http://2012.igem.org/wiki/index.php?title=Special:Contributions/Napatel&feed=atom&limit=50&target=Napatel&year=&month=2012.igem.org - User contributions [en]2024-03-29T12:51:35ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Team:Arizona_State/NotebookTeam:Arizona State/Notebook2012-10-22T22:50:49Z<p>Napatel: </p>
<hr />
<div><html><br />
<!-- Made by Abhi & Jordan with help from the "https://2011.igem.org/Team:Imperial_College_London" page --><br />
<head><br />
<style type="text/css"><br />
#top-section {<br />
width: 975px;<br />
height: 0px;<br />
background-color: transparent;<br />
border: none;<br />
}<br />
#p-logo { display: none; }<br />
#search-controls { display: none; }<br />
<br />
#content {<br />
position: relative;<br />
background-image:url(http://upload.wikimedia.org/wikipedia/commons/4/4b/Section_paper_tile.png);<br />
width: 975px;<br />
margin: 0 auto;<br />
padding-top:20px;<br />
padding-left:0px;<br />
padding-right:0px;<br />
padding-bottom:0px;<br />
color: black;<br />
border: none;<br />
line-height: 1.5em;<br />
z-index: 2;<br />
}<br />
<br />
a {color:#t;}<br />
a:link {color:#93B825;}<br />
a:visited {color:#728F1D;}<br />
a:hover {color:#93B825;}<br />
a:active {color:#93B825;}<br />
a[name]:hover {text-decoration:none;} <br />
<br />
h1 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 2.2em;<br />
margin: 0 0 0 0;<br />
padding: 20px 20px 12px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h2 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.7em;<br />
margin: 0 0 0 0;<br />
padding: 18px 20px 7px 20px;<br />
border-bottom: none;<br />
} <br />
<br />
h3 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.4em;<br />
margin: 0 0 0 0;<br />
padding: 16px 20px 2px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h4 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.1em;<br />
margin: 0 0 0 0;<br />
padding: 13.5px 20px 1px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
p {<br />
font-family: helvetica,sans-serif;<br />
background: transparent;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
margin: 0 0 0 0;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
.figText {<br />
font-family: helvetica,sans-serif;<br />
font-style: italic<br />
font-weight: bold;<br />
font-size: 1em;<br />
color:maroon;<br />
line-height: 1.7em;<br />
text-align: center;<br />
margin: 0 0 0 0;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
</style><br />
</head><br />
</html><br />
__NOTOC__<br />
<!---{{:Team:Arizona_State/Template:NBCalendar}}---><br />
==June 07==<br />
===Strep===<br />
* Transformation (LSE)<br />
** Transformed DNA:<br />
*** lacZ (well 4:12G, I732019)<br />
*** p + lacO (well 1:6G, R0011)<br />
** Cells: neb10beta (donated)<br />
** Protocol from: http://www.neb.com/nebecomm/products/productc3019.asp<br />
** Controls: puc19, no DNA (8 plates)<br />
<br />
==June 08==<br />
===Strep===<br />
* Transformation results<br />
** puc19: growth<br />
[[File: ASUiGEM2012_plate06712(3).jpg|200px]]<br />
** negative control: no growth<br />
[[File: ASUiGEM2012_plate06712(1).jpg|200px]]<br />
** lacZ, lacO: possible small colonies<br />
[[File: ASUiGEM2012_plate06712(2).jpg|200px]]<br />
[[File: ASUiGEM2012_plate06712(4).jpg|200px]]<br />
* liquid culture in amp media (100 ug / ml):<br />
** no growth of lacZ, lacO<br />
** growth of puc19<br />
<br />
==June 12==<br />
===General===<br />
* DH5a Competent Cell Prep<br />
** Streak plated cells on LB no amp plate, let grow overnight<br />
<br />
==June 13==<br />
===Strep===<br />
* Transformation (LSE)<br />
** Transformed DNA:<br />
*** lacZ (well 4:12G, I732019)<br />
*** p + lacO (well 1:6G, R0011)<br />
** Cells: DH5 alpha (donated)<br />
** Protocol from: http://openwetware.org/wiki/Haynes:Assembly101 (30 minute transformation)<br />
** Controls: puc19, no DNA (8 plates)<br />
[[File:ASUiGEM2012_plates061212.jpg|200px]]<br />
===General===<br />
* DH5a Chemically Competent cell prep<br />
** Grew 2 seed colonies from streak plate in LB no amp<br />
** Grew controls to test for contamination<br />
*** Both Seed colonies grew, no contamination present<br />
<br />
==June 14==<br />
===General===<br />
* Competent cell prep<br />
** Prepared CaCl2 buffer solution and CaCl2 glycerol buffer solution<br />
** Grew seed colony in 400mL LB no amp<br />
<br />
==June 15==<br />
===General===<br />
* Competent cell prep<br />
** Centrifuged falcon test tubes containing liquid colonies<br />
** Resuspended in CaCl2 buffer solution and incubated for 15 mins<br />
** Centrifuged and resuspended in CaCl2 glycerol buffer solution<br />
** Chilled overnight<br />
<br />
==June 16==<br />
===General===<br />
* Competent cell prep<br />
** Aliquotted 200uL into test tubes<br />
** Stored in -80C<br />
<br />
==June 17==<br />
===General===<br />
* Streak plated prepared competent cells on LB no amp plate<br />
** Colonies observed<br />
** No picture<br />
<br />
==June 18==<br />
===Strep===<br />
* Digest: Lac Z (X and P) and p + lacO (S and P)<br />
* Protocol: http://openwetware.org/wiki/Haynes:Assembly101<br />
* Gel extraction - Sigma Aldrich Gel Kit<br />
[[File:ASUiGEM2012_digest061812.jpg|200px]]<br />
<br />
==June 19==<br />
===Strep===<br />
* Ligation<br />
** P+lacO+Lac Z (samples still need to be tested)<br />
** Control (No DNA)<br />
===General===<br />
* Transformation (LSE)<br />
** Transformed DNA:<br />
*** T7 promoter BBa_I712074<br />
*** Constitutive promoter BBa_J23102<br />
** Cells: DH5 alpha (donated)<br />
** Protocol from: http://tools.invitrogen.com/content/sfs/manuals/subcloningefficiencydh5alpha_man.pdf (30 minute transformation)<br />
** Controls: puc19, no DNA<br />
** Plated 2 copies of each (100 ul, 250 ul) on LB amp plates.<br />
*Made 50 LB Amp plates.<br />
<br />
==June 20==<br />
===Strep===<br />
* PCR<br />
** Lac Z<br />
*** Primers: Standard BBa F and R primers (http://partsregistry.org/Primers/Catalog)<br />
*** 1000 fold dilution DNA used<br />
*** Protocol <br />
**** PCR water - 74.4 uL<br />
**** 1000 fold dilution DNA - 6 uL<br />
**** dNTP (10mM) - 2.4 uL<br />
**** F and R primers (10 uM) - 6 uL each<br />
**** 5x HF buffer - 24 uL<br />
**** Phusion DNA polymerase - 1.2 uL<br />
* Digest<br />
** P+Lac O<br />
*** S and P<br />
*** Treated with Antartic Phosphatase (avoids religation) <br />
* Plated negative control on LB Amp plate<br />
* Liquid cultures of T7 promoter and constitutive promoter<br />
===General===<br />
* Transformation (LSE)<br />
** Transformed DNA:<br />
*** RBS (well 1:1H BBa_B0030)<br />
*** TetR GFP (well 2:8A Part:BBa_I13522)<br />
** Cells: DH5 alpha (donated)<br />
** Protocol from: http://tools.invitrogen.com/content/sfs/manuals/subcloningefficiencydh5alpha_man.pdf (30 minute transformation)<br />
** Controls: puc19, no DNA<br />
<br />
==June 21==<br />
===General===<br />
* Made Liquid Cultures of E.coli transformed with RBS B0030<br />
* Made Liquid Cultures of E.coli transformed with TetR GFP<br />
* miniprepped and nanodropped T7 promoter BBa_I712074 and Constitutive promoter BBa_J23102 liquid cultures<br />
* liquid cultures:<br />
** RBS1<br />
** RBS2 (duplicate_<br />
** GFP1<br />
** puc19<br />
** negative controls<br />
** 5 ml LB amp<br />
** overnight cultures<br />
* replated GFP1 & 2 (duplicates)<br />
* Nanodropped plasmid DNA samples<br />
** Constitutive promoter 1: 2.554 ng/uL<br />
** Constitutive promoter 2: 2.345 ng/uL<br />
** T7 promoter 1: 3.369 ng/uL<br />
** T7 promoter 2: 3.049 ng/uL<br />
<br />
==June 22==<br />
===Strep===<br />
* PCR clean up (Sigma Aldrich Kit) Lac Z samples<br />
* Digest Lac Z with X and P<br />
* Nano Drop the PCR clean samples:<br />
** Lac O: 2.554 ug/uL<br />
** Lac Z: 3.369 ug/uL<br />
* Gel<br />
** [[File:ASUiGEM2012_gel062212(1).jpg|200px]]<br />
* PCR<br />
** Lac Z (25ul rxn)<br />
*** Primers: Standard BBa F and R primers (http://partsregistry.org/Primers/Catalog) <br />
*** Varied Concentration DNA samples <br />
*** Syzygy Mean Green MM<br />
*** Lac Z samples - 10 fold D, 100 fold D, 1000 fold D and Regular DNA.<br />
[[File:ASUiGEM2012_gel062212(2).jpg|200px]]<br />
* PCR cleaned samples<br />
===General===<br />
* Miniprepped liquid cultures: RBS (well 1:1H BBa_B0030) and TetR GFP (well 2:8A Part:BBa_I13522)<br />
* Picked colonies:<br />
** 1 colony from double terminator (dt1) plate<br />
** 1 colony from t7 polymerase (pol1) plate<br />
** 1 colony from puc19 plate (positive control)<br />
** 1 colony from dh5a plate (negative control)<br />
* started liquid cultures of each colony (5 mL LB amp each)<br />
<br />
==June 26==<br />
===General===<br />
* Transformation:<br />
** Transformed DNA:<br />
*** double terminator (B0017, 2:6K)<br />
*** T7 RNA polymerase (I715038, 2:15C)<br />
*** puc19, negative control<br />
** Protocol from: http://tools.invitrogen.com/content/sfs/manuals/subcloningefficiencydh5alpha_man.pdf (30 minute transformation)<br />
** Cells: dh5a<br />
<br />
==June 27==<br />
===General===<br />
* 6-26 transformation results:<br />
** Controls correct<br />
** 2x terminator: ~19 colonies<br />
** RNA pol: 1 colony<br />
* Liquid cultures including controls<br />
<br />
==June 28==<br />
===General===<br />
* Miniprepped double terminator (B0017, 2:6K) and T7 RNA polymerase (I715038, 2:15C) liquid cultures<br />
<br />
==July 2==<br />
===General===<br />
* Cleaned up liquid waste<br />
* Made SOB media<br />
===Magainin===<br />
* Finalized oligos for magainin construct<br />
<br />
==July 3==<br />
===General===<br />
* Third attempt of putting the bricks together. And samples were plated on X-gal plates to show that the construct worked.<br />
[[File:ASUiGEM2012_plates07212.jpg|200px]]<br />
* Autoclaved SOB media<br />
* Added glucose to make SOC media<br />
* Nanodropped double terminator (B0017, 2:6K) [DT1: 24.5, DT2: 29.6] and T7 RNA polymerase (I715038, 2:15C) [P1: 64.6, P2: 55.3] liquid cultures<br />
<br />
==July 12==<br />
===Magainin===<br />
* Searched for split beta gal fragment. Alpha fragment (BBa_I732006) was found on the distribution plates and transformed (NEB 10B).<br />
<br />
==July 14==<br />
===Magainin===<br />
* Designed primers to remove the stop codon on the alpha fragment. Also attained two flexible linkers from Dr. Haynes and transformed them.<br />
[[File:ASUiGEM2012_plates071412(1).jpg|200px]]<br />
[[File:ASUiGEM2012_plates071412(2).jpg|200px]]<br />
[[File:ASUiGEM2012_plates071412(3).jpg|200px]]<br />
<br />
==July 15==<br />
===Magainin===<br />
* Ran a miniprep of Bgal alpha 1&2, T7 and PSV<br />
* Procedure from GenElute HP PLasmid Miniprep Kit (Sigma-Aldrich)<br />
<br />
==July 16==<br />
===Strep===<br />
* Transformation of PLflex (part: BBa_J176040) and PLflex4 (part: BBa_J176130) linkers. <br />
[[File:ASUiGEM2012_plates071612.jpg|200px]]<br />
* Incubate at 37C for 8 hours for DH 5alpha turbo cells<br />
* Inoculated 5 mL LB/AMP media in 15 mL culture tubes and added the colony. Incubated in 37C overnight.<br />
<br />
==July 17==<br />
===Strep===<br />
* Miniprep of pLFlex DH5alpha and pLFlex 4 DH5alpha<br />
* Procedure comes from Zymo Research's Zyppy Kit. <br />
* Ran the spectrophotometer to determine the concentration for the miniprep DNA for the linker pLFlex and linker pLFlex 4<br />
* Concentrations were: <br />
** pLFlex: 73.792 ng/uL<br />
** pLFlex 4: 38.587 ng/uL<br />
* Absorbance ratios were:<br />
** pLFlex: 1.864<br />
** pLFlex 4: 1.851<br />
* Ran the miniprep for pLFlex and pLFlex 4 again.<br />
* Same procedure<br />
* Ran the spectrophotometer again<br />
* Concentrations were: <br />
** pLFlex: 48.095 ng/uL<br />
** pLFlex 4: 18.214 ng/uL<br />
* Absorbance ratios were:<br />
** pLFlex: 1.79<br />
** pLFlex 4: 1.85<br />
* Transformation was successful but 8-9 hour growth period was not sufficient for DH5 alpha.<br />
<br />
==July 23==<br />
===Strep===<br />
* Plated BBa_K283010 (Streptavidin) on LB amp plate from the agar stab provided from the iGEM head-quarters.<br />
* Incubated the dish overnight at 37 C.<br />
[[Image:ASUiGEM2012_plates072312.jpg|200px]]<br />
* Plate 1: pipet tip, colonies are in wells, neither distinct nor segregated<br />
* Plate 2: inoculating loop, numerous non-distinct colonies on the plate<br />
<br />
==July 24==<br />
===Topo===<br />
* Plasmids arrived courtesy of University of Pennsylvania School of Medicine<br />
* pET29a vectors containing coding sequence for Topoisomerase mutants CSCS and CSCS D168A described here<br />
<br />
==July 25==<br />
===Strep===<br />
* Ran a miniprep of streptavidin BBa_K283010<br />
* Protocol from Zymo Research's Zyppy Plasmid Miniprep Kit<br />
===Topo===<br />
* Tranformed CSCS topo 0 plasmid and CSCS D168A topo into DH5a Turbo cells (with neg control and Puc19 neg control)<br />
* Plated on Kanamycin plates<br />
<br />
==July 26==<br />
===Topo===<br />
* Picked colonies colonies from Topo 0 and Topo D168A and grew liquid cultures in Kan media<br />
<br />
==July 27==<br />
===Topo===<br />
* Miniprepped liquid colonies and nanodropped.<br />
* Plasmid concentrations<br />
** Topo O: 63.7 ng/uL <br />
** Topo D168A1: 125.4 ng/uL<br />
** Topo D168A2: 116.6 ng/uL<br />
<br />
==July 30==<br />
===General===<br />
* Prepared Kan Media and Kan Plates<br />
<br />
==July 31==<br />
===Topo===<br />
* PCR amplified polylinker sequence of Topo plasmid with Promega GoTaq protocol<br />
** Used pET29a upstream forward primer and T7 terminator reverse primer<br />
<br />
==August 3==<br />
===Topo===<br />
* Submitted pET29a Topoisomerase plasmid to Biodesign for sequencing<br />
* Resuspended GFPT1 and GFPT2 oligos with molecular grade (nuclease-free) H2O.<br />
** Final Concentration 100uM<br />
*** (gfpt1 top1, gfpt2 top1, gfpt1 top2, gftp2 top2, gfpt1 bot1, gfpt2 bot1, gfpt1 bot2, gfpt2 bot2)<br />
*** (3uL of each oligo + 2uL 10x annealing buffer, 6uL molecular grade H2O. 20uL Reactions)<br />
* Heated for 5 minutes at 100C. Let cool to room temperature on the heating block, stored at -20C.<br />
* Digested BBa_I13522 with XbaI and PstI.<br />
* Attempted ligating annealed oligos into a digested plasmid from Ryan (realized it was cut with E and P).<br />
<br />
==August 6==<br />
===Topo===<br />
* Annealed oligos for GFPT1 and GFPT2 (target probes)<br />
* Ligated oligos with digested GFP plasmid (BBa_I13522)<br />
* Transformed into competent DH5alpha<br />
* Added SOC and incubated at 37C for 15 minutes.<br />
* Plated on amp treated plates.<br />
<br />
==August 7==<br />
===Topo===<br />
* Only one colony on each plate (both were white)<br />
* Picked colonies and started 5mL LB amp cultures of each, stored at 37C<br />
* Stored plates in 37C<br />
<br />
==August 8==<br />
===Topo===<br />
* Picked the colonies again and started new liquid cultures (5mL LB amp).<br />
* Discarded cultures for 8/7/12<br />
<br />
==August 9==<br />
===Topo=== <br />
* Miniprepped 3mL of each 8/8/12 culture and nanodropped:<br />
** gfpt1 - 155 ng/uL<br />
** gfpt2 - 114 ng/uL<br />
* Digested gfpt1 and gfpt2 with X and P<br />
* Ran on a 1% agarose gel with the digested GFP plasmid and hyperladder V<br />
[[File:ASUiGEM2012_gel080912.jpg|200px]]<br />
* Didn't work<br />
* Made glyercol stocks with aliquot of the remaining liquid cultures<br />
<br />
==August 10==<br />
===Magainin===<br />
* PCR of Alpha-4, 1-omega, omega, and alpha fragments using corrected primers<br />
<br />
==August 13==<br />
===Magainin===<br />
* Ran gel of split beta gal fragments. Confirmed 3 out of the 4 fragments except for the alpha-4 fragment. <Br\><br />
[[File: ASUiGEM2012_gel081312.jpeg|200px]]<br />
===Topo===<br />
* Prepared sequencing samples<br />
* Sample w/ Primer: <br />
** GFPT1 w/ VF2 GFPT1 w/ VR GFPT2 w/ VF2 GFPT2 w/ VR<br />
** 200ng of DNA + 16 pmol of primer<br />
* Annealed oligos again GFPT1/2<br />
* Repeated ligation of oligos with digested GFP plasmid (BBa_I13522)<br />
* Followed Haynes assembly protocol instead of standard DH5alpha protocol. (http://openwetware.org/wiki/Haynes:Assembly101)<br />
* Transformed ligations into competent DH5alpha<br />
* Plated on amp treated plates<br />
<br />
==August 14==<br />
===Topo===<br />
* Took pictures of plates<br />
* Green-white screened plates<br />
* Picked 4 white colonies from each of gfpt1/2 plates<br />
* Made 5mL LB amp cultures of each colony<br />
* Delivered GFPT1/2 dna samples to biodesign for sequencing (samples from 8/13/12)<br />
===Magainin===<br />
* Assembled magainin insert via Overlapping oligo assembly<br />
* Digested pUC 19 plasmid with EcoRI and PstI<br />
* Transformed Magainin insert into digested pUC 19 plasmid. Failed. Probably too much X-gal on plate.<br />
Ran gel for the beta gal alpha-4 fragment. Failed. Fragment not in the correct size-band. <Br\><br />
[[File: ASUiGEM2012_gel081412.jpeg|200px]]<br />
<br />
==August 15==<br />
===Topo===<br />
*[http://129.219.2.10/home2/dnalims/fragment/32/21/pfasta/topo0_T7Term.seq Topo 0], [http://129.219.2.10/home2/dnalims/fragment/32/21/pfasta/D168Atopo1_T7Term.seq D168A Topo1], and [http://129.219.2.10/home2/dnalims/fragment/32/21/pfasta/D168Atopo2_T7Term.seq D168A Topo2] sequence results<br />
* Miniprepped 3mL of each liquid culture of GFPT1/2<br />
* Prepared glycerol stocks using 100uL of each liquid culture<br />
* Nanodropped samples:<br />
** GFPT1-1 - 172.6 ng/uL <br />
** GFPT1-2 - 203.7 ng/uL<br />
** GFPT1-3 - 197.4 ng/uL<br />
** GFPT1-4 - 178.9 ng/uL<br />
** GFPT2-1 - 107.3 ng/uL<br />
** GFPT2-2 - 131.2 ng/uL<br />
** GFPT2-3 - 145.5 ng/uL <br />
** GFPT2-4 - 172.0 ng/uL<br />
<br />
==August 16==<br />
===Magainin===<br />
* Replated magainin insert + plasmid into the grid. Failed. All blue colonies meaning that no insert.<Br\><br />
Tried gel for all gel-isolated fragments. Failed. Did not get a band in the 2000 bp region. Only got things below 200 bp.<BR\><br />
[[Image:ASUiGEM2012_gel081612.jpeg|200px]]<br />
<br />
==August 17==<br />
===Topo===<br />
* GFPT1 sequence confirmed<br />
* Prepared aliquots of GFPT2 minipreps from 8/15/12 for sequencing<br />
* Delivered GFPT2 samples to biodesign for sequencing<br />
<br />
==August 18==<br />
===Strep===<br />
* PCR’ed Streptavidin (biobrick) and omega fragment of beta (PSV plasmid) and confirmed size on a gel. <br />
Streptavidin was digested with E and S. Also, both flexible linkers attained from Dr. Haynes were digested with E and X and dephosphorlated. <br />
[[File:ASUiGEM2012_gel081812.jpg|200px]]<br />
<br />
==August 19==<br />
===Strep===<br />
* Restricted PLFlex and PLFlex 4 with ecori and xbai.<br />
* Restricted Bgala with Xbai and psti<br />
* Used Hayne's Lab Protocol<br />
* GFPT2 sequences confirmed<br />
<br />
==August 22==<br />
===Strep===<br />
* Transformed the two constructs.<br />
[[File:ASUiGEM2012_plates082212.jpg|200px]]<br />
* The two constructs were confirmed on gel and were ligated together to attain Streptavidin + pLFlex and Streptavidin+pLFlex4.<br />
[[File:ASUiGEM2012_gel082212.jpg|200px]]<br />
<br />
==August 27==<br />
===Topo===<br />
* Revived GFPT1 (from 8/9/12) and GFPT2 (2-2 from 8/15/12) cultures from glycerol scrapes<br />
* Made 4mL cultures in LB Amp<br />
<br />
==August 29==<br />
===Topo===<br />
* Discarded GFPT1/2 cultures from 8/27/12<br />
* Revived GFPT1 (from 8/9/12) and GFPT2 (2-2 from 8/15/12) cultures from glycerol scrapes<br />
* Made 4mL cultures in LB Amp<br />
* Digested GFPT1/2 with X and S<br />
* Ran a 1% agarose gel with GFPT1/2 digestions<br />
[[File:ASUiGEM2012_gel082912.jpg|200px]]<br />
* Cut out inserts and GFPT2 backbone and stored in 4C for gel extraction and tandum repeat assembly experiments<br />
<br />
==August 30==<br />
===Topo===<br />
* Prepared extra glyercol stocks of GFPT1/2 cultures from 8/29/12<br />
* Miniprepped 3mL of each culture, stored at -20C<br />
<br />
==September 2==<br />
===Strep===<br />
* Digested strep+pLFlex4(L4) with S and P and pLflex(L) with E and X and inserted alpha and omega fragments of beta gal.<br />
* Transformed these constructs<br />
[[File:ASUiGEM2012_plates09212.jpg|200px]]<br />
<br />
==September 10==<br />
===Strep===<br />
* Assembled:<br />
** Strep+L4+α which was a success<br />
** Strep+L4+ω which was a success<br />
** Strep+L which was a success<br />
*All digested samples were confirmed on a 1% agarose gel<br />
[[File:ASUiGEM2012_gel091012.jpg|200px]]<br />
<br />
==September 18==<br />
===Strep===<br />
* Assembled:<br />
** Prsf Duest+Strep+L4+α which failed<br />
** Prsf Duet+Strep+L4+ω which failed<br />
** Strep+L+α which was a success<br />
** Strep+L4+ω which was a success<br />
* All digested samples were confirmed on a 1% agarose gel<br />
** No picture of the gel.<br />
<br />
==September 19==<br />
===Strep===<br />
* Assembled<br />
** Prsf Duest+Strep+L4+α which failed<br />
** Prsf Duest+Strep+L4+ω which failed<br />
** Prsf Duest+Strep+L+α which failed<br />
** Prsf Duest+Strep+L+ω which failed<br />
* All digested samples were confirmed on a 1% agarose gel<br />
===Topo===<br />
* Set up VF2/VR endpoint PCR for double transform minipreps<br />
** 1-1, 1-1I, 1-2, 1-2I, 1-3, 1-3I, 2-1, 2-1I, 2-2, 2-2I, 2-3, 2-3I, GFPT1 (positive controls), GFPT2 (positive controls)<br />
* Annealing temp set to 55C for 25 cycles<br />
* Resuspended GFPT1 probe and GFPT2 probe oligos in molecular grade H2O (Final concentration: 100uM), stored at -20C<br />
<br />
==September 21==<br />
===Strep===<br />
* Miniprepped all the streps samples and digested them.<br />
<br />
==September 22==<br />
===Strep===<br />
* Assembles with new Prsf samples<br />
** Prsf Duest+Strep+L4+α which failed<br />
** Prsf Duest+Strep+L4+ω which failed<br />
** Prsf Duest+Strep+L+α which failed<br />
** Prsf Duest+Strep+L+ω which failed<br />
* Failed because outgrowth step want provided.<br />
* All digested samples were confirmed on a 1% agarose gel<br />
<br />
==September 25==<br />
===Topo===<br />
* Resuspended pSB1A2 FWD and pSB1A2 REV (amp resistance primers) oligos in molecular grade H2O (Final concentration: 100uM), stored at -20C<br />
* Prepared 1.6uM dilutions (500uL)<br />
* Did endpoint PCR using pSB1A2 primer pair on<br />
** Topo, Topo IPTG, Topo D168A, Topo D168A IPTG, 1-1, 1-1I, 2-1, 2-1I, GFPT1, GFPT2<br />
* Did endpoint PCR using VF2/VR primer pair on<br />
** Topo, Topo IPTG, Topo D168A, Topo D168A IPTG<br />
* Annealing temp 55C for 25 cycles, stored products at -20C<br />
* Made 3mL liquid cultures of the shipping vector (pSB1C3 with RFP insert) in DH5alpha in chloramphenicol resistant LB<br />
* Made 10mL liquid cultures of:<br />
** Topo in kanamycin<br />
** topo D168A in kanamycin<br />
** topo + GFPT1 in kanamycin + ampicillin<br />
** topo + GFPT2 in kanamycin + ampicillin<br />
* stored @ 37C<br />
<br />
==September 26==<br />
===Strep===<br />
* Assembled<br />
** Prsf Duest+Strep+L4+α which was a Success<br />
** Prsf Duest+Strep+L4+ω which was a Success<br />
** Prsf Duest+Strep+L+α which was a Success<br />
** Prsf Duest+Strep+L+ω which was a Success<br />
===Topo===<br />
* Picked two new colonies for topo + GFPT2 and grew 10mL cultures of amp+kan LB broth for each<br />
* Ran a gel with Hyperladder I, GFPT1 pSB1A2, GFPT2 pSB1A2, Topo pSB1A2, Topo D168A<br />
[[File:ASUiGEM2012_gel092612-1.jpg|200px]]<br />
* Ran a gel with PCR samples from 9/19 and 9/25 Hyperladder I, 1-1, 1-1I, 2-1, 2-1I, 2-1I(VF), 2-1(VF), 1-1I(VF), 1-1(VF), Hyperladder I<br />
[[File:ASUiGEM2012_gel092612-2.jpg|200px]]<br />
* Samples in wells 2-5 used the pSB1A2 primer pair. Samples in wells 6-9 used VF2/VR primer pair.<br />
* Revived GFPT1/2 from glycerol stocks (from 8/9 and 8/15) in 5mL LB amp each.<br />
* Nanodropped miniprepped DNA samples:<br />
** pSB1C3 I - 253.75 ng/uL<br />
** pSB1C3 II - 258.38 ng/uL<br />
** Topo - 24.84 ng/uL<br />
** Topo I - 17.33 ng/uL<br />
** Topo D168A - 7.24 ng/uL<br />
** Topo D168A I - 15.62 ng/uL<br />
** 1-1 - 16.49 ng/uL<br />
** 1-1I - 16.46 ng/uL<br />
** 2-1 - 142.05 ng/uL<br />
** 2-1I - 16.98 ng/uL<br />
* Picked new colonies from Topo, Topo D168A, Topo + G1, Topo + G2 and made 1mL colonies in their respective medias<br />
* Stored at -37C<br />
<br />
==September 27==<br />
===Strep===<br />
* Testing R0011 promoter. Digested R0011 with S and P generated the following assembly:<br />
** R0011+Strep+L4+α which failed<br />
** R0011+Strep+L4+ω which failed<br />
** R0011+Strep+L+α which failed<br />
** R0011+Strep+L+ω which was a Success<br />
===Topo===<br />
* Prepared serial dilutions of GFPT2 plasmid 1:10, 1:100, 1:1000, 1:10000<br />
* Prepared primer mixes for pSB and VF/VR primers<br />
* Prepared realtime PCR plate, ran RT-qPCR with annealing temp 57<br />
* Miniprepped GFPT1/2 cultures from 9/26<br />
* Nanodropped Miniprepped DNA:<br />
** GFPT1 - 276.12 ng/uL<br />
** GFPT2 - 219.84 ng/uL<br />
* Used 100uL of each 1mL culture from 9/26 to seed 10 mL cultures in their respective media<br />
* Added 10uL of 1M IPTG to each culture ~4 hours after seeding<br />
* Removed cells from 37C ~4 hours after IPTG inducing<br />
* Pelleted and lysed following the bugbuster protocol (http://openwetware.org/wiki/User:Behzad_Damadzadeh/Notebook/PcTF_Subcloning_in_E-coli/2012/05/22) (used lysonase for Topo and Topo D168A only)<br />
* HIS purified proteins using the Zymo HIS purification kit<br />
* Digested pSB1C3 plasmid with X and P<br />
* Sent protein samples (HIS purified samples from 9/19, 20uL) and ssDNA control (GFPT1/2 probe oligos 20uL @ 10uM) for mass spec<br />
[[File:ASUiGEM2012_massspectopo.png|200px]]<br />
<br />
==September 28== <br />
===Topo===<br />
* Tested another promoter (P2547) for the construct and repeated the assembly from 9/27.<br />
* Resuspended 8 new oligos, final volume 100 uM each<br />
* Annealed pet29 top/bot oligos<br />
* Redid the RT-PCR, 3x primer concentration, added 1:1 plasmid concentration<br />
* Made 1.6uM aliquots of primer stocks 1-7 (including topo add X primer previously ordered)<br />
* Diluted aliquot of Topo D168A plasmid 4:10<br />
* Diluted PSV plasmid 2:20<br />
* Performed Endpoint PCR on:<br />
** Topo D168A using primers 1,2 and primers 1,3<br />
* PSV using primers 4-5 and primers 6-7<br />
* 4 samples with low primer concentration, 4 samples with twice as much primer (labelled 'H')<br />
* Miniprepped Topo1 2, Topo1 3, Topo1 4 (biobricked Topo D168A without T7, multiple colonies from ligation into shipping vector)<br />
* Nanodropped:<br />
** Topo1 2 - 63.63 ng/uL<br />
** Topo1 3 - 75.07 ng/uL<br />
** Topo1 4 - 184.93 ng/uL<br />
* 1mL chloramphenicol cultures of GFPT1/GFPT2 in shipping vector prepared<br />
* Digested Topo1 2, Topo1 3, Topo1 4 with E and P<br />
* Ran digested Topo plasmids on 1% agarose gel with Hyperladder I<br />
[[File:ASUiGEM2012_gel092812.jpg|200px]]<br />
* Revived cultures of 2xGFPT1, 2xGFPT2, Topo, and Topo D168A (4 mL cultures each in their respective medias)<br />
* T5 exonuclease treated miniprepped plasmids (1-1, 1-1I)<br />
* A1 1-1I + t5<br />
* B1 1-1 + t5<br />
* A2 1-1I untreated<br />
* B2 1-1 untreated<br />
<br />
==September 29==<br />
===Strep===<br />
* Assembly was successful as liquid cultures were made. It was realized that due to the lack of beta gal negative strains the omega fragment couldn’t be tested and R0011 wouldn't code for the protein due to the lack of an RBS. <br />
* J61100 and J61101 constitutive promoters were extracted from the distribution plates and an additional promoter, pLux-Lac+RBS, were used to prove that the probe functions as desired.<br />
* Following assemblies were set up:<br />
** Plated on 50ul xgal LB amp Plates<br />
** J61100+ α<br />
** J61100+ strep+L+α (1a)<br />
** J61100+ strep+L+α (2c)<br />
** J61100+ strep +L +α(2b)<br />
** J61101+ α<br />
** J61101+strep+L+α(1a)<br />
** J61101+strep+L+α (2c)<br />
** J61101+strep+L+ α (2b)<br />
** plux-lac1+rbs+α<br />
** plux-lac1+rbs+strep+L+α(1a)<br />
** plux-lac1+rbs+strep+L+α(2c)<br />
** plux-lac1+rbs+strep+L+α(2b)<br />
** plux-lac2+rbs+α<br />
** plux-lac2+rbs+strep+L+α (1a)<br />
** plux-lac2+rbs+strep+L+α (2c)<br />
** plux-lac2+rbs+strep+L+α (2b)<br />
* Following were plated on 50ul X-Gal and 25ul IPTG LB AMP plates (no growth expected)<br />
** plux-lac1+rbs+α <br />
** plux-lac2+rbs+strep+L+α (1a)<br />
** plux-lac2+rbs+strep+L+α (2c) <br />
** plux-lac2+rbs+strep+L+α (2b)<br />
* Plate pictures:<br />
[[File:ASUiGEM2012_plate092912(1).jpg|200px]]<br />
[[File:ASUiGEM2012_plate092912(2).jpg|200px]]<br />
[[File:ASUiGEM2012_plate092912(3).jpg|200px]]<br />
[[File:ASUiGEM2012_24hrbgal.jpg|200px]]<br />
[[File:ASUiGEM2012_plate092912(5).jpg|200px]]<br />
[[File:ASUiGEM2012_plate092912(6).jpg|200px]]<br />
[[File:ASUiGEM2012_plate092912(7).jpg|200px]]<br />
[[File:ASUiGEM2012_plate092912(8).jpg|200px]]<br />
===Topo===<br />
* Miniprepped GFPT1, GFPT2, Topo, and Topo D168A (Topo cultures separated into 3mL and 1mL minipreps)<br />
* Nanodropped miniprepped DNA:<br />
** GFPT1 I - 275.29 ng/uL<br />
** GFPT1 II - 101.08 ng/uL<br />
** GFPT2 I - 222.11 ng/uL<br />
** GFPT2 II - 230.52 ng/uL<br />
** Topo I - 117.97 ng/uL<br />
** Topo II - 70.28 ng/uL<br />
** Topo D168A I - 69.47 ng/uL<br />
** Topo D168A II - 51.87 ng/uL<br />
* HIS purified crude lysates from 9/27/12 (Topo, Topo D168A, Topo + GFPT1, Topo + GFPT2, all IPTG induced)<br />
* Digested Topo I plasmid (pet29a) with E and X<br />
* Ran a gel with Hyperladder I, 1-2 1-3 4-5 and 6-7 PCR products, pet29a digestion, and pSB1C3 digestion<br />
[[File:ASUiGEM2012_gel092912_fragment_pcr_confrmation_smaller_(1).jpg|200px]]<br />
* Confirmed that PCR made amplicons<br />
[[File:ASUiGEM2012_gel092912-1.JPG|200px]]<br />
* Excised bands for digested pet29a and pSB1C3 plasmids<br />
* Gel extracted 4 gel fragments (2 wells per sample: digested pSB1C3 plasmid, digested pet29a plasmid)<br />
* Nanodropped gel extractions:<br />
** Digested pSB1C3 - 25.54 ng/uL<br />
** Digested pet29a - 22.95 ng/uL<br />
* Set up a bradford assay of topo, topo D168A, topo + G1, topo + G2 (5uL protein, 10uL protein, 20uL protein + 200uL reagent)<br />
* Used ~100uL aliquot of BL21 competent glycerol stock to seed 10mL of LB medium (no antibiotic), stored at 37C<br />
* Ran 1% agarose gel with samples: A1, B1, A2, B2 and Hyperladder I<br />
[[File:ASUiGEM2012_gel092912_alpha,_s%2Bl%2Ba_1a,s%2Bl%2Ba_2c,s%2Bl%2Ba_(2b)-2.jpg|200px]]<br />
* Did bug buster protocol to lyse BL21 control culture (used lysonase)<br />
* Ligated digested pet29a with pet29 top/bot annealed oligos<br />
* Transformed ligation using invitrogen DH5alpha transformation protocol<br />
* Prepared LB kanamycin plates<br />
* plated transformed ligations on prewarmed kanamycin plates<br />
<br />
==September 30==<br />
===Topo===<br />
* All assemblies were successful and went as planned. Blue colonies were picked to generate liquid cultures and streak plates to have a better visual result. <br />
* Pet29a plates did not grow<br />
* Kinase treated pet29a oligos<br />
* Annealed kinase treated pet29a oligos<br />
* Ligated digested pet29a (from gel extraction) with kinase treated oligos<br />
* Transformed ligations into DH5alpha, used topo plasmid as a positive control<br />
* Plated transformations on kanamycin plates and stored overnight at 37C<br />
* HIS purified BL21 control crude lysate<br />
* Set up a bradford assay with:<br />
** uninduced & induced topo protein extractions from 9/19<br />
** uninduced & induced topo D168A protein extractions from 9/19<br />
** BL21 control lysate<br />
** Topo, Topo D168A, Topo + G1, Topo + G2 from 9/27<br />
[[File:ASUiGEM2012_BradfordAssay.jpg|200px]]<br />
* All samples prepared (10uL protein, 20uL protein + 200uL reagent)<br />
* Miniprepped GFPT1 1,2,3 and GFPT2 (17,18,26) (~600uL of each) (1mL liquid cultures made from colonies on the chloramphenicol plates of GFPT1 and GFPT2 ligated into the shipping vector)<br />
* Nanodropped:<br />
** GFPT1-1 - 38.5 ng/uL<br />
** GFPT1-2 - 77.6 ng/uL<br />
** GFPT1-3 - 74.8 ng/uL<br />
** GFPT2-17 - 61.6 ng/uL<br />
** GFPT2-18 - 65.9 ng/uL<br />
** GFPT2-26 - 64.2 ng/uL<br />
* Ran a 1% agarose gel with 1-1, 1-2, 1-3, 2-17, 2-18, 2-26 plasmid miniprep samples and Hyperladder I<br />
[[File:ASUiGEM2012_gel093012-1.jpg|200px]]<br />
* Prepared a 1:2 dilution of GFPT2 plasmid from 9/27 miniprep<br />
* Treated 5uL of diluted plasmid with 5uL of water, BL21 protein, topo protein, topo D168A protein<br />
* Incubated 30 minutes at 37C<br />
* Ran a 1% agarose gel with protein treated target plasmid samples and Hyperladder I<br />
[[File:ASUiGEM2012_gel093012-2.jpg|200px]]<br />
* Digested GFPT2 plasmid with X (let run at 37C for 30 minutes)<br />
* Used DNA clean up kit on digested GFPT2<br />
* Nanodropped digested GFPT2:<br />
** GFPT2(X) - 39.85 ng/uL<br />
* Prepared DNA seq samples using VF2 and VR<br />
* Sample# - PrimerPair - DNA sample (sample 1, GFPT2 uncut + VF2; sample 2, GFPT2 uncut + VR)<br />
** 1/2 - FWD/REV - uncut GFPT2 plasmid<br />
** 3/4 - FWD/REV - cut GFPT2 plamid<br />
** 5/6 - FWD/REV - 2:1 uncut:cut GFPT2 plasmid mixture<br />
** 7/8 - FWD/REV - 1:1 uncut:cut GFPT2 plasmid mixture<br />
** 9/10 - FWD/REV - 1:2 uncut:cut GFPT2 plasmid mixture<br />
** 11/12 - FWD/REV - 1-2 miniprep sample from 9/19 double transformations<br />
** 13/14 - FWD/REV - 1-2I<br />
** 15/16 - FWD/REV - 1-3<br />
** 17/18 - FWD/REV - 1-3I<br />
** 19/20 - FWD/REV - 2-1<br />
** 21/22 - FWD/REV - 2-1I<br />
** 23/24 - FWD/REV - 2-2<br />
** 25/26 - FWD/REV - 2-2I<br />
** 27/28 - FWD/REV - 2-3<br />
** 29/30 - FWD/REV - 2-3I<br />
<br />
==October 1==<br />
===Strep===<br />
* Strep samples were minipreped and digested. The samples were inserted into the shipping vector.<br />
* Minipreps of:<br />
** J61011 + S + L + ALPHA 2B<br />
** J61100 + S + L + ALPHA 2B<br />
** J61100 + S + L + ALPHA 2C<br />
** PLUX2 + RBS + ALPHA 1A<br />
** PLUX2 + RBS + ALPHA 1A (2)<br />
** PLUX + S + L + ALPHA 2C<br />
** J61101 + S + L + ALPHA 1A<br />
** J61101 + S + L + ALPHA 1A (2)<br />
** PLUX2 + RBS + S + L + ALPHA 2B<br />
** PLUX2 + RBS + S + L + ALPHA 2B (2)<br />
** J61101 + S + L + ALPHA 2C<br />
** PLUX + S + L + ALPHA 2B<br />
* Ran Twice when finding concentrations:<br />
** J61101 + S + L + ALPHA 1A <br />
** J61101 + S + L + ALPHA 2B<br />
* Restricted all the above and: <br />
** Strep + Linker + OMEGA<br />
** Strep + Linker-4 + OMEGA<br />
* with:<br />
** X+P<br />
* Gel confirmed<br />
[[File:ASUiGEM2012_gel100112.JPG|200px]]<br />
* Ligated into pSB1C3 shipping vector and transformed into BL21(DE3) cells.<br />
* Prepared all 14 above samples for sequencing.<br />
<br />
==October 2==<br />
===Strep===<br />
* Transformation failed and DNA was turned in for sequencing.<br />
===Topo===<br />
* Prepared PCR tubes with 10uL Topo1 4 (25ng/uL topo d168a in the shipping vector), 10uL GFPT2-26 (25ng/uL GFPT2 in the shipping vector), and 10uL GFPT1-3 (25ng/uL GFPT1 in the shipping vector)<br />
* Labelled the tubes K891234, K891999, K891000 respectively and shipped overnight to iGEM Headquarters<br />
* Topo D168A treated DNA samples, incubated for 10 minutes at 37C:<br />
** Omega fragment PCR amplicon<br />
** Topo coding sequence PCR<br />
** GFPT1 VF2/VR PCR amplicon<br />
* Ran a 1% agarose gel containing untreated omega PCR, untreated topo PCR, untreated GFPT1 PCR, treated omega PCR, treated topo PCR, treated GFPT1 PCR, and Hyperladder I<br />
[[File:ASUiGEM_gel100212.jpg|200px]]<br />
<br />
==October 3==<br />
===Topo===<br />
* Protein treated GFPT2 plasmid, incubated for 10 minutes at 37C:<br />
** BL21 HIS-purified Control Lysate<br />
** Topo<br />
** Topo D168A<br />
* Ran a 1% agarose gel containing GFPT1, GFPT1 + BL21 protein, GFPT1 + Topo, GFPT1 + Topo D168A, Topo D168A (no DNA), and Hyperladder I<br />
[[File:Photo10031712_annotated.jpg|200px]]<br />
<br />
==October 18==<br />
===Magainin===<br />
* Overlapping oligo assembly of Magainin + Linker + His-tag<br />
* Ligated assembly into GFP vector BBa_I13522 for green-white screen<br />
* Transformed into DH5a cells and incubated overnight with negative control<br />
<br />
==October 19==<br />
===Magainin===<br />
* Picked a single white colony from overnight plate and made liquid culture.<br />
<br />
==October 20==<br />
===Magainin===<br />
* Miniprepped Magainin + Linker + His-tag +BBa_I13522 (274 ng/uL)<br />
* Cut with S+P and ligated to alpha-4 fragment cut with X+P.<br />
* Cut with S+P and ligated to omega fragment cut with X+P. <br />
* Transformed both ligations into DH5a cells with negative control<br />
<br />
==October 21==<br />
===Magainin===<br />
* Picked single colonies of both Magainin + Linker + His-tag + alpha-4 and Magainin + Linker + His-tag + omega and made liquid cultures.</div>Napatelhttp://2012.igem.org/Team:Arizona_State/FollowUsTeam:Arizona State/FollowUs2012-10-21T06:19:33Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<head><br />
<style type="text/css"><br />
/* use, put this in <a>: class="linkopacity" */<br />
a.linkopacity img<br />
