http://2012.igem.org/wiki/index.php?title=Special:Contributions/FourEyeGuy1962&feed=atom&limit=50&target=FourEyeGuy1962&year=&month=2012.igem.org - User contributions [en]2024-03-28T10:17:00ZFrom 2012.igem.orgMediaWiki 1.16.0http://2012.igem.org/Team:Columbia-Cooper-NYC/AcknowledgementsTeam:Columbia-Cooper-NYC/Acknowledgements2013-01-12T00:33:23Z<p>FourEyeGuy1962: /* Acknowledgements */</p>
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= Acknowledgements =<br />
<br />
Adam Cerini: Copper team, research, Maker Faire<br />
<br />
Marjana Chowdhury: Wiki team, Copper team<br />
<br />
Ciera Lowe: Genetics team, Maker Faire, Wiki team<br />
<br />
Anna Mai: Copper team, Wiki team, Maker Faire<br />
<br />
Yuta Makita: Wiki team, Genetics team, Maker Faire<br />
<br />
Nicholas Mannarino: Genetics team, Maker Faire<br />
<br />
Aakash Mansukhani: Copper team<br />
<br />
Joeseph Mercedes: Copper team, Wiki team<br />
<br />
Steven Neuhaus: Genetics team, research, Wiki team, Maker Faire<br />
<br />
Kirsten Nicassio: Genetics team, research, Wiki team<br />
<br />
Udochukwu (Ud) Okorafor: Copper team, Wiki team, Maker Faire<br />
<br />
Saimon Sharif: Genetics team, research<br />
<br />
Richard Shi: Copper team<br />
<br />
Jeffery Xu: Copper team, Maker Faire<br />
<br />
Vincent Xu: Copper team, Wiki team, Maker Faire<br />
<br />
<br />
<br />
We graciously thank the following parties for helping to fund this year's IGEM project:<br />
<br />
*Columbia University Fu Foundation School of Engineering and Applied Science.<br />
<br />
*The Cooper Union Joint Activities Committee for funding student clubs.<br />
<br />
*The Rose-Sandholm Biology Initiative to help us build up our laboratory offerings for students at The Cooper Union. <br />
<br />
<br />
A special thanks to the following iGEM teams and people:<br />
*Dr. Scott Banta for overseeing our project, providing invaluable advice and allowing us to work in his lab at Columbia.<br />
*Dr. Alan West for his expertise in copper etching.<br />
*Dr. David Orbach for overseeing our project, generating novel ideas and approaches to our goal and allowing us to work in the Kanbar Center at Cooper.<br />
*Dionne Lutz for walking the genetic team through countless protocols, supervising our work in the Kanbar lab, helping organize our Maker Faire table and providing motivation and optimism.<br />
*Sudipta Majumdar for helping us construct plasmids and patiently teaching us new protocols.<br />
*Kevin Dooley for help with expression experiments, providing us with a GFP gene and identifying and removing cut sites within our biobrick and answering questions as we became acquainted with Dr. Banta's lab.<br />
*Tushar Patel for providing us with a GFP gene and answering questions as we became acquainted with Dr. Banta's lab.<br />
*Jason Candreva for being extremely patient with us, teaching us various transformation protocols with ecoli and ferrooxidans and answering every question we threw at him.<br />
*Sara Chuang for initializing the iGEM team. <br />
* iGEM Team Uppsala University for sending us the following parts: BBa_K592004, BBa_K592005, BBa_K592006, BBa_K592009, BBa_K592010, and BBa_K592016<br />
* iGEM Team ETH Zurich for sending us E. coli codon-optimized Pif3 and PhyB<br />
* Dr. Nicole Frankenberg-Dinkel for her advice and for sending plasmids pASK-fphAN753s and pTDho1</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Columbia_notebook_2Team:Columbia-Cooper-NYC/Columbia notebook 22013-01-08T07:36:05Z<p>FourEyeGuy1962: /* Columbia Genetics Lab Notebook */</p>
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__NOTOC__ <br />
<br />
= Columbia Genetics Lab Notebook =<br />
__NOTOC__<br />
<div class="content-header-box"><br />
== July, 2012 ==<br />
</div><br />
<div class="content-body-box"><br />
==== Thursday, 5th ====<br />
* Re-hydrated plasmids with 50µl of LB and Kanamycin solution<br />
* Stored solution at 37°C incubator overnight<br />
==== Friday, 6th ====<br />
* Purified pET26b vector using standard DNA purification protocol<br />
==== Monday, 9th ====<br />
* Received kill gene Bba-K124017 from plate 3, 20M<br />
* Re-hydrated DNA according to standard iGEM re-hydration protocol<br />
==== Tuesday, 10th ====<br />
* Contacted professors at Germany in hopes to receive copies of fungal phytochrome FphA<br />
==== Wednesday, 11th ====<br />
* Received confirmation by professors at Germany for FphA to be sent to Columbia University<br />
* Conducted transformation using electroporation with competent bacteria (marked by resistance to Kanamycin)<br />
*# Control: 1µl of deionized water with abt. and 60µl of bacteria cells<br />
*# Variable: 1µl of re-hydrated kill gene and 60µl of bacteria cells<br />
* Placed both samples after electroporation into 200µl of preprepared LB<br />
* Placed samples in shaker 37°C for 30 minutes<br />
==== Thursday, 12th ====<br />
* Grew 1 colony of transformed bacteria in 5mL of Kanamycin and LB solution<br />
** Note: Using pET20b vector over pET26b vector from glycerol stock solution<br />
==== Friday, 13th ====<br />
* Isolated 4 samples of plasmid using standard plasmid isolation protocol<br />
*# 2 samples: kill gene<br />
*# 2 samples: pET20b vector<br />
==== Monday, 16th ====<br />
* Re-hydrated two biobrick parts in plasmid pSB2K3 according to standard iGEM re-hydration protocol <br />
*# BBa-I16009 (PcyA) from plate 1, 20F<br />
*# BBa-I16008 (ho1) from plate 2, 13J<br />
* Electroporated 1µl of each biobrick into separate E. coli at 1800V<br />
* Added 100µl LB broth into each sample<br />
* Placed samples at 33.4°C for 20 minutes<br />
* Samples were plated to be grown overnight<br />
<br />
==== Tuesday, 17th ====<br />
* Placed 5ml each of LB/Kan into two centrifuge tube for PCB creation<br />
*# Label P: PcyA<br />
*# Label h: ho1<br />
* Placed samples in 37°C incubator<br />
<br />
==== Wednesday, 18th ====<br />
* Purified ho1 and PcyA plasmids using standard DNA purification protocol<br />
* Placed purified DNA into glycerol stock (LB/Kan) and stored at -80°C<br />
<br />
==== Thursday, 19th ====<br />
* Purified GFP using standard DNA purification protocol<br />
* Prepared glycerol stock solution (500µl GFP/500µl 80% glycerol) and stored at -80°C<br />
<br />
==== Tuesday, 24th ====<br />
* Re-hydrated four biobrick parts according to standard iGEM re-hydration protocol<br />
*# Inducible plasmid (pSB1AK3-J04500) from plate 4, 12A<br />
*# GFP (pSB1A2-E0040) from plate 1, 14K<br />
*# High copy plasmid pSB1T3-J044500 from plate 1, 7A<br />
*# Low copy plasmid (pSB3C5-J044500) from plate 1, 3C<br />
* Electroporated competent E. coli with each of the four above genes separetely<br />
* Created Kan, Amp, Cam, Tetra, and Amp/Kan plates<br />
<br />
==== Wednesday, 25th ====<br />
* Streaked pSB1T3-J04450<br />
* Created LB solution with Kan or Amp or Cam<br />
<br />
==== Thursday, 26th ====<br />
* Prepared Glycerol stock for inducible promoter, GFP, and low-copy plasmid<br />
* Picked a single colony from pSB1T3-J04450 and let it grow overnight in 37C<br />
* Recorded and measured the DNA concentrations of following at 260nm:<br />
*# Kill gene<br />
*# PcyA<br />
*# ho1<br />
*# GFP<br />
*# Inducible promoter<br />
*# Low copy CAM plasmid<br />
* Followed digestion and ligation protocol; setup explained below:<br />
*# Upstream: ho1; Downstream: PcyA; Destination plasmid: Low-copy CAM<br />
*# Upstream: Inducible promoter; Downstream: GFP; Destination plasmid: Low-copy CAM<br />
*# Upstream: Inducible promoter; Downstream: Kill; Destination plasmid: High-copy TET (pSB1T3)<br />
* After completion, store samples at -20C<br />
<br />
==== Friday, 27th ====<br />
* Electroporated ligated samples from previous day: GFP, PCB, Kill<br />
* Followed standard plasmid isolation protocol for pSB1T3-J04450 (TET plasmid)<br />
<br />
==== Saturday, 28th ====<br />
* Check plates from electroporation from previous day<br />
<br />
==== Monday, 30th ====<br />
* Stored pif3 and phyB that arrived from Sweden<br />
* Relocated and reorganized the iGEM biobrick kit and glycerol stocks<br />
* Picked colonies for following DNA:<br />
*# Inducible promotor (pSB1AK3_J04500)<br />
*# GFP (pSB1A2_E0040)<br />
*# Low copy CAM plasmid (pSB3C5_J04150)<br />
* Added 10µl of ho1 and PcyA to 5ml of antibiotics<br />
* Electroporated following DNA:<br />
*# Inducible promoter IPTG/kill gene in BL21 cells<br />
*# Inducible promoter IPTG/GFP in BL21 cells<br />
*# PCB in α cells<br />
* Transferred successful electroporated cells to eppendorf tube with 100μL of LB and placed in 37C shaker<br />
==== Tuesday, 31st ====<br />
* Prepared glycerol stock of the following:<br />
*#GFP<br />
*#Inducible promoter (IPTG)<br />
*#Low copy CAM plasmid<br />
