetically modified bacteria, in the unlikely event that members of the public came into contact with the bacteria used in our project we anticipate that there would be '''no threat to public safety''' as we are using non-pathogenic strains. <br />
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*environmental safety?<br />
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While we appreciate that pathogenic strains of the species we are using exist, we are using disabled, non-pathogenic strains that should otherwise interact in an identical manner with the environment. We therefore anticipate that any released bacteria would be '''disadvantaged''' and are not expected to survive outside of the favorable conditions engineered in the lab.<br />
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'''2. Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,'''<br />
*did you document these issues in the Registery?<br />
*how did you manage to handle the safety issue?<br />
*how could other teams learn from your experience<br />
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Our biobricks are designed to create a biological system whereby a bacterial cell takes in metal ions and this induces a light output. None of our biobricks increase either the pathogenicity of the bacteria used or the range of usable hosts. <br />
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'''Our biobricks do not raise any safety issues.'''<br />
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'''3. Is there a local biosafety group, committee or review board at your institution?'''<br />
*If yes, what does your local biosafety group think about your project?<br />
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Departmental Codes of Practice for GM organisms were also consulted before we began our project. We have thus been cleared to work with bacteria that have been classified as being "unlikely to cause human disease". <br />
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Our project and protocols have been reviewed and accepted by our advisers and the departmental safety officer as suitable. <br />
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As we are a UK team there are also national biosafety regulations ([[http://www.hse.gov.uk/biosafety/gmo/law.htm here]]) that we were made aware of before beginning our project. We have complied with all of these guidelines, and hence have worked well within the law. <br />
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*If no, which specific biosafety rules or guidelines do you have to consider in your country<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 />
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Biosafety was a major consideration when planning our project and many (we feel) quite brilliant project ideas were discarded because they posed significant safety risks or the procedures it would be necessary to implement to work safely were unfeasible within the time scale of the project.<br />
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===Additional safety information===<br />
*'''[[Team:Cambridge/Safety/RiskAssessments|Risk Assessments]]''' Risk assessments for any experiments we do and safety information for carrying out any of the protocols listed on this wiki.<br />
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*'''[[Team:Cambridge/Safety/MSDS|MSDS Sheets]]''' Materials Safety Data Sheets for the reagents used in the course of our project.<br />
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*'''[[Team:Cambridge/Protocols|Protocols]]''' Protocols used in the course of our project.<br />
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*'''Waste procedure summary''' A copy of several waste safety posters around the department:<br />
[[File:cam_waste_chart.jpg|centre|720px]]<br />
<br />
{{Template:Team:Cambridge/CAM_2012_TEMPLATE_FOOT}}</div>CharlotteBG