{<br />
filter:alpha(opacity=90); /* For IE8 and earlier */<br />
opacity: 0.9;<br />
}<br />
a.linkopacity:hover img<br />
{<br />
filter:alpha(opacity=100); /* For IE8 and earlier */<br />
opacity: 1.0;<br />
}<br />
</style><br />
</head><br />
<br />
<body><br />
<br /><br />
<h1>Follow Us</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br /><br />
<br />
<br />
<table align="center"><br />
<tr><br />
<td><br />
<a class="linkopacity" href="https://www.facebook.com/pages/ASU-iGEM/196387053746045?fref=ts"><br />
<img src="https://static.igem.org/mediawiki/2012/c/cf/Screen_Shot_2012-10-20_at_10.28.39_PM.png" width="150" /><br />
</a><br />
</td><br />
<br />
<td><p></p></td><br />
<br />
<td><br />
<a class="linkopacity" href="https://twitter.com/asu_igem"><br />
<img src="https://static.igem.org/mediawiki/2012/9/9f/Screen_Shot_2012-10-20_at_10.28.49_PM.png" width="150" /><br />
</a><br />
</td><br />
<br />
<td><p></p></td><br />
<br />
<td><br />
<a class="linkopacity" href="http://www.flickr.com/"><br />
<img src="https://static.igem.org/mediawiki/2012/a/a2/Screen_Shot_2012-10-20_at_10.29.02_PM.png" width="150" /><br />
</a><br />
</td><br />
<br />
</tr><br />
</table><br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/NotebookTeam:Arizona State/Notebook2012-10-21T05:42:50Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
__NOTOC__<br />
<br />
{{:Team:Arizona_State/Template:NBCalendar}}<br />
<br />
==June 07==<br />
===Strep===<br />
* Transformation (LSE)<br />
** Transformed DNA:<br />
*** lacZ (well 4:12G, I732019)<br />
*** p + lacO (well 1:6G, R0011)<br />
** Cells: neb10beta (donated)<br />
** Protocol from: http://www.neb.com/nebecomm/products/productc3019.asp<br />
** Controls: puc19, no DNA (8 plates)<br />
<br />
==June 08==<br />
===Strep===<br />
* Transformation results<br />
** puc19: growth<br />
[[File: ASUiGEM2012_plate06712(3).jpg|200px]]<br />
** negative control: no growth<br />
[[File: ASUiGEM2012_plate06712(1).jpg|200px]]<br />
** lacZ, lacO: possible small colonies<br />
[[File: ASUiGEM2012_plate06712(2).jpg|200px]]<br />
[[File: ASUiGEM2012_plate06712(4).jpg|200px]]<br />
* liquid culture in amp media (100 ug / ml):<br />
** no growth of lacZ, lacO<br />
** growth of puc19<br />
<br />
==June 12==<br />
===General===<br />
* DH5a Competent Cell Prep<br />
** Streak plated cells on LB no amp plate, let grow overnight<br />
<br />
==June 13==<br />
===Strep===<br />
* Transformation (LSE)<br />
** Transformed DNA:<br />
*** lacZ (well 4:12G, I732019)<br />
*** p + lacO (well 1:6G, R0011)<br />
** Cells: DH5 alpha (donated)<br />
** Protocol from: http://openwetware.org/wiki/Haynes:Assembly101 (30 minute transformation)<br />
** Controls: puc19, no DNA (8 plates)<br />
[[File:ASUiGEM2012_plates061212.jpg|200px]]<br />
===General===<br />
* DH5a Chemically Competent cell prep<br />
** Grew 2 seed colonies from streak plate in LB no amp<br />
** Grew controls to test for contamination<br />
*** Both Seed colonies grew, no contamination present<br />
<br />
==June 14==<br />
===General===<br />
* Competent cell prep<br />
** Prepared CaCl2 buffer solution and CaCl2 glycerol buffer solution<br />
** Grew seed colony in 400mL LB no amp<br />
<br />
==June 15==<br />
===General===<br />
* Competent cell prep<br />
** Centrifuged falcon test tubes containing liquid colonies<br />
** Resuspended in CaCl2 buffer solution and incubated for 15 mins<br />
** Centrifuged and resuspended in CaCl2 glycerol buffer solution<br />
** Chilled overnight<br />
<br />
==June 16==<br />
===General===<br />
* Competent cell prep<br />
** Aliquotted 200uL into test tubes<br />
** Stored in -80C<br />
<br />
==June 17==<br />
===General===<br />
* Streak plated prepared competent cells on LB no amp plate<br />
** Colonies observed<br />
** No picture<br />
<br />
==June 18==<br />
===Strep===<br />
* Digest: Lac Z (X and P) and p + lacO (S and P)<br />
* Protocol: http://openwetware.org/wiki/Haynes:Assembly101<br />
* Gel extraction - Sigma Aldrich Gel Kit<br />
[[File:ASUiGEM2012_digest061812.jpg|200px]]<br />
<br />
==June 19==<br />
===Strep===<br />
* Ligation<br />
** P+lacO+Lac Z (samples still need to be tested)<br />
** Control (No DNA)<br />
===General===<br />
* Transformation (LSE)<br />
** Transformed DNA:<br />
*** T7 promoter BBa_I712074<br />
*** Constitutive promoter BBa_J23102<br />
** Cells: DH5 alpha (donated)<br />
** Protocol from: http://tools.invitrogen.com/content/sfs/manuals/subcloningefficiencydh5alpha_man.pdf (30 minute transformation)<br />
** Controls: puc19, no DNA<br />
** Plated 2 copies of each (100 ul, 250 ul) on LB amp plates.<br />
*Made 50 LB Amp plates.<br />
<br />
==June 20==<br />
===Strep===<br />
* PCR<br />
** Lac Z<br />
*** Primers: Standard BBa F and R primers (http://partsregistry.org/Primers/Catalog)<br />
*** 1000 fold dilution DNA used<br />
*** Protocol <br />
**** PCR water - 74.4 uL<br />
**** 1000 fold dilution DNA - 6 uL<br />
**** dNTP (10mM) - 2.4 uL<br />
**** F and R primers (10 uM) - 6 uL each<br />
**** 5x HF buffer - 24 uL<br />
**** Phusion DNA polymerase - 1.2 uL<br />
* Digest<br />
** P+Lac O<br />
*** S and P<br />
*** Treated with Antartic Phosphatase (avoids religation) <br />
* Plated negative control on LB Amp plate<br />
* Liquid cultures of T7 promoter and constitutive promoter<br />
===General===<br />
* Transformation (LSE)<br />
** Transformed DNA:<br />
*** RBS (well 1:1H BBa_B0030)<br />
*** TetR GFP (well 2:8A Part:BBa_I13522)<br />
** Cells: DH5 alpha (donated)<br />
** Protocol from: http://tools.invitrogen.com/content/sfs/manuals/subcloningefficiencydh5alpha_man.pdf (30 minute transformation)<br />
** Controls: puc19, no DNA<br />
<br />
==June 21==<br />
===General===<br />
* Made Liquid Cultures of E.coli transformed with RBS B0030<br />
* Made Liquid Cultures of E.coli transformed with TetR GFP<br />
* miniprepped and nanodropped T7 promoter BBa_I712074 and Constitutive promoter BBa_J23102 liquid cultures<br />
* liquid cultures:<br />
** RBS1<br />
** RBS2 (duplicate_<br />
** GFP1<br />
** puc19<br />
** negative controls<br />
** 5 ml LB amp<br />
** overnight cultures<br />
* replated GFP1 & 2 (duplicates)<br />
* Nanodropped plasmid DNA samples<br />
** Constitutive promoter 1: 2.554 ng/uL<br />
** Constitutive promoter 2: 2.345 ng/uL<br />
** T7 promoter 1: 3.369 ng/uL<br />
** T7 promoter 2: 3.049 ng/uL<br />
<br />
==June 22==<br />
===Strep===<br />
* PCR clean up (Sigma Aldrich Kit) Lac Z samples<br />
* Digest Lac Z with X and P<br />
* Nano Drop the PCR clean samples:<br />
** Lac O: 2.554 ug/uL<br />
** Lac Z: 3.369 ug/uL<br />
* Gel<br />
** [[File:ASUiGEM2012_gel062212(1).jpg|200px]]<br />
* PCR<br />
** Lac Z (25ul rxn)<br />
*** Primers: Standard BBa F and R primers (http://partsregistry.org/Primers/Catalog) <br />
*** Varied Concentration DNA samples <br />
*** Syzygy Mean Green MM<br />
*** Lac Z samples - 10 fold D, 100 fold D, 1000 fold D and Regular DNA.<br />
[[File:ASUiGEM2012_gel062212(2).jpg|200px]]<br />
* PCR cleaned samples<br />
===General===<br />
* Miniprepped liquid cultures: RBS (well 1:1H BBa_B0030) and TetR GFP (well 2:8A Part:BBa_I13522)<br />
* Picked colonies:<br />
** 1 colony from double terminator (dt1) plate<br />
** 1 colony from t7 polymerase (pol1) plate<br />
** 1 colony from puc19 plate (positive control)<br />
** 1 colony from dh5a plate (negative control)<br />
* started liquid cultures of each colony (5 mL LB amp each)<br />
<br />
==June 26==<br />
===General===<br />
* Transformation:<br />
** Transformed DNA:<br />
*** double terminator (B0017, 2:6K)<br />
*** T7 RNA polymerase (I715038, 2:15C)<br />
*** puc19, negative control<br />
** Protocol from: http://tools.invitrogen.com/content/sfs/manuals/subcloningefficiencydh5alpha_man.pdf (30 minute transformation)<br />
** Cells: dh5a<br />
<br />
==June 27==<br />
===General===<br />
* 6-26 transformation results:<br />
** Controls correct<br />
** 2x terminator: ~19 colonies<br />
** RNA pol: 1 colony<br />
* Liquid cultures including controls<br />
<br />
==June 28==<br />
===General===<br />
* Miniprepped double terminator (B0017, 2:6K) and T7 RNA polymerase (I715038, 2:15C) liquid cultures<br />
<br />
==July 2==<br />
===General===<br />
* Cleaned up liquid waste<br />
* Made SOB media<br />
===Magainin===<br />
* Finalized oligos for magainin construct<br />
<br />
==July 3==<br />
===General===<br />
* Third attempt of putting the bricks together. And samples were plated on X-gal plates to show that the construct worked.<br />
[[File:ASUiGEM2012_plates07212.jpg|200px]]<br />
* Autoclaved SOB media<br />
* Added glucose to make SOC media<br />
* Nanodropped double terminator (B0017, 2:6K) [DT1: 24.5, DT2: 29.6] and T7 RNA polymerase (I715038, 2:15C) [P1: 64.6, P2: 55.3] liquid cultures<br />
<br />
==July 12==<br />
===Magainin===<br />
* Searched for split beta gal fragment. Alpha fragment (BBa_I732006) was found on the distribution plates and transformed (NEB 10B).<br />
<br />
==July 14==<br />
===Magainin===<br />
* Designed primers to remove the stop codon on the alpha fragment. Also attained two flexible linkers from Dr. Haynes and transformed them.<br />
[[File:ASUiGEM2012_plates071412(1).jpg|200px]]<br />
[[File:ASUiGEM2012_plates071412(2).jpg|200px]]<br />
[[File:ASUiGEM2012_plates071412(3).jpg|200px]]<br />
<br />
==July 15==<br />
===Magainin===<br />
* Ran a miniprep of Bgal alpha 1&2, T7 and PSV<br />
* Procedure from GenElute HP PLasmid Miniprep Kit (Sigma-Aldrich)<br />
<br />
==July 16==<br />
===Strep===<br />
* Transformation of PLflex (part: BBa_J176040) and PLflex4 (part: BBa_J176130) linkers. <br />
[[File:ASUiGEM2012_plates071612.jpg|200px]]<br />
* Incubate at 37C for 8 hours for DH 5alpha turbo cells<br />
* Inoculated 5 mL LB/AMP media in 15 mL culture tubes and added the colony. Incubated in 37C overnight.<br />
<br />
==July 17==<br />
===Strep===<br />
* Miniprep of pLFlex DH5alpha and pLFlex 4 DH5alpha<br />
* Procedure comes from Zymo Research's Zyppy Kit. <br />
* Ran the spectrophotometer to determine the concentration for the miniprep DNA for the linker pLFlex and linker pLFlex 4<br />
* Concentrations were: <br />
** pLFlex: 73.792 ng/uL<br />
** pLFlex 4: 38.587 ng/uL<br />
* Absorbance ratios were:<br />
** pLFlex: 1.864<br />
** pLFlex 4: 1.851<br />
* Ran the miniprep for pLFlex and pLFlex 4 again.<br />
* Same procedure<br />
* Ran the spectrophotometer again<br />
* Concentrations were: <br />
** pLFlex: 48.095 ng/uL<br />
** pLFlex 4: 18.214 ng/uL<br />
* Absorbance ratios were:<br />
** pLFlex: 1.79<br />
** pLFlex 4: 1.85<br />
* Transformation was successful but 8-9 hour growth period was not sufficient for DH5 alpha.<br />
<br />
==July 23==<br />
===Strep===<br />
* Plated BBa_K283010 (Streptavidin) on LB amp plate from the agar stab provided from the iGEM head-quarters.<br />
* Incubated the dish overnight at 37 C.<br />
[[Image:ASUiGEM2012_plates072312.jpg|200px]]<br />
* Plate 1: pipet tip, colonies are in wells, neither distinct nor segregated<br />
* Plate 2: inoculating loop, numerous non-distinct colonies on the plate<br />
<br />
==July 24==<br />
===Topo===<br />
* Plasmids arrived courtesy of University of Pennsylvania School of Medicine<br />
* pET29a vectors containing coding sequence for Topoisomerase mutants CSCS and CSCS D168A described here<br />
<br />
==July 25==<br />
===Strep===<br />
* Ran a miniprep of streptavidin BBa_K283010<br />
* Protocol from Zymo Research's Zyppy Plasmid Miniprep Kit<br />
===Topo===<br />
* Tranformed CSCS topo 0 plasmid and CSCS D168A topo into DH5a Turbo cells (with neg control and Puc19 neg control)<br />
* Plated on Kanamycin plates<br />
<br />
==July 26==<br />
===Topo===<br />
* Picked colonies colonies from Topo 0 and Topo D168A and grew liquid cultures in Kan media<br />
<br />
==July 27==<br />
===Topo===<br />
* Miniprepped liquid colonies and nanodropped.<br />
* Plasmid concentrations<br />
** Topo O: 63.7 ng/uL <br />
** Topo D168A1: 125.4 ng/uL<br />
** Topo D168A2: 116.6 ng/uL<br />
<br />
==July 30==<br />
===General===<br />
* Prepared Kan Media and Kan Plates<br />
<br />
==July 31==<br />
===Topo===<br />
* PCR amplified polylinker sequence of Topo plasmid with Promega GoTaq protocol<br />
** Used pET29a upstream forward primer and T7 terminator reverse primer<br />
<br />
==August 3==<br />
===Topo===<br />
* Submitted pET29a Topoisomerase plasmid to Biodesign for sequencing<br />
* Resuspended GFPT1 and GFPT2 oligos with molecular grade (nuclease-free) H2O.<br />
** Final Concentration 100uM<br />
*** (gfpt1 top1, gfpt2 top1, gfpt1 top2, gftp2 top2, gfpt1 bot1, gfpt2 bot1, gfpt1 bot2, gfpt2 bot2)<br />
*** (3uL of each oligo + 2uL 10x annealing buffer, 6uL molecular grade H2O. 20uL Reactions)<br />
* Heated for 5 minutes at 100C. Let cool to room temperature on the heating block, stored at -20C.<br />
* Digested BBa_I13522 with XbaI and PstI.<br />
* Attempted ligating annealed oligos into a digested plasmid from Ryan (realized it was cut with E and P).<br />
<br />
==August 6==<br />
===Topo===<br />
* Annealed oligos for GFPT1 and GFPT2 (target probes)<br />
* Ligated oligos with digested GFP plasmid (BBa_I13522)<br />
* Transformed into competent DH5alpha<br />
* Added SOC and incubated at 37C for 15 minutes.<br />
* Plated on amp treated plates.<br />
<br />
==August 7==<br />
===Topo===<br />
* Only one colony on each plate (both were white)<br />
* Picked colonies and started 5mL LB amp cultures of each, stored at 37C<br />
* Stored plates in 37C<br />
<br />
==August 8==<br />
===Topo===<br />
* Picked the colonies again and started new liquid cultures (5mL LB amp).<br />
* Discarded cultures for 8/7/12<br />
<br />
==August 9==<br />
===Topo=== <br />
* Miniprepped 3mL of each 8/8/12 culture and nanodropped:<br />
** gfpt1 - 155 ng/uL<br />
** gfpt2 - 114 ng/uL<br />
* Digested gfpt1 and gfpt2 with X and P<br />
* Ran on a 1% agarose gel with the digested GFP plasmid and hyperladder V<br />
[[File:ASUiGEM2012_gel080912.jpg|200px]]<br />
* Didn't work<br />
* Made glyercol stocks with aliquot of the remaining liquid cultures<br />
<br />
==August 10==<br />
===Magainin===<br />
* PCR of Alpha-4, 1-omega, omega, and alpha fragments using corrected primers<br />
<br />
==August 13==<br />
===Magainin===<br />
* Ran gel of split beta gal fragments. Confirmed 3 out of the 4 fragments except for the alpha-4 fragment. <Br\><br />
[[File: ASUiGEM2012_gel081312.jpeg|200px]]<br />
===Topo===<br />
* Prepared sequencing samples<br />
* Sample w/ Primer: <br />
** GFPT1 w/ VF2 GFPT1 w/ VR GFPT2 w/ VF2 GFPT2 w/ VR<br />
** 200ng of DNA + 16 pmol of primer<br />
* Annealed oligos again GFPT1/2<br />
* Repeated ligation of oligos with digested GFP plasmid (BBa_I13522)<br />
* Followed Haynes assembly protocol instead of standard DH5alpha protocol. (http://openwetware.org/wiki/Haynes:Assembly101)<br />
* Transformed ligations into competent DH5alpha<br />
* Plated on amp treated plates<br />
<br />
==August 14==<br />
===Topo===<br />
* Took pictures of plates<br />
* Green-white screened plates<br />
* Picked 4 white colonies from each of gfpt1/2 plates<br />
* Made 5mL LB amp cultures of each colony<br />
* Delivered GFPT1/2 dna samples to biodesign for sequencing (samples from 8/13/12)<br />
===Magainin===<br />
* Assembled magainin insert via Overlapping oligo assembly<br />
* Digested pUC 19 plasmid with EcoRI and PstI<br />
* Transformed Magainin insert into digested pUC 19 plasmid. Failed. Probably too much X-gal on plate.<br />
Ran gel for the beta gal alpha-4 fragment. Failed. Fragment not in the correct size-band. <Br\><br />
[[File: ASUiGEM2012_gel081412.jpeg|200px]]<br />
<br />
==August 15==<br />
===Topo===<br />
*[http://129.219.2.10/home2/dnalims/fragment/32/21/pfasta/topo0_T7Term.seq Topo 0], [http://129.219.2.10/home2/dnalims/fragment/32/21/pfasta/D168Atopo1_T7Term.seq D168A Topo1], and [http://129.219.2.10/home2/dnalims/fragment/32/21/pfasta/D168Atopo2_T7Term.seq D168A Topo2] sequence results<br />
* Miniprepped 3mL of each liquid culture of GFPT1/2<br />
* Prepared glycerol stocks using 100uL of each liquid culture<br />
* Nanodropped samples:<br />
** GFPT1-1 - 172.6 ng/uL <br />
** GFPT1-2 - 203.7 ng/uL<br />
** GFPT1-3 - 197.4 ng/uL<br />
** GFPT1-4 - 178.9 ng/uL<br />
** GFPT2-1 - 107.3 ng/uL<br />
** GFPT2-2 - 131.2 ng/uL<br />
** GFPT2-3 - 145.5 ng/uL <br />
** GFPT2-4 - 172.0 ng/uL<br />
<br />
==August 16==<br />
===Magainin===<br />
* Replated magainin insert + plasmid into the grid. Failed. All blue colonies meaning that no insert.<Br\><br />
Tried gel for all gel-isolated fragments. Failed. Did not get a band in the 2000 bp region. Only got things below 200 bp.<BR\><br />
[[Image:ASUiGEM2012_gel081612.jpeg|200px]]<br />
<br />
==August 17==<br />
===Topo===<br />
* GFPT1 sequence confirmed<br />
* Prepared aliquots of GFPT2 minipreps from 8/15/12 for sequencing<br />
* Delivered GFPT2 samples to biodesign for sequencing<br />
<br />
==August 18==<br />
===Strep===<br />
* PCR’ed Streptavidin (biobrick) and omega fragment of beta (PSV plasmid) and confirmed size on a gel. <br />
Streptavidin was digested with E and S. Also, both flexible linkers attained from Dr. Haynes were digested with E and X and dephosphorlated. <br />
[[File:ASUiGEM2012_gel081812.jpg|200px]]<br />
<br />
==August 19==<br />
===Strep===<br />
* Restricted PLFlex and PLFlex 4 with ecori and xbai.<br />
* Restricted Bgala with Xbai and psti<br />
* Used Hayne's Lab Protocol<br />
* GFPT2 sequences confirmed<br />
<br />
==August 22==<br />
===Strep===<br />
* Transformed the two constructs.<br />
[[File:ASUiGEM2012_plates082212.jpg|200px]]<br />
* The two constructs were confirmed on gel and were ligated together to attain Streptavidin + pLFlex and Streptavidin+pLFlex4.<br />
[[File:ASUiGEM2012_gel082212.jpg|200px]]<br />
<br />
==August 27==<br />
===Topo===<br />
* Revived GFPT1 (from 8/9/12) and GFPT2 (2-2 from 8/15/12) cultures from glycerol scrapes<br />
* Made 4mL cultures in LB Amp<br />
<br />
==August 29==<br />
===Topo===<br />
* Discarded GFPT1/2 cultures from 8/27/12<br />
* Revived GFPT1 (from 8/9/12) and GFPT2 (2-2 from 8/15/12) cultures from glycerol scrapes<br />
* Made 4mL cultures in LB Amp<br />
* Digested GFPT1/2 with X and S<br />
* Ran a 1% agarose gel with GFPT1/2 digestions<br />
[[File:ASUiGEM2012_gel082912.jpg|200px]]<br />
* Cut out inserts and GFPT2 backbone and stored in 4C for gel extraction and tandum repeat assembly experiments<br />
<br />
==August 30==<br />
===Topo===<br />
* Prepared extra glyercol stocks of GFPT1/2 cultures from 8/29/12<br />
* Miniprepped 3mL of each culture, stored at -20C<br />
<br />
==September 2==<br />
===Strep===<br />
* Digested strep+pLFlex4(L4) with S and P and pLflex(L) with E and X and inserted alpha and omega fragments of beta gal.<br />
* Transformed these constructs<br />
[[File:ASUiGEM2012_plates09212.jpg|200px]]<br />
<br />
==September 10==<br />
===Strep===<br />
* Assembled:<br />
** Strep+L4+α which was a success<br />
** Strep+L4+ω which was a success<br />
** Strep+L which was a success<br />
*All digested samples were confirmed on a 1% agarose gel<br />
[[File:ASUiGEM2012_gel091012.jpg|200px]]<br />
<br />
==September 18==<br />
===Strep===<br />
* Assembled:<br />
** Prsf Duest+Strep+L4+α which failed<br />
** Prsf Duet+Strep+L4+ω which failed<br />
** Strep+L+α which was a success<br />
** Strep+L4+ω which was a success<br />
* All digested samples were confirmed on a 1% agarose gel<br />
** No picture of the gel.<br />
<br />
==September 19==<br />
===Strep===<br />
* Assembled<br />
** Prsf Duest+Strep+L4+α which failed<br />
** Prsf Duest+Strep+L4+ω which failed<br />
** Prsf Duest+Strep+L+α which failed<br />
** Prsf Duest+Strep+L+ω which failed<br />
* All digested samples were confirmed on a 1% agarose gel<br />
===Topo===<br />
* Set up VF2/VR endpoint PCR for double transform minipreps<br />
** 1-1, 1-1I, 1-2, 1-2I, 1-3, 1-3I, 2-1, 2-1I, 2-2, 2-2I, 2-3, 2-3I, GFPT1 (positive controls), GFPT2 (positive controls)<br />
* Annealing temp set to 55C for 25 cycles<br />
* Resuspended GFPT1 probe and GFPT2 probe oligos in molecular grade H2O (Final concentration: 100uM), stored at -20C<br />
<br />
==September 21==<br />
===Strep===<br />
* Miniprepped all the streps samples and digested them.<br />
<br />
==September 22==<br />
===Strep===<br />
* Assembles with new Prsf samples<br />
** Prsf Duest+Strep+L4+α which failed<br />
** Prsf Duest+Strep+L4+ω which failed<br />
** Prsf Duest+Strep+L+α which failed<br />
** Prsf Duest+Strep+L+ω which failed<br />
* Failed because outgrowth step want provided.<br />
* All digested samples were confirmed on a 1% agarose gel<br />
<br />
==September 25==<br />
===Topo===<br />
* Resuspended pSB1A2 FWD and pSB1A2 REV (amp resistance primers) oligos in molecular grade H2O (Final concentration: 100uM), stored at -20C<br />
* Prepared 1.6uM dilutions (500uL)<br />
* Did endpoint PCR using pSB1A2 primer pair on<br />
** Topo, Topo IPTG, Topo D168A, Topo D168A IPTG, 1-1, 1-1I, 2-1, 2-1I, GFPT1, GFPT2<br />
* Did endpoint PCR using VF2/VR primer pair on<br />
** Topo, Topo IPTG, Topo D168A, Topo D168A IPTG<br />
* Annealing temp 55C for 25 cycles, stored products at -20C<br />
* Made 3mL liquid cultures of the shipping vector (pSB1C3 with RFP insert) in DH5alpha in chloramphenicol resistant LB<br />
* Made 10mL liquid cultures of:<br />
** Topo in kanamycin<br />
** topo D168A in kanamycin<br />
** topo + GFPT1 in kanamycin + ampicillin<br />
** topo + GFPT2 in kanamycin + ampicillin<br />
* stored @ 37C<br />
<br />
==September 26==<br />
===Strep===<br />
* Assembled<br />
** Prsf Duest+Strep+L4+α which was a Success<br />
** Prsf Duest+Strep+L4+ω which was a Success<br />
** Prsf Duest+Strep+L+α which was a Success<br />
** Prsf Duest+Strep+L+ω which was a Success<br />
===Topo===<br />
* Picked two new colonies for topo + GFPT2 and grew 10mL cultures of amp+kan LB broth for each<br />
* Ran a gel with Hyperladder I, GFPT1 pSB1A2, GFPT2 pSB1A2, Topo pSB1A2, Topo D168A<br />
[[File:ASUiGEM2012_gel092612-1.jpg|200px]]<br />
* Ran a gel with PCR samples from 9/19 and 9/25 Hyperladder I, 1-1, 1-1I, 2-1, 2-1I, 2-1I(VF), 2-1(VF), 1-1I(VF), 1-1(VF), Hyperladder I<br />
[[File:ASUiGEM2012_gel092612-2.jpg|200px]]<br />
* Samples in wells 2-5 used the pSB1A2 primer pair. Samples in wells 6-9 used VF2/VR primer pair.<br />
* Revived GFPT1/2 from glycerol stocks (from 8/9 and 8/15) in 5mL LB amp each.<br />
* Nanodropped miniprepped DNA samples:<br />
** pSB1C3 I - 253.75 ng/uL<br />
** pSB1C3 II - 258.38 ng/uL<br />
** Topo - 24.84 ng/uL<br />
** Topo I - 17.33 ng/uL<br />
** Topo D168A - 7.24 ng/uL<br />
** Topo D168A I - 15.62 ng/uL<br />
** 1-1 - 16.49 ng/uL<br />
** 1-1I - 16.46 ng/uL<br />
** 2-1 - 142.05 ng/uL<br />
** 2-1I - 16.98 ng/uL<br />
* Picked new colonies from Topo, Topo D168A, Topo + G1, Topo + G2 and made 1mL colonies in their respective medias<br />
* Stored at -37C<br />
<br />
==September 27==<br />
===Strep===<br />
* Testing R0011 promoter. Digested R0011 with S and P generated the following assembly:<br />
** R0011+Strep+L4+α which failed<br />
** R0011+Strep+L4+ω which failed<br />
** R0011+Strep+L+α which failed<br />
** R0011+Strep+L+ω which was a Success<br />
===Topo===<br />
* Prepared serial dilutions of GFPT2 plasmid 1:10, 1:100, 1:1000, 1:10000<br />
* Prepared primer mixes for pSB and VF/VR primers<br />
* Prepared realtime PCR plate, ran RT-qPCR with annealing temp 57<br />
* Miniprepped GFPT1/2 cultures from 9/26<br />
* Nanodropped Miniprepped DNA:<br />
** GFPT1 - 276.12 ng/uL<br />
** GFPT2 - 219.84 ng/uL<br />
* Used 100uL of each 1mL culture from 9/26 to seed 10 mL cultures in their respective media<br />
* Added 10uL of 1M IPTG to each culture ~4 hours after seeding<br />
* Removed cells from 37C ~4 hours after IPTG inducing<br />
* Pelleted and lysed following the bugbuster protocol (http://openwetware.org/wiki/User:Behzad_Damadzadeh/Notebook/PcTF_Subcloning_in_E-coli/2012/05/22) (used lysonase for Topo and Topo D168A only)<br />
* HIS purified proteins using the Zymo HIS purification kit<br />
* Digested pSB1C3 plasmid with X and P<br />
* Sent protein samples (HIS purified samples from 9/19, 20uL) and ssDNA control (GFPT1/2 probe oligos 20uL @ 10uM) for mass spec<br />
[[File:ASUiGEM2012_massspectopo.png|200px]]<br />
<br />
==September 28== <br />
===Topo===<br />
* Tested another promoter (P2547) for the construct and repeated the assembly from 9/27.<br />
* Resuspended 8 new oligos, final volume 100 uM each<br />
* Annealed pet29 top/bot oligos<br />
* Redid the RT-PCR, 3x primer concentration, added 1:1 plasmid concentration<br />
* Made 1.6uM aliquots of primer stocks 1-7 (including topo add X primer previously ordered)<br />
* Diluted aliquot of Topo D168A plasmid 4:10<br />
* Diluted PSV plasmid 2:20<br />
* Performed Endpoint PCR on:<br />
** Topo D168A using primers 1,2 and primers 1,3<br />
* PSV using primers 4-5 and primers 6-7<br />
* 4 samples with low primer concentration, 4 samples with twice as much primer (labelled 'H')<br />
* Miniprepped Topo1 2, Topo1 3, Topo1 4 (biobricked Topo D168A without T7, multiple colonies from ligation into shipping vector)<br />
* Nanodropped:<br />
** Topo1 2 - 63.63 ng/uL<br />
** Topo1 3 - 75.07 ng/uL<br />
** Topo1 4 - 184.93 ng/uL<br />
* 1mL chloramphenicol cultures of GFPT1/GFPT2 in shipping vector prepared<br />
* Digested Topo1 2, Topo1 3, Topo1 4 with E and P<br />
* Ran digested Topo plasmids on 1% agarose gel with Hyperladder I<br />
[[File:ASUiGEM2012_gel092812.jpg|200px]]<br />
* Revived cultures of 2xGFPT1, 2xGFPT2, Topo, and Topo D168A (4 mL cultures each in their respective medias)<br />
* T5 exonuclease treated miniprepped plasmids (1-1, 1-1I)<br />
* A1 1-1I + t5<br />
* B1 1-1 + t5<br />
* A2 1-1I untreated<br />
* B2 1-1 untreated<br />
<br />
==September 29==<br />
===Strep===<br />
* Assembly was successful as liquid cultures were made. It was realized that due to the lack of beta gal negative strains the omega fragment couldn’t be tested and R0011 wouldn't code for the protein due to the lack of an RBS. <br />
* J61100 and J61101 constitutive promoters were extracted from the distribution plates and an additional promoter, pLux-Lac+RBS, were used to prove that the probe functions as desired.<br />
* Following assemblies were set up:<br />
** Plated on 50ul xgal LB amp Plates<br />
** J61100+ α<br />
** J61100+ strep+L+α (1a)<br />
** J61100+ strep+L+α (2c)<br />
** J61100+ strep +L +α(2b)<br />
** J61101+ α<br />
** J61101+strep+L+α(1a)<br />
** J61101+strep+L+α (2c)<br />
** J61101+strep+L+ α (2b)<br />
** plux-lac1+rbs+α<br />
** plux-lac1+rbs+strep+L+α(1a)<br />
** plux-lac1+rbs+strep+L+α(2c)<br />
** plux-lac1+rbs+strep+L+α(2b)<br />
** plux-lac2+rbs+α<br />
** plux-lac2+rbs+strep+L+α (1a)<br />
** plux-lac2+rbs+strep+L+α (2c)<br />
** plux-lac2+rbs+strep+L+α (2b)<br />
* Following were plated on 50ul X-Gal and 25ul IPTG LB AMP plates (no growth expected)<br />
** plux-lac1+rbs+α <br />
** plux-lac2+rbs+strep+L+α (1a)<br />
** plux-lac2+rbs+strep+L+α (2c) <br />
** plux-lac2+rbs+strep+L+α (2b)<br />
* Plate pictures:<br />
[[File:ASUiGEM2012_plate092912(1).jpg|200px]]<br />
[[File:ASUiGEM2012_plate092912(2).jpg|200px]]<br />
[[File:ASUiGEM2012_plate092912(3).jpg|200px]]<br />
[[File:ASUiGEM2012_24hrbgal.jpg|200px]]<br />
[[File:ASUiGEM2012_plate092912(5).jpg|200px]]<br />
[[File:ASUiGEM2012_plate092912(6).jpg|200px]]<br />
[[File:ASUiGEM2012_plate092912(7).jpg|200px]]<br />
[[File:ASUiGEM2012_plate092912(8).jpg|200px]]<br />
===Topo===<br />
* Miniprepped GFPT1, GFPT2, Topo, and Topo D168A (Topo cultures separated into 3mL and 1mL minipreps)<br />
* Nanodropped miniprepped DNA:<br />
** GFPT1 I - 275.29 ng/uL<br />
** GFPT1 II - 101.08 ng/uL<br />
** GFPT2 I - 222.11 ng/uL<br />
** GFPT2 II - 230.52 ng/uL<br />
** Topo I - 117.97 ng/uL<br />
** Topo II - 70.28 ng/uL<br />
** Topo D168A I - 69.47 ng/uL<br />
** Topo D168A II - 51.87 ng/uL<br />
* HIS purified crude lysates from 9/27/12 (Topo, Topo D168A, Topo + GFPT1, Topo + GFPT2, all IPTG induced)<br />
* Digested Topo I plasmid (pet29a) with E and X<br />
* Ran a gel with Hyperladder I, 1-2 1-3 4-5 and 6-7 PCR products, pet29a digestion, and pSB1C3 digestion<br />
[[File:ASUiGEM2012_gel092912_fragment_pcr_confrmation_smaller_(1).jpg|200px]]<br />
* Confirmed that PCR made amplicons<br />
[[File:ASUiGEM2012_gel092912-1.JPG|200px]]<br />
* Excised bands for digested pet29a and pSB1C3 plasmids<br />
* Gel extracted 4 gel fragments (2 wells per sample: digested pSB1C3 plasmid, digested pet29a plasmid)<br />
* Nanodropped gel extractions:<br />
** Digested pSB1C3 - 25.54 ng/uL<br />
** Digested pet29a - 22.95 ng/uL<br />
* Set up a bradford assay of topo, topo D168A, topo + G1, topo + G2 (5uL protein, 10uL protein, 20uL protein + 200uL reagent)<br />
* Used ~100uL aliquot of BL21 competent glycerol stock to seed 10mL of LB medium (no antibiotic), stored at 37C<br />
* Ran 1% agarose gel with samples: A1, B1, A2, B2 and Hyperladder I<br />
[[File:ASUiGEM2012_gel092912_alpha,_s%2Bl%2Ba_1a,s%2Bl%2Ba_2c,s%2Bl%2Ba_(2b)-2.jpg|200px]]<br />
* Did bug buster protocol to lyse BL21 control culture (used lysonase)<br />
* Ligated digested pet29a with pet29 top/bot annealed oligos<br />
* Transformed ligation using invitrogen DH5alpha transformation protocol<br />
* Prepared LB kanamycin plates<br />
* plated transformed ligations on prewarmed kanamycin plates<br />
<br />
==September 30==<br />
===Topo===<br />
* All assemblies were successful and went as planned. Blue colonies were picked to generate liquid cultures and streak plates to have a better visual result. <br />
* Pet29a plates did not grow<br />
* Kinase treated pet29a oligos<br />
* Annealed kinase treated pet29a oligos<br />
* Ligated digested pet29a (from gel extraction) with kinase treated oligos<br />
* Transformed ligations into DH5alpha, used topo plasmid as a positive control<br />
* Plated transformations on kanamycin plates and stored overnight at 37C<br />
* HIS purified BL21 control crude lysate<br />
* Set up a bradford assay with:<br />
** uninduced & induced topo protein extractions from 9/19<br />
** uninduced & induced topo D168A protein extractions from 9/19<br />
** BL21 control lysate<br />
** Topo, Topo D168A, Topo + G1, Topo + G2 from 9/27<br />
[[File:ASUiGEM2012_BradfordAssay.jpg|200px]]<br />
* All samples prepared (10uL protein, 20uL protein + 200uL reagent)<br />
* Miniprepped GFPT1 1,2,3 and GFPT2 (17,18,26) (~600uL of each) (1mL liquid cultures made from colonies on the chloramphenicol plates of GFPT1 and GFPT2 ligated into the shipping vector)<br />
* Nanodropped:<br />
** GFPT1-1 - 38.5 ng/uL<br />
** GFPT1-2 - 77.6 ng/uL<br />
** GFPT1-3 - 74.8 ng/uL<br />
** GFPT2-17 - 61.6 ng/uL<br />
** GFPT2-18 - 65.9 ng/uL<br />
** GFPT2-26 - 64.2 ng/uL<br />
* Ran a 1% agarose gel with 1-1, 1-2, 1-3, 2-17, 2-18, 2-26 plasmid miniprep samples and Hyperladder I<br />
[[File:ASUiGEM2012_gel093012-1.jpg|200px]]<br />
* Prepared a 1:2 dilution of GFPT2 plasmid from 9/27 miniprep<br />
* Treated 5uL of diluted plasmid with 5uL of water, BL21 protein, topo protein, topo D168A protein<br />
* Incubated 30 minutes at 37C<br />
* Ran a 1% agarose gel with protein treated target plasmid samples and Hyperladder I<br />
[[File:ASUiGEM2012_gel093012-2.jpg|200px]]<br />
* Digested GFPT2 plasmid with X (let run at 37C for 30 minutes)<br />
* Used DNA clean up kit on digested GFPT2<br />
* Nanodropped digested GFPT2:<br />
** GFPT2(X) - 39.85 ng/uL<br />
* Prepared DNA seq samples using VF2 and VR<br />
* Sample# - PrimerPair - DNA sample (sample 1, GFPT2 uncut + VF2; sample 2, GFPT2 uncut + VR)<br />
** 1/2 - FWD/REV - uncut GFPT2 plasmid<br />
** 3/4 - FWD/REV - cut GFPT2 plamid<br />
** 5/6 - FWD/REV - 2:1 uncut:cut GFPT2 plasmid mixture<br />
** 7/8 - FWD/REV - 1:1 uncut:cut GFPT2 plasmid mixture<br />
** 9/10 - FWD/REV - 1:2 uncut:cut GFPT2 plasmid mixture<br />
** 11/12 - FWD/REV - 1-2 miniprep sample from 9/19 double transformations<br />
** 13/14 - FWD/REV - 1-2I<br />
** 15/16 - FWD/REV - 1-3<br />
** 17/18 - FWD/REV - 1-3I<br />
** 19/20 - FWD/REV - 2-1<br />
** 21/22 - FWD/REV - 2-1I<br />
** 23/24 - FWD/REV - 2-2<br />
** 25/26 - FWD/REV - 2-2I<br />
** 27/28 - FWD/REV - 2-3<br />
** 29/30 - FWD/REV - 2-3I<br />
<br />
==October 1==<br />
===Strep===<br />
* Strep samples were minipreped and digested. The samples were inserted into the shipping vector.<br />
* Minipreps of:<br />
** J61011 + S + L + ALPHA 2B<br />
** J61100 + S + L + ALPHA 2B<br />
** J61100 + S + L + ALPHA 2C<br />
** PLUX2 + RBS + ALPHA 1A<br />
** PLUX2 + RBS + ALPHA 1A (2)<br />
** PLUX + S + L + ALPHA 2C<br />
** J61101 + S + L + ALPHA 1A<br />
** J61101 + S + L + ALPHA 1A (2)<br />
** PLUX2 + RBS + S + L + ALPHA 2B<br />
** PLUX2 + RBS + S + L + ALPHA 2B (2)<br />
** J61101 + S + L + ALPHA 2C<br />
** PLUX + S + L + ALPHA 2B<br />
* Ran Twice when finding concentrations:<br />
** J61101 + S + L + ALPHA 1A <br />
** J61101 + S + L + ALPHA 2B<br />
* Restricted all the above and: <br />
** Strep + Linker + OMEGA<br />
** Strep + Linker-4 + OMEGA<br />
* with:<br />
** X+P<br />
* Gel confirmed<br />
[[File:ASUiGEM2012_gel100112.JPG|200px]]<br />
* Ligated into pSB1C3 shipping vector and transformed into BL21(DE3) cells.<br />
* Prepared all 14 above samples for sequencing.<br />
<br />
==October 2==<br />
===Strep===<br />
* Transformation failed and DNA was turned in for sequencing.<br />
===Topo===<br />
* Prepared PCR tubes with 10uL Topo1 4 (25ng/uL topo d168a in the shipping vector), 10uL GFPT2-26 (25ng/uL GFPT2 in the shipping vector), and 10uL GFPT1-3 (25ng/uL GFPT1 in the shipping vector)<br />
* Labelled the tubes K891234, K891999, K891000 respectively and shipped overnight to iGEM Headquarters<br />
* Topo D168A treated DNA samples, incubated for 10 minutes at 37C:<br />
** Omega fragment PCR amplicon<br />
** Topo coding sequence PCR<br />
** GFPT1 VF2/VR PCR amplicon<br />
* Ran a 1% agarose gel containing untreated omega PCR, untreated topo PCR, untreated GFPT1 PCR, treated omega PCR, treated topo PCR, treated GFPT1 PCR, and Hyperladder I<br />
[[File:ASUiGEM_gel100212.jpg|200px]]<br />
<br />
==October 3==<br />
===Topo===<br />
* Protein treated GFPT2 plasmid, incubated for 10 minutes at 37C:<br />
** BL21 HIS-purified Control Lysate<br />
** Topo<br />
** Topo D168A<br />
* Ran a 1% agarose gel containing GFPT1, GFPT1 + BL21 protein, GFPT1 + Topo, GFPT1 + Topo D168A, Topo D168A (no DNA), and Hyperladder I<br />
[[File:Photo10031712_annotated.jpg|200px]]<br />
<br />
==October 18==<br />
===Magainin===<br />
* Overlapping oligo assembly of Magainin + Linker + His-tag<br />
* Ligated assembly into GFP vector BBa_I13522 for green-white screen<br />
* Transformed into DH5a cells and incubated overnight with negative control<br />
<br />
==October 19==<br />
===Magainin===<br />
* Picked a single white colony from overnight plate and made liquid culture.<br />
==October 20==<br />
===Magainin===<br />
* Miniprepped Magainin + Linker + His-tag +BBa_I13522 (274 ng/uL)<br />
* Cut with S+P and ligated to alpha-4 fragment cut with X+P.<br />
* Cut with S+P and ligated to omega fragment cut with X+P. <br />
* Transformed both ligations into DH5a cells with negative control</div>Napatelhttp://2012.igem.org/Team:Arizona_State/PhotosTeam:Arizona State/Photos2012-10-17T06:26:17Z<p>Napatel: Replaced content with "{{:Team:Arizona_State/Template:Header}}"</p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}</div>Napatelhttp://2012.igem.org/Team:Arizona_State/PhotosTeam:Arizona State/Photos2012-10-17T06:10:43Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<head><br />
<br />
<script type="text/javascript"><br />
var image1=new Image()<br />
image1.src="https://static.igem.org/mediawiki/2012/c/c8/002_copy.jpg"<br />
var image2=new Image()<br />
image2.src="https://static.igem.org/mediawiki/2012/c/ce/004_copy.jpg"<br />
var image3=new Image()<br />
image3.src="https://static.igem.org/mediawiki/2012/f/f6/006_copy.jpg"<br />
var image4=new Image()<br />
image4.src="https://static.igem.org/mediawiki/2012/3/31/007_copy.jpg"<br />
var image5=new Image()<br />
image5.src="https://static.igem.org/mediawiki/2012/c/cf/008_copy.jpg"<br />
</script><br />
<br />
</head><br />
<br />
<br />
<body><br />
<h1>Photos</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<!---props to: http://www.javascriptkit.com/howto/show2.shtml---><br />
<br /><br />
<div align="center"><br />
<img src="https://static.igem.org/mediawiki/2012/c/c8/002_copy.jpg" name="slide" width="800" /><br />
<script><br />
//variable that will increment through the images<br />
var step=1<br />
function slideit(){<br />
//if browser does not support the image object, exit.<br />
if (!document.images)<br />
return<br />
document.images.slide.src=eval("image"+step+".src")<br />