*#pcyA<br />
*#ho1<br />
* Isolated ho1 and PcyA using standard plasmid isolation protocol<br />
<br />
</div><br />
<br />
== August, 2012 ==<br />
<div class="content-body-box"><br />
==== Wednesday, 1st ====<br />
* Applied IPTG to samples of bacteria with GFP or kill gene and placed back in incubator at 37C<br />
* Electroporated the following plasmids:<br />
*# IPTG inducible promoter/kill gene into BL21 cells<br />
*# IPTG inducible promoter/GFP into BL21 cells<br />
*# phyB into α select cells<br />
*# pif3 into α select cells<br />
* Followed the PCR purification protocol for samples 1, 2 listed above<br />
* Chemically transformed the following using standard heat shock protocol provided by Bioline:<br />
*# IPTG inducible promoter/kill gene into BL21 cells<br />
*# IPTG inducible promoter/GFP into BL21 cells<br />
* Plated PCB onto LB/CAM plate<br />
* Plated Pif3 and phyB on KAN plates<br />
* Plated 500μL of GFP containing cells among two plates each LB/CAM (with and without IPTG)<br />
* Placed all samples in 37C incubator<br />
<br />
==== Thursday, 2nd ====<br />
* Selected colonies from PhyB from the LB/Kan plate<br />
* Prepared CAM plates<br />
* Selected colonies from GFP control<br />
* Received agar stabs from Uppsala<br />
<br />
==== Friday, 3rd ====<br />
* Placed 60μL of IPTG to half of control plate for reconfirmation of results<br />
* Streaked GFP (with IPTG inducible promoter) and Pif3 on plates<br />
<br />
==== Saturday, 4th ====<br />
* Streaked all 6 Uppsala (labelled below) parts from stabs onto plates:<br />
*# Upps 1: pSB1K3-B0034-YF1-B0034-FixJ<br />
*# Upps 2: pSB1K3-YF1<br />
*# Upps 3: pSB1K3-FixJ<br />
*# Upps 4: pSB1C3-PfixK2<br />
*# Upps 5: pSB1A3-amilCP<br />
*# Upps 6: pSB1C3 - amilGFP<br />
* Prepared glycerol stock for phyB (ETHZ)<br />
* Isolated phyB by following standard plasmid isolation protocol<br />
* Electroporated fphA and ho1 from Germany<br />
* Created LB/TET, LB/CAM, LB/Amp, LB/Kan plates<br />
<br />
==== Sunday, 5th ====<br />
* Pulled colonies from 6 iGEM parts and ho1 from Germany<br />
* Streaked fphA from Germany<br />
* Pulled colonies for Upps 2, 3, 4, 5, 6<br />
* Streaked Upps 1, 3, 4, 6<br />
* Parafilmed all plates and placed in 4C<br />
* Sorted and threw out unnecessary plates<br />
<br />
==== Monday, 6th ====<br />
* Pulled colonies from fphA and Upps 1<br />
* Isolated plasmids for the following samples following standard plasmid isolation protocol:<br />
*# 6 iGEM parts<br />
*# Upps 2-6<br />
*# ho1<br />
* Reconfirmed that TET plates are valid<br />
<br />
==== Tuesday, 7th ====<br />
* Prepared glycerol stock and isolated the plasmid using standard plasmid isolation protocol for following:<br />
*# fphA from Germany<br />
*# Upps 1 (pSB1K3-B0034-YF1-B0034-FixJ)<br />
* Prepared digestion by measuring OD at 260nm for following:<br />
*# Upps 1<br />
*# Upps 4<br />
*# Upps 5<br />
*# Upps 6<br />
*# Kill Gene<br />
*# Inducible promoter containing plasmid<br />
* Prepared digestions and ligated with following setup using the 3A assembly protocol provided from Bioline:<br />
*# Upstream: Upps 4; Downstream: Upps 5; Destination Plasmid: High Copy TET plasmid<br />
*# Upstream: Upps 4; Downstream: Upps 6; Destination Plasmid: High Copy TET plasmid<br />
*# Upstream: Upps 4; Downstream: Kill gene; Destination Plasmid: Low Copy CAM plasmid<br />
*# Upstream: Inducible promoter; Downstream: Upps 5; Destination Plasmid: High Copy TET plasmid<br />
*# Upstream: Inducible promoter; Downstream: Upps 6; Destination Plasmid: High Copy TET plasmid<br />
*# Upstream: Inducible promoter; Downstream: Kill gene; Destination Plasmid: High Copy TET plasmid<br />
<br />
==== Wednesday, 8th ====<br />
* Pulled colony from GFP streak<br />
* Isolated following using standard plasmid isolation protocol:<br />
*# Low Copy CAM plasmid<br />
*# High Copy TET plasmid<br />
*# Inducible promoter<br />
* Checked optical density and applied necessary dilutions for GFP<br />
* Prepared two samples of GFP: sample with IPTG and sample without IPTG<br />
* Place samples in shaker to grow overnight<br />
<br />
==== Thursday, 9th ====<br />
* Diluted GFP solutions to match proper optical density<br />
* Pulled colony for ho1 as backup and place in 37C inbucator<br />
<br />
==== Friday, 10th ====<br />
* Remade 200 mL each of antibiotic solutions for CAM, TET, Kan, Amp<br />
* Conducted digestions and ligations using the 3A assembly method following the protocols provided by bioline of following:<br />
*# Upstream: Upps 4; Downstream: Kill gene; Destination Plasmid: High Copy TET plasmid<br />
*# Upstream: Inducible promoter; Downstream: Upps 5; Destination Plasmid: Low Copy CAM plasmid<br />
*# Upstream: Inducible promoter; Downstream: Upps 6; Destination Plasmid: Low Copy CAM plasmid<br />
*# Upstream: Inducible promoter; Downstream; Kill gene; Destination Plamid: Low Copy CAM plasmid<br />
* Followed the butanol purification protocol for ligated material containing inducible promoter from 7th and 10th<br />
<br />
==== Saturday, 11th ====<br />
* Reviewed the solutions for diluted GFP and observed no significant results<br />
* Reorganized samples in fridges and incubators<br />
<br />
==== Monday, 13th ====<br />
* Chemically transformed competent cells (BL21) with plasmids below using bioline protocol (used 1/2 of recommended amount)<br />
*# IPTG-Upps 5-Low Copy (CAM)<br />
*# IPTG-Upps 6-Low Copy (CAM)<br />
*# IPTG-Kill gene-Low Copy (CAM)<br />
*# CAM control plasmid<br />
*# PUC19 control plasmid<br />
* Electroporated competent cells (α-select) with plasmids below using bioline protocol<br />
*# Upps 4-Kill gene-High Copy (TET)<br />
*# Upps 4-Upps 5-High Copy (TET)<br />
*# Upps 4-Upps 6-High Copy (TET)<br />
*# PUC19 control plasmid<br />
*# High copy TET control plasmid<br />
''Note 1: TET control sparked''<br />
<br />
''Note 2: Upps 4-Upps 5-TET sparked''<br />
<br />
''Note 3: Original DNA for Upps 4-Upps 5-TET was pink''<br />
* Placed transformed samples in growth media and placed in 37°C shaker<br />
* Made 60ml of 1% agar gel for running gel electrophoresis (2 rows of 12 wells each noted below for gel) to check digestion and ligation<br />
** First row<br />
**# 2 log ladder<br />
**# Upps 4<br />
**# blank<br />
**# High Copy TET plasmid<br />
**# Upps 4 (2)<br />
**# Upps 6<br />
**# High Copy TET plasmid (2)<br />
**# Upps 4 (3)<br />
**# Kill gene<br />
**# High Copy TET plasmid (3)<br />
**# PCB<br />
**# High Copy TET plasmid (4)<br />
** Second row<br />
**# 2 log ladder<br />
**# Inducible promoter-IPTG<br />
**# Kill gene (2)<br />
**# High Copy TET plasmid (5)<br />
**# Inducible promoter-IPTG (2)<br />
**# Upps 6 (2)<br />
**# High Copy TET plasmid (6)<br />
**# Inducible promoter-IPTG (3)<br />
**# Upps 5 (2)<br />
**# High Copy TET plasmid (7)<br />
* Ran gel for 25 minutes at constant 150V<br />
* Took picture under UV light<br />
* Created TET and CAM plates<br />
<br />
==== Tuesday, 14th ====<br />
''Note: Work done below was conducted at the Kanbar Lab at the Cooper Union''<br />
* Prepared CAM from .250g of 25mg/mL CAM powder with 10mL of EtOH<br />
* Prepared LB/glucose media<br />
* Heat shocked DH5α competent cells with Inducible promoter/GFP/Low Copy CAM plasmid<br />
<br />
==== Wednesday, 15th ====<br />
* Diluted bacteria cultures with following plasmids to 200x LB/CAM and placed in 37°C shaker<br />
*# IPTG-Upps 5-Low Copy (CAM)<br />
*# IPTG-Upps 6-Low Copy (CAM)<br />
*# IPTG-Kill gene-Low Copy (CAM)<br />
* Purified above plasmids and CAM control plasmid using standard purification protocol and prepared glycerol stocks<br />
* Added appropriate buffers to IPTG-Upps 5 and IPTG-Upps 6 and centrifuged for 10 minutes to determine for a pellet<br />
* Measured OD 600 of following samples<br />
*# IPTG-Upps 5-Low Copy (CAM): .160A<br />
*# IPTG-Upps 6-Low Copy (CAM): .038A<br />
* Inserted 1µl of 1M IPTG into cultures<br />
* Placed all samples in 37°C overnight<br />
''Note: conducted the below procedures at the Kanbar Lab''<br />
* Observed no growth for inducible promoter/GFP/low copy CAM plasmid<br />
<br />
==== Thursday, 16th ====<br />
* Measured OD 600 for 200x diluted bacterial solution containing plasmids with promoter inducible with IPTG<br />
*# IPTG-Upps 5-Low Copy (CAM): .040A<br />
*# IPTG-Upps 6-Low Copy (CAM): .032A<br />
*# IPTG-Kill gene-Low Copy (CAM): .028A<br />
* Noted that cell concentration was dense, decided to dilute solution with 75µl cells and 925µl LB/CAM solution<br />
* Placed diluted cell solution into 37°C incubator for 40 minutes<br />
* Inserted 1µl of 1M IPTG into cultures<br />
* Placed all samples in 37°C overnight<br />
==== Friday, 17th ====<br />
''Note: IPTG induced I-U5 and I-U6 appear to give no color change (no expression)''<br />
* Electroporate the following genes:<br />
*# Upps 4-Upps 6-High copy TET (sparked first time, redid trial)<br />
*# Upps 4-Kill-High copy TET<br />
*# Upps 4-Kill-Low copy CAM<br />
*# pUC19 control DNA (AMP resistance)<br />
* Placed all samples in 37°C overnight<br />
''Note2: Only adding 25µl of competent cells instead of 50µl mentioned in the<br />
<br />
==== Saturday, 18th ====<br />
* Observed none of the electroporated DNA grew, but observed colonies for control<br />
* Placed all samples back in the 37°C incubator<br />
==== Monday, 20th ====<br />
* Measured the optical density for the following:<br />
*# Upps 6 (with inducible promoter)<br />
*# Kill gene<br />
*# GFP<br />
*# Upps 5 (with inducible promoter)<br />
* Diluted the concentrated primer into a primer stock that would be used for DNA sequencing<br />
* Sent following DNA for sequencing (at Genewiz)<br />
*# Inducible promoter-GFP-Low Copy CAM plasmid<br />
*# Inducible promoter-Upps 5-Low Copy CAM plasmid<br />
*# Inducible promoter-Upps 6-Low Copy CAM plasmid<br />
*# Inducible promoter-Kill gene-Low Copy CAM plasmid<br />
* Analyzed gel and concluded following:<br />
*# The digestion for TET high copy plasmid did not work<br />
*# The digestion for Upps 4, 5, 6 appeared to have worked<br />
*# All other digestions are inconclusive results<br />
==== Tuesday, 21st ====<br />
* Made additional Amp/CAM and Amp/TET plates<br />
* Measured the optical density for the following:<br />
*# Upps 1<br />
*# Kill gene<br />
*# High copy TET plasmid<br />
* Followed the standard digestion protocol provided by bioline or the following:<br />
*# Upps 1 (Upstream)<br />
*# Kill gene (Downstream)<br />
*# High copy TET plasmid (Destination plasmid)<br />
* Re-organized iGEM boxes by throwing out previous digestions of High Copy TET plasmids<br />
* Re-hydrated following biobricks from standard rehydration protocol:<br />
*# Constitutive promoter-BBa_J130002 (P1, 13B)<br />
*# Low-copy TET plasmid-PSB3T5 (P1, 7C)<br />
*# High-copy CAM plasmid-PSB1C3 (P1, 3A)<br />
*# High-copy Amp/CAM plasmid-PSB1AC3 (P1, 9A)<br />
*# High-copy Amp/TET plasmid-PSB1AT3 (P1, 13A)<br />
* Made 60ml of 1% agar gel for running gel electrophoresis (2 rows of 12 wells each noted below for gel) to check digestion and ligation<br />
** First row<br />
**# 2 log ladder<br />
**# old TET high copy plasmid<br />
**# old Kill gene<br />
**# Upps 5<br />
**# IPTG inducible promoter<br />
** Second row<br />
**# 2 log ladder<br />
**# newly digested TET high copy plasmid<br />
**# newly digested Kill gene<br />
**# Upps 1<br />
* Ran gel for 25 minutes at constant 150V<br />
* Took picture under UV light<br />
==== Wednesday, 22nd ====<br />
* Conducted ligations for the following using a vector to insert ratio of 1:3<br />
*# Sample 1: Inducible promoter (upstream insert)-Kill gene (Downstream insert)-pSB3C5 (vector)<br />
*# Sample 2: Inducible promoter (upstream insert)-Upps 5 (Downstream insert)-pSB3C5 (vector)<br />
*# Sample 3: Inducible promoter (upstream insert)-Upps 6 (Downstream insert)-pSB3C5 (vector)<br />
*# Sample 4: Upps 4 (upstream insert)-Kill gene (Downstream insert)-pSB1T3 (vector)<br />
*# Sample 5: Upps 4 (upstream insert)-Upps 5 (Downstream insert)-pSB1T3 (vector)<br />
*# Sample 6: Upps 4 (upstream insert)-Upps 6 (Downstream insert)-pSB1T3 (vector)<br />
*# Sample 7: Control pSB3C5 (1:0 vector to insert ratio)<br />
*# Sample 8: Control pSB1T3 (1:0 vector to insert ratio)<br />
''Note: above ligations will be done with T4 buffer and ligase from both the Biobrick kit and Columbia's lab''<br />
<br />
''Note 2: label all sample using iGEM ligase and buffer with prefix N''<br />
<br />
''Note 3: label all sample using Columbia lab's ligase and buffer with B''<br />
* Electroporated the following using the standard protocol provided by Bioline:<br />
*# Constitutive promoter-BBa_J130002<br />
*# Low-copy TET plasmid-PSB3T5 <br />
*# High-copy CAM plasmid-PSB1C3<br />
*# High-copy Amp/CAM plasmid-PSB1AC3 <br />
*# High-copy Amp/TET plasmid-PSB1AT3 <br />
*# PUC19 control plasmid<br />
* Chemically transformed the following using the heat shock protocol:<br />
*# N1, N2, N3, N7, B1, B2, B3, B7 into BL21 (DE) pLysZ orange cells<br />
*# GFP IPTG given by graduate student at Columbia into BL21 (DE) green cells<br />
*# PUC19 into BL21 (DE) pLysZ orange cells<br />
*# PUC19 into BL21 (DE) green cells<br />
* Purified ligated protocol for electroporation following QIAquick PCR purification protocol<br />
* Plated all chemically transformed and electroporated cells<br />
<br />
==== Thursday, 23rd ====<br />
''Note: Observed no growth with pSB1T3, BL21 pLyse''<br />
<br />
''Note 2: Observed growth with PUC19 and other BL21''<br />
* Streaked sample N5<br />
* Found following 3 restriction sites (to be double checked by graduate student):<br />
*# NgomIV: CCGCCGGC<br />
*# EcoRI: GAATTC<br />
*# PstI: CTGCAG<br />
==== Friday, 24th ====<br />
* Diluted IPTG driven cultures to 200x with fresh LB/antibiotic solution<br />
* Followed standard plasmid isolation protocol for everything except the following:<br />
*# 1 sample of graduate student's GFP<br />
*# Sample of pSB1C3 (the high copy CAM plasmid)<br />
* Checked optical densities of samples B1-B3 and graduate student's GFP<br />
* Created two subsamples each of B1-B3; applied 1M IPTG to half of the subsamples<br />
* Applied 1M IPTG to into one of the samples of graduate student's IPTG-GFP<br />
==== Saturday, 25th ====<br />
* Checked IPTG "induced" samples and observed no expression<br />
* Measured optical density for following samples and diluted the samples:<br />
*# GFP by graduate student-pre-dilution: 2.0, post dilution: 0.710<br />
*# IPTG-kill (N1)-pre-dilution: 2.4, post dilution: 0.736<br />
*# IPTG-U5 (N2)-pre-dilution: 1.9, post dilution: 0.740<br />
*# IPTG-U6 (N5)-pre-dilution: 2.4, post dilution: 0.630<br />
*# IPTG-U5 (B2)-pre-dilution: 1.9, post dilution: 0.681<br />
*# IPTG-U6 (B3)-pre-dilution: 1.9, post dilution: 0.651<br />
* Applied 1.5μL of 1M IPTG with 1.5mL of each sample and place in 25C shaker<br />
* Followed standard plasmid isolation protocol for N1 and N5<br />
==== Monday, 27th ====<br />
* Observe expression of graduate student's GFP<br />
* Measured optical densities for following:<br />
** Ligated samples:<br />
**# N1-N3 <br />
**# B1-B3<br />
** Mini-prepped:<br />
**# Upps1-Upps6<br />
**# pSB1C3<br />
**# pSB1T3<br />
**# pSB1AT3<br />
**# pSB1AC3<br />
**# pSB1A2<br />
* Sent above samples for sequencing<br />
* Followed protocol from bioline for digestion:<br />
*# Downstream: Upps 1 <br />
*# Upstream: Constitutive promoter <br />
*# Destination plasmid: pSB3T5<br />
*# Destination plasmid: pSB1C3<br />
*# Destination plasmid: pSB1AC3<br />
*# Destination plasmid: pSB1AT3<br />
* Streaked out Upps 1 from agar stab<br />
<br />
==== Tuesday, 28th ====<br />
* Reviewed results from the sequencing from Genewiz<br />
* Design and send new primer (nev) for sequencing<br />
* Conducted ligations for the following using a vector to insert ratio of 1:3<br />
*# Constitutive promoter (upstream insert)-Upps 1 (downstream insert)-pSB1C3 (vector)<br />
*# Constitutive promoter (upstream insert)-Upps 1 (downstream insert)-pSB3T5 (vector)<br />
*# Constitutive promoter (upstream insert)-Upps 1 (downstream insert)-pSB1AT3 (vector)<br />
*# Constitutive promoter (upstream insert)-Upps 1 (downstream insert)-pSB1AC3 (vector)<br />
* Electroporated the above 4 ligations without purifying the ligations<br />
* Plated cells into respective plates<br />
* Picked colonies for Upps 1-YF1/FixJ<br />
==== Wednesday, 29th ====<br />
* Conducted ligations for the following using a vector to insert ratio of 1:3<br />
*# Upps 4 (upstream insert)-Upps 5 (downstream insert)-pSB1C3 (vector)<br />
*# Upps 4 (upstream insert)-Upps 6 (downstream insert)-pSB1C3 (vector)<br />
*# Upps 4 (upstream insert)-Kill gene (downstream insert)-pSB1C3 (vector)<br />
*# Upps 4 (upstream insert)-Upps 5 (downstream insert)-pSB1AC3 (vector)<br />
*# Upps 4 (upstream insert)-Upps 6 (downstream insert)-pSB1AC3 (vector)<br />
*# Upps 4 (upstream insert)-Kill gene (downstream insert)-pSB1AC3 (vector)<br />
* Extracted Upps 1 (Kan) from glycerol stock from -80C freezer<br />
* Followed graduate student's quickchange protocol and labelled N1-N4, E1-E4, P1-P4 with the labeling as following:<br />
*# Sample 1: HF only<br />
*# Sample 2: HF and 1.5μL DMSO<br />
*# Sample 3: GC only<br />
*# Sample 4: GC and 1.5μL DMSO<br />
*# Prefix N: NgoMIV mutation<br />
*# Prefix E: EcoRI mutation<br />
*# Prefix P: PsH mutation<br />
==== Thursday, 30th ====<br />
* Followed standard plasmid isolation protocol for Upps 1<br />