if (step<5)<br />
step++<br />
else<br />
step=1<br />
//call function "slideit()" every 5 seconds<br />
setTimeout("slideit()",5000)<br />
}<br />
slideit()<br />
</script><br />
</div><br />
<br /><br />
<div align="center"><b>Water Collection</b></div><br />
<br /><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<br />
<!---<embed src="https://static.igem.org/mediawiki/2012/d/db/Untitled-1.swf" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" wmode="transparent" height="400" width="900">---></div>Napatelhttp://2012.igem.org/Team:Arizona_State/PhotosTeam:Arizona State/Photos2012-10-17T06:10:25Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<head><br />
<br />
<script type="text/javascript"><br />
var image1=new Image()<br />
image1.src="https://static.igem.org/mediawiki/2012/c/c8/002_copy.jpg"<br />
var image2=new Image()<br />
image2.src="https://static.igem.org/mediawiki/2012/c/ce/004_copy.jpg"<br />
var image3=new Image()<br />
image3.src="https://static.igem.org/mediawiki/2012/f/f6/006_copy.jpg"<br />
var image4=new Image()<br />
image4.src="https://static.igem.org/mediawiki/2012/3/31/007_copy.jpg"<br />
var image5=new Image()<br />
image5.src="https://static.igem.org/mediawiki/2012/c/cf/008_copy.jpg"<br />
</script><br />
<br />
</head><br />
<br />
<br />
<body><br />
<h2>Photos</h2><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<!---props to: http://www.javascriptkit.com/howto/show2.shtml---><br />
<br /><br />
<div align="center"><br />
<img src="https://static.igem.org/mediawiki/2012/c/c8/002_copy.jpg" name="slide" width="800" /><br />
<script><br />
//variable that will increment through the images<br />
var step=1<br />
function slideit(){<br />
//if browser does not support the image object, exit.<br />
if (!document.images)<br />
return<br />
document.images.slide.src=eval("image"+step+".src")<br />
if (step<5)<br />
step++<br />
else<br />
step=1<br />
//call function "slideit()" every 5 seconds<br />
setTimeout("slideit()",5000)<br />
}<br />
slideit()<br />
</script><br />
</div><br />
<br /><br />
<div align="center"><b>Water Collection</b></div><br />
<br /><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<br />
<!---<embed src="https://static.igem.org/mediawiki/2012/d/db/Untitled-1.swf" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" wmode="transparent" height="400" width="900">---></div>Napatelhttp://2012.igem.org/Team:Arizona_State/PhotosTeam:Arizona State/Photos2012-10-17T06:09:49Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<head><br />
<br />
<script type="text/javascript"><br />
var image1=new Image()<br />
image1.src="https://static.igem.org/mediawiki/2012/c/c8/002_copy.jpg"<br />
var image2=new Image()<br />
image2.src="https://static.igem.org/mediawiki/2012/c/ce/004_copy.jpg"<br />
var image3=new Image()<br />
image3.src="https://static.igem.org/mediawiki/2012/f/f6/006_copy.jpg"<br />
var image4=new Image()<br />
image4.src="https://static.igem.org/mediawiki/2012/3/31/007_copy.jpg"<br />
var image5=new Image()<br />
image5.src="https://static.igem.org/mediawiki/2012/c/cf/008_copy.jpg"<br />
</script><br />
<br />
</head><br />
<br />
<br />
<body><br />
<h1>Community Outreach</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<!---props to: http://www.javascriptkit.com/howto/show2.shtml---><br />
<br /><br />
<div align="center"><br />
<img src="https://static.igem.org/mediawiki/2012/c/c8/002_copy.jpg" name="slide" width="800" /><br />
<script><br />
//variable that will increment through the images<br />
var step=1<br />
function slideit(){<br />
//if browser does not support the image object, exit.<br />
if (!document.images)<br />
return<br />
document.images.slide.src=eval("image"+step+".src")<br />
if (step<5)<br />
step++<br />
else<br />
step=1<br />
//call function "slideit()" every 5 seconds<br />
setTimeout("slideit()",5000)<br />
}<br />
slideit()<br />
</script><br />
</div><br />
<br /><br />
<div align="center"><b>ASU iGEM guest speaking at Bioscience High School</b></div><br />
<br /><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<br />
<!---<embed src="https://static.igem.org/mediawiki/2012/d/db/Untitled-1.swf" type="application/x-shockwave-flash" pluginspage="http://www.macromedia.com/go/getflashplayer" wmode="transparent" height="400" width="900">---></div>Napatelhttp://2012.igem.org/Team:Arizona_State/PhotosTeam:Arizona State/Photos2012-10-17T06:09:22Z<p>Napatel: Created page with "{{:Team:Arizona_State/Template:Header}}"</p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}</div>Napatelhttp://2012.igem.org/Team:Arizona_State/Template:HeaderTeam:Arizona State/Template:Header2012-10-17T06:08:58Z<p>Napatel: </p>
<hr />
<div><html lang="en"><br />
<!-- Made by Abhi & Jordan with help from the "https://2011.igem.org/Team:Imperial_College_London" page --><br />
<head><br />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /><br />
<style type="text/css"><br />
#top-section {<br />
width: 975px;<br />
height: 20px;<br />
background-color: transparent;<br />
border: none;<br />
}<br />
<br />
#p-logo { display: none; }<br />
#search-controls { display: none; }<br />
.firstHeading { display: none; }<br />
#contentSub { margin: 0 0 0 0; }<br />
iframe { padding: 10px 20px 10px 20px; }<br />
<br />
body {<br />
background-color:#000000;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/c/c8/BackgroundNew.jpg); <br />
background-size:100%;<br />
background-position:center; background-attachment:fixed;<br />
}<br />
<br />
.right-menu li a, .right-menu li a:hover {<br />
color: #3c6b27;<br />
background-color: transparent;<br />
}<br />
<br />
#iGEMLogo {<br />
position: absolute;<br />
top:40px;<br />
left:20px;<br />
}<br />
<br />
#ProjectTitle {<br />
position: relative;<br />
text-align:center;<br />
}<br />
<br />
#ASULogo {<br />
position: absolute;<br />
top:45px;<br />
right:25px;<br />
}<br />
<br />
#menucontainer {<br />
overflow:visible;<br />
position:relative;<br />
z-index:3;<br />
}<br />
<br />
#content {<br />
position: relative;<br />
width: 975px;<br />
margin: 0 auto;<br />
padding-top:20px;<br />
padding-left:0px;<br />
padding-right:0px;<br />
padding-bottom:0px;<br />
//background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/4/4b/2012ASUiGemLogo.png);<br />
//background-repeat:no-repeat;<br />
//background-position:center;<br />
//background-attachment:fixed;<br />
color: black;<br />
border: none;<br />
line-height: 1.5em;<br />
z-index: 2;<br />
}<br />
<br />
#bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 {<br />
margin-bottom: 0;<br />
}<br />
<br />
a {color:#t;}<br />
a:link {color:#93B825;}<br />
a:visited {color:#728F1D;}<br />
a:hover {color:#93B825;}<br />
a:active {color:#93B825;}<br />
a[name]:hover {text-decoration:none;} <br />
<br />
a.sitemap:link,a.sitemap:visited {color:#680000;font-decoration:none;}<br />
a.sitemap:hover,a.sitemap:active {color:#680000;font-decoration:underline;}<br />
<br />
h1 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 2.2em;<br />
margin: 0 0 0 0;<br />
padding: 20px 20px 12px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h2 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.7em;<br />
margin: 0 0 0 0;<br />
padding: 18px 20px 7px 20px;<br />
border-bottom: none;<br />
} <br />
<br />
h3 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.4em;<br />
margin: 0 0 0 0;<br />
padding: 16px 20px 2px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h4 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.1em;<br />
margin: 0 0 0 0;<br />
padding: 13.5px 20px 1px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
p {<br />
font-family: helvetica,sans-serif;<br />
//color: #ffffff;<br />
background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/e/ea/Layer.png);<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
margin: 0 0 0 0;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
table {<br />
background: transparent;<br />
} th {<br />
background-color:maroon;<br />
color:gold;<br />
}<br />
<br />
.border {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
}<br />
<br />
.borderMagnify {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
margin-left:-9px;<br />
margin-right:9px;<br />
}<br />
<br />
.imgbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.vidbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.newouterbox {<br />
background-color:#FF944D;<br />
border:1px solid #CCCCCC;<br />
margin:20px;<br />
padding-bottom:0px;<br />
}<br />
<br />
.newinnerbox {<br />
border:1px solid #CCCCCC;<br />
margin:10px 20px 20px 20px;<br />
padding-top:0px;<br />
padding-bottom:13px;<br />
background-color:#ffffff;<br />
}<br />
<br />
.newtext {<br />
text-align:center;<br />
background-color:#FF944D;<br />
color:#000000;<br />
}<br />
<br />
ul.a {<br />
margin: 0 0 0 40px;<br />
list-style-image: none;<br />
list-style-type:disc;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
ol.a {<br />
margin: 0 0 0 30px;<br />
list-style-position:inside;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
#BackToTop {<br />
position:fixed;<br />
bottom:0;<br />
right:0;<br />
}<br />
<br />
#Sitemap {<br />
position:fixed;<br />
bottom:0;<br />
left:0;<br />
}<br />
<br />
/*** Start of Styling for menu bar ***/<br />
/*** ESSENTIAL STYLES ***/<br />
a.collapseLink {<br />
font-weight:bold;<br />
font-size:1em;<br />
color:#225323;<br />
}<br />
.sf-menu, .sf-menu * {<br />
margin:0;<br />
padding:0;<br />
list-style:none;<br />
}<br />
.sf-menu {<br />
line-height:1.0;<br />
}<br />
.sf-menu ul {<br />
position:absolute;<br />
top:999em;<br />
width:195px; /* left offset of submenus need to match (see below) */<br />
}<br />
.sf-menu ul li {<br />
width:100%;<br />
}<br />
.sf-menu li:hover {<br />
visibility:inherit; /* fixes IE7 'sticky bug' */<br />
}<br />
.sf-menu li {<br />
float:left;<br />
position:relative;<br />
width:195px;<br />
}<br />
.sf-menu a {<br />
display:block;<br />
position:relative;<br />
}<br />
.sf-menu li:hover ul, .sf-menu li.sfHover ul {<br />
left:0;<br />
top:2.5em; /* match top ul list item height */<br />
z-index:99;<br />
}<br />
ul.sf-menu li:hover li ul, ul.sf-menu li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li:hover ul, ul.sf-menu li li.sfHover ul {<br />
left:15.3em; /* match ul width */<br />
top:0;<br />
}<br />
ul.sf-menu li li:hover li ul, ul.sf-menu li li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul {<br />
left:10em; /* match ul width */<br />
top:0;<br />
}<br />
<br />
/*** DEMO SKIN ***/<br />
.sf-menu {<br />
float:left;<br />
margin-bottom:1em;<br />
}<br />
.sf-menu a {<br />
border-left:1px solid #fff;<br />
border-top:1px solid #826554;<br />
padding:0.37em 1em 0.37em 1em;<br />
text-decoration:none;<br />
font-family:'helveticaneue', sans-serif;<br />
font-size:1.3em;<br />
}<br />
.sf-menu a, .sf-menu a:visited { /* visited pseudo selector so IE6 applies text colour*/<br />
color:#efefef;<br />
}<br />
.sf-menu li, .sf-menu li li, .sf-menu li li li {<br />
background:#990000;<br />
}<br />
.sf-menu li:hover, .sf-menu li.sfHover, .sf-menu a:focus, .sf-menu a:hover, .sf-menu a:active {<br />
background:#b30000;<br />
outline:0;<br />
}<br />
<br />
/*** arrows **/<br />
.sf-menu a.sf-with-ul {<br />
cursor:default; <br />
padding-right:2.25em;<br />
min-width:1px; /* trigger IE7 hasLayout so spans position accurately */<br />
}<br />
.sf-sub-indicator {<br />
position:absolute;<br />
display:block;<br />
right:.75em;<br />
top:1.05em; /* IE6 only */<br />
width:10px;<br />
height:10px;<br />
text-indent:-999em;<br />
overflow:hidden;<br />
background:url('https://static.igem.org/mediawiki/2011/2/2f/ICL_MenuArrow.png') no-repeat -10px -100px;<br />
/* 8-bit indexed alpha png. IE6 gets solid image only */<br />
}<br />
a > .sf-sub-indicator { /* give all except IE6 the correct values */<br />
top:.8em;<br />
background-position:0 -100px; /* use translucent arrow for modern browsers*/<br />
}<br />
/* apply hovers to modern browsers */<br />
a:focus > .sf-sub-indicator,<br />
a:hover > .sf-sub-indicator,<br />
a:active > .sf-sub-indicator,<br />
li:hover > a > .sf-sub-indicator,<br />
li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px -100px; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/* point right for anchors in subs */<br />
.sf-menu ul .sf-sub-indicator { background-position: -10px 0; }<br />
.sf-menu ul a > .sf-sub-indicator { background-position: 0 0; }<br />
/* apply hovers to modern browsers */<br />
.sf-menu ul a:focus > .sf-sub-indicator,<br />
.sf-menu ul a:hover > .sf-sub-indicator,<br />
.sf-menu ul a:active > .sf-sub-indicator,<br />
.sf-menu ul li:hover > a > .sf-sub-indicator,<br />
.sf-menu ul li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px 0; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/*** shadows for all but IE6 ***/<br />
.sf-shadow ul {<br />
background:url('https://static.igem.org/mediawiki/2011/9/9f/ICL_Shadow.png') no-repeat bottom right;<br />
padding:0 8px 9px 0;<br />
-moz-border-radius-bottomleft:17px;<br />
-moz-border-radius-topright:17px;<br />
-webkit-border-top-right-radius:17px;<br />
-webkit-border-bottom-left-radius:17px;<br />
}<br />
<br />
.sf-shadow ul.sf-shadow-off {<br />
background:transparent;<br />
}<br />
</style><br />
<br />
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/hoverIntent?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/superfishjs?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/magnifier?action=raw&ctype=text/js"><br />
/***********************************************<br />
* jQuery Image Magnify- (c) Dynamic Drive DHTML code library (www.dynamicdrive.com)<br />
* This notice MUST stay intact for legal use<br />
* Visit Dynamic Drive at http://www.dynamicdrive.com/ for this script and 100s more<br />
***********************************************/<br />
</script><br />
<br />
<script type="text/javascript"><br />
var $ = jQuery;<br />
jQuery.imageMagnify.zIndexcounter = 1000;<br />
</script><br />
<br />
<script><br />
$(document).ready(function() {<br />
$("sup").click(function () {<br />
if ($(this).html().substr(0,1)=="[")<br />
{<br />
if ($('.technology').length>0)<br />
{<br />
ddaccordion.expandone('technology', $('.technology').length-1)<br />
setTimeout("window.scrollBy(0,50000)",200)<br />
}<br />
else window.scrollBy(0,50000)<br />
}<br />
});<br />
$("sup").mouseover(function () {<br />
if ($(this).html().substr(0,1)=="[") $(this).css('cursor', 'pointer');<br />
});<br />
});<br />
</script><br />
<br />
<script> <br />
$(document).ready(function() { <br />
$('ul.sf-menu').superfish({ <br />
}); <br />
});<br />
</script><br />
</head><br />
<br />
<body><br />
<a name="top"></a><br />
<!-----<br />
<div id='iGEMLogo'><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:120px;" /><br />
</a><br />
</div><br />
<br />
<div id='ProjectTitle'><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/5/5f/CRSYS.png" style="width:550px;" /><br />
<!---Before: https://static.igem.org/mediawiki/2012/d/db/2012_Project_logo.png---><!----<br />
</a><br />
</div><br />
<br />
<div id='ASULogo'><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="150" height="70" /><br />
</div><br />
-----><br />
<div id='header' align="center"><br />
<table width="950"><br />
<tr><br />
<td><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:100px;" /><br />
</a><br />
</td><br />
<td align="center"><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/9/9a/AsuCrsysLogothingy.png" style="width:591px;" /><br />
</a><br />
</td><br />
<td><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="125" /><br />
</td><br />
</table><br />
<br /><br />
</div><br />
<br />
<br />
<br />
<div id="BackToTop"><br />
<a href="#top"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2d/ArrowColorChanged.png" width="50px" /><br />
</a><br />
</div><br />
<br />
<div id="Sitemap"><br />
<a href='https://2012.igem.org/Team:Arizona_State/Sitemap'><br />
<img src="https://static.igem.org/mediawiki/2012/3/30/SiteMapColorChange.png" width="100px" /><br />
</a><br />
</div><br />
<br />
<div id='menucontainer'><br />
<ul class="sf-menu sf-navbar"><br />
<li><a class="sf-with-ul" href="">Project<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State">Home</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Problem">The Problem</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Chimeric_Reporter">DNA-Protein Chimera Biosensor</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Magainin">Cell Surface Biosensor</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Safety">Safety</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Notebook">Notebook</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/References">References</a><br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Team<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Team">Members</a></li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Attributions">Attributions</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2012">Official Team Profile</a></li><br />
</ul><br />
</li><br />
<br />
<li><a class="sf-with-ul" href="#">Results<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Data">Data</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Parts">BioBricks</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Accomplishments">Judging Criteria</a> </li><br />
</ul><br />
</li><br />
<li><a class="sf-with-ul" href="#">Human Practices<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/International">International Hygiene Plan</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Community">Community Outreach</a> </li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/University">University Outreach</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/FieldApplications">Case Studies</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/HPModeling">Epidemiological Modeling</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Ethical_Conditions">Ethical Considerations</a> </li> <br />
<br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Extras<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Media">Media</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Photos">Photos</a> </li> <br />
</ul><br />
</li> <br />
</ul> <br />
</div><br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/Template:HeaderTeam:Arizona State/Template:Header2012-10-17T06:08:02Z<p>Napatel: </p>
<hr />
<div><html lang="en"><br />
<!-- Made by Abhi & Jordan with help from the "https://2011.igem.org/Team:Imperial_College_London" page --><br />
<head><br />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /><br />
<style type="text/css"><br />
#top-section {<br />
width: 975px;<br />
height: 20px;<br />
background-color: transparent;<br />
border: none;<br />
}<br />
<br />
#p-logo { display: none; }<br />
#search-controls { display: none; }<br />
.firstHeading { display: none; }<br />
#contentSub { margin: 0 0 0 0; }<br />
iframe { padding: 10px 20px 10px 20px; }<br />
<br />
body {<br />
background-color:#000000;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/c/c8/BackgroundNew.jpg); <br />
background-size:100%;<br />
background-position:center; background-attachment:fixed;<br />
}<br />
<br />
.right-menu li a, .right-menu li a:hover {<br />
color: #3c6b27;<br />
background-color: transparent;<br />
}<br />
<br />
#iGEMLogo {<br />
position: absolute;<br />
top:40px;<br />
left:20px;<br />
}<br />
<br />
#ProjectTitle {<br />
position: relative;<br />
text-align:center;<br />
}<br />
<br />
#ASULogo {<br />
position: absolute;<br />
top:45px;<br />
right:25px;<br />
}<br />
<br />
#menucontainer {<br />
overflow:visible;<br />
position:relative;<br />
z-index:3;<br />
}<br />
<br />
#content {<br />
position: relative;<br />
width: 975px;<br />
margin: 0 auto;<br />
padding-top:20px;<br />
padding-left:0px;<br />
padding-right:0px;<br />
padding-bottom:0px;<br />
//background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/4/4b/2012ASUiGemLogo.png);<br />
//background-repeat:no-repeat;<br />
//background-position:center;<br />
//background-attachment:fixed;<br />
color: black;<br />
border: none;<br />
line-height: 1.5em;<br />
z-index: 2;<br />
}<br />
<br />
#bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 {<br />
margin-bottom: 0;<br />
}<br />
<br />
a {color:#t;}<br />
a:link {color:#93B825;}<br />
a:visited {color:#728F1D;}<br />
a:hover {color:#93B825;}<br />
a:active {color:#93B825;}<br />
a[name]:hover {text-decoration:none;} <br />
<br />
a.sitemap:link,a.sitemap:visited {color:#680000;font-decoration:none;}<br />
a.sitemap:hover,a.sitemap:active {color:#680000;font-decoration:underline;}<br />
<br />
h1 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 2.2em;<br />
margin: 0 0 0 0;<br />
padding: 20px 20px 12px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h2 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.7em;<br />
margin: 0 0 0 0;<br />
padding: 18px 20px 7px 20px;<br />
border-bottom: none;<br />
} <br />
<br />
h3 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.4em;<br />
margin: 0 0 0 0;<br />
padding: 16px 20px 2px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h4 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.1em;<br />
margin: 0 0 0 0;<br />
padding: 13.5px 20px 1px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
p {<br />
font-family: helvetica,sans-serif;<br />
//color: #ffffff;<br />
background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/e/ea/Layer.png);<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
margin: 0 0 0 0;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
table {<br />
background: transparent;<br />
} th {<br />
background-color:maroon;<br />
color:gold;<br />
}<br />
<br />
.border {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
}<br />
<br />
.borderMagnify {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
margin-left:-9px;<br />
margin-right:9px;<br />
}<br />
<br />
.imgbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.vidbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.newouterbox {<br />
background-color:#FF944D;<br />
border:1px solid #CCCCCC;<br />
margin:20px;<br />
padding-bottom:0px;<br />
}<br />
<br />
.newinnerbox {<br />
border:1px solid #CCCCCC;<br />
margin:10px 20px 20px 20px;<br />
padding-top:0px;<br />
padding-bottom:13px;<br />
background-color:#ffffff;<br />
}<br />
<br />
.newtext {<br />
text-align:center;<br />
background-color:#FF944D;<br />
color:#000000;<br />
}<br />
<br />
ul.a {<br />
margin: 0 0 0 40px;<br />
list-style-image: none;<br />
list-style-type:disc;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
ol.a {<br />
margin: 0 0 0 30px;<br />
list-style-position:inside;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
#BackToTop {<br />
position:fixed;<br />
bottom:0;<br />
right:0;<br />
}<br />
<br />
#Sitemap {<br />
position:fixed;<br />
bottom:0;<br />
left:0;<br />
}<br />
<br />
/*** Start of Styling for menu bar ***/<br />
/*** ESSENTIAL STYLES ***/<br />
a.collapseLink {<br />
font-weight:bold;<br />
font-size:1em;<br />
color:#225323;<br />
}<br />
.sf-menu, .sf-menu * {<br />
margin:0;<br />
padding:0;<br />
list-style:none;<br />
}<br />
.sf-menu {<br />
line-height:1.0;<br />
}<br />
.sf-menu ul {<br />
position:absolute;<br />
top:999em;<br />
width:195px; /* left offset of submenus need to match (see below) */<br />
}<br />
.sf-menu ul li {<br />
width:100%;<br />
}<br />
.sf-menu li:hover {<br />
visibility:inherit; /* fixes IE7 'sticky bug' */<br />
}<br />
.sf-menu li {<br />
float:left;<br />
position:relative;<br />
width:195px;<br />
}<br />
.sf-menu a {<br />
display:block;<br />
position:relative;<br />
}<br />
.sf-menu li:hover ul, .sf-menu li.sfHover ul {<br />
left:0;<br />
top:2.5em; /* match top ul list item height */<br />
z-index:99;<br />
}<br />
ul.sf-menu li:hover li ul, ul.sf-menu li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li:hover ul, ul.sf-menu li li.sfHover ul {<br />
left:15.3em; /* match ul width */<br />
top:0;<br />
}<br />
ul.sf-menu li li:hover li ul, ul.sf-menu li li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul {<br />
left:10em; /* match ul width */<br />
top:0;<br />
}<br />
<br />
/*** DEMO SKIN ***/<br />
.sf-menu {<br />
float:left;<br />
margin-bottom:1em;<br />
}<br />
.sf-menu a {<br />
border-left:1px solid #fff;<br />
border-top:1px solid #826554;<br />
padding:0.37em 1em 0.37em 1em;<br />
text-decoration:none;<br />
font-family:'helveticaneue', sans-serif;<br />
font-size:1.3em;<br />
}<br />
.sf-menu a, .sf-menu a:visited { /* visited pseudo selector so IE6 applies text colour*/<br />
color:#efefef;<br />
}<br />
.sf-menu li, .sf-menu li li, .sf-menu li li li {<br />
background:#990000;<br />
}<br />
.sf-menu li:hover, .sf-menu li.sfHover, .sf-menu a:focus, .sf-menu a:hover, .sf-menu a:active {<br />
background:#b30000;<br />
outline:0;<br />
}<br />
<br />
/*** arrows **/<br />
.sf-menu a.sf-with-ul {<br />
cursor:default; <br />
padding-right:2.25em;<br />
min-width:1px; /* trigger IE7 hasLayout so spans position accurately */<br />
}<br />
.sf-sub-indicator {<br />
position:absolute;<br />
display:block;<br />
right:.75em;<br />
top:1.05em; /* IE6 only */<br />
width:10px;<br />
height:10px;<br />
text-indent:-999em;<br />
overflow:hidden;<br />
background:url('https://static.igem.org/mediawiki/2011/2/2f/ICL_MenuArrow.png') no-repeat -10px -100px;<br />
/* 8-bit indexed alpha png. IE6 gets solid image only */<br />
}<br />
a > .sf-sub-indicator { /* give all except IE6 the correct values */<br />
top:.8em;<br />
background-position:0 -100px; /* use translucent arrow for modern browsers*/<br />
}<br />
/* apply hovers to modern browsers */<br />
a:focus > .sf-sub-indicator,<br />
a:hover > .sf-sub-indicator,<br />
a:active > .sf-sub-indicator,<br />
li:hover > a > .sf-sub-indicator,<br />
li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px -100px; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/* point right for anchors in subs */<br />
.sf-menu ul .sf-sub-indicator { background-position: -10px 0; }<br />
.sf-menu ul a > .sf-sub-indicator { background-position: 0 0; }<br />
/* apply hovers to modern browsers */<br />
.sf-menu ul a:focus > .sf-sub-indicator,<br />
.sf-menu ul a:hover > .sf-sub-indicator,<br />
.sf-menu ul a:active > .sf-sub-indicator,<br />
.sf-menu ul li:hover > a > .sf-sub-indicator,<br />
.sf-menu ul li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px 0; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/*** shadows for all but IE6 ***/<br />
.sf-shadow ul {<br />
background:url('https://static.igem.org/mediawiki/2011/9/9f/ICL_Shadow.png') no-repeat bottom right;<br />
padding:0 8px 9px 0;<br />
-moz-border-radius-bottomleft:17px;<br />
-moz-border-radius-topright:17px;<br />
-webkit-border-top-right-radius:17px;<br />
-webkit-border-bottom-left-radius:17px;<br />
}<br />
<br />
.sf-shadow ul.sf-shadow-off {<br />
background:transparent;<br />
}<br />
</style><br />
<br />
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/hoverIntent?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/superfishjs?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/magnifier?action=raw&ctype=text/js"><br />
/***********************************************<br />
* jQuery Image Magnify- (c) Dynamic Drive DHTML code library (www.dynamicdrive.com)<br />
* This notice MUST stay intact for legal use<br />
* Visit Dynamic Drive at http://www.dynamicdrive.com/ for this script and 100s more<br />
***********************************************/<br />
</script><br />
<br />
<script type="text/javascript"><br />
var $ = jQuery;<br />
jQuery.imageMagnify.zIndexcounter = 1000;<br />
</script><br />
<br />
<script><br />
$(document).ready(function() {<br />
$("sup").click(function () {<br />
if ($(this).html().substr(0,1)=="[")<br />
{<br />
if ($('.technology').length>0)<br />
{<br />
ddaccordion.expandone('technology', $('.technology').length-1)<br />
setTimeout("window.scrollBy(0,50000)",200)<br />
}<br />
else window.scrollBy(0,50000)<br />
}<br />
});<br />
$("sup").mouseover(function () {<br />
if ($(this).html().substr(0,1)=="[") $(this).css('cursor', 'pointer');<br />
});<br />
});<br />
</script><br />
<br />
<script> <br />
$(document).ready(function() { <br />
$('ul.sf-menu').superfish({ <br />
}); <br />
});<br />
</script><br />
</head><br />
<br />
<body><br />
<a name="top"></a><br />
<!-----<br />
<div id='iGEMLogo'><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:120px;" /><br />
</a><br />
</div><br />
<br />
<div id='ProjectTitle'><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/5/5f/CRSYS.png" style="width:550px;" /><br />
<!---Before: https://static.igem.org/mediawiki/2012/d/db/2012_Project_logo.png---><!----<br />
</a><br />
</div><br />
<br />
<div id='ASULogo'><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="150" height="70" /><br />
</div><br />
-----><br />
<div id='header' align="center"><br />
<table width="950"><br />
<tr><br />
<td><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:100px;" /><br />
</a><br />
</td><br />
<td align="center"><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/9/9a/AsuCrsysLogothingy.png" style="width:591px;" /><br />
</a><br />
</td><br />
<td><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="125" /><br />
</td><br />
</table><br />
<br /><br />
</div><br />
<br />
<br />
<br />
<div id="BackToTop"><br />
<a href="#top"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2d/ArrowColorChanged.png" width="50px" /><br />
</a><br />
</div><br />
<br />
<div id="Sitemap"><br />
<a href='https://2012.igem.org/Team:Arizona_State/Sitemap'><br />
<img src="https://static.igem.org/mediawiki/2012/3/30/SiteMapColorChange.png" width="100px" /><br />
</a><br />
</div><br />
<br />
<div id='menucontainer'><br />
<ul class="sf-menu sf-navbar"><br />
<li><a class="sf-with-ul" href="">Project<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State">Home</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Problem">The Problem</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Magainin">Cell Surface Biosensor</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Chimeric_Reporter">DNA-Protein Chimera Biosensor</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Notebook">Notebook</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/References">References</a><br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Team<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Team">Members</a></li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Attributions">Attributions</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2012">Official Team Profile</a></li><br />
</ul><br />
</li><br />
<br />
<li><a class="sf-with-ul" href="#">Results<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Data">Data</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Parts">BioBricks</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Accomplishments">Judging Criteria</a> </li><br />
</ul><br />
</li><br />
<li><a class="sf-with-ul" href="#">Human Practices<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/International">International Hygiene Plan</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Community">Community Outreach</a> </li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/University">University Outreach</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/FieldApplications">Case Studies</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/HPModeling">Epidemiological Modeling</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Ethical_Conditions">Ethical Considerations</a> </li> <br />
<br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Extras<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Safety">Safety</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Media">Media</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Photos">Photos</a> </li> <br />
</ul><br />
</li> <br />
</ul> <br />
</div><br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_StateTeam:Arizona State2012-10-17T00:00:27Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Project Overview</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Arizona State's 2012 iGEM project aims to develop a portable water-borne pathogen biosensor. The team is looking towards addressing problems that prevent existing biosensor technologies from being effectively used in the field. Specifically, we are working on a sensor that is cheap, portable, robust, easily customizable, and produces a quick response. Our vision is to build a user-friendly device that does not require any technical expertise to operate. <br />
</p><br />
<p><br />
<h4 style="text-align:center;">Figure 1: Biosensor Production Pipeline</h4><br />
</p><br />
<p><br />
<table width="950"><br />
<tr><br />
<td align="center"><br />
<img src="https://static.igem.org/mediawiki/2012/1/12/ASUiGEM2012_productionpipeline.png" width="400"><br />
</td><br />
</table><br />
</p> <br />
<br />
<h1>Abstract</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Diarrheic pathogens including <i>E.coli</i> O157:H7 serotype, <i>Campylobacter</i>, <i>Shigella</i>, and <i>Salmonella</i> often contaminate drinking water supplies in developing nations and are responsible for approximately 1.5 million worldwide annual deaths. Current technologies for detection of bacteria include DNA hybridization FRET signaling, electrical detection via immobilized antimicrobial peptides, and PCR amplification followed by gel visualization. Our method of bacterial detection fills a niche in biosensor technology. Our design implies lower costs, higher portability, and a more rapid signal output than most bacterial biosensors. Additionally, our interchangeable DNA probe confers modularity, allowing for a range of bacterial detection. Using a novel split beta-galactosidase complementation assay, we have designed three unique chimeric proteins that recognize and bind to specific pathogenic markers and create a functioning beta-galactosidase enzyme. This functioning enzyme unit then cleaves X-gal and produces a colorimetric output signal. Our research demonstrates success in initial stages of chimeric protein assembly. <br />
</p><br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<br /><br />
<br />
<br /><br />
<br />
<div align="center"><br />
<b>Contact Us</b><br />
<br /><br />
Arizona State University<br />
<br /><br />
ECG 334, PO BOX 9709<br />
<br /><br />
Tempe, Arizona 85287<br />
</div><br />
<br />
</body><br />
</html><br />
{{:Team:Arizona_State/Template:twitter}}<br />
{{:Team:Arizona_State/sitemap}}</div>Napatelhttp://2012.igem.org/Team:Arizona_StateTeam:Arizona State2012-10-16T23:59:33Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Project Overview</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Arizona State's 2012 iGEM project aims to develop a portable water-borne pathogen biosensor. The team is looking towards addressing problems that prevent existing biosensor technologies from being effectively used in the field. Specifically, our team is working on a sensor that is cheap, portable, robust easily customizable, and produces a cheap response. Our vision is to build a user-friendly device that does not require any technical expertise to operate. <br />
</p><br />
<p><br />
<h4 style="text-align:center;">Figure 1: Biosensor Production Pipeline</h4><br />
</p><br />
<p><br />
<table width="950"><br />
<tr><br />
<td align="center"><br />
<img src="https://static.igem.org/mediawiki/2012/1/12/ASUiGEM2012_productionpipeline.png" width="400"><br />
</td><br />
</table><br />
</p> <br />
<br />
<h1>Abstract</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Diarrheic pathogens including <i>E.coli</i> O157:H7 serotype, <i>Campylobacter</i>, <i>Shigella</i>, and <i>Salmonella</i> often contaminate drinking water supplies in developing nations and are responsible for approximately 1.5 million worldwide annual deaths. Current technologies for detection of bacteria include DNA hybridization FRET signaling, electrical detection via immobilized antimicrobial peptides, and PCR amplification followed by gel visualization. Our method of bacterial detection fills a niche in biosensor technology. Our design implies lower costs, higher portability, and a more rapid signal output than most bacterial biosensors. Additionally, our interchangeable DNA probe confers modularity, allowing for a range of bacterial detection. Using a novel split beta-galactosidase complementation assay, we have designed three unique chimeric proteins that recognize and bind to specific pathogenic markers and create a functioning beta-galactosidase enzyme. This functioning enzyme unit then cleaves X-gal and produces a colorimetric output signal. Our research demonstrates success in initial stages of chimeric protein assembly. <br />
</p><br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<br /><br />
<br />
<br /><br />
<br />
<div align="center"><br />
<b>Contact Us</b><br />
<br /><br />
Arizona State University<br />
<br /><br />
ECG 334, PO BOX 9709<br />
<br /><br />
Tempe, Arizona 85287<br />
</div><br />
<br />
</body><br />
</html><br />
{{:Team:Arizona_State/Template:twitter}}<br />
{{:Team:Arizona_State/sitemap}}</div>Napatelhttp://2012.igem.org/Team:Arizona_StateTeam:Arizona State2012-10-16T23:52:51Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Project Overview</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Arizona State's 2012 iGEM project aims to develop a portable water-borne pathogen biosensor. The team is looking towards addressing problems that prevent existing biosensor technologies from being effectively used in the field. Specifically, our team is working on a sensor that is cheap, portable, robust easily customizable, and produces a cheap response. Our vision is to build a user-friendly device that does not require any technical expertise to operate. <br />
</p><br />
<p><br />
<b><i>Figure 1: Biosensor Production Pipeline</i></b><br />
</p><br />
<p><br />
<img src="https://static.igem.org/mediawiki/2012/1/12/ASUiGEM2012_productionpipeline.png" width="800"><br />
</p> <br />
<br />
<h1>Abstract</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Diarrheic pathogens including <i>E.coli</i> O157:H7 serotype, <i>Campylobacter</i>, <i>Shigella</i>, and <i>Salmonella</i> often contaminate drinking water supplies in developing nations and are responsible for approximately 1.5 million worldwide annual deaths. Current technologies for detection of bacteria include DNA hybridization FRET signaling, electrical detection via immobilized antimicrobial peptides, and PCR amplification followed by gel visualization. Our method of bacterial detection fills a niche in biosensor technology. Our design implies lower costs, higher portability, and a more rapid signal output than most bacterial biosensors. Additionally, our interchangeable DNA probe confers modularity, allowing for a range of bacterial detection. Using a novel split beta-galactosidase complementation assay, we have designed three unique chimeric proteins that recognize and bind to specific pathogenic markers and create a functioning beta-galactosidase enzyme. This functioning enzyme unit then cleaves X-gal and produces a colorimetric output signal. Our research demonstrates success in initial stages of chimeric protein assembly. <br />
</p><br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<br /><br />
<br />
<br /><br />
<br />
<div align="center"><br />
<b>Contact Us</b><br />
<br /><br />
Arizona State University<br />
<br /><br />
ECG 334, PO BOX 9709<br />
<br /><br />
Tempe, Arizona 85287<br />
</div><br />
<br />
</body><br />
</html><br />
{{:Team:Arizona_State/Template:twitter}}<br />
{{:Team:Arizona_State/sitemap}}</div>Napatelhttp://2012.igem.org/File:ASUiGEM2012_productionpipeline.pngFile:ASUiGEM2012 productionpipeline.png2012-10-16T23:51:48Z<p>Napatel: </p>
<hr />
<div></div>Napatelhttp://2012.igem.org/Team:Arizona_State/ProblemTeam:Arizona State/Problem2012-10-16T23:48:40Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Our Problem</h1><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Viewed as a minor inconvenience in the developed world, diarrhea can be a death sentence in developing countries. Diarrhea can be life threatening as it causes severe dehydration as a result of extensive fluid loss. An estimated 2.0 billion cases of diarrhea occur each year amongst children under five years of age. Of these cases, 1.5 million children die. The major pathogens that most frequently cause acute childhood diarrhea cases are bacterial pathogens such as <i>E. coli, Shigella, Campylobacter and Salmonella</i>. The ASU iGEM team plans to develop an inexpensive way for communities to test the purity of water sources- and identify the specific pathogens in the water source- in efforts of reducing the incidence of childhood diarrhea and ultimately decreasing mortality rates. Existing biosensors for water-borne pathogens are either costly, unaccessible to developing countries, require large machinery to operate, difficult to use without training, and not very reliable. For example, immunoassays, which uses antibodies specific for certain antigens on pathogenic diarrhea, have a good turnaround time. However, not all antigens have available antibodies that can be used for detection, and those antibodies that are available can be very costly. <br />
</p><br />
<p><br />
<b><i>Figure 1: Epidemiology map indicating disability-adjusted life year for diarrhea per 100,000 inhabitants (2004)</i></b><br />
</p><br />
<img src="https://static.igem.org/mediawiki/2012/0/03/Asuigem_diseasemap.png" width="800"><br />
<br /><br />
<br /><br />
<br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h1>Quantitative considerations</h1><br />
<br />
<p><b>What concentration of pathogens causes sickness?</b><br />
<br />
<p>In determining what kinds of scenarios our biosensor would work in, a concentration had to be determined for what would be considered an outbreak. Based on research that was found for our project, patients' stool samples were tested for antibodies. An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen). <br />
<br /><br />
<p><b>What specific design approaches did we take to try to reduce false positives, while making the biosensor effective? </b><br />
<p> A coliform count is defined as a test of water contamination in which the number of the colonies of coliform-bacteria <i>Escherichia coli (E.coli)</i> per 100 milliliter of water is counted. The result is expressed as “Coliform Microbial Density” and indicates the extent of fecal matter present in it. According to common water quality standards water can have about 200 colonies, and about 1000 in recreational water” (Business Dictionary). <br />
<p><br />
Environmental Protection Agency standards define non-potable water as a sample that contains one bacterium per 100 mL.<br />
</p><br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Why are we doing this?</h2><br />
<br />
<p><br />
<p><b>What do we hope to accomplish/want to figure out?</b><br />
<p><br />
For this project we are hoping to make our biosensor as user friendly and most cost effective product as possible. In the process in making this design we also wanted to address the results from using the biosensor. We wanted our project to give results in real time and be able to determine the phenotype of the potential pathogen. <br />
<br /><br />
<p><b>Who are we doing this for? What do we care about? </b><br />
<p> This project is primarily based on its applications. We wanted to develop a low-cost biosensor that could be implemented in developing countries. This is because pathogenic bacteria causes diarrhea which is one of the world's leading global health issues. By designing our biosensor it would be a potential solution to this problem. <br />
<br />
<br /><br />
<p><b>What is our ultimate goal?</b><br />
<p>Our ultimate goal for the project is to be able to see our biosensor used in developing nations. Ideally our biosensor would be able to be used as an early detection device in order to prevent future pathogenic outbreaks. This would be a solution to not only maintaining a healthy water supply but also to also improve the overall sanitation of developing nations. <br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/ProblemTeam:Arizona State/Problem2012-10-16T23:47:18Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Our Problem</h1><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Viewed as a minor inconvenience in the developed world, diarrhea can be a death sentence in developing countries. Diarrhea can be life threatening as it causes severe dehydration as a result of extensive fluid loss. An estimated 2.0 billion cases of diarrhea occur each year amongst children under five years of age. Of these cases, 1.5 million children die. The major pathogens that most frequently cause acute childhood diarrhea cases are bacterial pathogens such as <i>E. coli, Shigella, Campylobacter and Salmonella</i>. The ASU iGEM team plans to develop an inexpensive way for communities to test the purity of water sources- and identify the specific pathogens in the water source- in efforts of reducing the incidence of childhood diarrhea and ultimately decreasing mortality rates. Existing biosensors for water-borne pathogens are either costly, unaccessible to developing countries, require large machinery to operate, difficult to use without training, and not very reliable. For example, immunoassays, which uses antibodies specific for certain antigens on pathogenic diarrhea, have a good turnaround time. However, not all antigens have available antibodies that can be used for detection, and those antibodies that are available can be very costly. <br />
</p><br />
<p><br />
<b><i>Figure 1: Epidemiology map indicating disability-adjusted life year for diarrhea per 100,000 inhabitants (2004)</i></b><br />
</p><br />
<img src="https://static.igem.org/mediawiki/2012/0/03/Asuigem_diseasemap.png" width="800"><br />
<br /><br />
<br /><br />
<br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h1>Quantitative considerations</h1><br />
<br />
<p><b>What concentration of pathogens causes sickness?</b><br />
<br />
<p>In determining what kinds of scenarios our biosensor would work in, a concentration had to be determined for what would be considered an outbreak. Based on research that was found for our project, patients' stool samples were tested for antibodies. An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen). <br />
<br /><br />
<p><b>What specific design approaches did we take to try to reduce false positives, while making the biosensor effective? </b><br />
<p> A coliform count is defined as a test of water contamination in which the number of the colonies of coliform-bacteria <i>Escherichia coli (E.coli)</i> per 100 milliliter of water is counted. The result is expressed as “Coliform Microbial Density” and indicates the extent of fecal matter present in it. According to common water quality standards water can have about 200 colonies, and about 1000 in recreational water” (Business Dictionary). <br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Why are we doing this?</h2><br />
<br />
<p><br />
<p><b>What do we hope to accomplish/want to figure out?</b><br />
<p><br />
For this project we are hoping to make our biosensor as user friendly and most cost effective product as possible. In the process in making this design we also wanted to address the results from using the biosensor. We wanted our project to give results in real time and be able to determine the phenotype of the potential pathogen. <br />
<br /><br />
<p><b>Who are we doing this for? What do we care about? </b><br />
<p> This project is primarily based on its applications. We wanted to develop a low-cost biosensor that could be implemented in developing countries. This is because pathogenic bacteria causes diarrhea which is one of the world's leading global health issues. By designing our biosensor it would be a potential solution to this problem. <br />
<br />
<br /><br />
<p><b>What is our ultimate goal?</b><br />
<p>Our ultimate goal for the project is to be able to see our biosensor used in developing nations. Ideally our biosensor would be able to be used as an early detection device in order to prevent future pathogenic outbreaks. This would be a solution to not only maintaining a healthy water supply but also to also improve the overall sanitation of developing nations. <br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/ProblemTeam:Arizona State/Problem2012-10-16T23:46:55Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Our Problem</h1><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Viewed as a minor inconvenience in the developed world, diarrhea can be a death sentence in developing countries. Diarrhea can be life threatening as it causes severe dehydration as a result of extensive fluid loss. An estimated 2.0 billion cases of diarrhea occur each year amongst children under five years of age. Of these cases, 1.5 million children die. The major pathogens that most frequently cause acute childhood diarrhea cases are bacterial pathogens such as <i>E. coli, Shigella, Campylobacter and Salmonella</i>. The ASU iGEM team plans to develop an inexpensive way for communities to test the purity of water sources- and identify the specific pathogens in the water source- in efforts of reducing the incidence of childhood diarrhea and ultimately decreasing mortality rates. Existing biosensors for water-borne pathogens are either costly, unaccessible to developing countries, require large machinery to operate, difficult to use without training, and not very reliable. For example, immunoassays, which uses antibodies specific for certain antigens on pathogenic diarrhea, have a good turnaround time. However, not all antigens have available antibodies that can be used for detection, and those antibodies that are available can be very costly. <br />
</p><br />
<p><br />
<b><i>Figure 1: Epidemiology map indicating disability-adjusted life year for diarrhea per 100,000 inhabitants (2004)</i></b><br />
</p><br />
<img src="https://static.igem.org/mediawiki/2012/0/03/Asuigem_diseasemap.png" width="800"><br />
<br /><br />
<br /><br />
<br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Quantitative considerations</h2><br />
<br />
<p><b>What concentration of pathogens causes sickness?</b><br />
<br />
<p>In determining what kinds of scenarios our biosensor would work in, a concentration had to be determined for what would be considered an outbreak. Based on research that was found for our project, patients' stool samples were tested for antibodies. An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen). <br />
<br /><br />
<p><b>What specific design approaches did we take to try to reduce false positives, while making the biosensor effective? </b><br />
<p> A coliform count is defined as a test of water contamination in which the number of the colonies of coliform-bacteria <i>Escherichia coli (E.coli)</i> per 100 milliliter of water is counted. The result is expressed as “Coliform Microbial Density” and indicates the extent of fecal matter present in it. According to common water quality standards water can have about 200 colonies, and about 1000 in recreational water” (Business Dictionary). <br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Why are we doing this?</h2><br />
<br />
<p><br />
<p><b>What do we hope to accomplish/want to figure out?</b><br />
<p><br />
For this project we are hoping to make our biosensor as user friendly and most cost effective product as possible. In the process in making this design we also wanted to address the results from using the biosensor. We wanted our project to give results in real time and be able to determine the phenotype of the potential pathogen. <br />
<br /><br />
<p><b>Who are we doing this for? What do we care about? </b><br />
<p> This project is primarily based on its applications. We wanted to develop a low-cost biosensor that could be implemented in developing countries. This is because pathogenic bacteria causes diarrhea which is one of the world's leading global health issues. By designing our biosensor it would be a potential solution to this problem. <br />
<br />
<br /><br />
<p><b>What is our ultimate goal?</b><br />
<p>Our ultimate goal for the project is to be able to see our biosensor used in developing nations. Ideally our biosensor would be able to be used as an early detection device in order to prevent future pathogenic outbreaks. This would be a solution to not only maintaining a healthy water supply but also to also improve the overall sanitation of developing nations. <br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/ProblemTeam:Arizona State/Problem2012-10-16T23:46:36Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Detailed Problem Description</h1><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Our Problem</h2><br />
<br />
<p><br />
Viewed as a minor inconvenience in the developed world, diarrhea can be a death sentence in developing countries. Diarrhea can be life threatening as it causes severe dehydration as a result of extensive fluid loss. An estimated 2.0 billion cases of diarrhea occur each year amongst children under five years of age. Of these cases, 1.5 million children die. The major pathogens that most frequently cause acute childhood diarrhea cases are bacterial pathogens such as <i>E. coli, Shigella, Campylobacter and Salmonella</i>. The ASU iGEM team plans to develop an inexpensive way for communities to test the purity of water sources- and identify the specific pathogens in the water source- in efforts of reducing the incidence of childhood diarrhea and ultimately decreasing mortality rates. Existing biosensors for water-borne pathogens are either costly, unaccessible to developing countries, require large machinery to operate, difficult to use without training, and not very reliable. For example, immunoassays, which uses antibodies specific for certain antigens on pathogenic diarrhea, have a good turnaround time. However, not all antigens have available antibodies that can be used for detection, and those antibodies that are available can be very costly. <br />
</p><br />
<p><br />
<b><i>Figure 1: Epidemiology map indicating disability-adjusted life year for diarrhea per 100,000 inhabitants (2004)</i></b><br />
</p><br />
<img src="https://static.igem.org/mediawiki/2012/0/03/Asuigem_diseasemap.png" width="800"><br />
<br /><br />
<br /><br />
<br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Quantitative considerations</h2><br />
<br />
<p><b>What concentration of pathogens causes sickness?</b><br />
<br />
<p>In determining what kinds of scenarios our biosensor would work in, a concentration had to be determined for what would be considered an outbreak. Based on research that was found for our project, patients' stool samples were tested for antibodies. An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen). <br />
<br /><br />
<p><b>What specific design approaches did we take to try to reduce false positives, while making the biosensor effective? </b><br />
<p> A coliform count is defined as a test of water contamination in which the number of the colonies of coliform-bacteria <i>Escherichia coli (E.coli)</i> per 100 milliliter of water is counted. The result is expressed as “Coliform Microbial Density” and indicates the extent of fecal matter present in it. According to common water quality standards water can have about 200 colonies, and about 1000 in recreational water” (Business Dictionary). <br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Why are we doing this?</h2><br />
<br />
<p><br />
<p><b>What do we hope to accomplish/want to figure out?</b><br />
<p><br />
For this project we are hoping to make our biosensor as user friendly and most cost effective product as possible. In the process in making this design we also wanted to address the results from using the biosensor. We wanted our project to give results in real time and be able to determine the phenotype of the potential pathogen. <br />
<br /><br />
<p><b>Who are we doing this for? What do we care about? </b><br />
<p> This project is primarily based on its applications. We wanted to develop a low-cost biosensor that could be implemented in developing countries. This is because pathogenic bacteria causes diarrhea which is one of the world's leading global health issues. By designing our biosensor it would be a potential solution to this problem. <br />
<br />
<br /><br />
<p><b>What is our ultimate goal?</b><br />
<p>Our ultimate goal for the project is to be able to see our biosensor used in developing nations. Ideally our biosensor would be able to be used as an early detection device in order to prevent future pathogenic outbreaks. This would be a solution to not only maintaining a healthy water supply but also to also improve the overall sanitation of developing nations. <br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/ProblemTeam:Arizona State/Problem2012-10-16T23:46:16Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Detailed Problem Description</h1><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>What is the problem we want to solve?</h2><br />
<br />
<p><br />
Viewed as a minor inconvenience in the developed world, diarrhea can be a death sentence in developing countries. Diarrhea can be life threatening as it causes severe dehydration as a result of extensive fluid loss. An estimated 2.0 billion cases of diarrhea occur each year amongst children under five years of age. Of these cases, 1.5 million children die. The major pathogens that most frequently cause acute childhood diarrhea cases are bacterial pathogens such as <i>E. coli, Shigella, Campylobacter and Salmonella</i>. The ASU iGEM team plans to develop an inexpensive way for communities to test the purity of water sources- and identify the specific pathogens in the water source- in efforts of reducing the incidence of childhood diarrhea and ultimately decreasing mortality rates. Existing biosensors for water-borne pathogens are either costly, unaccessible to developing countries, require large machinery to operate, difficult to use without training, and not very reliable. For example, immunoassays, which uses antibodies specific for certain antigens on pathogenic diarrhea, have a good turnaround time. However, not all antigens have available antibodies that can be used for detection, and those antibodies that are available can be very costly. <br />
</p><br />
<p><br />
<b><i>Figure 1: Epidemiology map indicating disability-adjusted life year for diarrhea per 100,000 inhabitants (2004)</i></b><br />
</p><br />
<img src="https://static.igem.org/mediawiki/2012/0/03/Asuigem_diseasemap.png" width="800"><br />
<br /><br />
<br /><br />
<br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Quantitative considerations</h2><br />
<br />
<p><b>What concentration of pathogens causes sickness?</b><br />
<br />
<p>In determining what kinds of scenarios our biosensor would work in, a concentration had to be determined for what would be considered an outbreak. Based on research that was found for our project, patients' stool samples were tested for antibodies. An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen). <br />
<br /><br />
<p><b>What specific design approaches did we take to try to reduce false positives, while making the biosensor effective? </b><br />
<p> A coliform count is defined as a test of water contamination in which the number of the colonies of coliform-bacteria <i>Escherichia coli (E.coli)</i> per 100 milliliter of water is counted. The result is expressed as “Coliform Microbial Density” and indicates the extent of fecal matter present in it. According to common water quality standards water can have about 200 colonies, and about 1000 in recreational water” (Business Dictionary). <br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Why are we doing this?</h2><br />
<br />
<p><br />
<p><b>What do we hope to accomplish/want to figure out?</b><br />
<p><br />
For this project we are hoping to make our biosensor as user friendly and most cost effective product as possible. In the process in making this design we also wanted to address the results from using the biosensor. We wanted our project to give results in real time and be able to determine the phenotype of the potential pathogen. <br />
<br /><br />
<p><b>Who are we doing this for? What do we care about? </b><br />
<p> This project is primarily based on its applications. We wanted to develop a low-cost biosensor that could be implemented in developing countries. This is because pathogenic bacteria causes diarrhea which is one of the world's leading global health issues. By designing our biosensor it would be a potential solution to this problem. <br />
<br />
<br /><br />
<p><b>What is our ultimate goal?</b><br />
<p>Our ultimate goal for the project is to be able to see our biosensor used in developing nations. Ideally our biosensor would be able to be used as an early detection device in order to prevent future pathogenic outbreaks. This would be a solution to not only maintaining a healthy water supply but also to also improve the overall sanitation of developing nations. <br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/ProblemTeam:Arizona State/Problem2012-10-16T23:41:12Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Detailed Problem Description</h1><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>What is the problem we want to solve?</h2><br />
<br />
<p><br />
Viewed as a minor inconvenience in the developed world, diarrhea can be a death sentence in developing countries. Diarrhea can be life threatening as it causes severe dehydration as a result of extensive fluid loss. An estimated 2.0 billion cases of diarrhea occur each year amongst children under five years of age. Of these cases, 1.5 million children die. The major pathogens that most frequently cause acute childhood diarrhea cases are bacterial pathogens such as <i>E. coli, Shigella, Campylobacter and Salmonella</i>. The ASU iGEM team plans to develop an inexpensive way for communities to test the purity of water sources- and identify the specific pathogens in the water source- in efforts of reducing the incidence of childhood diarrhea and ultimately decreasing mortality rates. Existing biosensors for water-borne pathogens are either costly, unaccessible to developing countries, require large machinery to operate, difficult to use without training, and not very reliable. For example, immunoassays, which uses antibodies specific for certain antigens on pathogenic diarrhea, have a good turnaround time. However, not all antigens have available antibodies that can be used for detection, and those antibodies that are available can be very costly. <br />
<img src="https://static.igem.org/mediawiki/2012/0/03/Asuigem_diseasemap.png" width="800"><br />
<br /><br />
<br /><br />
<br />
</p><br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Quantitative considerations</h2><br />
<br />
<p><b>What concentration of pathogens causes sickness?</b><br />
<br />
<p>In determining what kinds of scenarios our biosensor would work in, a concentration had to be determined for what would be considered an outbreak. Based on research that was found for our project, patients' stool samples were tested for antibodies. An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen). <br />
<br /><br />
<p><b>What specific design approaches did we take to try to reduce false positives, while making the biosensor effective? </b><br />
<p> A coliform count is defined as a test of water contamination in which the number of the colonies of coliform-bacteria <i>Escherichia coli (E.coli)</i> per 100 milliliter of water is counted. The result is expressed as “Coliform Microbial Density” and indicates the extent of fecal matter present in it. According to common water quality standards water can have about 200 colonies, and about 1000 in recreational water” (Business Dictionary). <br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Why are we doing this?</h2><br />
<br />
<p><br />
<p><b>What do we hope to accomplish/want to figure out?</b><br />
<p><br />
For this project we are hoping to make our biosensor as user friendly and most cost effective product as possible. In the process in making this design we also wanted to address the results from using the biosensor. We wanted our project to give results in real time and be able to determine the phenotype of the potential pathogen. <br />
<br /><br />
<p><b>Who are we doing this for? What do we care about? </b><br />
<p> This project is primarily based on its applications. We wanted to develop a low-cost biosensor that could be implemented in developing countries. This is because pathogenic bacteria causes diarrhea which is one of the world's leading global health issues. By designing our biosensor it would be a potential solution to this problem. <br />
<br />
<br /><br />
<p><b>What is our ultimate goal?</b><br />
<p>Our ultimate goal for the project is to be able to see our biosensor used in developing nations. Ideally our biosensor would be able to be used as an early detection device in order to prevent future pathogenic outbreaks. This would be a solution to not only maintaining a healthy water supply but also to also improve the overall sanitation of developing nations. <br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/ProblemTeam:Arizona State/Problem2012-10-16T23:41:02Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Detailed Problem Description</h1><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>What is the problem we want to solve?</h2><br />
<br />
<p><br />
Viewed as a minor inconvenience in the developed world, diarrhea can be a death sentence in developing countries. Diarrhea can be life threatening as it causes severe dehydration as a result of extensive fluid loss. An estimated 2.0 billion cases of diarrhea occur each year amongst children under five years of age. Of these cases, 1.5 million children die. The major pathogens that most frequently cause acute childhood diarrhea cases are bacterial pathogens such as <i>E. coli, Shigella, Campylobacter and Salmonella</i>. The ASU iGEM team plans to develop an inexpensive way for communities to test the purity of water sources- and identify the specific pathogens in the water source- in efforts of reducing the incidence of childhood diarrhea and ultimately decreasing mortality rates. Existing biosensors for water-borne pathogens are either costly, unaccessible to developing countries, require large machinery to operate, difficult to use without training, and not very reliable. For example, immunoassays, which uses antibodies specific for certain antigens on pathogenic diarrhea, have a good turnaround time. However, not all antigens have available antibodies that can be used for detection, and those antibodies that are available can be very costly. <br />
<img src="https://static.igem.org/mediawiki/2012/0/03/Asuigem_diseasemap.png" width="800" height="600"><br />
<br /><br />
<br /><br />
<br />
</p><br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Quantitative considerations</h2><br />
<br />
<p><b>What concentration of pathogens causes sickness?</b><br />
<br />
<p>In determining what kinds of scenarios our biosensor would work in, a concentration had to be determined for what would be considered an outbreak. Based on research that was found for our project, patients' stool samples were tested for antibodies. An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen). <br />
<br /><br />
<p><b>What specific design approaches did we take to try to reduce false positives, while making the biosensor effective? </b><br />
<p> A coliform count is defined as a test of water contamination in which the number of the colonies of coliform-bacteria <i>Escherichia coli (E.coli)</i> per 100 milliliter of water is counted. The result is expressed as “Coliform Microbial Density” and indicates the extent of fecal matter present in it. According to common water quality standards water can have about 200 colonies, and about 1000 in recreational water” (Business Dictionary). <br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Why are we doing this?</h2><br />
<br />
<p><br />
<p><b>What do we hope to accomplish/want to figure out?</b><br />
<p><br />
For this project we are hoping to make our biosensor as user friendly and most cost effective product as possible. In the process in making this design we also wanted to address the results from using the biosensor. We wanted our project to give results in real time and be able to determine the phenotype of the potential pathogen. <br />
<br /><br />
<p><b>Who are we doing this for? What do we care about? </b><br />
<p> This project is primarily based on its applications. We wanted to develop a low-cost biosensor that could be implemented in developing countries. This is because pathogenic bacteria causes diarrhea which is one of the world's leading global health issues. By designing our biosensor it would be a potential solution to this problem. <br />
<br />
<br /><br />
<p><b>What is our ultimate goal?</b><br />
<p>Our ultimate goal for the project is to be able to see our biosensor used in developing nations. Ideally our biosensor would be able to be used as an early detection device in order to prevent future pathogenic outbreaks. This would be a solution to not only maintaining a healthy water supply but also to also improve the overall sanitation of developing nations. <br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/File:Asuigem_diseasemap.pngFile:Asuigem diseasemap.png2012-10-16T23:39:39Z<p>Napatel: </p>
<hr />
<div></div>Napatelhttp://2012.igem.org/Team:Arizona_StateTeam:Arizona State2012-10-16T23:35:10Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Project Overview</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Arizona State's 2012 iGEM project aims to develop a portable water-borne pathogen biosensor. The team is looking towards addressing problems that prevent existing biosensor technologies from being effectively used in the field. Specifically, our team is working on a sensor that is cheap, portable, robust easily customizable, and produces a cheap response. Our vision is to build a user-friendly device that does not require any technical expertise to operate. <br />
</p><br />
<br />
<br />
<br />
<h1>Abstract</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Diarrheic pathogens including <i>E.coli</i> O157:H7 serotype, <i>Campylobacter</i>, <i>Shigella</i>, and <i>Salmonella</i> often contaminate drinking water supplies in developing nations and are responsible for approximately 1.5 million worldwide annual deaths. Current technologies for detection of bacteria include DNA hybridization FRET signaling, electrical detection via immobilized antimicrobial peptides, and PCR amplification followed by gel visualization. Our method of bacterial detection fills a niche in biosensor technology. Our design implies lower costs, higher portability, and a more rapid signal output than most bacterial biosensors. Additionally, our interchangeable DNA probe confers modularity, allowing for a range of bacterial detection. Using a novel split beta-galactosidase complementation assay, we have designed three unique chimeric proteins that recognize and bind to specific pathogenic markers and create a functioning beta-galactosidase enzyme. This functioning enzyme unit then cleaves X-gal and produces a colorimetric output signal. Our research demonstrates success in initial stages of chimeric protein assembly. <br />
</p><br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<br /><br />
<br />
<br /><br />
<br />
<div align="center"><br />
<b>Contact Us</b><br />
<br /><br />
Arizona State University<br />
<br /><br />
ECG 334, PO BOX 9709<br />
<br /><br />
Tempe, Arizona 85287<br />
</div><br />
<br />
</body><br />
</html><br />
{{:Team:Arizona_State/Template:twitter}}<br />
{{:Team:Arizona_State/sitemap}}</div>Napatelhttp://2012.igem.org/Team:Arizona_StateTeam:Arizona State2012-10-16T23:28:27Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<center><img src="https://static.igem.org/mediawiki/2012/f/f3/CrSYS.JPG" width="800" length="1000"></center><br />
<br />
<body><br />
<h1>Project Overview</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Arizona State's 2012 iGEM project aims to develop a portable water-borne pathogen biosensor. The team is looking towards addressing problems that prevent existing biosensor technologies from being effectively used in the field. Specifically, our team is working on a sensor that is cheap, portable, robust easily customizable, and produces a cheap response. Our vision is to build a user-friendly device that does not require any technical expertise to operate. <br />
</p><br />
<br />
<br />
<br />
<h1>Abstract</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Diarrheic pathogens including <i>E.coli</i> O157:H7 serotype, <i>Campylobacter</i>, <i>Shigella</i>, and <i>Salmonella</i> often contaminate drinking water supplies in developing nations and are responsible for approximately 1.5 million worldwide annual deaths. Current technologies for detection of bacteria include DNA hybridization FRET signaling, electrical detection via immobilized antimicrobial peptides, and PCR amplification followed by gel visualization. Our method of bacterial detection fills a niche in biosensor technology. Our design implies lower costs, higher portability, and a more rapid signal output than most bacterial biosensors. Additionally, our interchangeable DNA probe confers modularity, allowing for a range of bacterial detection. Using a novel split beta-galactosidase complementation assay, we have designed three unique chimeric proteins that recognize and bind to specific pathogenic markers and create a functioning beta-galactosidase enzyme. This functioning enzyme unit then cleaves X-gal and produces a colorimetric output signal. Our research demonstrates success in initial stages of chimeric protein assembly. <br />