* Transformed U4-U5, U4-U6, U4-kill in 2 different plasmids<br />
* Ran gels of Quickchange product<br />
*# Column 1: miniprepped plasmid<br />
*# Column 2-5: N1-N4<br />
*# Column 6-9: E1-E4<br />
*# Column 10-13: P1-P4<br />
* Re-ligated Constitutive promoter-Upps 1<br />
<br />
</div><br />
== September, 2012 ==<br />
<div class="content-body-box"><br />
==== Wednesday, 5th ====<br />
''Note: All work done from this day on was done at the Kanbar lab at the Cooper Union''<br />
* Single digested the J13002<br />
* Placed the digest above and other digests to be run on gels into -20C freezer<br />
* Made 4 50mL 1% agarose gels<br />
* Followed standard plasmid isolation protocol for kill gene<br />
==== Friday, 7th ====<br />
* Ran two gels to check digests<br />
** Gel Number 1<br />
**# Marker<br />
**# Upps 1<br />
**# Inducible promoter 1<br />
**# Inducible promoter 2<br />
**# pSB3T5<br />
**# pSB1C3<br />
**# Low Copy Vector 1<br />
**# Low Copy Vector 2<br />
** Gel Number 2<br />
**# Marker<br />
**# Kill gene<br />
**# PcyA<br />
**# TetR 1<br />
**# TetR 2<br />
**# GFP from biobrick kit<br />
**# GFP from Tushar<br />
**# GFP from Kevin<br />
* Conducted digestions for the following:<br />
*# Inducible promoter digested with EcoRI&Spe with Buffer E and Buffer Multi (for 30 min.)<br />
*# TetR digested with EcoRI with Buffer H<br />
*# TetR digested with Spe with Buffer B<br />
*# Upps 1 digested with Xba&Pst with Buffer H<br />
*# Kill gene digested with Xba&Pst with Buffer H<br />
*# GFP digested with Xba&Pst with Buffer H<br />
*# pSB3T5 with EcoRI&Pst with Buffer H<br />
*# Low copy plasmid 2 digested with EcoRI&Pst with Buffer H<br />
*# pSB1C3 digested with EcoR&Pst with Buffer H<br />
''Note: Digests 7-9 was done in Antartic Phosphotase Treat 30 min in 37C and 15 min in 65C''<br />
* Conducted ligations for the following (followed by chemical transformations:<br />
*# Upstream: Inducible promoter; Downstream: Upps 1; Destination plasmid: Low copy plasmid 2<br />
*# Upstream: Inducible promoter; Downstream: Kill; Destination plasmid: Low copy plasmid 2<br />
*# Upstream: Inducible promoter; Downstream: GFP; Destination plasmid: Low copy plasmid 2<br />
* Conducted additional chemical transformations with the following vectors:<br />
*# pET20b<br />
*# pET26b<br />
*# pUC19<br />
* Conducted following additional ligations, reference numbers correlate to numbers shown above for this day's digestions<br />
*# Label A: 2 and 9<br />
*# Label B: 3 and 4 and 9<br />
*# Label C: 1 and 4 and 8<br />
*# Label D: 1 and 5 and 8<br />
*# Label E: 1 and 6 and 8<br />
*# Label F: 3 and 4<br />
*# Label G: 3 and 5<br />
*# Label H: 3 and 6<br />
<br />
==== Tuesday, 11th ====<br />
* Observed the following:<br />
*# Inducible promoter-GFP-Low Copy CAM Plasmid had 3 pink clones (IPTG applied)<br />
*# Inducible promoter-GFP-Low Copy CAM Plasmid had 3 pink clones (NO IPTG)<br />
*# Inducible promoter-Upps 1-Low Copy CAM Plasmid had 32 pink clones<br />
*# Inducible promoter-Kill gene-Low Copy CAM Plasmid had 50 pink clones<br />
''Note 1: Destination plasmid/vector contained J04450 biobrick part, explained pink clones''<br />
<br />
''Note 2: All vectors were all treated with Antartic Phophotase, expect no religation of J04450 with LC vector''<br />
* Digested Kill gene and GFP with E and P<br />
* AP Treat Kill gene with X and P, GFP with X and P<br />
* Conducted ligations for the following:<br />
*# GFP (E and P) with pSB1C3 (E and P, AP treated)<br />
*# GFP (X and D, AP treated) with TetR/s<br />
* Condcuted transformations for the following:<br />
*# Ligation F from 9/7, TetR, Upps 1(X and P)<br />
*# Kill gene, pSB1C3<br />
*# GFP, pSB1C3<br />
*# GFP, TetR<br />
* Mini-cultured pET20b and pET26b<br />
<br />
==== Wednesday, 12th ====<br />
* Observed following from the transformations from 9/11<br />
*# TetR/GFP-successful with about 250 colonies<br />
*# TetR/Upps 1-successful with about 200 colonies<br />
*# No growth with Kill&pCB1C3, GFP&pCB1C3 <br />
* Prepared colony PCR for TetR&GFP, and TetR&Upps 1 on Amp grid plate (had A-D columns and 1-4 rows)<br />
*# Resuspended single colonies in 4μL deionized water<br />
*# Transferred 3μL colony suspension to Amp grid<br />
*# Stored remaining 1μL as PCR template<br />
*# Grew Amp grid plate in 37C overnight<br />
''Note 1: GFP/TetR: A and B with 1-4 each''<br />
<br />
''Note 2: Upps 1/TetR: C and D with 1-4 each''<br />
* PCR reaction contained following mixture:<br />
** 1x PCR Rxn<br />
*# 1.0μL of 10x buffer<br />
*# 0.4μL of dNTP<br />
*# 0.4μL of Primer F<br />
*# 0.4μL of Primer R<br />
*# 1.0μL of template mentioned above<br />
*# 0.4μL of tag<br />
*# 6.4μL of deionized water<br />
** 17x PCR Rxn<br />
*# 17μL of 10x buffer<br />
*# 6.8μL of dNTP<br />
*# 6.8μL of Primer F<br />
*# 6.8μL of Primer R<br />
*# 6.8μL of tag<br />
*# 108.8μL of deionized water<br />
* PCR reactions conducted with following protocol:<br />
*# Denature at 95C for 10 min.<br />
*# Denature at 95C for additional 30 sec.<br />
*# Anneal at 56C for 30 sec.<br />
*# Elongation at 70C for 60 sec.<br />
*# Elongation at 72C for 20 min.<br />
*# Hold at 4C for 39 cycles<br />
* Set up second half composite construction digests for following:<br />
*# Upps 1; Enzyme: EcoRI and SpeI; Buffer E*; Ratio: 1:2; Reaction vol.: 30μL<br />
*# Upps 4; Enzyme: EcoRI and SpeI; Buffer E*; Ratio: 1:2; Reaction vol.: 30μL<br />
*# Upps 5; Enzyme: Xba and Pst; Buffer H; Ratio: 1:1; Reaction vol.: 20μL<br />
*# Upps 6; Enzyme: Xba and Pst; Buffer H; Ratio: 1:1; Reaction vol.: 20μL<br />
*# Kill gene; Enzyme: Xba and Pst; Buffer H; Ratio: 1:1; Reaction vol.: 20μL<br />
*# Linearlized pSB1T3; Enzyme: EcoRI and Pst; Buffer H; Ratio: 1:1; Reaction vol.: 20μL<br />
*# Linearlized pSB1K3; Enzyme: EcoRI and Pst; Buffer H; Ratio: 1:1; Reaction vol.: 20μL<br />
*# Promoterless GFP; Enzyme: Xba; Buffer H; Ratio: N/A; Reaction vol.: 20μL<br />
*# pUC19; Enzyme: EcoRI; Buffer H; Ratio: N/A; Reaction vol.: 20μL<br />
''Note 3: for * buffers, will use buffer 2 or 4 in future''<br />
* Reactions took place for 1 hr. in 37C incubation and placed in -20C<br />
* Isolated pGLO and pET20b vectors using standard plasmid isolation protocol<br />
* Prepared glycerol stocks for pET20b and pET26b<br />
==== Thursday, 13th ====<br />
* Conducted fphA PCR mutogenesis with following (template = pASKfphA 753bp)<br />
** 1x PCR Rxn<br />
*# 2.0μL of 10x Buffer<br />
*# 0.4μL of dNTP<br />
*# 0.4μL of Primer F (EcoRI)<br />
*# 0.4μL of Primer R (EcoRI)<br />
*# 1.0μL of template<br />
*# 0.4μL of tag<br />
*# 15.4μL of deionized water<br />
** 3x PCR Rxn<br />
*# 6.0μL of 10x Buffer<br />
*# 1.2μL of dNTP<br />
*# 1.2μL of Primer F (EcoRI)<br />
*# 1.2μL of Primer R (EcoRI)<br />
*# 1.2μL of tag<br />
*# 46.2μL of deionized water<br />
* Set up 4 min. extension time with 55C for annealing temp for PCR program<br />
* Digested above mixture with Dpn1 at 37C for 1hr. after PCR<br />
* Transformed product into DH5α<br />
* Heat inactivated samples with Spe1 restriction digests from 9/12 at 80C for 20 min. and rest at 65C for 20 min.<br />
* Antartic treated the following (15 min. 37C, 5 min. 65C):<br />
*# Upps 4<br />
*# Promoterless GFP<br />
*# pUC19<br />
* Conducted ligations for the following for a total volume of 10μL<br />
*# Upps 4-Kill gene-pSB1K3<br />
*# Upps 4-Upps 5-pSB1K3<br />
*# Upps 4-Upps 6-pSB1K3<br />
*# TetR/Spe (from 9/7)-promoterless GFP<br />
*# pUC19<br />
* Transformed ligated DNA into DH5α<br />
* Ran gels for PCR Rxn and observed following:<br />
*# A3, B3 had 300 bp (estimated) product<br />
*# B1, B4 had 700 bp (estimated) product<br />
*# Everything else (including marker failed)<br />
*# Can not differentiate between ±TetR<br />
* Minicultured 4 TetR-Upps 1 cultures randomly <br />
==== Friday, 14th ====<br />
* Sterilized glycerol for stocks<br />
* Created more LB/Amp plates<br />
* Created more sterile miniculture tubes<br />
* Ran 100 bp optimization gel<br />
''Note 1: While 2µl DNA visble, should use minimum of 5µl/lane for system (SYBR)''<br />
* Repeated VF2-VR PCR on TetR&promoterless GFP (denoted A) and TetR&Upps 1 (denoted B)<br />
** 1x PCR Rxn<br />
**# 1.0μL of 10x Buffer<br />
**# 0.4μL of dNTP<br />
**# 0.4μL of Primer F (EcoRI)<br />
**# 0.4μL of Primer R (EcoRI)<br />
**# 1.0μL of template<br />
**# 0.4μL of tag<br />
**# 6.4μL of deionized water<br />
** 17x PCR Rxn<br />
**# 17.0μL of 10x Buffer<br />
**# 6.8μL of dNTP<br />
**# 6.8μL of Primer F (EcoRI)<br />
**# 6.8μL of Primer R (EcoRI)<br />
**# 6.8μL of tag<br />
**# 108.8μL of deionized water<br />
''Note 2: Will pick 7 colonies from each and have 4 minicultures of B-will use 1µl±1 colony''<br />
* After review of primers, changed PCR program as follows:<br />
*# Increased annealing temp to 60C<br />
*# Increased extension temp to 70C<br />
*# Reduced cycles to 30<br />
==== Thursday, 20th ====<br />
* Reviewed order of custom primer from Invitrogen (primer ordered: 9/17)<br />
* Rehydrated primers<br />
* Ran PCR Rxn with following:<br />
*# Annealing temperature: 61C<br />
*# Elongation time: 3 minutes<br />
*# 30 cycles<br />
<br />
==== Monday, 24th ====<br />
* Reviewed plates and observed the following:<br />
** Noted plenty of colonies on both plates, as expected<br />
** Plates with pSB1C3-J04450 based vector had many pink colonies and 8-10 white clones<br />
** Considering both vectors were alkaline phosphatase treated, will assume treatment failed for both vectors<br />
** Will currently disregard Upps 3 based vector transformations<br />
* Picked following colonies for miniculture:<br />
*# pSB1C3-FphA<br />
*# Upps 4-Kill gene<br />
*# Upps 4-Upps 6<br />
*# TetR-Upps 1<br />
* Minicultured the following from glycerol stocks<br />
*# Upps 1<br />
*# Upps 4<br />
*# TetR<br />
<br />
==== Tuesday, 25th ====<br />
* Ran a gel to verify following plasmids:<br />
** Sizing Gel 1<br />
**# Kill gene 1 (OK)<br />
**# Kill gene 2 (OK)<br />
**# FphA1 (too small - discard)<br />
**# FphA2 (OK)<br />
**# Upps 1 (too big - discard)<br />
**# B0034 RBS (OK, faint)<br />
** Sizing Gel 2<br />
**# Upps 4-Kill gene 1 (OK)<br />
**# Upps 4-Kill gene 2 (OK)<br />
**# Upps 4-Upps 6 (OK)<br />
**# Upps 4-Upps 6 (too big - discard)<br />
**# Upps 4 (OK)<br />
**# B0030 RBS.1 (OK, but really faint)<br />
''Note 1: the parenthesis denote observations/analysis of gel''<br />
* Isolated plasmids using standard miniprep protocol for the minicultures from previous day<br />
* Set up PCR site directed mutagenesis using pSB1C3-FphA as template <br />
''Note 2: used protocol from 9/13 and EcoRI primer set''<br />
* Rehydrated the following using standard iGEM rehydration protocol<br />
*# BBa_J23100 (plate 1, 18C [Amp])<br />
*# BBa_J23101 (plate 1, 18E [Amp])<br />
*# Bba_J23102 (plate 1, 18G [Amp])<br />
* Transformed the above rehydrated biobricks into DH5α<br />
<br />
==== Wednesday, 26th ====<br />
* Digested the PCR Rxn with DpnI<br />
* Transformed pSB1C3-FphA into DH5α<br />
* Digested the following: <br />
*# BBa_B0034 RBS with SpeI<br />
*# Upps4 with XbaI<br />
*# Kill gene with XbaI<br />
* Ligated the following (was predigested with EcoRI): <br />
*# RBS-Upps 4<br />
*# RBS-Kill gene<br />
* Gel extracted the bands of the following:<br />
*# RBS-Upp4 Target 2352bp, erroneous 2155bp<br />
*# RBS-Kill Target 3441bp, erroneous 2155bp<br />
* Minicultured the following:<br />
*# Upps 1<br />
*# Promoterless GFP<br />
*# Promoters 100-102<br />
<br />
==== Wednesday, 27th ====<br />
* Made minipreps from minicultures from previous day, ran qualitative gel, and concluded the following:<br />
*# Upps 1 had poor yield<br />
*# Promoterless GFP showed no growth<br />
* Conducted digestions of the following: (yielded 2x volume)<br />
*# RBS with SpeI<br />
*# Promoter 102 with SpeI <br />
*# Upps 1 with XbaI<br />
*# Promoterless GFP with XbaI<br />
* Conducted ligations of the following using digestion with 1x volume of EcoRI: (yielded 2x volume)<br />
*# Promoter 102-Upps 1<br />
*# Promoter 102-Promoterless GFP<br />
*# RBS-Upps 4<br />
*# Ribosome Binding Site-Kill gene<br />
* Ran 1x volume on gel to purify and gel extract target band<br />
* Transformed the above in DH5α using standard heat shock protocol<br />
* Observed the PCR site mutagenesis yielded no colonies<br />
<br />
==== Friday, 28th ====<br />
* Observed that Ribosome Binding Site-Kill gene worked and everything else did not <br />
* Conducted minicultures for the following: <br />
*# Ribosome Bidning Site-Kill gene<br />
*# Promoterless GFP with Kan resistance<br />
*# Upps 1<br />
*# Upps 4<br />
* Conducted digestions of the following: <br />
*# Upps 1 with XbaI<br />
*# Inducible Promoter with SpeI<br />
*# Upps 1 with EcoRI/SpeI<br />
*# Upps 4 with XbaI/PstI<br />
*# pSB1A3 (linearized DNA) with EcoRI/PstI<br />
*# pSB3T5 with EcoRI/PstI<br />
* Conducted ligations of the following:<br />
*# Promoter 100-Upps 1<br />
*# Promoter 101-Upps 1<br />
*# Promoter 102-Upps 1<br />
*# Inducible Promoter-Upps 1<br />
*# Promoter 102-promoterless GFP<br />
*# Upps 1-Upps 4-pSB1A3<br />
*# Upp1-Upp4-pSB3T5<br />
* Transformed the above ligated products into DH5α using heat shock protocol<br />
<br />
==== Saturday, 29th ====<br />
* Observed that Promoter 102-GFP worked and everythign else did not<br />
* Conducted digestions of the following:<br />
*# Upps 1 with EcoRI&SpeI<br />
*# Upps 4-Kill with XbaI&PstI<br />
*# Upps 4-Upps 6 with XbaI&PstI<br />
*# pSB1C3-J04450 with EcoRI&PstI<br />
* Conducted ligations of the following:<br />
*# Upps 1-Upps 4-Kill gene-pSB1C3 destination plasmid<br />
*# Upps 1-Upps 4-Upps6-pSB1C3 destination plasmid<br />
* Transformed the above ligated products into DH5α using a heat shock protocol<br />
* Transformed the following into JM109:<br />
*# Promoter 100-Upps 1<br />
*# Promoter 101-Upps 1<br />
*# Promoter 102-Upps 1<br />
*# Inducible Promoter-Upps 1<br />
<br />
</div><br />
== October, 2012 ==<br />
<div class="content-body-box"><br />
==== Monday, 1st ====<br />
* Observed that all of the plates grew colonies<br />
* Prepared minicultures of the following:<br />
*# Upps 1-Upps 4-Kill gene-pSB1C3 destination plasmid <br />
*# Upps 1-Upps 4-Upps 6-pSB1C3 destination plasmid<br />
*# Promoter 102-Upps 1 <br />
*# Inducible promoter-Upps 1<br />
<br />
==== Tuesday, 2nd ====<br />
* Isolated following plasmids by following standard plasmid isolation protocol and submitted parts:<br />
*# pSB1C3-FphA<br />
*# Upps 4-Kill gene<br />
*# Upps 1-Upps 4-Kill gene<br />
*# Upps 1-Upps 4-Upps 6<br />
*# Promoter 102-Upps 1<br />
*# Inducible promoter-Upps 1<br />
<br />
<br />
<br />
<br />
<br />
</div></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Liquid_MediaTeam:Columbia-Cooper-NYC/Making Liquid Media2013-01-07T07:47:13Z<p>FourEyeGuy1962: /* Liquid Media Protocol */</p>
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== Liquid Media Protocol ==<br />
<br />
For 1 liter of liquid media: <br />
<OL><br />
<LI>Combine in a large beaker, while stirring with a magnetic bar:<br />
<UL><br />
<LI>1 L of distilled water<br />
<LI>0.8 g of ammonium sulfate (NH4)2SO4<br />
<LI>1.0 g of magnesium sulfate MgSO4<br />
<LI>0.4 g of dipotassium phosphate K2HPO4<br />
<LI>5.0 mL of MD-TMS<br />
</UL><br />
<LI>Using sulfuric acid (H2SO4), adjust pH of solution to 2.1. (This should take about 0.5 mL of H2SO4.)<br />
<LI>Add 20 g of FeSO4*7H20<br />
<LI>Using sulfuric acid, adjust pH of solution to 1.8-1.85<br />
<LI>Once solution appears homogeneous, filter sterilize<br />
</OL><br />
<br />
<i>Credit for protocol goes to Jason Candreva, Research Associate, Columbia University</i><br />
<br />
Return to [[Team:Columbia-Cooper-NYC/Protocols|Protocols Page]]</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2013-01-07T07:45:03Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
<br />
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<br />
'''Liquid Media'''<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick (computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start.<br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. Thus, the data shows that the bacteria can accelerate the etching of copper in liquid media and the following copper consumption rates were obtained:<br />
<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 2]]<br />
<br />
Note that the bacterial rate is ~3x greater than the background rate or that the bacteria increase the etching by ~230% relative to the background rate.<br />
<br />
<br />
'''Solid Media'''<br />
<br />
In order to achieve controlled etching, liquid media cannot be used because the bacteria is mobile. Therefore, solid media is explored. (Refer to [https://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_Media Solid Media Protocol] for solutions used and how to make solid media.) 15 mL of solid media are poured onto a petri dish and four pieces of 2 cm x 2 cm copper are placed inside the media and allowed to harden. Afterwards, ~ 5 mL of OD 15 bacteria (as well as no bacteria) are placed on top of the solid media, spread evenly using sterile glass beads, and placed in an incubator at approximately room temperature for 12 days. Every 3 days, a petri dish with bacteria and a petri dish without bacteria are taken out and all the copper pieces are massed and thrown out. <br />
[[File:solid_media_only.png|600px|thumb|center|Figure 3]]<br />
<br />