</p><br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<br /><br />
<br />
<br /><br />
<br />
<div align="center"><br />
<b>Contact Us</b><br />
<br /><br />
Arizona State University<br />
<br /><br />
ECG 334, PO BOX 9709<br />
<br /><br />
Tempe, Arizona 85287<br />
</div><br />
<br />
</body><br />
</html><br />
{{:Team:Arizona_State/Template:twitter}}<br />
{{:Team:Arizona_State/sitemap}}</div>Napatelhttp://2012.igem.org/Team:Arizona_State/HPModelingTeam:Arizona State/HPModeling2012-10-16T23:22:34Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<h1>Epidemiological Modeling</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
We can use Bayesian techniques to estimate natural frequency of the quantity to be measured (pathogen presence) as well as to analyze the accuracy and reliability of our device.<br />
<br />
Baye's rule gives us the probability of an actual positive event given that our sensor outputs "true". To evaluate this probability we need three pieces of data: specificity ('''A'''), sensitivity ('''B'''), and the "natural frequency" ('''C''') of the event. Sensitivity and specificity are evaluated based on experimental results and are defined below. Estimation of the "natural frequency" of a disease vector is more complex, and can be handled using a Bayesian network or other sophisticated statistical devices. This Bayesian network should be constructed using data from studies such as those referenced in [https://2012.igem.org/Team:Arizona_State/FieldApplications <i>Escherichia Coli</i> Case Studies].<br />
----<br />
<center><br />
{| class="wikitable" align="center" style="text-align:center; border:none; background:transparent;"<br />
|colspan="2" rowspan="2" style="border:none;"|<br />
|colspan="2" style="background:#ffdead;"|'''Condition'''<br />
|-<br />
|Condition Positive<br />
|Condition Negative<br />
|-<br />
|rowspan="2" style="background:#ffdead;"|'''Sensor<br />Outcome'''<br />
|Sensor<br />Outcome<br />Positive<br />
|<span style="color:#006600;">'''True Positive'''</span><br />
|<span style="color:#cc0000;">'''False Positive'''</span><br />
|style="background:#ffdead;"|Positive predictability =<br />TP<div style="border-top:1px solid;">TP + FP</div><br />
|-<br />
|Sensor<br />Outcome<br />Negative<br />
|<span style="color:#cc0000;">'''False Negative'''</span><br />
|<span style="color:#006600;">'''True Negative'''</span><br />
|style="background:#ffdead;"|Negative predictability =<br />TN<div style="border-top:1px solid;">TN + FN</div><br />
|-<br />
|colspan="2" style="border:none;" |<br />
|style="background:#ffdead;"|Sensitivity =<br />TP<div style="border-top:1px solid;">TP + TN</div><br />
|style="background:#ffdead;"|Specificity =<br />TN<div style="border-top:1px solid;">TN + FP</div><br />
|}<br />
</center><br />
<br />
* '''Sensitivity''': proportion of true positives accurately measured<br />
* '''Specificity''': proportion of true negatives accurately measured<br />
* '''Positive predictability''': proportion of positive sensor results that are true positives<br />
* '''Negative predictability''': proportion of negative sensor results that are true negatives<br />
<br />
Once we have experimental data giving us values for the table above, we can use Bayes' theorem to estimate the probability of an actual event given a positive sensor reading. To aid in these calculations we have attached an excel spreadsheet: [[File:Bayesian formulas.xls|Bayes' rule]].</div>Napatelhttp://2012.igem.org/Team:Arizona_State/Template:HeaderTeam:Arizona State/Template:Header2012-10-16T22:50:55Z<p>Napatel: </p>
<hr />
<div><html lang="en"><br />
<!-- Made by Abhi & Jordan with help from the "https://2011.igem.org/Team:Imperial_College_London" page --><br />
<head><br />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /><br />
<style type="text/css"><br />
#top-section {<br />
width: 975px;<br />
height: 20px;<br />
background-color: transparent;<br />
border: none;<br />
}<br />
<br />
#p-logo { display: none; }<br />
#search-controls { display: none; }<br />
.firstHeading { display: none; }<br />
#contentSub { margin: 0 0 0 0; }<br />
iframe { padding: 10px 20px 10px 20px; }<br />
<br />
body {<br />
background-color:#000000;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/c/c8/BackgroundNew.jpg); <br />
background-size:100%;<br />
background-position:center; background-attachment:fixed;<br />
}<br />
<br />
.right-menu li a, .right-menu li a:hover {<br />
color: #3c6b27;<br />
background-color: transparent;<br />
}<br />
<br />
#iGEMLogo {<br />
position: absolute;<br />
top:40px;<br />
left:20px;<br />
}<br />
<br />
#ProjectTitle {<br />
position: relative;<br />
text-align:center;<br />
}<br />
<br />
#ASULogo {<br />
position: absolute;<br />
top:45px;<br />
right:25px;<br />
}<br />
<br />
#menucontainer {<br />
overflow:visible;<br />
position:relative;<br />
z-index:3;<br />
}<br />
<br />
#content {<br />
position: relative;<br />
width: 975px;<br />
margin: 0 auto;<br />
padding-top:20px;<br />
padding-left:0px;<br />
padding-right:0px;<br />
padding-bottom:0px;<br />
//background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/4/4b/2012ASUiGemLogo.png);<br />
//background-repeat:no-repeat;<br />
//background-position:center;<br />
//background-attachment:fixed;<br />
color: black;<br />
border: none;<br />
line-height: 1.5em;<br />
z-index: 2;<br />
}<br />
<br />
#bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 {<br />
margin-bottom: 0;<br />
}<br />
<br />
a {color:#t;}<br />
a:link {color:#93B825;}<br />
a:visited {color:#728F1D;}<br />
a:hover {color:#93B825;}<br />
a:active {color:#93B825;}<br />
a[name]:hover {text-decoration:none;} <br />
<br />
a.sitemap:link,a.sitemap:visited {color:#680000;font-decoration:none;}<br />
a.sitemap:hover,a.sitemap:active {color:#680000;font-decoration:underline;}<br />
<br />
h1 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 2.2em;<br />
margin: 0 0 0 0;<br />
padding: 20px 20px 12px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h2 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.7em;<br />
margin: 0 0 0 0;<br />
padding: 18px 20px 7px 20px;<br />
border-bottom: none;<br />
} <br />
<br />
h3 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.4em;<br />
margin: 0 0 0 0;<br />
padding: 16px 20px 2px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h4 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.1em;<br />
margin: 0 0 0 0;<br />
padding: 13.5px 20px 1px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
p {<br />
font-family: helvetica,sans-serif;<br />
//color: #ffffff;<br />
background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/e/ea/Layer.png);<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
margin: 0 0 0 0;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
table {<br />
background: transparent;<br />
} th {<br />
background-color:maroon;<br />
color:gold;<br />
}<br />
<br />
.border {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
}<br />
<br />
.borderMagnify {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
margin-left:-9px;<br />
margin-right:9px;<br />
}<br />
<br />
.imgbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.vidbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.newouterbox {<br />
background-color:#FF944D;<br />
border:1px solid #CCCCCC;<br />
margin:20px;<br />
padding-bottom:0px;<br />
}<br />
<br />
.newinnerbox {<br />
border:1px solid #CCCCCC;<br />
margin:10px 20px 20px 20px;<br />
padding-top:0px;<br />
padding-bottom:13px;<br />
background-color:#ffffff;<br />
}<br />
<br />
.newtext {<br />
text-align:center;<br />
background-color:#FF944D;<br />
color:#000000;<br />
}<br />
<br />
ul.a {<br />
margin: 0 0 0 40px;<br />
list-style-image: none;<br />
list-style-type:disc;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
ol.a {<br />
margin: 0 0 0 30px;<br />
list-style-position:inside;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
#BackToTop {<br />
position:fixed;<br />
bottom:0;<br />
right:0;<br />
}<br />
<br />
#Sitemap {<br />
position:fixed;<br />
bottom:0;<br />
left:0;<br />
}<br />
<br />
/*** Start of Styling for menu bar ***/<br />
/*** ESSENTIAL STYLES ***/<br />
a.collapseLink {<br />
font-weight:bold;<br />
font-size:1em;<br />
color:#225323;<br />
}<br />
.sf-menu, .sf-menu * {<br />
margin:0;<br />
padding:0;<br />
list-style:none;<br />
}<br />
.sf-menu {<br />
line-height:1.0;<br />
}<br />
.sf-menu ul {<br />
position:absolute;<br />
top:999em;<br />
width:195px; /* left offset of submenus need to match (see below) */<br />
}<br />
.sf-menu ul li {<br />
width:100%;<br />
}<br />
.sf-menu li:hover {<br />
visibility:inherit; /* fixes IE7 'sticky bug' */<br />
}<br />
.sf-menu li {<br />
float:left;<br />
position:relative;<br />
width:195px;<br />
}<br />
.sf-menu a {<br />
display:block;<br />
position:relative;<br />
}<br />
.sf-menu li:hover ul, .sf-menu li.sfHover ul {<br />
left:0;<br />
top:2.5em; /* match top ul list item height */<br />
z-index:99;<br />
}<br />
ul.sf-menu li:hover li ul, ul.sf-menu li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li:hover ul, ul.sf-menu li li.sfHover ul {<br />
left:15.3em; /* match ul width */<br />
top:0;<br />
}<br />
ul.sf-menu li li:hover li ul, ul.sf-menu li li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul {<br />
left:10em; /* match ul width */<br />
top:0;<br />
}<br />
<br />
/*** DEMO SKIN ***/<br />
.sf-menu {<br />
float:left;<br />
margin-bottom:1em;<br />
}<br />
.sf-menu a {<br />
border-left:1px solid #fff;<br />
border-top:1px solid #826554;<br />
padding:0.37em 1em 0.37em 1em;<br />
text-decoration:none;<br />
font-family:'helveticaneue', sans-serif;<br />
font-size:1.3em;<br />
}<br />
.sf-menu a, .sf-menu a:visited { /* visited pseudo selector so IE6 applies text colour*/<br />
color:#efefef;<br />
}<br />
.sf-menu li, .sf-menu li li, .sf-menu li li li {<br />
background:#990000;<br />
}<br />
.sf-menu li:hover, .sf-menu li.sfHover, .sf-menu a:focus, .sf-menu a:hover, .sf-menu a:active {<br />
background:#b30000;<br />
outline:0;<br />
}<br />
<br />
/*** arrows **/<br />
.sf-menu a.sf-with-ul {<br />
cursor:default; <br />
padding-right:2.25em;<br />
min-width:1px; /* trigger IE7 hasLayout so spans position accurately */<br />
}<br />
.sf-sub-indicator {<br />
position:absolute;<br />
display:block;<br />
right:.75em;<br />
top:1.05em; /* IE6 only */<br />
width:10px;<br />
height:10px;<br />
text-indent:-999em;<br />
overflow:hidden;<br />
background:url('https://static.igem.org/mediawiki/2011/2/2f/ICL_MenuArrow.png') no-repeat -10px -100px;<br />
/* 8-bit indexed alpha png. IE6 gets solid image only */<br />
}<br />
a > .sf-sub-indicator { /* give all except IE6 the correct values */<br />
top:.8em;<br />
background-position:0 -100px; /* use translucent arrow for modern browsers*/<br />
}<br />
/* apply hovers to modern browsers */<br />
a:focus > .sf-sub-indicator,<br />
a:hover > .sf-sub-indicator,<br />
a:active > .sf-sub-indicator,<br />
li:hover > a > .sf-sub-indicator,<br />
li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px -100px; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/* point right for anchors in subs */<br />
.sf-menu ul .sf-sub-indicator { background-position: -10px 0; }<br />
.sf-menu ul a > .sf-sub-indicator { background-position: 0 0; }<br />
/* apply hovers to modern browsers */<br />
.sf-menu ul a:focus > .sf-sub-indicator,<br />
.sf-menu ul a:hover > .sf-sub-indicator,<br />
.sf-menu ul a:active > .sf-sub-indicator,<br />
.sf-menu ul li:hover > a > .sf-sub-indicator,<br />
.sf-menu ul li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px 0; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/*** shadows for all but IE6 ***/<br />
.sf-shadow ul {<br />
background:url('https://static.igem.org/mediawiki/2011/9/9f/ICL_Shadow.png') no-repeat bottom right;<br />
padding:0 8px 9px 0;<br />
-moz-border-radius-bottomleft:17px;<br />
-moz-border-radius-topright:17px;<br />
-webkit-border-top-right-radius:17px;<br />
-webkit-border-bottom-left-radius:17px;<br />
}<br />
<br />
.sf-shadow ul.sf-shadow-off {<br />
background:transparent;<br />
}<br />
</style><br />
<br />
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/hoverIntent?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/superfishjs?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/magnifier?action=raw&ctype=text/js"><br />
/***********************************************<br />
* jQuery Image Magnify- (c) Dynamic Drive DHTML code library (www.dynamicdrive.com)<br />
* This notice MUST stay intact for legal use<br />
* Visit Dynamic Drive at http://www.dynamicdrive.com/ for this script and 100s more<br />
***********************************************/<br />
</script><br />
<br />
<script type="text/javascript"><br />
var $ = jQuery;<br />
jQuery.imageMagnify.zIndexcounter = 1000;<br />
</script><br />
<br />
<script><br />
$(document).ready(function() {<br />
$("sup").click(function () {<br />
if ($(this).html().substr(0,1)=="[")<br />
{<br />
if ($('.technology').length>0)<br />
{<br />
ddaccordion.expandone('technology', $('.technology').length-1)<br />
setTimeout("window.scrollBy(0,50000)",200)<br />
}<br />
else window.scrollBy(0,50000)<br />
}<br />
});<br />
$("sup").mouseover(function () {<br />
if ($(this).html().substr(0,1)=="[") $(this).css('cursor', 'pointer');<br />
});<br />
});<br />
</script><br />
<br />
<script> <br />
$(document).ready(function() { <br />
$('ul.sf-menu').superfish({ <br />
}); <br />
});<br />
</script><br />
</head><br />
<br />
<body><br />
<a name="top"></a><br />
<!-----<br />
<div id='iGEMLogo'><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:120px;" /><br />
</a><br />
</div><br />
<br />
<div id='ProjectTitle'><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/5/5f/CRSYS.png" style="width:550px;" /><br />
<!---Before: https://static.igem.org/mediawiki/2012/d/db/2012_Project_logo.png---><!----<br />
</a><br />
</div><br />
<br />
<div id='ASULogo'><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="150" height="70" /><br />
</div><br />
-----><br />
<div id='header' align="center"><br />
<table width="950"><br />
<tr><br />
<td><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:100px;" /><br />
</a><br />
</td><br />
<td align="center"><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/9/9a/AsuCrsysLogothingy.png" style="width:591px;" /><br />
</a><br />
</td><br />
<td><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="125" /><br />
</td><br />
</table><br />
<br /><br />
</div><br />
<br />
<br />
<br />
<div id="BackToTop"><br />
<a href="#top"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2d/ArrowColorChanged.png" width="50px" /><br />
</a><br />
</div><br />
<br />
<div id="Sitemap"><br />
<a href='https://2012.igem.org/Team:Arizona_State/Sitemap'><br />
<img src="https://static.igem.org/mediawiki/2012/3/30/SiteMapColorChange.png" width="100px" /><br />
</a><br />
</div><br />
<br />
<div id='menucontainer'><br />
<ul class="sf-menu sf-navbar"><br />
<li><a class="sf-with-ul" href="">Project<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State">Home</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Problem">The Problem</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Magainin">Cell Surface Biosensor</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Chimeric_Reporter">DNA-Protein Chimera Biosensor</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Notebook">Notebook</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/References">References</a><br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Team<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Team">Members</a></li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Attributions">Attributions</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2012">Official Team Profile</a></li><br />
</ul><br />
</li><br />
<br />
<li><a class="sf-with-ul" href="#">Results<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Data">Data</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Parts">BioBricks</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Accomplishments">Judging Criteria</a> </li><br />
</ul><br />
</li><br />
<li><a class="sf-with-ul" href="#">Human Practices<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/International">International Hygiene Plan</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Community">Community Outreach</a> </li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/University">University Outreach</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/FieldApplications">Case Studies</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/HPModeling">Epidemiological Modeling</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Ethical_Conditions">Ethical Considerations</a> </li> <br />
<br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Extras<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Safety">Safety</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Media">Media</a> </li> <br />
</ul><br />
</li> <br />
</ul> <br />
</div><br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/Template:HeaderTeam:Arizona State/Template:Header2012-10-16T22:45:15Z<p>Napatel: </p>
<hr />
<div><html lang="en"><br />
<!-- Made by Abhi & Jordan with help from the "https://2011.igem.org/Team:Imperial_College_London" page --><br />
<head><br />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /><br />
<style type="text/css"><br />
#top-section {<br />
width: 975px;<br />
height: 20px;<br />
background-color: transparent;<br />
border: none;<br />
}<br />
<br />
#p-logo { display: none; }<br />
#search-controls { display: none; }<br />
.firstHeading { display: none; }<br />
#contentSub { margin: 0 0 0 0; }<br />
iframe { padding: 10px 20px 10px 20px; }<br />
<br />
body {<br />
background-color:#000000;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/c/c8/BackgroundNew.jpg); <br />
background-size:100%;<br />
background-position:center; background-attachment:fixed;<br />
}<br />
<br />
.right-menu li a, .right-menu li a:hover {<br />
color: #3c6b27;<br />
background-color: transparent;<br />
}<br />
<br />
#iGEMLogo {<br />
position: absolute;<br />
top:40px;<br />
left:20px;<br />
}<br />
<br />
#ProjectTitle {<br />
position: relative;<br />
text-align:center;<br />
}<br />
<br />
#ASULogo {<br />
position: absolute;<br />
top:45px;<br />
right:25px;<br />
}<br />
<br />
#menucontainer {<br />
overflow:visible;<br />
position:relative;<br />
z-index:3;<br />
}<br />
<br />
#content {<br />
position: relative;<br />
width: 975px;<br />
margin: 0 auto;<br />
padding-top:20px;<br />
padding-left:0px;<br />
padding-right:0px;<br />
padding-bottom:0px;<br />
//background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/4/4b/2012ASUiGemLogo.png);<br />
//background-repeat:no-repeat;<br />
//background-position:center;<br />
//background-attachment:fixed;<br />
color: black;<br />
border: none;<br />
line-height: 1.5em;<br />
z-index: 2;<br />
}<br />
<br />
#bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 {<br />
margin-bottom: 0;<br />
}<br />
<br />
a {color:#t;}<br />
a:link {color:#93B825;}<br />
a:visited {color:#728F1D;}<br />
a:hover {color:#93B825;}<br />
a:active {color:#93B825;}<br />
a[name]:hover {text-decoration:none;} <br />
<br />
a.sitemap:link,a.sitemap:visited {color:#680000;font-decoration:none;}<br />
a.sitemap:hover,a.sitemap:active {color:#680000;font-decoration:underline;}<br />
<br />
h1 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 2.2em;<br />
margin: 0 0 0 0;<br />
padding: 20px 20px 12px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h2 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.7em;<br />
margin: 0 0 0 0;<br />
padding: 18px 20px 7px 20px;<br />
border-bottom: none;<br />
} <br />
<br />
h3 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.4em;<br />
margin: 0 0 0 0;<br />
padding: 16px 20px 2px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h4 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.1em;<br />
margin: 0 0 0 0;<br />
padding: 13.5px 20px 1px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
p {<br />
font-family: helvetica,sans-serif;<br />
//color: #ffffff;<br />
background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/e/ea/Layer.png);<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
margin: 0 0 0 0;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
table {<br />
background: transparent;<br />
} th {<br />
background-color:maroon;<br />
color:gold;<br />
}<br />
<br />
.border {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
}<br />
<br />
.borderMagnify {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
margin-left:-9px;<br />
margin-right:9px;<br />
}<br />
<br />
.imgbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.vidbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.newouterbox {<br />
background-color:#FF944D;<br />
border:1px solid #CCCCCC;<br />
margin:20px;<br />
padding-bottom:0px;<br />
}<br />
<br />
.newinnerbox {<br />
border:1px solid #CCCCCC;<br />
margin:10px 20px 20px 20px;<br />
padding-top:0px;<br />
padding-bottom:13px;<br />
background-color:#ffffff;<br />
}<br />
<br />
.newtext {<br />
text-align:center;<br />
background-color:#FF944D;<br />
color:#000000;<br />
}<br />
<br />
ul.a {<br />
margin: 0 0 0 40px;<br />
list-style-image: none;<br />
list-style-type:disc;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
ol.a {<br />
margin: 0 0 0 30px;<br />
list-style-position:inside;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
#BackToTop {<br />
position:fixed;<br />
bottom:0;<br />
right:0;<br />
}<br />
<br />
#Sitemap {<br />
position:fixed;<br />
bottom:0;<br />
left:0;<br />
}<br />
<br />
/*** Start of Styling for menu bar ***/<br />
/*** ESSENTIAL STYLES ***/<br />
a.collapseLink {<br />
font-weight:bold;<br />
font-size:1em;<br />
color:#225323;<br />
}<br />
.sf-menu, .sf-menu * {<br />
margin:0;<br />
padding:0;<br />
list-style:none;<br />
}<br />
.sf-menu {<br />
line-height:1.0;<br />
}<br />
.sf-menu ul {<br />
position:absolute;<br />
top:999em;<br />
width:195px; /* left offset of submenus need to match (see below) */<br />
}<br />
.sf-menu ul li {<br />
width:100%;<br />
}<br />
.sf-menu li:hover {<br />
visibility:inherit; /* fixes IE7 'sticky bug' */<br />
}<br />
.sf-menu li {<br />
float:left;<br />
position:relative;<br />
width:195px;<br />
}<br />
.sf-menu a {<br />
display:block;<br />
position:relative;<br />
}<br />
.sf-menu li:hover ul, .sf-menu li.sfHover ul {<br />
left:0;<br />
top:2.5em; /* match top ul list item height */<br />
z-index:99;<br />
}<br />
ul.sf-menu li:hover li ul, ul.sf-menu li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li:hover ul, ul.sf-menu li li.sfHover ul {<br />
left:15.3em; /* match ul width */<br />
top:0;<br />
}<br />
ul.sf-menu li li:hover li ul, ul.sf-menu li li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul {<br />
left:10em; /* match ul width */<br />
top:0;<br />
}<br />
<br />
/*** DEMO SKIN ***/<br />
.sf-menu {<br />
float:left;<br />
margin-bottom:1em;<br />
}<br />
.sf-menu a {<br />
border-left:1px solid #fff;<br />
border-top:1px solid #826554;<br />
padding:0.37em 1em 0.37em 1em;<br />
text-decoration:none;<br />
font-family:'helveticaneue', sans-serif;<br />
font-size:1.3em;<br />
}<br />
.sf-menu a, .sf-menu a:visited { /* visited pseudo selector so IE6 applies text colour*/<br />
color:#efefef;<br />
}<br />
.sf-menu li, .sf-menu li li, .sf-menu li li li {<br />
background:#990000;<br />
}<br />
.sf-menu li:hover, .sf-menu li.sfHover, .sf-menu a:focus, .sf-menu a:hover, .sf-menu a:active {<br />
background:#b30000;<br />
outline:0;<br />
}<br />
<br />
/*** arrows **/<br />
.sf-menu a.sf-with-ul {<br />
cursor:default; <br />
padding-right:2.25em;<br />
min-width:1px; /* trigger IE7 hasLayout so spans position accurately */<br />
}<br />
.sf-sub-indicator {<br />
position:absolute;<br />
display:block;<br />
right:.75em;<br />
top:1.05em; /* IE6 only */<br />
width:10px;<br />
height:10px;<br />
text-indent:-999em;<br />
overflow:hidden;<br />
background:url('https://static.igem.org/mediawiki/2011/2/2f/ICL_MenuArrow.png') no-repeat -10px -100px;<br />
/* 8-bit indexed alpha png. IE6 gets solid image only */<br />
}<br />
a > .sf-sub-indicator { /* give all except IE6 the correct values */<br />
top:.8em;<br />
background-position:0 -100px; /* use translucent arrow for modern browsers*/<br />
}<br />
/* apply hovers to modern browsers */<br />
a:focus > .sf-sub-indicator,<br />
a:hover > .sf-sub-indicator,<br />
a:active > .sf-sub-indicator,<br />
li:hover > a > .sf-sub-indicator,<br />
li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px -100px; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/* point right for anchors in subs */<br />
.sf-menu ul .sf-sub-indicator { background-position: -10px 0; }<br />
.sf-menu ul a > .sf-sub-indicator { background-position: 0 0; }<br />
/* apply hovers to modern browsers */<br />
.sf-menu ul a:focus > .sf-sub-indicator,<br />
.sf-menu ul a:hover > .sf-sub-indicator,<br />
.sf-menu ul a:active > .sf-sub-indicator,<br />
.sf-menu ul li:hover > a > .sf-sub-indicator,<br />
.sf-menu ul li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px 0; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/*** shadows for all but IE6 ***/<br />
.sf-shadow ul {<br />
background:url('https://static.igem.org/mediawiki/2011/9/9f/ICL_Shadow.png') no-repeat bottom right;<br />
padding:0 8px 9px 0;<br />
-moz-border-radius-bottomleft:17px;<br />
-moz-border-radius-topright:17px;<br />
-webkit-border-top-right-radius:17px;<br />
-webkit-border-bottom-left-radius:17px;<br />
}<br />
<br />
.sf-shadow ul.sf-shadow-off {<br />
background:transparent;<br />
}<br />
</style><br />
<br />
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/hoverIntent?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/superfishjs?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/magnifier?action=raw&ctype=text/js"><br />
/***********************************************<br />
* jQuery Image Magnify- (c) Dynamic Drive DHTML code library (www.dynamicdrive.com)<br />
* This notice MUST stay intact for legal use<br />
* Visit Dynamic Drive at http://www.dynamicdrive.com/ for this script and 100s more<br />
***********************************************/<br />
</script><br />
<br />
<script type="text/javascript"><br />
var $ = jQuery;<br />
jQuery.imageMagnify.zIndexcounter = 1000;<br />
</script><br />
<br />
<script><br />
$(document).ready(function() {<br />
$("sup").click(function () {<br />
if ($(this).html().substr(0,1)=="[")<br />
{<br />
if ($('.technology').length>0)<br />
{<br />
ddaccordion.expandone('technology', $('.technology').length-1)<br />
setTimeout("window.scrollBy(0,50000)",200)<br />
}<br />
else window.scrollBy(0,50000)<br />
}<br />
});<br />
$("sup").mouseover(function () {<br />
if ($(this).html().substr(0,1)=="[") $(this).css('cursor', 'pointer');<br />
});<br />
});<br />
</script><br />
<br />
<script> <br />
$(document).ready(function() { <br />
$('ul.sf-menu').superfish({ <br />
}); <br />
});<br />
</script><br />
</head><br />
<br />
<body><br />
<a name="top"></a><br />
<!-----<br />
<div id='iGEMLogo'><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:120px;" /><br />
</a><br />
</div><br />
<br />
<div id='ProjectTitle'><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/5/5f/CRSYS.png" style="width:550px;" /><br />
<!---Before: https://static.igem.org/mediawiki/2012/d/db/2012_Project_logo.png---><!----<br />
</a><br />
</div><br />
<br />
<div id='ASULogo'><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="150" height="70" /><br />
</div><br />
-----><br />
<div id='header' align="center"><br />
<table width="950"><br />
<tr><br />
<td><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:100px;" /><br />
</a><br />
</td><br />
<td align="center"><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/9/9a/AsuCrsysLogothingy.png" style="width:591px;" /><br />
</a><br />
</td><br />
<td><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="125" /><br />
</td><br />
</table><br />
<br /><br />
</div><br />
<br />
<br />
<br />
<div id="BackToTop"><br />
<a href="#top"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2d/ArrowColorChanged.png" width="50px" /><br />
</a><br />
</div><br />
<br />
<div id="Sitemap"><br />
<a href='https://2012.igem.org/Team:Arizona_State/Sitemap'><br />
<img src="https://static.igem.org/mediawiki/2012/3/30/SiteMapColorChange.png" width="100px" /><br />
</a><br />
</div><br />
<br />
<div id='menucontainer'><br />
<ul class="sf-menu sf-navbar"><br />
<li><a class="sf-with-ul" href="">Project<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State">Home</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Problem">The Problem</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Magainin">Cell Surface Biosensor</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Chimeric_Reporter">DNA-Protein Chimera Biosensor</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Notebook">Notebook</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/References">References</a><br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Team<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Team">Members</a></li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Attributions">Attributions</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2012">Official Team Profile</a></li><br />
</ul><br />
</li><br />
<br />
<li><a class="sf-with-ul" href="#">Results<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Data">Data</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Parts">BioBricks</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Accomplishments">Judging Criteria</a> </li><br />
</ul><br />
</li><br />
<li><a class="sf-with-ul" href="#">Human Practices<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/International">International Hygiene Plan</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Community">Community Outreach</a> </li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/University">University Outreach</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/FieldApplications">Case Studies</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/HPModeling">Epidemiological Modeling</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Ethical_Conditions">Ethical Considerations</a> </li> <br />
<br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Extras<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Media">Media</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Safety">Safety</a> </li> <br />
</ul><br />
</li> <br />
</ul> <br />
</div><br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/Template:HeaderTeam:Arizona State/Template:Header2012-10-16T22:44:54Z<p>Napatel: </p>
<hr />
<div><html lang="en"><br />
<!-- Made by Abhi & Jordan with help from the "https://2011.igem.org/Team:Imperial_College_London" page --><br />
<head><br />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /><br />
<style type="text/css"><br />
#top-section {<br />
width: 975px;<br />
height: 20px;<br />
background-color: transparent;<br />
border: none;<br />
}<br />
<br />
#p-logo { display: none; }<br />
#search-controls { display: none; }<br />
.firstHeading { display: none; }<br />
#contentSub { margin: 0 0 0 0; }<br />
iframe { padding: 10px 20px 10px 20px; }<br />
<br />
body {<br />
background-color:#000000;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/c/c8/BackgroundNew.jpg); <br />
background-size:100%;<br />
background-position:center; background-attachment:fixed;<br />
}<br />
<br />
.right-menu li a, .right-menu li a:hover {<br />
color: #3c6b27;<br />
background-color: transparent;<br />
}<br />
<br />
#iGEMLogo {<br />
position: absolute;<br />
top:40px;<br />
left:20px;<br />
}<br />
<br />
#ProjectTitle {<br />
position: relative;<br />
text-align:center;<br />
}<br />
<br />
#ASULogo {<br />
position: absolute;<br />
top:45px;<br />
right:25px;<br />
}<br />
<br />
#menucontainer {<br />
overflow:visible;<br />
position:relative;<br />
z-index:3;<br />
}<br />
<br />
#content {<br />
position: relative;<br />
width: 975px;<br />
margin: 0 auto;<br />
padding-top:20px;<br />
padding-left:0px;<br />
padding-right:0px;<br />
padding-bottom:0px;<br />
//background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/4/4b/2012ASUiGemLogo.png);<br />
//background-repeat:no-repeat;<br />
//background-position:center;<br />
//background-attachment:fixed;<br />
color: black;<br />
border: none;<br />
line-height: 1.5em;<br />
z-index: 2;<br />
}<br />
<br />
#bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 {<br />
margin-bottom: 0;<br />
}<br />
<br />
a {color:#t;}<br />
a:link {color:#93B825;}<br />
a:visited {color:#728F1D;}<br />
a:hover {color:#93B825;}<br />
a:active {color:#93B825;}<br />
a[name]:hover {text-decoration:none;} <br />
<br />
a.sitemap:link,a.sitemap:visited {color:#680000;font-decoration:none;}<br />
a.sitemap:hover,a.sitemap:active {color:#680000;font-decoration:underline;}<br />
<br />
h1 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 2.2em;<br />
margin: 0 0 0 0;<br />
padding: 20px 20px 12px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h2 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.7em;<br />
margin: 0 0 0 0;<br />
padding: 18px 20px 7px 20px;<br />
border-bottom: none;<br />
} <br />
<br />
h3 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.4em;<br />
margin: 0 0 0 0;<br />
padding: 16px 20px 2px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h4 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.1em;<br />
margin: 0 0 0 0;<br />
padding: 13.5px 20px 1px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
p {<br />
font-family: helvetica,sans-serif;<br />
//color: #ffffff;<br />
background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/e/ea/Layer.png);<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
margin: 0 0 0 0;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
table {<br />
background: transparent;<br />
} th {<br />
background-color:maroon;<br />
color:gold;<br />
}<br />
<br />
.border {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
}<br />
<br />
.borderMagnify {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
margin-left:-9px;<br />
margin-right:9px;<br />
}<br />
<br />
.imgbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.vidbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.newouterbox {<br />
background-color:#FF944D;<br />
border:1px solid #CCCCCC;<br />
margin:20px;<br />
padding-bottom:0px;<br />
}<br />
<br />
.newinnerbox {<br />
border:1px solid #CCCCCC;<br />
margin:10px 20px 20px 20px;<br />
padding-top:0px;<br />
padding-bottom:13px;<br />
background-color:#ffffff;<br />
}<br />
<br />
.newtext {<br />
text-align:center;<br />
background-color:#FF944D;<br />
color:#000000;<br />
}<br />
<br />
ul.a {<br />
margin: 0 0 0 40px;<br />
list-style-image: none;<br />
list-style-type:disc;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
ol.a {<br />
margin: 0 0 0 30px;<br />
list-style-position:inside;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
#BackToTop {<br />
position:fixed;<br />
bottom:0;<br />
right:0;<br />
}<br />
<br />
#Sitemap {<br />
position:fixed;<br />
bottom:0;<br />
left:0;<br />
}<br />
<br />
/*** Start of Styling for menu bar ***/<br />
/*** ESSENTIAL STYLES ***/<br />
a.collapseLink {<br />
font-weight:bold;<br />
font-size:1em;<br />
color:#225323;<br />
}<br />
.sf-menu, .sf-menu * {<br />
margin:0;<br />
padding:0;<br />
list-style:none;<br />
}<br />
.sf-menu {<br />
line-height:1.0;<br />
}<br />
.sf-menu ul {<br />
position:absolute;<br />
top:999em;<br />
width:195px; /* left offset of submenus need to match (see below) */<br />
}<br />
.sf-menu ul li {<br />
width:100%;<br />
}<br />
.sf-menu li:hover {<br />
visibility:inherit; /* fixes IE7 'sticky bug' */<br />
}<br />
.sf-menu li {<br />
float:left;<br />
position:relative;<br />
width:195px;<br />
}<br />
.sf-menu a {<br />
display:block;<br />
position:relative;<br />
}<br />
.sf-menu li:hover ul, .sf-menu li.sfHover ul {<br />
left:0;<br />
top:2.5em; /* match top ul list item height */<br />
z-index:99;<br />
}<br />
ul.sf-menu li:hover li ul, ul.sf-menu li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li:hover ul, ul.sf-menu li li.sfHover ul {<br />
left:15.3em; /* match ul width */<br />
top:0;<br />
}<br />
ul.sf-menu li li:hover li ul, ul.sf-menu li li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul {<br />
left:10em; /* match ul width */<br />
top:0;<br />
}<br />
<br />
/*** DEMO SKIN ***/<br />
.sf-menu {<br />
float:left;<br />
margin-bottom:1em;<br />
}<br />
.sf-menu a {<br />
border-left:1px solid #fff;<br />
border-top:1px solid #826554;<br />
padding:0.37em 1em 0.37em 1em;<br />
text-decoration:none;<br />
font-family:'helveticaneue', sans-serif;<br />
font-size:1.3em;<br />
}<br />
.sf-menu a, .sf-menu a:visited { /* visited pseudo selector so IE6 applies text colour*/<br />
color:#efefef;<br />
}<br />
.sf-menu li, .sf-menu li li, .sf-menu li li li {<br />
background:#990000;<br />
}<br />
.sf-menu li:hover, .sf-menu li.sfHover, .sf-menu a:focus, .sf-menu a:hover, .sf-menu a:active {<br />
background:#b30000;<br />
outline:0;<br />
}<br />
<br />
/*** arrows **/<br />
.sf-menu a.sf-with-ul {<br />
cursor:default; <br />
padding-right:2.25em;<br />
min-width:1px; /* trigger IE7 hasLayout so spans position accurately */<br />
}<br />
.sf-sub-indicator {<br />
position:absolute;<br />
display:block;<br />
right:.75em;<br />
top:1.05em; /* IE6 only */<br />
width:10px;<br />
height:10px;<br />
text-indent:-999em;<br />
overflow:hidden;<br />
background:url('https://static.igem.org/mediawiki/2011/2/2f/ICL_MenuArrow.png') no-repeat -10px -100px;<br />
/* 8-bit indexed alpha png. IE6 gets solid image only */<br />
}<br />
a > .sf-sub-indicator { /* give all except IE6 the correct values */<br />
top:.8em;<br />
background-position:0 -100px; /* use translucent arrow for modern browsers*/<br />
}<br />
/* apply hovers to modern browsers */<br />
a:focus > .sf-sub-indicator,<br />
a:hover > .sf-sub-indicator,<br />
a:active > .sf-sub-indicator,<br />
li:hover > a > .sf-sub-indicator,<br />
li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px -100px; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/* point right for anchors in subs */<br />
.sf-menu ul .sf-sub-indicator { background-position: -10px 0; }<br />
.sf-menu ul a > .sf-sub-indicator { background-position: 0 0; }<br />
/* apply hovers to modern browsers */<br />
.sf-menu ul a:focus > .sf-sub-indicator,<br />
.sf-menu ul a:hover > .sf-sub-indicator,<br />
.sf-menu ul a:active > .sf-sub-indicator,<br />
.sf-menu ul li:hover > a > .sf-sub-indicator,<br />
.sf-menu ul li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px 0; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/*** shadows for all but IE6 ***/<br />
.sf-shadow ul {<br />
background:url('https://static.igem.org/mediawiki/2011/9/9f/ICL_Shadow.png') no-repeat bottom right;<br />
padding:0 8px 9px 0;<br />
-moz-border-radius-bottomleft:17px;<br />
-moz-border-radius-topright:17px;<br />
-webkit-border-top-right-radius:17px;<br />
-webkit-border-bottom-left-radius:17px;<br />
}<br />
<br />
.sf-shadow ul.sf-shadow-off {<br />
background:transparent;<br />
}<br />
</style><br />
<br />
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/hoverIntent?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/superfishjs?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/magnifier?action=raw&ctype=text/js"><br />
/***********************************************<br />
* jQuery Image Magnify- (c) Dynamic Drive DHTML code library (www.dynamicdrive.com)<br />
* This notice MUST stay intact for legal use<br />
* Visit Dynamic Drive at http://www.dynamicdrive.com/ for this script and 100s more<br />
***********************************************/<br />
</script><br />
<br />
<script type="text/javascript"><br />
var $ = jQuery;<br />
jQuery.imageMagnify.zIndexcounter = 1000;<br />
</script><br />
<br />
<script><br />
$(document).ready(function() {<br />
$("sup").click(function () {<br />
if ($(this).html().substr(0,1)=="[")<br />
{<br />
if ($('.technology').length>0)<br />
{<br />
ddaccordion.expandone('technology', $('.technology').length-1)<br />
setTimeout("window.scrollBy(0,50000)",200)<br />
}<br />
else window.scrollBy(0,50000)<br />
}<br />
});<br />
$("sup").mouseover(function () {<br />
if ($(this).html().substr(0,1)=="[") $(this).css('cursor', 'pointer');<br />
});<br />
});<br />
</script><br />
<br />
<script> <br />
$(document).ready(function() { <br />
$('ul.sf-menu').superfish({ <br />
}); <br />
});<br />
</script><br />
</head><br />
<br />
<body><br />
<a name="top"></a><br />
<!-----<br />
<div id='iGEMLogo'><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:120px;" /><br />
</a><br />
</div><br />
<br />
<div id='ProjectTitle'><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/5/5f/CRSYS.png" style="width:550px;" /><br />
<!---Before: https://static.igem.org/mediawiki/2012/d/db/2012_Project_logo.png---><!----<br />
</a><br />
</div><br />
<br />
<div id='ASULogo'><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="150" height="70" /><br />
</div><br />
-----><br />
<div id='header' align="center"><br />
<table width="950"><br />
<tr><br />
<td><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:100px;" /><br />
</a><br />
</td><br />
<td align="center"><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/9/9a/AsuCrsysLogothingy.png" style="width:591px;" /><br />
</a><br />
</td><br />
<td><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="125" /><br />
</td><br />
</table><br />
<br /><br />
</div><br />
<br />
<br />
<br />
<div id="BackToTop"><br />
<a href="#top"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2d/ArrowColorChanged.png" width="50px" /><br />
</a><br />
</div><br />
<br />
<div id="Sitemap"><br />
<a href='https://2012.igem.org/Team:Arizona_State/Sitemap'><br />
<img src="https://static.igem.org/mediawiki/2012/3/30/SiteMapColorChange.png" width="100px" /><br />
</a><br />
</div><br />
<br />
<div id='menucontainer'><br />
<ul class="sf-menu sf-navbar"><br />
<li><a class="sf-with-ul" href="">Project<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State">Home</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Problem">The Problem</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Magainin">Cell Surface Biosensor</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Chimeric_Reporter">DNA-Protein Chimera Biosensor</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Notebook">Notebook</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/References">References</a><br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Team<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Team">Members</a></li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Attributions">Attributions</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2012">Official Team Profile</a></li><br />
</ul><br />
</li><br />
<br />
<li><a class="sf-with-ul" href="#">Results<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Data">Data</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Parts">BioBricks</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Accomplishments">Judging Criteria</a> </li><br />
</ul><br />
</li><br />
<li><a class="sf-with-ul" href="#">Human Practices<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/International">International Hygiene Plan</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Community">Community Outreach</a> </li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/University">University Outreach</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/FieldApplications">Case Studies</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/HPModeling">Modeling</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Ethical_Conditions">Ethical Considerations</a> </li> <br />
<br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Extras<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Media">Media</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Safety">Safety</a> </li> <br />
</ul><br />
</li> <br />
</ul> <br />
</div><br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/MagaininTeam:Arizona State/Magainin2012-10-16T05:55:05Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Pathogenic Cell Surface Biosensor</h1><br />
<h2>Overview</h2><br />
<p><br />
Current methods of water-borne pathogen detection require expensive equipment that often isn't modular or accessible to developing countries. Thus, current sensors are limited to specific bacterial strains or are too broad and produce false positive tests. One of the projects this year's ASU iGEM undertook was building a split-enzyme engineered fusion protein consisting of the Magainin peptide and the split alpha and omega fragments of beta-galactosidase.<br />
</p><br />
<h2>Magainin</h2><br />
<p><br />
Magainins</html><sup>[http://www.chemicalbook.com/ChemicalProductProperty_EN_CB1199778.htm]</sup><html> are a class of proteins found in the skin of <i>Xenopus laevis</i></html><sup>[http://en.wikipedia.org/wiki/Xenopus_laevis]</sup><html> - the African clawed frog - that contain antimicrobial properties. Both Magainin 1 and 2 are closely related peptides that each contain 23 amino acids and only differ by two amino acid substitutions. These two peptides have broad spectrum antimicrobial activity, including: gram-positive and gram-negative bacteria, viruses, protozoa, yeasts and fungi, and are hemolytic and cytotoxic to cancer cells</html><sup>[http://www.pnas.org/content/85/3/910.full.pdf]</sup><html>. The mechanism for antimicrobial activity in Magainin 1 and 2 involves the disruption the plasma membranes of target cells via electrostatic interactions between the negatively charged phospholipid bilayer and the positively-charged amino-terminus of the Magainin peptide. <br />
</p><br />
<p><br />
Functionally, this interaction allowed us to take advantage of the electrostatic interaction between the Magainin-1 peptide and the lipid bilayer of bacteria to design a bacterial biosensor that confers a signal based on the binding of multiple Magainin peptides to a bacterial membrane (Figure A). <br />
</p><br />
<br />
<h2>Biosensor Design Concept</h2><br />
<p><br />
<image src="https://static.igem.org/mediawiki/2012/0/03/ASUiGEM2012_magainindesigconcept.png" width="450" height="300"><br />
</p><br />
<p><br />
Figure A depicts the Magainin-Linker-Split Beta-galactosidase biosensor design concept. In close proximity, the two subunits of beta-galactosidase, Alpha and Omega, interact to form a complete, fully-functional unit. Because Magainin peptides congregate and form a toroidal pore</html><sup>[http://www.springerlink.com/content/tg476537mk033550/]</sup><html> when binding to the membranes of bacteria, the close proximity of the linked split beta-galactosidase units can be achieved. Previous research indicates that this reporter system can be applied to mammalian cell detection with different ligands in close proximity. The novel approach of this project involves linking Magainin to the beta-galactosidase reporter system to detect pathogenic bacteria. The benefit of this system is its modularity. The magainin peptide can be switched out with other antimicrobial peptides - which may have better binding affinities to other bacterial strains - via BioBrick assembly, creating a system that can be engineered to potentially detect any bacterial strain.<br />
</p><br />
<br />
<h2>Results & Progress Map</h2><br />
<p><br />
<image src="https://static.igem.org/mediawiki/2012/3/3e/ASUiGEM2012_magaininoutline1.jpg" width="900" height="300"><br />
</p><br />
<p><br />
Project progress has been completed up to cloning in the pET29 expression vector. Three of the four fragments of the split beta-galactosidase - omega, alpha-1, and 1-omega - have been isolated from the beta-galactosidase plasmid (shown below). Alpha-1 and 1-Omega, which have been isolated, complement each other to create a functional beta-galactosidase unit. Transformation of the alpha fragment in BL21(DE3) strains naturally coding for the Omega fragment have shown complementation <i>in vivo</i>, indicating that the split beta-galactosidase reporter system functioned as desired.<br />
</p><br />
<p><br />
Expression of the full Magainin-Linker-Bgal construct in BL21(DE3) strains will continue post-Regional jamboree. <br />
</p><br />
<div id='header' align="center"><br />
<table width="950"><br />
<tr><br />
<td><br />
<img src="https://static.igem.org/mediawiki/2012/2/2f/ASUiGEM2012_alphaomega.png" width="300" height="400"></td><br />
<td><br />
<br />
<image src="https://static.igem.org/mediawiki/2012/5/5d/ASUiGEM2012_1omega.png" align="right" width="550" height="400"><br />
</tr><br />
</table><br />
</div><br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/Chimeric_ReporterTeam:Arizona State/Chimeric Reporter2012-10-04T04:01:33Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<html><br />
<body><br />
<h1>DNA-Protein Chimera Biosensor</h1><br />
<h2>Overview</h2><br />
<p><br />
There are various biosensors on the market but the state of the art technology is based upon Polymerase Chain Reaction and nanotechnology, which involves gold plated probes and requires specialized skills to use. Despite the extreme accuracy of the device, the affordability, and longer diagnostic time has made the technology scarce in the field. In order to make biosensing technology more accessible to those with few resources and the greatest need, the team worked on generating a cost effective, highly accurate and user-friendly organic biosensor. The components of the sensor will be produced in non-pathogenic E. coli. The sensor is made up of a protein head and DNA tail. The protein head is an enzyme that turns a colorless substrate (X-gal) blue. The enzyme is split in half, so that when the sensor is dissolved in water it cannot produce blue color. When pathogenic target DNA is present, two DNA sensor tails bind the target, the split enzyme assembles, and blue color is produced. Color provides a user-friendly output that is familiar to non-skilled users. <br />
</p><br />
<br />
<h2>Streptavidin</h2><br />
<p><br />
Purified and extracted from the bacteria Streptomyces avidinii, Streptavidin posses a high binding affinity for biotin, with a dissociation constant of 10^-14–10^–16 M ( Laitinen et al.). With such high dissociation constant, the bonding of streptavidin to biotin is considered as one of the strongest non covalent bonding in nature. Due to its high binding affinity to biotin, streptavidin serves as one of the major component of this project. <br />
</p><br />
<p><br />
As a proof of concept for our design, our team designed and assembled fusions of streptavidin (strep) and the split beta-galactosidase (bgal) fragments. Because of streptavidin's high biotin binding affinity, it will allow our fusion proteins to easily bind onto the ends of biotinylated DNA fragments.<br />
</p><br />
<p><br />
<br />
The addition of a poly-histidine tag (His-tag) makes it possible to generate the fusion proteins in E. Coli, then isolate and purify them using a nickle binding column. Mixtures of His-purified strep-tagged bgal fragments and single stranded biotinylated DNA will generate DNA-Protein Chimera 'probes' as the streptavidin binds to the biotinylated end of the DNA. <br />
</p><br />
<p><br />
<br />
By creating probes using complementary strands of DNA of varying lengths, we can confirm that DNA-Protein Chimeric probes generated in E. Coli will create a colorimetric response when kept in close proximity. This will allow us to characterize the behavior of split bgal fusion probes as a function of the distance that they are separated - which can be controlled by altering the length of the ssDNA, or by creating two probes that bind to the same template ssDNA at different sites separated by a variable length.<br />
</p><br />
<br />
<h2>Topoisomerase</h2><br />
<p><br />
<img src="https://static.igem.org/mediawiki/2012/8/8f/TopoDiagram.png" width="800" height="500"><br />
</p><br />
<p><br />
The wild type form of topoisomerase binds to the DNA sequence (YCCTT) in E. Coli. It regulates the winding of the DNA by making a nick after the second T. This allows for the rotation of the strands to relieve torsional stress. Afterwards, the DNA strands are religated. In 2006, Bushman et al. have shown that the smallpox topoisomerase double cysteine mutant D168A mutates the tyrosine responsible for covalent bonding to the 5’ phosphate at the DNA nicking. This mutant form prevents religation, and thus causes the majority of the DNA to stay in the covalently bonded complex.<br />
</p><br />
<h2>Design Scheme</h2><br />
<p><br />
In our design, we plan to use topoisomerase to nick a specific covalently bonded sequence and peel off a section of single stranded DNA. We have designed a template plasmid that includes tandem YCCTT recognition sites with template strand in between, and is complementary to a section of coding sequence of GFP. By inducing topoisomerase/split bgal fusion protein expression, we will be able to generate Chimeric probes <i>in vivo</i> that can be easily His-tag purified and tested. We plan to use a KEIO strain with one copy of this coding sequence in the <i>E. Coli</i> genome in order to test the function of our chimeric probes on cell lysates and mock water samples.<br />
</p><br />
<h2>Reporter System</h2><br />
<p><br />
Basilion et al. from Case Western in 2010 have shown that they were able to make a split beta-galactosidase complementation assay with relatively reliable assay results In the assay, alpha-4/omega, which has a higher specificity, is the most successful split beta galactosidase assay. It is thus used to eliminate false positive. Additionally, we are adapting alpha and 1-omega, which is less specific but has a higher signal, for the same protocol to eliminate false negative.<br />
</p><br />
<p><br />
Basilion et al. also demonstrated success in creating fusion proteins with a split-beta galactosidase fragment and antibody specific to their target. Modifying this, we plan to make a fusion of our mutant topoisomerase and our split-beta galactosidase fragments. This effectively creates a probe that when assembled contains topoisomerase bound both to a single stranded DNA hybridization probe and a split-beta galactosidase fragment. By incubating the two probes that recognize adjacent DNA sequences, we can test for the presence of DNA sequences in a bacterial genome.<br />
</p></div>Napatelhttp://2012.igem.org/Team:Arizona_State/AttributionsTeam:Arizona State/Attributions2012-10-04T03:59:26Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<h1>Attributions</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
*Rohit: Media Preparation/ Magainin<br />
*Amanda: Media Preparation Team/ Human Practices<br />
*Hyder: Topo Chimeric Protein Production/ Topo Target Plasmid Design and Building <br />
*Ryan: Topo Chimeric Protein Production<br />
*Abhi: Split Beta Gal Assay Development for the Chimeric Reporter (DNA probe)<br />
*Maddie: Split Beta Gal Assay Development for the Chimeric Reporter (DNA probe)/ Human Practices<br />
*Nisarg: Magainin Assembly/ Split Beta Gal Assay Development for Magainin/ Topo/ AlumniGEM<br />
*Ellen: Magainin Assembly<br />
*Ethan: Modeling<br />
<br />
<h1>Acknowledgements</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<b>We would like to thank the following individuals:</b><br />
<br />
*Dr. Karmella Haynes for providing us guidance and support throughout the whole iGEM process. She generously opened her lab for the iGEM team and provided access to various equipments such as a thermocycler, spectrophotometer and a Light Cycler. In addition to providing us access to various equipments, she also donated various reagents contributing to the success of our projects.<br />
<br />
*Dr. Xiao Wang for serving as one of the team mentors. Wang Lab provided us with lab space during the summer and also provided us with cells and reagents. <br />
<br />
*Dr. Vincent Pizziconi for serving as one of the team mentors and providing us with aspiring words throughout the summer. Dr. Pizziconi opened his lab, the Biomedical Engineering Design Studio and the conference room for this years iGEM team.<br />
<br />
*Dr. Miles Orchinik and Dr. Tsafrir Mor for providing us lab space during the summer. Additionally, we would like to thank Dr. Gary Tahmahkera for giving us continual support in answering any questions we had while we were there.<br />
<br />
*Kylie Standage-Beier for providing us with feedbacks on our projects and helping troubleshoot our experiments. He also generously donated cells, few DNA samples and few reagents due to back ordering. <br />
<br />
*Alizee Jenck who ran mass spectrometry for us to determine whether or not topoisomerase was covalently bound to single stranded DNA.<br />
<br />
*Jordan Nguyen for setting up the foundation for our Wiki.<br />
<br />
*James Alling for helping us edit our abstract as well as providing guidance for our ethics essay.<br />
<br />
*Rene Davis for helping us proofread our writing and providing advice. <br />
<br />
<br />
*Eric Trang for helping us with creating the logo.<br />
<br />
*Dr. Thomas E. Grys, Mayo Clinic, for providing his feedback on the project and suggesting different applications of the device. <br />
<br />
<br />
<b>In terms of research materials, we would like to thank:</b><br />
<br />
*Case Western for providing us with the split-beta gal fragment sequences.<br />
<br />
*The University of Pennsylvania for the Topoisomerase samples.<br />
<br />
<br />
<b>In terms of funding, we would like to thank:</b><br />
<br />
*Ira A. Fulton Schools of Engineering at Arizona State University<br />
<br />
*College of Liberal Arts and Sciences at Arizona State University <br />
<br />
*School of Biological Health Systems Engineering at Arizona State University<br />
<br />
*School of Life Sciences at Arizona State University<br />
<br />
*School of Politics and Global Studies at Arizona State University<br />
<br />
*Barrett, the Honors College at Arizona State University<br />
<br />
*Department of Chemistry and Biochemistry at Arizona State University</div>Napatelhttp://2012.igem.org/Team:Arizona_State/AccomplishmentsTeam:Arizona State/Accomplishments2012-10-04T03:58:09Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<html><br />
<body><br />
<p><br />
<h4>Requirements for a Bronze Medal:</h4><br />
<p><br />
&#10003; Register the team, have a great summer, and plan to have fun at the Regional Jamboree.<br />
</p><br />
<p><br />
&#10003; Successfully complete and submit this iGEM 2012 Judging form.<br />
</p><br />
<p><br />
&#10003; Create and share a Description of the team's project using the iGEM wiki and the team's parts using the Registry of Standard Biological Parts.<br />
</p><br />
<p><br />
&#10003; Plan to present a Poster and Talk at the iGEM Jamboree.<br />
</p><br />
<p><br />
&#10003; Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Standard Biological Parts. Including:<br />
</p><br />
<p><br />
&#10003; Primary nucleic acid sequence<br />
</p><br />
<p><br />
&#10003; Description of function<br />
</p><br />
<p><br />
&#10003; Authorship<br />
</p><br />
<p><br />
&#10003; Safety notes, if relevant.<br />
</p><br />
<p><br />
&#10003; Acknowedgment of sources and references<br />
</p><br />
<p><br />
&#10003; Submit DNA for at least one new BioBrick Part or Device to the Registry.<br />
</p><br />
<p><br />
<h4>Additional Requirements for a Silver Medal:</h4><br />
</p><br />
<p><br />
&#10003; Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected; characterize the operation of your new part/device. <br />
</p><br />
<p><br />
&#10003; Enter this information and other documentation on the part's 'Main Page' section of the Registry. Part Number(s): BBa_K891000, BBa_K891234, BBa_K891999<br />
</p><br />
<p><br />
<h4>Additional Requirements for a Gold Medal: (one OR more)</h4><br />
<p><br />
&#10003; 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 />
</p></div>Napatelhttp://2012.igem.org/Team:Arizona_State/AccomplishmentsTeam:Arizona State/Accomplishments2012-10-04T03:56:59Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<html><br />
<body><br />
<p><br />
<h4>Requirements for a Bronze Medal:</h4><br />
<p><br />
&#10003; Register the team, have a great summer, and plan to have fun at the Regional Jamboree.<br />
</p><br />
<p><br />
&#10003; Successfully complete and submit this iGEM 2012 Judging form.<br />
</p><br />
<p><br />
&#10003; Create and share a Description of the team's project using the iGEM wiki and the team's parts using the Registry of Standard Biological Parts.<br />
</p><br />
<p><br />
&#10003; Plan to present a Poster and Talk at the iGEM Jamboree.<br />
</p><br />
<p><br />
&#10003; Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Standard Biological Parts. Including:<br />
</p><br />
<p><br />
&#10003; Primary nucleic acid sequence<br />
</p><br />
<p><br />
&#10003; Description of function<br />
</p><br />
<p><br />
&#10003; Authorship<br />
</p><br />
<p><br />
&#10003; Safety notes, if relevant.<br />
</p><br />
<p><br />
&#10003; Acknowedgment of sources and references<br />
</p><br />
<p><br />
&#10003; Submit DNA for at least one new BioBrick Part or Device to the Registry.<br />
</p><br />
<p><br />
<h4>Additional Requirements for a Silver Medal:</h4><br />
</p><br />
<p><br />
&#10003; Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected; characterize the operation of your new part/device. Enter this information and other documentation on the part's 'Main Page' section of the Registry. Part Number(s): BBa_K891000, BBa_K891234, BBa_K891999<br />
</p><br />
<p><br />
<h4>Additional Requirements for a Gold Medal: (one OR more)</h4><br />
<p><br />
&#10003; 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 />
</p></div>Napatelhttp://2012.igem.org/Team:Arizona_State/ProblemTeam:Arizona State/Problem2012-10-04T03:52:12Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Detailed Problem Description</h1><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>What is the problem we want to solve?</h2><br />
<br />
<p><br />
Viewed as a minor inconvenience in the developed world, diarrhea can be a death sentence in developing countries. Diarrhea can be life threatening as it causes severe dehydration as a result of extensive fluid loss. An estimated 2.0 billion cases of diarrhea occur each year amongst children under five years of age. Of these cases, 1.5 million children die. The major pathogens that most frequently cause acute childhood diarrhea cases are bacterial pathogens such as <i>E. coli, Shigella, Campylobacter and Salmonella</i>. The ASU iGEM team plans to develop an inexpensive way for communities to test the purity of water sources- and identify the specific pathogens in the water source- in efforts of reducing the incidence of childhood diarrhea and ultimately decreasing mortality rates. Existing biosensors for water-borne pathogens are either costly, unaccessible to developing countries, require large machinery to operate, difficult to use without training, and not very reliable. For example, immunoassays, which uses antibodies specific for certain antigens on pathogenic diarrhea, have a good turnaround time. However, not all antigens have available antibodies that can be used for detection, and those antibodies that are available can be very costly. <br />
</font><br />
<br /><br />
<br /><br />
<br />
</p><br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Quantitative considerations</h2><br />
<br />
<p>What concentration of pathogens causes sickness?</font><br />
<p>In determining what kinds of scenarios our biosensor would work in, a concentration had to be determined for what would be considered an outbreak. Based on research that was found for our project, patients' stool samples were tested for antibodies. An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen). <br />
<br /><br />
What specific design approaches did we take to try to reduce false positives, while making the biosensor effective?<br />
<p> A coliform count is defined as a test of water contamination in which the number of the colonies of coliform-bacteria <i>Escherichia coli (E.coli)</i> per 100 milliliter of water is counted. The result is expressed as “Coliform Microbial Density” and indicates the extent of fecal matter present in it. According to common water quality standards water can have about 200 colonies, and about 1000 in recreational water” (Business Dictionary). <br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Why are we doing this?</h2><br />
<br />
<p><br />
What do we hope to accomplish/want to figure out?<br />
<p><br />
For this project we are hoping to make our biosensor as user friendly and most cost effective product as possible. In the process in making this design we also wanted to address the results from using the biosensor. We wanted our project to give results in real time and be able to determine the phenotype of the potential pathogen. <br />
<br /><br />
Who are we doing this for? What do we care about? <br />
<p> This project is primarily based on its applications. We wanted to develop a low-cost biosensor that could be implemented in developing countries. This is because pathogenic bacteria causes diarrhea which is one of the world's leading global health issues. By designing our biosensor it would be a potential solution to this problem. <br />
<br />
<br /><br />
What is our ultimate goal?<br />
<p>Our ultimate goal for the project is to be able to see our biosensor used in developing nations. Ideally our biosensor would be able to be used as an early detection device in order to prevent future pathogenic outbreaks. This would be a solution to not only maintaining a healthy water supply but also to also improve the overall sanitation of developing nations. <br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/ProblemTeam:Arizona State/Problem2012-10-04T03:51:51Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<body><br />
<h1>Detailed Problem Description</h1><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>What is the problem we want to solve?</h2><br />
<br />
<p><br />
Viewed as a minor inconvenience in the developed world, diarrhea can be a death sentence in developing countries. Diarrhea can be life threatening as it causes severe dehydration as a result of extensive fluid loss. An estimated 2.0 billion cases of diarrhea occur each year amongst children under five years of age. Of these cases, 1.5 million children die. The major pathogens that most frequently cause acute childhood diarrhea cases are bacterial pathogens such as <i>E. coli, Shigella, Campylobacter and Salmonella</i>. The ASU iGEM team plans to develop an inexpensive way for communities to test the purity of water sources- and identify the specific pathogens in the water source- in efforts of reducing the incidence of childhood diarrhea and ultimately decreasing mortality rates. Existing biosensors for water-borne pathogens are either costly, unaccessible to developing countries, require large machinery to operate, difficult to use without training, and not very reliable. For example, immunoassays, which uses antibodies specific for certain antigens on pathogenic diarrhea, have a good turnaround time. However, not all antigens have available antibodies that can be used for detection, and those antibodies that are available can be very costly. <br />
</font><br />
<br /><br />
<br /><br />
<br />
</p><br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Quantitative considerations</h2><br />
<br />
<p>What concentration of pathogens causes sickness?</font><br />
<p>In determining what kinds of scenarios our biosensor would work in, a concentration had to be determined for what would be considered an outbreak. Based on research that was found for our project, patients' stool samples were tested for antibodies. An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen). <br />
<br /><br />
What specific design approaches did we take to try to reduce false positives, while making the biosensor effective?<br />
<p> A coliform count is defined as a test of water contamination in which the number of the colonies of coliform-bacteria Escherichia coli (E.coli) per 100 milliliter of water is counted. The result is expressed as “Coliform Microbial Density” and indicates the extent of fecal matter present in it. According to common water quality standards water can have about 200 colonies, and about 1000 in recreational water” (Business Dictionary). <br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<h2>Why are we doing this?</h2><br />
<br />
<p><br />
What do we hope to accomplish/want to figure out?<br />
<p><br />
For this project we are hoping to make our biosensor as user friendly and most cost effective product as possible. In the process in making this design we also wanted to address the results from using the biosensor. We wanted our project to give results in real time and be able to determine the phenotype of the potential pathogen. <br />
<br /><br />
Who are we doing this for? What do we care about? <br />
<p> This project is primarily based on its applications. We wanted to develop a low-cost biosensor that could be implemented in developing countries. This is because pathogenic bacteria causes diarrhea which is one of the world's leading global health issues. By designing our biosensor it would be a potential solution to this problem. <br />
<br />
<br /><br />
What is our ultimate goal?<br />
<p>Our ultimate goal for the project is to be able to see our biosensor used in developing nations. Ideally our biosensor would be able to be used as an early detection device in order to prevent future pathogenic outbreaks. This would be a solution to not only maintaining a healthy water supply but also to also improve the overall sanitation of developing nations. <br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_StateTeam:Arizona State2012-10-04T03:51:34Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<html><br />
<center><img src="https://static.igem.org/mediawiki/2012/f/f3/CrSYS.JPG" width="800" length="1000"></center><br />
<br />
<body><br />
<h1>Project Overview</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Arizona State's 2012 iGEM project aims to develop a portable water-borne pathogen biosensor feasible for real-time field application. To achieve both specificity and portability, the team is constructing two biosensors, each capable of detecting a specific pathogenic marker in water-borne bacteria. The first system, a split-enzyme engineered fusion protein, selectively binds to pathogen membranes in water samples and induces a colorimetric response. The second system will detect specific DNA sequences in pathogenic bacteria and activate a similar colorimetric change. The advantage of this design over previous designs in the field lies in the cheap production of probes and the enzymatic chain reaction. In this way, samples can be tested in the field with minimal cost and high sensitivity.<br />
<br />
</p><br />
<br />
<br />
<br />
<h1>Abstract</h1><br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<p><br />
Diarrheic pathogens including <i>E.coli</i> O157:H7 serotype, campylobacter, shigella, and salmonella often contaminate drinking water supplies in developing nations and are responsible for approximately 1.5 million worldwide annual deaths. Current technologies for detection of bacteria include DNA hybridization FRET signaling, electrical detection via immobilized antimicrobial peptides, and PCR amplification followed by gel visualization. Our method of bacterial detection fills a niche in biosensor technology. Our design implies lower costs, higher portability, and a more rapid signal output than most bacterial biosensors. Additionally, our interchangeable DNA probe confers modularity, allowing for a range of bacterial detection. Using a novel split beta-galactosidase complementation assay, we have designed three unique chimeric proteins that recognize and bind to specific pathogenic markers and create a functioning beta-galactosidase enzyme. This functioning enzyme unit then cleaves x-gal and produces a colorimetric output signal. Our research demonstrates success in initial stages of chimeric protein assembly. <br />
</p><br />
<br /><br />
<br />
<hr style="color: #800000; height:3px;" /><br />
<br />
<br /><br />
<br />
<br /><br />
<br />
<div align="center"><br />
<b>Contact Us</b><br />
<br /><br />
Arizona State University<br />
<br /><br />
ECG 334, PO BOX 9709<br />
<br /><br />
Tempe, Arizona 85287<br />
</div><br />
<br />
</body><br />
</html><br />
{{:Team:Arizona_State/Template:twitter}}<br />
{{:Team:Arizona_State/sitemap}}</div>Napatelhttp://2012.igem.org/Team:Arizona_State/AccomplishmentsTeam:Arizona State/Accomplishments2012-10-04T03:51:10Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
Requirements for a Bronze Medal:<br />
&#10003; Register the team, have a great summer, and plan to have fun at the Regional Jamboree.<br />
Successfully complete and submit this iGEM 2012 Judging form.<br />
Create and share a Description of the team's project using the iGEM wiki and the team's parts using the Registry of Standard Biological Parts.<br />