The plot above shows the total average % decrease of copper vs. days. The data here is inconclusive because most of the data points are very close to each other, suggesting that the bacterial etching rate is slow and not faster than the background etching rate. <br />
<br />
<br />
'''Hybrid Media'''<br />
<br />
Since bacteria will not accelerate the etching of copper in solid media alone while bacteria in liquid media does, a combination of liquid and solid media (or hybrid media) will be explored. <br />
<br />
To make sure that hybrid media can work, experiments were done where cubes of solid media enclosed copper pieces were placed in flasks with 100 mL liquid media containing a pellet of bacteria in a shaker. Controls without bacteria were also used. After shaking for several days, and measuring the masses of the copper, it was found that the flasks with bacteria in them had on average ~11.6% copper mass lost since the start while the flasks without bacteria had on average ~1.4% copper mass lost since the start. This shows that bacteria can accelerate the etching of copper in hybrid media. The problem now is to decrease the amount of liquid media used. <br />
<br />
The set-up for the hybrid experiments is the same as the one for solid media except that variable amounts of liquid media are added on top of the solid media before bacteria (if any) were inoculated. <br />
<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
The plot above shows the average % copper lost due solely to the bacteria (bacteria - background) for different amounts of liquid media on solid media. As long as the data points are above zero, the bacteria accelerates the etching of copper in hybrid media using the corresponding amount of liquid media. Thus, volumes of down to 2 mL still work, albeit slow, and we have narrowed the range of liquid media down to between 1 and 2 mL. Note that this doesn't work for the 1 mL case because of the negative percents. <br />
<br />
<br />
<br />
<br />
'''Plasmids Submitted to the Parts Registry:'''<br />
<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in E. Coli:<br />
<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006, we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007, we do not have the additional IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls, we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is to provide information on how sensitive the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab without inducing cell lysis. However, we do not expect this to be the case.<br />
<br />
<br />
'''Depth Etching Rate'''<br />
<br />
As an attempt to obtain a bacterial depth etching rate (the genetically modified A. Ferrooxidans isn't ready yet), experiments using hybrid media (15 mL of solid and of liquid media) with four pieces of 2 cm x 2 cm copper in each petri dish as well as 1 mL OD 0.5 bacteria (if non-control cases) were placed in an incubator. In addition, the coppers were painted with nail polish everywhere but a strip down the center on both sides, which we found out prevents etching from occurring. The nail polish simulates the final result with the genetically modified bacteria because it acts as the illuminated spots that trigger cell death and thus no etching in that region. The masses were obtained after several days and the density of copper along with the non-lacquer covered surface area were used to calculate a depth rate.<br />
<br />
[[File:new_copper_depth.png|600px|thumb|center|Figure 5]]<br />
<br />
The plot above shows the average depth etched vs. days and by subtracting the slopes, the bacteria alone provides a depth etching rate of approximately 2.24 microns/day.</div>FourEyeGuy1962http://2012.igem.org/File:New_copper_depth.pngFile:New copper depth.png2013-01-07T07:44:31Z<p>FourEyeGuy1962: </p>
<hr />
<div></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2013-01-07T07:41:40Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
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<br />
'''Liquid Media'''<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick (computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start.<br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. Thus, the data shows that the bacteria can accelerate the etching of copper in liquid media and the following copper consumption rates were obtained:<br />
<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 2]]<br />
<br />
Note that the bacterial rate is ~3x greater than the background rate or that the bacteria increase the etching by ~230% relative to the background rate.<br />
<br />
<br />
'''Solid Media'''<br />
<br />
In order to achieve controlled etching, liquid media cannot be used because the bacteria is mobile. Therefore, solid media is explored. (Refer to [https://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_Media Solid Media Protocol] for solutions used and how to make solid media.) 15 mL of solid media are poured onto a petri dish and four pieces of 2 cm x 2 cm copper are placed inside the media and allowed to harden. Afterwards, ~ 5 mL of OD 15 bacteria (as well as no bacteria) are placed on top of the solid media, spread evenly using sterile glass beads, and placed in an incubator at approximately room temperature for 12 days. Every 3 days, a petri dish with bacteria and a petri dish without bacteria are taken out and all the copper pieces are massed and thrown out. <br />
[[File:solid_media_only.png|600px|thumb|center|Figure 3]]<br />
<br />
The plot above shows the total average % decrease of copper vs. days. The data here is inconclusive because most of the data points are very close to each other, suggesting that the bacterial etching rate is slow and not faster than the background etching rate. <br />
<br />
<br />
'''Hybrid Media'''<br />
<br />
Since bacteria will not accelerate the etching of copper in solid media alone while bacteria in liquid media does, a combination of liquid and solid media (or hybrid media) will be explored. <br />
<br />
To make sure that hybrid media can work, experiments were done where cubes of solid media enclosed copper pieces were placed in flasks with 100 mL liquid media containing a pellet of bacteria in a shaker. Controls without bacteria were also used. After shaking for several days, and measuring the masses of the copper, it was found that the flasks with bacteria in them had on average ~11.6% copper mass lost since the start while the flasks without bacteria had on average ~1.4% copper mass lost since the start. This shows that bacteria can accelerate the etching of copper in hybrid media. The problem now is to decrease the amount of liquid media used. <br />
<br />
The set-up for the hybrid experiments is the same as the one for solid media except that variable amounts of liquid media are added on top of the solid media before bacteria (if any) were inoculated. <br />
<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
The plot above shows the average % copper lost due solely to the bacteria (bacteria - background) for different amounts of liquid media on solid media. As long as the data points are above zero, the bacteria accelerates the etching of copper in hybrid media using the corresponding amount of liquid media. Thus, volumes of down to 2 mL still work, albeit slow, and we have narrowed the range of liquid media down to between 1 and 2 mL. Note that this doesn't work for the 1 mL case because of the negative percents. <br />
<br />
<br />
<br />
<br />
'''Plasmids Submitted to the Parts Registry:'''<br />
<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in E. Coli:<br />
<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006, we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007, we do not have the additional IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls, we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is to provide information on how sensitive the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab without inducing cell lysis. However, we do not expect this to be the case.<br />
<br />
<br />
'''Depth Etching Rate'''<br />
<br />
As an attempt to obtain a bacterial depth etching rate (the genetically modified A. Ferrooxidans isn't ready yet), experiments using hybrid media (15 mL of solid and of liquid media) with four pieces of 2 cm x 2 cm copper in each petri dish as well as 1 mL OD 0.5 bacteria (if non-control cases) were placed in an incubator. In addition, the coppers were painted with nail polish everywhere but a strip down the center on both sides, which we found out prevents etching from occurring. The nail polish simulates the final result with the genetically modified bacteria because it acts as the illuminated spots that trigger cell death and thus no etching in that region. The masses were obtained after several days and the density of copper along with the non-lacquer covered surface area were used to calculate a depth rate.<br />
<br />
[[File:copper depth.png|600px|thumb|center|Figure 5]]<br />
<br />
The plot above shows the average depth etched vs. days and by subtracting the slopes, the bacteria alone provides a depth etching rate of approximately 2.24 microns/day.</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2013-01-07T07:41:14Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
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'''Liquid Media'''<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick (computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start.<br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. Thus, the data shows that the bacteria can accelerate the etching of copper in liquid media and the following copper consumption rates were obtained:<br />
<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 2]]<br />
<br />
Note that the bacterial rate is ~3x greater than the background rate or that the bacteria increase the etching by ~230% relative to the background rate.<br />
<br />
<br />
'''Solid Media'''<br />
<br />
In order to achieve controlled etching, liquid media cannot be used because the bacteria is mobile. Therefore, solid media is explored. (Refer to [https://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_Media Solid Media Protocol] for solutions used and how to make solid media.) 15 mL of solid media are poured onto a petri dish and four pieces of 2 cm x 2 cm copper are placed inside the media and allowed to harden. Afterwards, ~ 5 mL of OD 15 bacteria (as well as no bacteria) are placed on top of the solid media, spread evenly using sterile glass beads, and placed in an incubator at approximately room temperature for 12 days. Every 3 days, a petri dish with bacteria and a petri dish without bacteria are taken out and all the copper pieces are massed and thrown out. <br />
[[File:solid_media_only.png|600px|thumb|center|Figure 3]]<br />
<br />
The plot above shows the total average % decrease of copper vs. days. The data here is inconclusive because most of the data points are very close to each other, suggesting that the bacterial etching rate is slow and not faster than the background etching rate. <br />
<br />
<br />
'''Hybrid Media'''<br />
<br />
Since bacteria will not accelerate the etching of copper in solid media alone while bacteria in liquid media does, a combination of liquid and solid media (or hybrid media) will be explored. <br />
<br />
To make sure that hybrid media can work, experiments were done where cubes of solid media enclosed copper pieces were placed in flasks with 100 mL liquid media containing a pellet of bacteria in a shaker. Controls without bacteria were also used. After shaking for several days, and measuring the masses of the copper, it was found that the flasks with bacteria in them had on average ~11.6% copper mass lost since the start while the flasks without bacteria had on average ~1.4% copper mass lost since the start. This shows that bacteria can accelerate the etching of copper in hybrid media. The problem now is to decrease the amount of liquid media used. <br />
<br />
The set-up for the hybrid experiments is the same as the one for solid media except that variable amounts of liquid media are added on top of the solid media before bacteria (if any) were inoculated. <br />
<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
The plot above shows the average % copper lost due solely to the bacteria (bacteria - background) for different amounts of liquid media on solid media. As long as the data points are above zero, the bacteria accelerates the etching of copper in hybrid media using the corresponding amount of liquid media. Thus, volumes of down to 2 mL still work, albeit slow, and we have narrowed the range of liquid media down to between 1 and 2 mL. Note that this doesn't work for the 1 mL case because of the negative percents. <br />
<br />
<br />
<br />
<br />
'''Plasmids Submitted to the Parts Registry:'''<br />
<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in E. Coli:<br />
<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006, we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007, we do not have the additional IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls, we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is to provide information on how sensitive the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab without inducing cell lysis. However, we do not expect this to be the case.<br />
<br />
<br />
'''Depth Etching Rate'''<br />
<br />
As an attempt to obtain a bacterial depth etching rate (the genetically modified A. Ferrooxidans isn't ready yet), experiments using hybrid media (15 mL of solid and of liquid media) with four pieces of 2 cm x 2 cm copper in each petri dish as well as 1 mL OD 0.5 bacteria (if non-control cases) were placed in an incubator. In addition, the coppers were painted with nail polish everywhere but a strip down the center on both sides, which we found out prevents etching from occurring. The nail polish simulates the final result with the genetically modified bacteria because it acts as the illuminated spots that trigger cell death and thus no etching in that region. The masses were obtained after several days and the density of copper along with the non-lacquer covered surface area were used to calculate a depth rate.<br />
<br />
[[File:Copper_depth.png|600px|thumb|center|Figure 5]]<br />
<br />
The plot above shows the average depth etched vs. days and by subtracting the slopes, the bacteria alone provides a depth etching rate of approximately 2.24 microns/day.</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2013-01-07T07:39:59Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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'''Liquid Media'''<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick (computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start.<br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. Thus, the data shows that the bacteria can accelerate the etching of copper in liquid media and the following copper consumption rates were obtained:<br />
<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 2]]<br />
<br />
Note that the bacterial rate is ~3x greater than the background rate or that the bacteria increase the etching by ~230% relative to the background rate.<br />
<br />
<br />
'''Solid Media'''<br />
<br />
In order to achieve controlled etching, liquid media cannot be used because the bacteria is mobile. Therefore, solid media is explored. (Refer to [https://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_Media Solid Media Protocol] for solutions used and how to make solid media.) 15 mL of solid media are poured onto a petri dish and four pieces of 2 cm x 2 cm copper are placed inside the media and allowed to harden. Afterwards, ~ 5 mL of OD 15 bacteria (as well as no bacteria) are placed on top of the solid media, spread evenly using sterile glass beads, and placed in an incubator at approximately room temperature for 12 days. Every 3 days, a petri dish with bacteria and a petri dish without bacteria are taken out and all the copper pieces are massed and thrown out. <br />
[[File:solid_media_only.png|600px|thumb|center|Figure 3]]<br />
<br />
The plot above shows the total average % decrease of copper vs. days. The data here is inconclusive because most of the data points are very close to each other, suggesting that the bacterial etching rate is slow and not faster than the background etching rate. <br />
<br />
<br />
'''Hybrid Media'''<br />
<br />
Since bacteria will not accelerate the etching of copper in solid media alone while bacteria in liquid media does, a combination of liquid and solid media (or hybrid media) will be explored. <br />
<br />
To make sure that hybrid media can work, experiments were done where cubes of solid media enclosed copper pieces were placed in flasks with 100 mL liquid media containing a pellet of bacteria in a shaker. Controls without bacteria were also used. After shaking for several days, and measuring the masses of the copper, it was found that the flasks with bacteria in them had on average ~11.6% copper mass lost since the start while the flasks without bacteria had on average ~1.4% copper mass lost since the start. This shows that bacteria can accelerate the etching of copper in hybrid media. The problem now is to decrease the amount of liquid media used. <br />
<br />
The set-up for the hybrid experiments is the same as the one for solid media except that variable amounts of liquid media are added on top of the solid media before bacteria (if any) were inoculated. <br />