Plan to present a Poster and Talk at the iGEM Jamboree.<br />
Enter information detailing at least one new standard BioBrick Part or Device in the Registry of Standard Biological Parts. Including:<br />
Primary nucleaic acid sequence<br />
Description of function<br />
Authorship<br />
Safety notes, if relevant.<br />
Acknowedgment of sources and references<br />
Submit DNA for at least one new BioBrick Part or Device to the Registry.<br />
<br />
Additional Requirements for a Silver Medal:<br />
Demonstrate that at least one new BioBrick Part or Device of your own design and construction works as expected; characterize the operation of your new part/device.<br />
Enter this information and other documentation on the part's 'Main Page' section of the Registry<br />
Part Number(s): BBa_K891000, BBa_K891234, BBa_K891999<br />
<br />
Additional Requirements for a Gold Medal: (one OR more)<br />
Improve an existing BioBrick Part or Device and enter this information back on the Experience Page of the Registry.<br />
Part Number(s): None<br />
Help another iGEM team by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.<br />
Link to this information on your wiki. Page name: None<br />
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 />
Link to this information on your wiki.</div>Napatelhttp://2012.igem.org/Team:Arizona_State/HPModelingTeam:Arizona State/HPModeling2012-10-04T03:44:39Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
We can use Bayesian techniques to estimate natural frequency of the quantity to be measured (pathogen presence) as well as to analyze the accuracy and reliability of our device.<br />
<br />
Baye's rule gives us the probability of an actual positive event given that our sensor outputs "true". To evaluate this probability we need three pieces of data: specificity ('''A'''), sensitivity ('''B'''), and the "natural frequency" ('''C''') of the event. Sensitivity and specificity are evaluated based on experimental results and are defined below. Estimation of the "natural frequency" of a disease vector is more complex, and can be handled using a Bayesian network or other sophisticated statistical devices. This Bayesian network should be constructed using data from studies such as those referenced in [https://2012.igem.org/Team:Arizona_State/FieldApplications <i>Escherichia Coli</i> Case Studies].<br />
----<br />
<center><br />
{| class="wikitable" align="center" style="text-align:center; border:none; background:transparent;"<br />
|colspan="2" rowspan="2" style="border:none;"|<br />
|colspan="2" style="background:#ffdead;"|'''Condition'''<br />
|-<br />
|Condition Positive<br />
|Condition Negative<br />
|-<br />
|rowspan="2" style="background:#ffdead;"|'''Sensor<br />Outcome'''<br />
|Sensor<br />Outcome<br />Positive<br />
|<span style="color:#006600;">'''True Positive'''</span><br />
|<span style="color:#cc0000;">'''False Positive'''</span><br />
|style="background:#ffdead;"|Positive predictability =<br />TP<div style="border-top:1px solid;">TP + FP</div><br />
|-<br />
|Sensor<br />Outcome<br />Negative<br />
|<span style="color:#cc0000;">'''False Negative'''</span><br />
|<span style="color:#006600;">'''True Negative'''</span><br />
|style="background:#ffdead;"|Negative predictability =<br />TN<div style="border-top:1px solid;">TN + FN</div><br />
|-<br />
|colspan="2" style="border:none;" |<br />
|style="background:#ffdead;"|Sensitivity =<br />TP<div style="border-top:1px solid;">TP + TN</div><br />
|style="background:#ffdead;"|Specificity =<br />TN<div style="border-top:1px solid;">TN + FP</div><br />
|}<br />
</center><br />
<br />
* '''Sensitivity''': proportion of true positives accurately measured<br />
* '''Specificity''': proportion of true negatives accurately measured<br />
* '''Positive predictability''': proportion of positive sensor results that are true positives<br />
* '''Negative predictability''': proportion of negative sensor results that are true negatives<br />
<br />
Once we have experimental data giving us values for the table above, we can use Bayes' theorem to estimate the probability of an actual event given a positive sensor reading. To aid in these calculations we have attached an excel spreadsheet: [[File:Bayesian formulas.xls|Bayes' rule]].</div>Napatelhttp://2012.igem.org/Team:Arizona_State/Ethical_ConditionsTeam:Arizona State/Ethical Conditions2012-10-04T03:40:23Z<p>Napatel: Created page with "{{:Team:Arizona_State/Template:Header}}"</p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}</div>Napatelhttp://2012.igem.org/Team:Arizona_State/FieldApplicationsTeam:Arizona State/FieldApplications2012-10-04T03:39:47Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<h1 style="font-family:Helvetica;color:maroon;" align="left"><i>Escherichia Coli</i> Case Studies</h1><br />
<br />
<br />
<b> Timeline of an outbreak: </b><br />
<br />
In order to implement the biosensor correctly, it is imperative to find data about how E-coli outbreaks progressed. Last year for example, there was on outbreak of E-coli O104:H4 in Germany. It was first detected in early May of 2011, by causing an increased frequency of hemolytic uremic syndrome (Rohde). As the E-coli outbreak continued to spread, traces of E-coli were present in different foods. According to Dr. Rohde in the Open-Source Genomic Analysis of Shiga-Toxin-Producing E.coli O104:H4 case study, the genomic events began with how the E-coli phenotype being determined (Rohde). It wasn’t until five days after the first detection of the E-coli did lab work begin (Rohde). Although this case study reference is a food E-coli outbreak, it continued to grow in size as more food was found to be contaminated. This scenrario is similar to a water based E-coli outbreak because typically in larger outbreaks it will affect more than one geographic area. Using this timeline as an example, between the first detection of the outbreak to the E-coli phenotype being determined, it was a period of three weeks. According to research, detection of the pathogen took a very small amount of time compared to determining the phenotype of the pathogen (Rohde). At this point in time there would have been many sick patients and even potentially deaths depending on the severity of the outbreak. With our biosensor, this time could be dramatically reduced. Our biosensor could detect ideally any pathogen of interest.<br />
<br />
<b> Finding the source of an outbreak? </b><br />
<br />
As defined an outbreak is an occurrence of disease greater than would otherwise be expected at a particular time and place (Business Dictionary). For an E-coli outbreak it is most common to see outbreaks take place when fecal matter is mixed in with the primary supply of water or in food. This is more common in developing countries that in more established countries such as most of Europe and the United States, although occurrences still take place in these areas. For example in Denmark, there was an outbreak of Campylobacter jejuni that happened between 1995-1996 (Engberg). This bacteria is similar to E-coli in that it behaves very similar. Campylobacter jejuni is the most commonly reported bacterial cause of diarrhea in humans in developing countries (Engberg). In December of 1995, a control procedure was performed to test the amount of nitrate in the ground water. In the process of testing this, a sewage pipe was damaged and then leaked into the ground water supply. It took over a month for the water pump to be turned off from the initial point of contamination (Engberg). For this particular case, a very high coliform count was found in the infected water. “A coliform count is defined as a test of water contamination in which the number of the colonies of coliform-bacteria Escherichia coli (E.coli) per 100 milliliter of water is counted. The result is expressed as “Coliform Microbial Density” and indicates the extent of fecal matter present in it. According to common water quality standards water can have about 200 colonies, and about 1000 in recreational water” (Business Dictionary). An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen).<br />
<br />
<br />
<b> What if the E-coli strain mutated or the E-coli was undetectable? What are the chances of a mutation occurring or what should be done if a mutation occurs? </b><br />
<br />
Currently there is a controversial hypothesis that although e coli can be detected it is viable but its non-culturable (Bogosian). This holds true for any bacteria that cannot be cultured by standard methods. A culturable bacterium is inoculated into a sterile microcosm, most commonly seawater or river water, and incubated for a number of days with regular monitoring (Bogosian). This would affect the timeline of an outbreak as well as infect more people with contaminated water. This poses as an obvious public health issue for developing nations who do not have the equipment or technology for this kind of situation. Thus far it has been shown that although this poses as a health risk, it has only been attributed to 22 deaths and 104 total cases in the United States in the last 70 years (Bgosian). It has been shown that although the E-coli are present, the cells actually die off based on their living conditions. A study was conducted to determine if changes in cell populations were due to cell death or to the cells developing into the non-culturable state (Bogosian). This proved to be very useful because the study tested what kinds of environment the E-coli cells would either decline in their populations or thrive to cause an outbreak. The conclusion that E-coli cells did not thrive in non-sterile environments (Bogosian). This proves that when an E-coli outbreak occurs it will be because the cells are in an optimum environment where they are able to grow readily. Although E-coli can be present in water does not mean an outbreak will occur. <br />
<br />
<br />
<b> How many tests should be done for an outbreak? </b><br />
<br />
In each of the case studies that were researched, it became apparent quickly that each outbreak has its own characteristics. For example, in 2011, there was an outbreak that took place in Germany where there was a very high incidence in adults, especially women (Rohde). There can also be instances where the outbreak is more toxic to visitors compared to residents or could affect children more so than adults. Since each outbreak is unique in its own way, it is difficult to determine how many tests should be done to determine the severity of the outbreak. According to case study about an outbreak that took place in Alpine, Wyoming, physicians began seeing more patients with bloody diarrhea (Olsen). More cases began showing up in not only Wyoming but also Utah and Washington (Olsen). During the lab investigation of this outbreak, serum was tested from town residents to check for IgM antibodies to the O157 lipopolysaccharides (Olsen). An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen). Prior to the outbreak, the Alpine municipal water system was tested multiple times each month for coliform counts. In this case, they were positive results for E-coli in April, May and June of that year (Olsen). It was in late June that the outbreak occurred, and by middle of July they had found the source of this occurrence. Once the outbreak was detected, stool samples from infected patients were then sent to a lab for further testing. In total, from the time that the outbreak began to the time that the source was found, took about 3-4 weeks (Olsen). During this time, tests were being done by multiple agencies such as the Wyoming State laboratory, and the Utah Department of Health State Laboratory (Olsen). <br />
<br />
<br />
<b> What are the current practices? </b><br />
<br />
E-coli outbreaks have been known to occur in many different sources, such as food, water, and plants. It has been shown that before an outbreak takes place in water, there are typically signs that E-coli is present (Olsen). This is because before an outbreak can occur the cells must be able to survive in their environment. In recent case studies it has been found that although E-coli were found to be present in the water supply, although the amount of E-coli was insufficient. It was not until after an outbreak occurred and patients began having symptoms did the amount of E-coli become a problem. Once the E-coli outbreak has occurred, it will usually take a few weeks to run tests. These experiments can be determining the phenotype of E-coli or just to determine how many people could potentially be affected by the outbreak. It is quite common during E-coli water outbreaks for the cohort case studies to take place. These studies determine the statistical analysis of the outbreak, where the analysts can see how the outbreak progressed with how many people it infected (Olsen). When E-coli are present in other sources such as food and plants, it is usually not known that this is the source until after the outbreak has already occurred. <br />
<br />
<br />
<b> How does the biosensor improve sanitation? Why is there a need for a real time/faster response for the biosensor needed? </b><br />
<br />
Improving sanitation and hygiene of water has been one of the primary goals for Arizona State’s iGEM team. As a result of producing a biosensor to detect pathogens, it has the ability to not only prevent outbreaks from occurring but also to minimize them. Our biosensor has the ability to be used to detect different kinds of pathogens. This is very useful because if an outbreak were to occur, the amount of time in spending on determining the phenotype of the pathogen, can then be spent on eliminating it from water sources. This is another reason why our biosensor can be so effective by being able to detect specific pathogens, but it is also able to give you the answers in real time. This eliminates even more time in the process of determining the pathogen. By being able to prevent an outbreak from occurring, we would be able to improve the sanitation of water, especially in developing countries. It is in developing nations where the outbreaks are the most prevalent.</div>Napatelhttp://2012.igem.org/Team:Arizona_State/FieldApplicationsTeam:Arizona State/FieldApplications2012-10-04T03:39:32Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<h1 style="font-family:Helvetica;color:maroon;" align="left"><i>Escherichia Coli</i> Case Studies</h1><br />
<br />
<br />
<b> Timeline of an outbreak: </b><br />
<br />
In order to implement the biosensor correctly, it is imperative to find data about how E-coli outbreaks progressed. Last year for example, there was on outbreak of E-coli O104:H4 in Germany. It was first detected in early May of 2011, by causing an increased frequency of hemolytic uremic syndrome (Rohde). As the E-coli outbreak continued to spread, traces of E-coli were present in different foods. According to Dr. Rohde in the Open-Source Genomic Analysis of Shiga-Toxin-Producing E.coli O104:H4 case study, the genomic events began with how the E-coli phenotype being determined (Rohde). It wasn’t until five days after the first detection of the E-coli did lab work begin (Rohde). Although this case study reference is a food E-coli outbreak, it continued to grow in size as more food was found to be contaminated. This scenrario is similar to a water based E-coli outbreak because typically in larger outbreaks it will affect more than one geographic area. Using this timeline as an example, between the first detection of the outbreak to the E-coli phenotype being determined, it was a period of three weeks. According to research, detection of the pathogen took a very small amount of time compared to determining the phenotype of the pathogen (Rohde). At this point in time there would have been many sick patients and even potentially deaths depending on the severity of the outbreak. With our biosensor, this time could be dramatically reduced. Our biosensor could detect ideally any pathogen of interest.<br />
<br />
<b> Finding the source of an outbreak? </b><br />
<br />
As defined an outbreak is an occurrence of disease greater than would otherwise be expected at a particular time and place (Business Dictionary). For an E-coli outbreak it is most common to see outbreaks take place when fecal matter is mixed in with the primary supply of water or in food. This is more common in developing countries that in more established countries such as most of Europe and the United States, although occurrences still take place in these areas. For example in Denmark, there was an outbreak of Campylobacter jejuni that happened between 1995-1996 (Engberg). This bacteria is similar to E-coli in that it behaves very similar. Campylobacter jejuni is the most commonly reported bacterial cause of diarrhea in humans in developing countries (Engberg). In December of 1995, a control procedure was performed to test the amount of nitrate in the ground water. In the process of testing this, a sewage pipe was damaged and then leaked into the ground water supply. It took over a month for the water pump to be turned off from the initial point of contamination (Engberg). For this particular case, a very high coliform count was found in the infected water. “A coliform count is defined as a test of water contamination in which the number of the colonies of coliform-bacteria Escherichia coli (E.coli) per 100 milliliter of water is counted. The result is expressed as “Coliform Microbial Density” and indicates the extent of fecal matter present in it. According to common water quality standards water can have about 200 colonies, and about 1000 in recreational water” (Business Dictionary). An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen).<br />
<br />
<br />
<b> What if the E-coli strain mutated or the E-coli was undetectable? What are the chances of a mutation occurring or what should be done if a mutation occurs? </b><br />
<br />
Currently there is a controversial hypothesis that although e coli can be detected it is viable but its non-culturable (Bogosian). This holds true for any bacteria that cannot be cultured by standard methods. A culturable bacterium is inoculated into a sterile microcosm, most commonly seawater or river water, and incubated for a number of days with regular monitoring (Bogosian). This would affect the timeline of an outbreak as well as infect more people with contaminated water. This poses as an obvious public health issue for developing nations who do not have the equipment or technology for this kind of situation. Thus far it has been shown that although this poses as a health risk, it has only been attributed to 22 deaths and 104 total cases in the United States in the last 70 years (Bgosian). It has been shown that although the E-coli are present, the cells actually die off based on their living conditions. A study was conducted to determine if changes in cell populations were due to cell death or to the cells developing into the non-culturable state (Bogosian). This proved to be very useful because the study tested what kinds of environment the E-coli cells would either decline in their populations or thrive to cause an outbreak. The conclusion that E-coli cells did not thrive in non-sterile environments (Bogosian). This proves that when an E-coli outbreak occurs it will be because the cells are in an optimum environment where they are able to grow readily. Although E-coli can be present in water does not mean an outbreak will occur. <br />
<br />
<br />
<b> How many tests should be done for an outbreak? </b><br />
<br />
In each of the case studies that were researched, it became apparent quickly that each outbreak has its own characteristics. For example, in 2011, there was an outbreak that took place in Germany where there was a very high incidence in adults, especially women (Rohde). There can also be instances where the outbreak is more toxic to visitors compared to residents or could affect children more so than adults. Since each outbreak is unique in its own way, it is difficult to determine how many tests should be done to determine the severity of the outbreak. According to case study about an outbreak that took place in Alpine, Wyoming, physicians began seeing more patients with bloody diarrhea (Olsen). More cases began showing up in not only Wyoming but also Utah and Washington (Olsen). During the lab investigation of this outbreak, serum was tested from town residents to check for IgM antibodies to the O157 lipopolysaccharides (Olsen). An antibody >1:320 for IgM or >1:160 for IgG was considered positive (Olsen). Prior to the outbreak, the Alpine municipal water system was tested multiple times each month for coliform counts. In this case, they were positive results for E-coli in April, May and June of that year (Olsen). It was in late June that the outbreak occurred, and by middle of July they had found the source of this occurrence. Once the outbreak was detected, stool samples from infected patients were then sent to a lab for further testing. In total, from the time that the outbreak began to the time that the source was found, took about 3-4 weeks (Olsen). During this time, tests were being done by multiple agencies such as the Wyoming State laboratory, and the Utah Department of Health State Laboratory (Olsen). <br />
<br />
<br />
<b> What are the current practices? </b><br />
E-coli outbreaks have been known to occur in many different sources, such as food, water, and plants. It has been shown that before an outbreak takes place in water, there are typically signs that E-coli is present (Olsen). This is because before an outbreak can occur the cells must be able to survive in their environment. In recent case studies it has been found that although E-coli were found to be present in the water supply, although the amount of E-coli was insufficient. It was not until after an outbreak occurred and patients began having symptoms did the amount of E-coli become a problem. Once the E-coli outbreak has occurred, it will usually take a few weeks to run tests. These experiments can be determining the phenotype of E-coli or just to determine how many people could potentially be affected by the outbreak. It is quite common during E-coli water outbreaks for the cohort case studies to take place. These studies determine the statistical analysis of the outbreak, where the analysts can see how the outbreak progressed with how many people it infected (Olsen). When E-coli are present in other sources such as food and plants, it is usually not known that this is the source until after the outbreak has already occurred. <br />
<br />
<br />
<b> How does the biosensor improve sanitation? Why is there a need for a real time/faster response for the biosensor needed? </b><br />
<br />
Improving sanitation and hygiene of water has been one of the primary goals for Arizona State’s iGEM team. As a result of producing a biosensor to detect pathogens, it has the ability to not only prevent outbreaks from occurring but also to minimize them. Our biosensor has the ability to be used to detect different kinds of pathogens. This is very useful because if an outbreak were to occur, the amount of time in spending on determining the phenotype of the pathogen, can then be spent on eliminating it from water sources. This is another reason why our biosensor can be so effective by being able to detect specific pathogens, but it is also able to give you the answers in real time. This eliminates even more time in the process of determining the pathogen. By being able to prevent an outbreak from occurring, we would be able to improve the sanitation of water, especially in developing countries. It is in developing nations where the outbreaks are the most prevalent.</div>Napatelhttp://2012.igem.org/Team:Arizona_State/HPModelingTeam:Arizona State/HPModeling2012-10-04T03:39:05Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}</div>Napatelhttp://2012.igem.org/Team:Arizona_State/Template:HeaderTeam:Arizona State/Template:Header2012-10-04T03:38:44Z<p>Napatel: </p>
<hr />
<div><html lang="en"><br />
<!-- Made by Abhi & Jordan with help from the "https://2011.igem.org/Team:Imperial_College_London" page --><br />
<head><br />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /><br />
<style type="text/css"><br />
#top-section {<br />
width: 975px;<br />
height: 20px;<br />
background-color: transparent;<br />
border: none;<br />
}<br />
<br />
#p-logo { display: none; }<br />
#search-controls { display: none; }<br />
.firstHeading { display: none; }<br />
#contentSub { margin: 0 0 0 0; }<br />
iframe { padding: 10px 20px 10px 20px; }<br />
<br />
body {<br />
background-color:#000000;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/c/c8/BackgroundNew.jpg); <br />
background-size:100%;<br />
background-position:center; background-attachment:fixed;<br />
}<br />
<br />
.right-menu li a, .right-menu li a:hover {<br />
color: #3c6b27;<br />
background-color: transparent;<br />
}<br />
<br />
#iGEMLogo {<br />
position: absolute;<br />
top:40px;<br />
left:20px;<br />
}<br />
<br />
#ProjectTitle {<br />
position: relative;<br />
text-align:center;<br />
}<br />
<br />
#ASULogo {<br />
position: absolute;<br />
top:45px;<br />
right:25px;<br />
}<br />
<br />
#menucontainer {<br />
overflow:visible;<br />
position:relative;<br />
z-index:3;<br />
}<br />
<br />
#content {<br />
position: relative;<br />
width: 975px;<br />
margin: 0 auto;<br />
padding-top:20px;<br />
padding-left:0px;<br />
padding-right:0px;<br />
padding-bottom:0px;<br />
//background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/4/4b/2012ASUiGemLogo.png);<br />
//background-repeat:no-repeat;<br />
//background-position:center;<br />
//background-attachment:fixed;<br />
color: black;<br />
border: none;<br />
line-height: 1.5em;<br />
z-index: 2;<br />
}<br />
<br />
#bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 {<br />
margin-bottom: 0;<br />
}<br />
<br />
a {color:#t;}<br />
a:link {color:#93B825;}<br />
a:visited {color:#728F1D;}<br />
a:hover {color:#93B825;}<br />
a:active {color:#93B825;}<br />
a[name]:hover {text-decoration:none;} <br />
<br />
a.sitemap:link,a.sitemap:visited {color:#680000;font-decoration:none;}<br />
a.sitemap:hover,a.sitemap:active {color:#680000;font-decoration:underline;}<br />
<br />
h1 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 2.2em;<br />
margin: 0 0 0 0;<br />
padding: 20px 20px 12px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h2 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.7em;<br />
margin: 0 0 0 0;<br />
padding: 18px 20px 7px 20px;<br />
border-bottom: none;<br />
} <br />
<br />
h3 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.4em;<br />
margin: 0 0 0 0;<br />
padding: 16px 20px 2px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h4 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.1em;<br />
margin: 0 0 0 0;<br />
padding: 13.5px 20px 1px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
p {<br />
font-family: helvetica,sans-serif;<br />
//color: #ffffff;<br />
background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/e/ea/Layer.png);<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
margin: 0 0 0 0;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
table {<br />
background: transparent;<br />
} th {<br />
background-color:maroon;<br />
color:gold;<br />
}<br />
<br />
.border {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
}<br />
<br />
.borderMagnify {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
margin-left:-9px;<br />
margin-right:9px;<br />
}<br />
<br />
.imgbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.vidbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.newouterbox {<br />
background-color:#FF944D;<br />
border:1px solid #CCCCCC;<br />
margin:20px;<br />
padding-bottom:0px;<br />
}<br />
<br />
.newinnerbox {<br />
border:1px solid #CCCCCC;<br />
margin:10px 20px 20px 20px;<br />
padding-top:0px;<br />
padding-bottom:13px;<br />
background-color:#ffffff;<br />
}<br />
<br />
.newtext {<br />
text-align:center;<br />
background-color:#FF944D;<br />
color:#000000;<br />
}<br />
<br />
ul.a {<br />
margin: 0 0 0 40px;<br />
list-style-image: none;<br />
list-style-type:disc;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
ol.a {<br />
margin: 0 0 0 30px;<br />
list-style-position:inside;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
#BackToTop {<br />
position:fixed;<br />
bottom:0;<br />
right:0;<br />
}<br />
<br />
#Sitemap {<br />
position:fixed;<br />
bottom:0;<br />
left:0;<br />
}<br />
<br />
/*** Start of Styling for menu bar ***/<br />
/*** ESSENTIAL STYLES ***/<br />
a.collapseLink {<br />
font-weight:bold;<br />
font-size:1em;<br />
color:#225323;<br />
}<br />
.sf-menu, .sf-menu * {<br />
margin:0;<br />
padding:0;<br />
list-style:none;<br />
}<br />
.sf-menu {<br />
line-height:1.0;<br />
}<br />
.sf-menu ul {<br />
position:absolute;<br />
top:999em;<br />
width:195px; /* left offset of submenus need to match (see below) */<br />
}<br />
.sf-menu ul li {<br />
width:100%;<br />
}<br />
.sf-menu li:hover {<br />
visibility:inherit; /* fixes IE7 'sticky bug' */<br />
}<br />
.sf-menu li {<br />
float:left;<br />
position:relative;<br />
width:195px;<br />
}<br />
.sf-menu a {<br />
display:block;<br />
position:relative;<br />
}<br />
.sf-menu li:hover ul, .sf-menu li.sfHover ul {<br />
left:0;<br />
top:2.5em; /* match top ul list item height */<br />
z-index:99;<br />
}<br />
ul.sf-menu li:hover li ul, ul.sf-menu li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li:hover ul, ul.sf-menu li li.sfHover ul {<br />
left:15.3em; /* match ul width */<br />
top:0;<br />
}<br />
ul.sf-menu li li:hover li ul, ul.sf-menu li li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul {<br />
left:10em; /* match ul width */<br />
top:0;<br />
}<br />
<br />
/*** DEMO SKIN ***/<br />
.sf-menu {<br />
float:left;<br />
margin-bottom:1em;<br />
}<br />
.sf-menu a {<br />
border-left:1px solid #fff;<br />
border-top:1px solid #826554;<br />
padding:0.37em 1em 0.37em 1em;<br />
text-decoration:none;<br />
font-family:'helveticaneue', sans-serif;<br />
font-size:1.3em;<br />
}<br />
.sf-menu a, .sf-menu a:visited { /* visited pseudo selector so IE6 applies text colour*/<br />
color:#efefef;<br />
}<br />
.sf-menu li, .sf-menu li li, .sf-menu li li li {<br />
background:#990000;<br />
}<br />
.sf-menu li:hover, .sf-menu li.sfHover, .sf-menu a:focus, .sf-menu a:hover, .sf-menu a:active {<br />
background:#b30000;<br />
outline:0;<br />
}<br />
<br />
/*** arrows **/<br />
.sf-menu a.sf-with-ul {<br />
cursor:default; <br />
padding-right:2.25em;<br />
min-width:1px; /* trigger IE7 hasLayout so spans position accurately */<br />
}<br />
.sf-sub-indicator {<br />
position:absolute;<br />
display:block;<br />
right:.75em;<br />
top:1.05em; /* IE6 only */<br />
width:10px;<br />
height:10px;<br />
text-indent:-999em;<br />
overflow:hidden;<br />
background:url('https://static.igem.org/mediawiki/2011/2/2f/ICL_MenuArrow.png') no-repeat -10px -100px;<br />
/* 8-bit indexed alpha png. IE6 gets solid image only */<br />
}<br />
a > .sf-sub-indicator { /* give all except IE6 the correct values */<br />
top:.8em;<br />
background-position:0 -100px; /* use translucent arrow for modern browsers*/<br />
}<br />
/* apply hovers to modern browsers */<br />
a:focus > .sf-sub-indicator,<br />
a:hover > .sf-sub-indicator,<br />
a:active > .sf-sub-indicator,<br />
li:hover > a > .sf-sub-indicator,<br />
li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px -100px; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/* point right for anchors in subs */<br />
.sf-menu ul .sf-sub-indicator { background-position: -10px 0; }<br />
.sf-menu ul a > .sf-sub-indicator { background-position: 0 0; }<br />
/* apply hovers to modern browsers */<br />
.sf-menu ul a:focus > .sf-sub-indicator,<br />
.sf-menu ul a:hover > .sf-sub-indicator,<br />
.sf-menu ul a:active > .sf-sub-indicator,<br />
.sf-menu ul li:hover > a > .sf-sub-indicator,<br />
.sf-menu ul li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px 0; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/*** shadows for all but IE6 ***/<br />
.sf-shadow ul {<br />
background:url('https://static.igem.org/mediawiki/2011/9/9f/ICL_Shadow.png') no-repeat bottom right;<br />
padding:0 8px 9px 0;<br />
-moz-border-radius-bottomleft:17px;<br />
-moz-border-radius-topright:17px;<br />
-webkit-border-top-right-radius:17px;<br />
-webkit-border-bottom-left-radius:17px;<br />
}<br />
<br />
.sf-shadow ul.sf-shadow-off {<br />
background:transparent;<br />
}<br />
</style><br />
<br />
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/hoverIntent?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/superfishjs?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/magnifier?action=raw&ctype=text/js"><br />
/***********************************************<br />
* jQuery Image Magnify- (c) Dynamic Drive DHTML code library (www.dynamicdrive.com)<br />
* This notice MUST stay intact for legal use<br />
* Visit Dynamic Drive at http://www.dynamicdrive.com/ for this script and 100s more<br />
***********************************************/<br />
</script><br />
<br />
<script type="text/javascript"><br />
var $ = jQuery;<br />
jQuery.imageMagnify.zIndexcounter = 1000;<br />
</script><br />
<br />
<script><br />
$(document).ready(function() {<br />
$("sup").click(function () {<br />
if ($(this).html().substr(0,1)=="[")<br />
{<br />
if ($('.technology').length>0)<br />
{<br />
ddaccordion.expandone('technology', $('.technology').length-1)<br />
setTimeout("window.scrollBy(0,50000)",200)<br />
}<br />
else window.scrollBy(0,50000)<br />
}<br />
});<br />
$("sup").mouseover(function () {<br />
if ($(this).html().substr(0,1)=="[") $(this).css('cursor', 'pointer');<br />
});<br />
});<br />
</script><br />
<br />
<script> <br />
$(document).ready(function() { <br />
$('ul.sf-menu').superfish({ <br />
}); <br />
});<br />
</script><br />
</head><br />
<br />
<body><br />
<a name="top"></a><br />
<!-----<br />
<div id='iGEMLogo'><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:120px;" /><br />
</a><br />
</div><br />
<br />
<div id='ProjectTitle'><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/5/5f/CRSYS.png" style="width:550px;" /><br />
<!---Before: https://static.igem.org/mediawiki/2012/d/db/2012_Project_logo.png---><!----<br />
</a><br />
</div><br />
<br />
<div id='ASULogo'><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="150" height="70" /><br />
</div><br />
-----><br />
<div id='header' align="center"><br />
<table width="950"><br />
<tr><br />
<td><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:100px;" /><br />
</a><br />
</td><br />
<td align="center"><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/9/9a/AsuCrsysLogothingy.png" style="width:591px;" /><br />
</a><br />
</td><br />
<td><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="125" /><br />
</td><br />
</table><br />
<br /><br />
</div><br />
<br />
<br />
<br />
<div id="BackToTop"><br />
<a href="#top"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2d/ArrowColorChanged.png" width="50px" /><br />
</a><br />
</div><br />
<br />
<div id="Sitemap"><br />
<a href='https://2012.igem.org/Team:Arizona_State/Sitemap'><br />
<img src="https://static.igem.org/mediawiki/2012/3/30/SiteMapColorChange.png" width="100px" /><br />
</a><br />
</div><br />
<br />
<div id='menucontainer'><br />
<ul class="sf-menu sf-navbar"><br />
<li><a class="sf-with-ul" href="#">Project<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State">Home</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Problem">Problem</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Magainin">Cell Surface Biosensor</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Chimeric_Reporter">DNA Biosensor</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/ssDNA">ssDNA Probe Design</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Notebook">Notebook</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/References">References</a><br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Team<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Team">Members</a></li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Attributions">Attributions</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2012">Official Team Profile</a></li><br />
</ul><br />
</li><br />
<br />
<li><a class="sf-with-ul" href="#">Results<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Data">Data</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Parts">BioBricks</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Accomplishments">Judging Criteria</a> </li><br />
</ul><br />
</li><br />
<li><a class="sf-with-ul" href="#">Human Practices<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/International">International Outreach</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Community">Community Outreach</a> </li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/University">University Outreach</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/FieldApplications">Case Studies</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/HPModeling">Modeling</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Ethical_Conditions">Ethical Considerations</a> </li> <br />
<br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Extras<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Media">Media</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Safety">Safety</a> </li> <br />
</ul><br />
</li> <br />
</ul> <br />
</div><br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/AttributionsTeam:Arizona State/Attributions2012-10-04T03:38:32Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<br />
<h2>Attributions</h2><br />
<br />
*Rohit: media preparation/Magainin<br />
*Amanda: media preparation team/human practices<br />
*Hyder: Topo chimeric protein production/ Topo target plasmid design and building <br />
*Ryan: Topo chimeric protein production<br />
*Abhi: Split beta gal assay development for the chimeric reporter (DNA probe)<br />
*Maddie: Split beta gal assay development for the chimeric reporter (DNA probe) / human practices<br />
*Nisarg: Magainin Assembly/Split beta gal assay development for Magainin/topo/AlumniGEM<br />
*Ellen: Magainin Assembly<br />
*Ethan: modeling<br />
<br />
<b>Thank you to:</b><br />
<br />
<ul><ul><br />
<br />
*Dr. Karmella Haynes for providing us guidance and support throughout the whole iGEM process. She generously opened her lab for the iGEM team and provided access to various equipments such as a thermocycler, spectrophotometer and a Light Cycler. In addition to providing us access to various equipments, she also donated various reagents contributing to the success of our projects.<br />
<br />
*Dr. Xiao Wang for serving as one of the team mentors. Wang Lab provided us with lab space during the summer and also provided us with cells and reagents. <br />
<br />
*Dr. Vincent Pizziconi for serving as one of the team mentors and providing us with aspiring words throughout the summer. Dr. Pizziconi opened his lab, the Biomedical Engineering Design Studio and the conference room for this years iGEM team.<br />
<br />
*Dr. Miles Orchinik and Dr. Tsafrir Mor for providing us lab space during the summer. Additionally, we would like to thank Dr. Gary Tahmahkera for giving us continual support in answering any questions we had while we were there.<br />
<br />
*Kylie Standage-Beier for providing us with feedbacks on our projects and helping troubleshoot our experiments. He also generously donated cells, few DNA samples and few reagents due to back ordering. <br />
<br />
*Alizee Jenck who ran mass spectrometry for us to determine whether or not topoisomerase was covalently bound to single stranded DNA.<br />
<br />
*Jordan Nguyen for setting up the foundation for our Wiki.<br />
<br />
*James Alling for helping us edit our abstract as well as providing guidance for our ethics essay.<br />
<br />
*Eric Trang for helping us with creating the logo.<br />
<br />
*Dr. Thomas E. Grys, Mayo Clinic, for providing his feedbacks on the project and suggesting different applications of the device. <br />
<br />
<b>In terms of research materials, we would like to thank:</b><br />
<br />
<br />
*Case Western for providing us with the split-beta gal fragment sequences.<br />
<br />
*The University of Pennsylvania for the Topoisomerase samples.<br />
<br />
<br />
<b>Also, we would like to thank our sponsors who help fund the project:</b><br />
<br />
*Ira A. Fulton School of Engineering<br />
<br />
*School of Biological Health Systems Engineering<br />
<br />
*School of Life Sciences<br />
<br />
*School of Politics and Global Studies<br />
<br />
*Barrett the Honors<br />
<br />
<br />
</ul></ul></div>Napatelhttp://2012.igem.org/Team:Arizona_State/AccomplishmentsTeam:Arizona State/Accomplishments2012-10-04T03:30:29Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<h1>Accomplishments</h1><br />
<br />
'''Experiments and Results'''<br />
*Researched a mutant form of Topoisomerase that is capable of peeling ssDNA off a template plasmid. <br />
*Confirmed Topo nicking interaction with plasmid DNA. <br />
*Confirmed alpha-omega complementation in strep-linker-split fragment<br />
<br />
<br />
'''Biobricks and Protocols'''<br />
*Submitted [https://2012.igem.org/Team:Arizona_State/Parts Biobricks]<br />
<br />
<br />
'''Human Practices'''<br />
<br />
'''Best Measurement Technique'''</div>Napatelhttp://2012.igem.org/Team:Arizona_State/Template:HeaderTeam:Arizona State/Template:Header2012-10-04T03:29:57Z<p>Napatel: </p>
<hr />
<div><html lang="en"><br />
<!-- Made by Abhi & Jordan with help from the "https://2011.igem.org/Team:Imperial_College_London" page --><br />
<head><br />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" /><br />
<style type="text/css"><br />
#top-section {<br />
width: 975px;<br />
height: 20px;<br />
background-color: transparent;<br />
border: none;<br />
}<br />
<br />
#p-logo { display: none; }<br />
#search-controls { display: none; }<br />
.firstHeading { display: none; }<br />
#contentSub { margin: 0 0 0 0; }<br />
iframe { padding: 10px 20px 10px 20px; }<br />
<br />
body {<br />
background-color:#000000;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/c/c8/BackgroundNew.jpg); <br />
background-size:100%;<br />
background-position:center; background-attachment:fixed;<br />
}<br />
<br />
.right-menu li a, .right-menu li a:hover {<br />
color: #3c6b27;<br />
background-color: transparent;<br />
}<br />
<br />
#iGEMLogo {<br />
position: absolute;<br />
top:40px;<br />
left:20px;<br />
}<br />
<br />
#ProjectTitle {<br />
position: relative;<br />
text-align:center;<br />
}<br />
<br />
#ASULogo {<br />
position: absolute;<br />
top:45px;<br />
right:25px;<br />
}<br />
<br />
#menucontainer {<br />
overflow:visible;<br />
position:relative;<br />
z-index:3;<br />
}<br />
<br />
#content {<br />
position: relative;<br />
width: 975px;<br />
margin: 0 auto;<br />
padding-top:20px;<br />
padding-left:0px;<br />
padding-right:0px;<br />
padding-bottom:0px;<br />
//background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/4/4b/2012ASUiGemLogo.png);<br />
//background-repeat:no-repeat;<br />
//background-position:center;<br />
//background-attachment:fixed;<br />
color: black;<br />
border: none;<br />
line-height: 1.5em;<br />
z-index: 2;<br />
}<br />
<br />
#bodyContent h1, #bodyContent h2, #bodyContent h3, #bodyContent h4, #bodyContent h5 {<br />
margin-bottom: 0;<br />
}<br />
<br />
a {color:#t;}<br />
a:link {color:#93B825;}<br />
a:visited {color:#728F1D;}<br />
a:hover {color:#93B825;}<br />
a:active {color:#93B825;}<br />
a[name]:hover {text-decoration:none;} <br />
<br />
a.sitemap:link,a.sitemap:visited {color:#680000;font-decoration:none;}<br />
a.sitemap:hover,a.sitemap:active {color:#680000;font-decoration:underline;}<br />
<br />
h1 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 2.2em;<br />
margin: 0 0 0 0;<br />
padding: 20px 20px 12px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h2 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.7em;<br />
margin: 0 0 0 0;<br />
padding: 18px 20px 7px 20px;<br />
border-bottom: none;<br />
} <br />
<br />
h3 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.4em;<br />
margin: 0 0 0 0;<br />
padding: 16px 20px 2px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
h4 {<br />
font-family: helvetica,sans-serif;<br />
color: #800000;<br />
background: transparent;<br />
font-weight: bold;<br />
font-size: 1.1em;<br />
margin: 0 0 0 0;<br />
padding: 13.5px 20px 1px 20px;<br />
border-bottom: none;<br />
}<br />
<br />
p {<br />
font-family: helvetica,sans-serif;<br />
//color: #ffffff;<br />
background: transparent;<br />
//background-image:url(https://static.igem.org/mediawiki/2012/e/ea/Layer.png);<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
margin: 0 0 0 0;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
table {<br />
background: transparent;<br />
} th {<br />
background-color:maroon;<br />
color:gold;<br />
}<br />
<br />
.border {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
}<br />
<br />
.borderMagnify {<br />
border:1px solid #B2B2B2;<br />
z-index:101;<br />
margin-left:-9px;<br />
margin-right:9px;<br />
}<br />
<br />
.imgbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.vidbox {<br />
margin:20px;<br />
padding:10px;<br />
border:1px solid black;<br />
text-align:center;<br />
}<br />
<br />
.newouterbox {<br />
background-color:#FF944D;<br />
border:1px solid #CCCCCC;<br />
margin:20px;<br />
padding-bottom:0px;<br />
}<br />
<br />
.newinnerbox {<br />
border:1px solid #CCCCCC;<br />
margin:10px 20px 20px 20px;<br />
padding-top:0px;<br />
padding-bottom:13px;<br />
background-color:#ffffff;<br />
}<br />
<br />
.newtext {<br />
text-align:center;<br />
background-color:#FF944D;<br />
color:#000000;<br />
}<br />
<br />
ul.a {<br />
margin: 0 0 0 40px;<br />
list-style-image: none;<br />
list-style-type:disc;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
ol.a {<br />
margin: 0 0 0 30px;<br />
list-style-position:inside;<br />
font-family: helvetica,sans-serif;<br />
color: #000000;<br />
background: #ffffff;<br />
font-weight: normal;<br />
font-size: 1em;<br />
line-height: 1.7em;<br />
text-align: justify;<br />
padding: 5px 20px 0px 20px;<br />
}<br />
<br />
#BackToTop {<br />
position:fixed;<br />
bottom:0;<br />
right:0;<br />
}<br />
<br />
#Sitemap {<br />
position:fixed;<br />
bottom:0;<br />
left:0;<br />
}<br />
<br />
/*** Start of Styling for menu bar ***/<br />
/*** ESSENTIAL STYLES ***/<br />
a.collapseLink {<br />
font-weight:bold;<br />
font-size:1em;<br />
color:#225323;<br />
}<br />
.sf-menu, .sf-menu * {<br />
margin:0;<br />
padding:0;<br />
list-style:none;<br />
}<br />
.sf-menu {<br />
line-height:1.0;<br />
}<br />
.sf-menu ul {<br />
position:absolute;<br />
top:999em;<br />
width:195px; /* left offset of submenus need to match (see below) */<br />
}<br />
.sf-menu ul li {<br />
width:100%;<br />
}<br />
.sf-menu li:hover {<br />
visibility:inherit; /* fixes IE7 'sticky bug' */<br />
}<br />
.sf-menu li {<br />
float:left;<br />
position:relative;<br />
width:195px;<br />
}<br />
.sf-menu a {<br />
display:block;<br />
position:relative;<br />
}<br />
.sf-menu li:hover ul, .sf-menu li.sfHover ul {<br />
left:0;<br />
top:2.5em; /* match top ul list item height */<br />
z-index:99;<br />
}<br />
ul.sf-menu li:hover li ul, ul.sf-menu li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li:hover ul, ul.sf-menu li li.sfHover ul {<br />
left:15.3em; /* match ul width */<br />
top:0;<br />
}<br />
ul.sf-menu li li:hover li ul, ul.sf-menu li li.sfHover li ul {<br />
top:-999em;<br />
}<br />
ul.sf-menu li li li:hover ul, ul.sf-menu li li li.sfHover ul {<br />
left:10em; /* match ul width */<br />
top:0;<br />
}<br />
<br />
/*** DEMO SKIN ***/<br />
.sf-menu {<br />
float:left;<br />
margin-bottom:1em;<br />
}<br />
.sf-menu a {<br />
border-left:1px solid #fff;<br />
border-top:1px solid #826554;<br />
padding:0.37em 1em 0.37em 1em;<br />
text-decoration:none;<br />
font-family:'helveticaneue', sans-serif;<br />
font-size:1.3em;<br />
}<br />
.sf-menu a, .sf-menu a:visited { /* visited pseudo selector so IE6 applies text colour*/<br />
color:#efefef;<br />
}<br />
.sf-menu li, .sf-menu li li, .sf-menu li li li {<br />
background:#990000;<br />
}<br />
.sf-menu li:hover, .sf-menu li.sfHover, .sf-menu a:focus, .sf-menu a:hover, .sf-menu a:active {<br />
background:#b30000;<br />
outline:0;<br />
}<br />
<br />
/*** arrows **/<br />
.sf-menu a.sf-with-ul {<br />
cursor:default; <br />
padding-right:2.25em;<br />
min-width:1px; /* trigger IE7 hasLayout so spans position accurately */<br />
}<br />
.sf-sub-indicator {<br />
position:absolute;<br />
display:block;<br />
right:.75em;<br />
top:1.05em; /* IE6 only */<br />
width:10px;<br />
height:10px;<br />
text-indent:-999em;<br />
overflow:hidden;<br />
background:url('https://static.igem.org/mediawiki/2011/2/2f/ICL_MenuArrow.png') no-repeat -10px -100px;<br />
/* 8-bit indexed alpha png. IE6 gets solid image only */<br />
}<br />
a > .sf-sub-indicator { /* give all except IE6 the correct values */<br />
top:.8em;<br />
background-position:0 -100px; /* use translucent arrow for modern browsers*/<br />
}<br />
/* apply hovers to modern browsers */<br />
a:focus > .sf-sub-indicator,<br />
a:hover > .sf-sub-indicator,<br />
a:active > .sf-sub-indicator,<br />
li:hover > a > .sf-sub-indicator,<br />
li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px -100px; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/* point right for anchors in subs */<br />
.sf-menu ul .sf-sub-indicator { background-position: -10px 0; }<br />
.sf-menu ul a > .sf-sub-indicator { background-position: 0 0; }<br />
/* apply hovers to modern browsers */<br />
.sf-menu ul a:focus > .sf-sub-indicator,<br />
.sf-menu ul a:hover > .sf-sub-indicator,<br />
.sf-menu ul a:active > .sf-sub-indicator,<br />
.sf-menu ul li:hover > a > .sf-sub-indicator,<br />
.sf-menu ul li.sfHover > a > .sf-sub-indicator {<br />
background-position:-10px 0; /* arrow hovers for modern browsers*/<br />
}<br />
<br />
/*** shadows for all but IE6 ***/<br />
.sf-shadow ul {<br />
background:url('https://static.igem.org/mediawiki/2011/9/9f/ICL_Shadow.png') no-repeat bottom right;<br />
padding:0 8px 9px 0;<br />
-moz-border-radius-bottomleft:17px;<br />
-moz-border-radius-topright:17px;<br />
-webkit-border-top-right-radius:17px;<br />
-webkit-border-bottom-left-radius:17px;<br />
}<br />
<br />
.sf-shadow ul.sf-shadow-off {<br />
background:transparent;<br />
}<br />
</style><br />
<br />
<script type="text/javascript" src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/hoverIntent?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/superfishjs?action=raw&ctype=text/js"><br />
</script> <br />
<script type="text/javascript" src="https://2011.igem.org/Team:Imperial_College_London/magnifier?action=raw&ctype=text/js"><br />
/***********************************************<br />
* jQuery Image Magnify- (c) Dynamic Drive DHTML code library (www.dynamicdrive.com)<br />
* This notice MUST stay intact for legal use<br />
* Visit Dynamic Drive at http://www.dynamicdrive.com/ for this script and 100s more<br />
***********************************************/<br />
</script><br />
<br />
<script type="text/javascript"><br />
var $ = jQuery;<br />
jQuery.imageMagnify.zIndexcounter = 1000;<br />
</script><br />
<br />
<script><br />
$(document).ready(function() {<br />
$("sup").click(function () {<br />
if ($(this).html().substr(0,1)=="[")<br />
{<br />
if ($('.technology').length>0)<br />
{<br />
ddaccordion.expandone('technology', $('.technology').length-1)<br />
setTimeout("window.scrollBy(0,50000)",200)<br />
}<br />
else window.scrollBy(0,50000)<br />
}<br />
});<br />
$("sup").mouseover(function () {<br />
if ($(this).html().substr(0,1)=="[") $(this).css('cursor', 'pointer');<br />
});<br />
});<br />
</script><br />
<br />
<script> <br />
$(document).ready(function() { <br />
$('ul.sf-menu').superfish({ <br />
}); <br />
});<br />
</script><br />
</head><br />
<br />
<body><br />
<a name="top"></a><br />
<!-----<br />
<div id='iGEMLogo'><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:120px;" /><br />
</a><br />
</div><br />
<br />
<div id='ProjectTitle'><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/5/5f/CRSYS.png" style="width:550px;" /><br />
<!---Before: https://static.igem.org/mediawiki/2012/d/db/2012_Project_logo.png---><!----<br />
</a><br />
</div><br />
<br />
<div id='ASULogo'><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="150" height="70" /><br />
</div><br />
-----><br />
<div id='header' align="center"><br />
<table width="950"><br />
<tr><br />
<td><br />
<a href='https://2012.igem.org/Main_Page'><br />
<img src="https://static.igem.org/mediawiki/2012/d/d6/IGEM_official_logo.png" style="width:100px;" /><br />
</a><br />
</td><br />
<td align="center"><br />
<a href='https://2012.igem.org/Team:Arizona_State'><br />
<img src="https://static.igem.org/mediawiki/2012/9/9a/AsuCrsysLogothingy.png" style="width:591px;" /><br />
</a><br />
</td><br />
<td><br />
<img src="http://afmarcom.com/blog/wp-content/uploads/2011/02/2011-02-25-asu.png" width="125" /><br />
</td><br />
</table><br />
<br /><br />
</div><br />
<br />
<br />
<br />
<div id="BackToTop"><br />
<a href="#top"><br />
<img src="https://static.igem.org/mediawiki/2012/2/2d/ArrowColorChanged.png" width="50px" /><br />
</a><br />
</div><br />
<br />
<div id="Sitemap"><br />
<a href='https://2012.igem.org/Team:Arizona_State/Sitemap'><br />
<img src="https://static.igem.org/mediawiki/2012/3/30/SiteMapColorChange.png" width="100px" /><br />
</a><br />
</div><br />
<br />
<div id='menucontainer'><br />
<ul class="sf-menu sf-navbar"><br />
<li><a class="sf-with-ul" href="#">Project<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State">Home</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Problem">Problem</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Magainin">Cell Surface Biosensor</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Chimeric_Reporter">DNA Biosensor</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/ssDNA">ssDNA Probe Design</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Notebook">Notebook</a><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/References">References</a><br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Team<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Team">Members</a></li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Attributions">Attributions</a></li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Acknowledgments">Acknowledgments</a></li><br />
<li><a href="https://igem.org/Team.cgi?year=2012">Official Team Profile</a></li><br />
</ul><br />
</li><br />
<br />
<li><a class="sf-with-ul" href="#">Results<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Data">Data</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Parts">BioBricks</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Accomplishments">Judging Criteria</a> </li><br />
</ul><br />
</li><br />
<li><a class="sf-with-ul" href="#">Human Practices<span class="sf-sub-indicator"> &#187;</span></a> <br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/International">International Outreach</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Community">Community Outreach</a> </li><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/University">University Outreach</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/FieldApplications">Case Studies</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/HPModeling">Modeling</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Ethical_Conditions">Ethical Considerations</a> </li> <br />
<br />
</ul> <br />
</li> <br />
<br />
<li><a class="sf-with-ul" href="#">Extras<span class="sf-sub-indicator"> &#187;</span></a><br />
<ul><br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Media">Media</a> </li> <br />
<li><a href="https://2012.igem.org/Team:Arizona_State/Safety">Safety</a> </li> <br />
</ul><br />
</li> <br />
</ul> <br />
</div><br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/ssDNATeam:Arizona State/ssDNA2012-10-04T03:29:20Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<html><br />
<body><br />
<h1>ssDNA Probe Design</h1><br />
<h2>Topoisomerase</h2><br />
<p><br />
<img src="https://static.igem.org/mediawiki/2012/8/8f/TopoDiagram.png" width="800" height="500"><br />
</p><br />
<p><br />
The wild type form of topoisomerase binds to the DNA sequence (YCCTT) in E. Coli. It regulates the winding of the DNA by making a nick after the second T. This allows for the rotation of the strands to relieve torsional stress. Afterwards, the DNA strands are religated. In 2006, Bushman et al. have shown that the smallpox topoisomerase double cysteine mutant D168A mutates the tyrosine responsible for covalent bonding to the 5’ phosphate at the DNA nicking. This mutant form prevents religation, and thus causes the majority of the DNA to stay in the covalently bonded complex.<br />
</p><br />
<h2>Design Scheme</h2><br />
<p><br />
In our design, we plan to use topoisomerase to nick a specific covalently bonded sequence and peel off a section of single stranded DNA. We have designed a template plasmid that includes tandem YCCTT recognition sites with template strand in between, and is complementary to a section of coding sequence of GFP. We plan to use a KEIO strain with one copy of this coding sequence in the E. Coli genome.<br />
</p><br />
<h2>Reporter System</h2><br />
<p><br />
Basilion et al. from Case Western in 2010 have shown that they were able to make a split beta-galactosidase complementation assay with relatively reliable assay results In the assay, alpha-4/omega, which has a higher specificity, is the most successful split beta galactosidase assay. It is thus used to eliminate false positive. Additionally, we are adapting alpha and 1-omega, which is less specific but has a higher signal, for the same protocol to eliminate false negative.<br />
</p><br />
<p><br />
Additionally, Basilion et al. also demonstrated success in creating fusion proteins with a split-beta galactosidase fragment and antibody specific to their target. Modifying this, we plan to make a fusion of our mutant topoisomerase and our split-beta galactosidase fragments. This effectively creates a probe that when assembled contains topoisomerase bound both to a single stranded DNA hybridization probe and a split-beta galactosidase fragment. By incubating the two probes that recognize adjacent DNA sequences, we can test for the presence of DNA sequences in a bacterial genome.<br />
</p><br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/ssDNATeam:Arizona State/ssDNA2012-10-04T03:29:00Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<html><br />
<body><br />
<h1>ssDNA Probe Design</h1><br />
<h2>Topoisomerase</h2><br />
<p><br />
<img src="https://static.igem.org/mediawiki/2012/8/8f/TopoDiagram.png" width="800" height="500"><br />
</p><br />
<p><br />
The wild type form of topoisomerase binds to the DNA sequence (YCCTT) in E. Coli. It regulates the winding of the DNA by making a nick after the second T. This allows for the rotation of the strands to relieve torsional stress. Afterwards, the DNA strands are religated. In 2006, Bushman et al. have shown that the smallpox topoisomerase double cysteine mutant D168A mutates the tyrosine responsible for covalent bonding to the 5’ phosphate at the DNA nicking. This mutant form prevents religation, and thus causes the majority of the DNA to stay in the covalently bonded complex.<br />
</p><br />
<h2>ssDNA Probe Design</h2><br />
<p><br />
In our design, we plan to use topoisomerase to nick a specific covalently bonded sequence and peel off a section of single stranded DNA. We have designed a template plasmid that includes tandem YCCTT recognition sites with template strand in between, and is complementary to a section of coding sequence of GFP. We plan to use a KEIO strain with one copy of this coding sequence in the E. Coli genome.<br />
</p><br />
<h2>Reporter System</h2><br />
<p><br />
Basilion et al. from Case Western in 2010 have shown that they were able to make a split beta-galactosidase complementation assay with relatively reliable assay results In the assay, alpha-4/omega, which has a higher specificity, is the most successful split beta galactosidase assay. It is thus used to eliminate false positive. Additionally, we are adapting alpha and 1-omega, which is less specific but has a higher signal, for the same protocol to eliminate false negative.<br />
</p><br />
<p><br />
Additionally, Basilion et al. also demonstrated success in creating fusion proteins with a split-beta galactosidase fragment and antibody specific to their target. Modifying this, we plan to make a fusion of our mutant topoisomerase and our split-beta galactosidase fragments. This effectively creates a probe that when assembled contains topoisomerase bound both to a single stranded DNA hybridization probe and a split-beta galactosidase fragment. By incubating the two probes that recognize adjacent DNA sequences, we can test for the presence of DNA sequences in a bacterial genome.<br />
</p><br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/TeamTeam:Arizona State/Team2012-10-04T03:28:01Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<br /><br />
<br /><br />
<hr style="color: #800000; height:4px;" /><br />
<h1 style="font-family:Helvetica;color:maroon;" align="left">Team</h1><br />
<br />
<html><br />
<body><br />
<br />
<br /><br />
<br /><br />
<br />
<div align="center"><a href="http://fulton.zenfolio.com/igem2012/e38c33173"><img src="http://fulton.zenfolio.com/img/s2/v61/p952316275-4.jpg" width="800" height="533" alt="FSE Photos: iGem2012 &emdash; " /></a></div><br />
<br />
<br /><br />
<hr style="color: #800000; height:4px;" /><br />
<h1 style="font-family:Helvetica;color:maroon;" align="left">Meet the Devils</h1><br />
<br /><br />
<br />
<br />
<div align="center"><br />
<table width="960"><br />
<tr><br />
<td width="200" scope="col"><a href="http://fulton.zenfolio.com/igem2012/e3d2bee6c"><img src="http://fulton.zenfolio.com/img/s1/v54/p1026289260-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td width="270" scope="col"><b>Abhinav Markus</b>, a junior Biomedical Engineering major, is our beloved "mom" of the group. He enjoys cloning and has lately been wanted for his awesome beard. He loves sports and can't let go of Hindi Music.</td><br />
<td width="200" scope="col"><a href="http://fulton.zenfolio.com/igem2012/e263dcf1a"><img src="http://fulton.zenfolio.com/img/s1/v48/p641584922-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td width="270" scope="col"><b>Nisarg Patel</b>, a junior molecular biosciences and biotechnology major, is the cool one in the group. He enjoys debate, sports, and riding flying carpets.</td><br />
</tr><br />
<tr><br />
<td scope="row"><a href="http://fulton.zenfolio.com/igem2012/e2fe55cf7"><img src="http://fulton.zenfolio.com/img/s1/v49/p803560695-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Hyder Hussain</b>, a junior biomedical engineering major, is the fun one on the team. He likes dragons, and is convinced that Ethan likes My Little Pony. </td><br />
<td><a href="http://fulton.zenfolio.com/igem2012/e2d8d2995"><img src="http://fulton.zenfolio.com/img/s2/v59/p764225941-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Ellen Qin</b>, a junior chemical engineering major, is the sweet one in the group. Her interests include: drawing, running, and her pillow.</td><br />
</tr><br />
<tr><br />
<td scope="row"><a href="http://fulton.zenfolio.com/igem2012/e38950bee"><img src="http://fulton.zenfolio.com/img/s1/v49/p949292014-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Amanda Ispas</b>, a senior biomedical engineering major, is the busy one in the group. Her interests include hanging out with friends and baseball.</td><br />
<td><a href="http://fulton.zenfolio.com/igem2012/e36f53531"><img src="http://fulton.zenfolio.com/img/s1/v55/p922039601-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Madeline Sands</b>, a senior anthropology major, is the superstar of the group. She gave us the initial idea to design a biosensor to use in third world countries. </td><br />
</tr><br />
<tr><br />
<td scope="row"><a href="http://fulton.zenfolio.com/igem2012/e37086686"><img src="http://fulton.zenfolio.com/img/s4/v64/p923297414-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Ryan Muller</b>, a sophomore biochemistry and molecular biology double major, is super talented. Did I tell you? He has this super awesome phage dance. Ladies watch out!</td><br />
<td><a href="http://fulton.zenfolio.com/igem2012/e3b699a56"><img src="http://fulton.zenfolio.com/img/s1/v48/p996776534-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Ethan Ward</b>, a senior biomedical engineering major, is our super chill "dad" of the team. His interests are programming and listening to music. </td><br />
</tr><br />
<tr><br />
<td scope="row"><img src="https://static.igem.org/mediawiki/2012/c/c3/ASUiGEM2012_rohit.png" width="196" height="196" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Rohit Rajan</b>, a sophomore biochemistry major, is the cat daddy of the group. His interest: being cooler than Nisarg. </td><br />
</tr><br />
</table><br />
</div><br />
<br />
<br />
<br />
<br /><br />
<hr style="color: #800000; height:4px;" /><br />
<h1 style="font-family:Helvetica;color:maroon;" align="left">Meet the Advisors</h1><br />
<br />
<br />
<div align="center"><br /><br />
<table width="830"><br />
<tr><br />
<td width="323" scope="col"><span style="font-family:Helvetica;font-size:15px"><img src="http://openwetware.org/images/6/60/SBHSE_lab_KHaynes_0212.jpg" width="305"/></span></td><br />
<td width="495" scope="col"><p style="font-family:Helvetica;font-size:15px"><b>Dr. Karmella Haynes</b></p><br />
<p><a href="http://www.biologicaldesign.asu.edu/node/123">Click here</a> to learn more about her.</p><br />
<span style="font-family:Helvetica;color:maroon;"></span></td><br />
</tr><br />
<tr><br />
<td scope="row"><span style="font-family:Helvetica;font-size:15px"><img src="http://engineering.asu.edu/sbhse/wp-content/uploads/2012/05/Wang_Xiao_Lab_0002a.jpg" /></span></td><br />
<td><p style="font-family:Helvetica;font-size:15px"><b>Dr. Xiao Wang</b></p><br />
<p><a href="http://www.biologicaldesign.asu.edu/node/118">Click here</a> to learn more about him.</p><br />
<span style="font-family:Helvetica;color:maroon;"></span></td><br />
</tr><br />
<tr><br />
<td scope="row"><img src="http://engineering.asu.edu/sbhse/wp-content/uploads/2012/05/Pizziconi-EOH.jpg" /></td><br />
<td><p style="font-family:Helvetica;font-size:15px"><b>Dr. Vincent Pizziconi</b></p><br />
<p><a href="http://engineering.asu.edu/sbhse/?page_id=601">Click here</a> to learn more about him.</p><br />
<span style="font-family:Helvetica;color:maroon;"></span></td><br />
</tr><br />
</table><br />
</div><br />
<br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/TeamTeam:Arizona State/Team2012-10-04T03:27:16Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<br /><br />
<br /><br />
<hr style="color: #800000; height:4px;" /><br />
<h1 style="font-family:Helvetica;color:maroon;" align="left">Team</h1><br />
<br />
<html><br />
<body><br />
<p><br />
This is the ASU iGem Team!! =)<br />
</p><br />
<br /><br />
<br /><br />
<br />
<div align="center"><a href="http://fulton.zenfolio.com/igem2012/e38c33173"><img src="http://fulton.zenfolio.com/img/s2/v61/p952316275-4.jpg" width="800" height="533" alt="FSE Photos: iGem2012 &emdash; " /></a></div><br />
<br />
<br /><br />
<hr style="color: #800000; height:4px;" /><br />
<h1 style="font-family:Helvetica;color:maroon;" align="left">Meet the Devils</h1><br />
<br /><br />
<br />
<br />
<div align="center"><br />
<table width="960"><br />
<tr><br />
<td width="200" scope="col"><a href="http://fulton.zenfolio.com/igem2012/e3d2bee6c"><img src="http://fulton.zenfolio.com/img/s1/v54/p1026289260-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td width="270" scope="col"><b>Abhinav Markus</b>, a junior Biomedical Engineering major, is our beloved "mom" of the group. He enjoys cloning and has lately been wanted for his awesome beard. He loves sports and can't let go of Hindi Music.</td><br />
<td width="200" scope="col"><a href="http://fulton.zenfolio.com/igem2012/e263dcf1a"><img src="http://fulton.zenfolio.com/img/s1/v48/p641584922-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td width="270" scope="col"><b>Nisarg Patel</b>, a junior molecular biosciences and biotechnology major, is the cool one in the group. He enjoys debate, sports, and riding flying carpets.</td><br />
</tr><br />
<tr><br />
<td scope="row"><a href="http://fulton.zenfolio.com/igem2012/e2fe55cf7"><img src="http://fulton.zenfolio.com/img/s1/v49/p803560695-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Hyder Hussain</b>, a junior biomedical engineering major, is the fun one on the team. He likes dragons, and is convinced that Ethan likes My Little Pony. </td><br />
<td><a href="http://fulton.zenfolio.com/igem2012/e2d8d2995"><img src="http://fulton.zenfolio.com/img/s2/v59/p764225941-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Ellen Qin</b>, a junior chemical engineering major, is the sweet one in the group. Her interests include: drawing, running, and her pillow.</td><br />
</tr><br />
<tr><br />
<td scope="row"><a href="http://fulton.zenfolio.com/igem2012/e38950bee"><img src="http://fulton.zenfolio.com/img/s1/v49/p949292014-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Amanda Ispas</b>, a senior biomedical engineering major, is the busy one in the group. Her interests include hanging out with friends and baseball.</td><br />
<td><a href="http://fulton.zenfolio.com/igem2012/e36f53531"><img src="http://fulton.zenfolio.com/img/s1/v55/p922039601-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Madeline Sands</b>, a senior anthropology major, is the superstar of the group. She gave us the initial idea to design a biosensor to use in third world countries. </td><br />
</tr><br />
<tr><br />
<td scope="row"><a href="http://fulton.zenfolio.com/igem2012/e37086686"><img src="http://fulton.zenfolio.com/img/s4/v64/p923297414-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Ryan Muller</b>, a sophomore biochemistry and molecular biology double major, is super talented. Did I tell you? He has this super awesome phage dance. Ladies watch out!</td><br />
<td><a href="http://fulton.zenfolio.com/igem2012/e3b699a56"><img src="http://fulton.zenfolio.com/img/s1/v48/p996776534-2.jpg" width="196" height="293" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Ethan Ward</b>, a senior biomedical engineering major, is our super chill "dad" of the team. His interests are programming and listening to music. </td><br />
</tr><br />
<tr><br />
<td scope="row"><img src="https://static.igem.org/mediawiki/2012/c/c3/ASUiGEM2012_rohit.png" width="196" height="196" alt="FSE Photos: iGem2012 &emdash; " /></a></td><br />
<td><b>Rohit Rajan</b>, a sophomore biochemistry major, is the cat daddy of the group. His interest: being cooler than Nisarg. </td><br />
</tr><br />
</table><br />
</div><br />
<br />
<br />
<br />
<br /><br />
<hr style="color: #800000; height:4px;" /><br />
<h1 style="font-family:Helvetica;color:maroon;" align="left">Meet the Advisors</h1><br />
<br />
<br />
<div align="center"><br /><br />
<table width="830"><br />
<tr><br />
<td width="323" scope="col"><span style="font-family:Helvetica;font-size:15px"><img src="http://openwetware.org/images/6/60/SBHSE_lab_KHaynes_0212.jpg" width="305"/></span></td><br />
<td width="495" scope="col"><p style="font-family:Helvetica;font-size:15px"><b>Dr. Karmella Haynes</b></p><br />
<p><a href="http://www.biologicaldesign.asu.edu/node/123">Click here</a> to learn more about her.</p><br />
<span style="font-family:Helvetica;color:maroon;"></span></td><br />
</tr><br />
<tr><br />
<td scope="row"><span style="font-family:Helvetica;font-size:15px"><img src="http://engineering.asu.edu/sbhse/wp-content/uploads/2012/05/Wang_Xiao_Lab_0002a.jpg" /></span></td><br />
<td><p style="font-family:Helvetica;font-size:15px"><b>Dr. Xiao Wang</b></p><br />
<p><a href="http://www.biologicaldesign.asu.edu/node/118">Click here</a> to learn more about him.</p><br />
<span style="font-family:Helvetica;color:maroon;"></span></td><br />
</tr><br />
<tr><br />
<td scope="row"><img src="http://engineering.asu.edu/sbhse/wp-content/uploads/2012/05/Pizziconi-EOH.jpg" /></td><br />
<td><p style="font-family:Helvetica;font-size:15px"><b>Dr. Vincent Pizziconi</b></p><br />
<p><a href="http://engineering.asu.edu/sbhse/?page_id=601">Click here</a> to learn more about him.</p><br />
<span style="font-family:Helvetica;color:maroon;"></span></td><br />
</tr><br />
</table><br />
</div><br />
<br />
<br />
</body><br />
</html></div>Napatelhttp://2012.igem.org/Team:Arizona_State/AttributionsTeam:Arizona State/Attributions2012-10-04T03:26:04Z<p>Napatel: </p>
<hr />
<div>{{:Team:Arizona_State/Template:Header}}<br />
<br />
<br />
<h2>Attributions</h2><br />
<br />
*Rohit: media preparation/Magainin<br />
*Amanda: media preparation team/human practices<br />
*Hyder: Topo chimeric protein production/ Topo target plasmid design and building <br />
*Ryan: Topo chimeric protein production<br />
*Abhi: Split beta gal assay development for the chimeric reporter (DNA probe)<br />
*Maddie: Split beta gal assay development for the chimeric reporter (DNA probe) / human practices<br />
*Nisarg: Magainin Assembly/Split beta gal assay development for Magainin/topo/AlumniGEM<br />
*Ellen: Magainin Assembly<br />
*Ethan: modeling</div>Napatel