<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
The plot above shows the average % copper lost due solely to the bacteria (bacteria - background) for different amounts of liquid media on solid media. As long as the data points are above zero, the bacteria accelerates the etching of copper in hybrid media using the corresponding amount of liquid media. Thus, volumes of down to 2 mL still work, albeit slow, and we have narrowed the range of liquid media down to between 1 and 2 mL. Note that this doesn't work for the 1 mL case because of the negative percents. <br />
<br />
<br />
<br />
<br />
'''Plasmids Submitted to the Parts Registry:'''<br />
<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in E. Coli:<br />
<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006, we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007, we do not have the additional IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls, we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is to provide information on how sensitive the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab without inducing cell lysis. However, we do not expect this to be the case.<br />
<br />
<br />
'''Depth Etching Rate'''<br />
<br />
As an attempt to obtain a bacterial depth etching rate (the genetically modified A. Ferrooxidans isn't ready yet), experiments using hybrid media (15 mL of solid and of liquid media) with four pieces of 2 cm x 2 cm copper in each petri dish as well as 1 mL OD 0.5 bacteria (if non-control cases) were placed in an incubator. In addition, the coppers were painted with nail polish everywhere but a strip down the center on both sides, which we found out prevents etching from occurring. The nail polish simulates the final result with the genetically modified bacteria because it acts as the illuminated spots that trigger cell death and thus no etching in that region. The masses were obtained after several days and the density of copper along with the non-lacquer covered surface area were used to calculate a depth rate.<br />
<br />
[[File:copper_depth.png|600px|thumb|center|Figure 5]]<br />
<br />
The plot above shows the average depth etched vs. days and by subtracting the slopes, the bacteria provides a depth etching rate of approximately 2.24 micron/day.</div>FourEyeGuy1962http://2012.igem.org/File:Depth_etched.pngFile:Depth etched.png2013-01-07T07:38:01Z<p>FourEyeGuy1962: uploaded a new version of &quot;File:Depth etched.png&quot;</p>
<hr />
<div>Average depth etched vs. days in solid media</div>FourEyeGuy1962http://2012.igem.org/File:Hybrid_media.pngFile:Hybrid media.png2013-01-07T07:35:12Z<p>FourEyeGuy1962: uploaded a new version of &quot;File:Hybrid media.png&quot;</p>
<hr />
<div>Average bacterial copper etching rate vs. days</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-27T04:00:55Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
<br />
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<br />
'''Liquid Media'''<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick (computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start.<br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. Thus, the data shows that the bacteria can accelerate the etching of copper in liquid media and the following copper consumption rates were obtained:<br />
<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 2]]<br />
<br />
Note that the bacterial rate is ~3x greater than the background rate or that the bacteria increase the etching by ~230% relative to the background rate.<br />
<br />
<br />
'''Solid Media'''<br />
<br />
In order to achieve controlled etching, liquid media cannot be used because the bacteria is mobile. Therefore, solid media is explored. (Refer to [https://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_Media Solid Media Protocol] for solutions used and how to make solid media.) 15 mL of solid media are poured onto a petri dish and four pieces of 2 cm x 2 cm copper are placed inside the media and allowed to harden. Afterwards, ~ 5 mL of OD 15 bacteria (as well as no bacteria) are placed on top of the solid media, spread evenly using sterile glass beads, and placed in an incubator at approximately room temperature for 12 days. Every 3 days, a petri dish with bacteria and a petri dish without bacteria are taken out and all the copper pieces are massed and thrown out. <br />
[[File:solid_media_only.png|600px|thumb|center|Figure 3]]<br />
<br />
The plot above shows the total average % decrease of copper vs. days. The data here is inconclusive because most of the data points are very close to each other, suggesting that the bacterial etching rate is slow and not faster than the background etching rate. <br />
<br />
<br />
'''Hybrid Media'''<br />
<br />
Since bacteria will not accelerate the etching of copper in solid media alone while bacteria in liquid media does, a combination of liquid and solid media (or hybrid media) will be explored. <br />
<br />
To make sure that hybrid media can work, experiments were done where cubes of solid media enclosed copper pieces were placed in flasks with 100 mL liquid media containing a pellet of bacteria in a shaker. Controls without bacteria were also used. After shaking for several days, and measuring the masses of the copper, it was found that the flasks with bacteria in them had on average ~11.6% copper mass lost since the start while the flasks without bacteria had on average ~1.4% copper mass lost since the start. This shows that bacteria can accelerate the etching of copper in hybrid media. The problem now is to decrease the amount of liquid media used. <br />
<br />
The set-up for the hybrid experiments is the same as the one for solid media except that variable amounts of liquid media are added on top of the solid media before bacteria (if any) were inoculated. <br />
<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
The plot above shows the average % copper lost due solely to the bacteria (bacteria - background) for different amounts of liquid media on solid media. As long as the data points are above zero, the bacteria accelerates the etching of copper in hybrid media using the corresponding amount of liquid media. Thus, volumes of down to 2 mL still work, albeit slow, and we have narrowed the range of liquid media down to between 1 and 2 mL. Note that this doesn't work for the 1 mL case because of the negative percents. <br />
<br />
<br />
<br />
<br />
'''Plasmids Submitted to the Parts Registry:'''<br />
<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in E. Coli:<br />
<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006, we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007, we do not have the additional IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls, we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is to provide information on how sensitive the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab without inducing cell lysis. However, we do not expect this to be the case.<br />
<br />
<br />
'''Depth Etching Rate'''<br />
<br />
As an attempt to obtain a bacterial depth etching rate (the genetically modified A. Ferrooxidans isn't ready yet), experiments using hybrid media (15 mL of solid and of liquid media) with four pieces of 2 cm x 2 cm copper in each petri dish as well as 1 mL OD 0.5 bacteria (if non-control cases) were placed in an incubator. In addition, the coppers were painted with nail polish everywhere but a strip down the center on both sides, which we found out prevents etching from occurring. The nail polish simulates the final result with the genetically modified bacteria because it acts as the illuminated spots that trigger cell death and thus no etching in that region. The masses were obtained after several days and the density of copper along with the non-lacquer covered surface area were used to calculate a depth rate.<br />
<br />
[[File:depth_etched.png|600px|thumb|center|Figure 5]]<br />
<br />
The plot above shows the average depth etched vs. days and by subtracting the slopes, we see that the bacteria provides a depth etching rate of approximately 1 micron/day.</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-27T03:56:06Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
<br />
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'''Liquid Media'''<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick ((computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start.<br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. Thus, the data shows that the bacteria can accelerate the etching of copper in liquid media and the following copper consumption rates were obtained:<br />
<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 2]]<br />
<br />
Note that the bacterial rate is ~3x greater than the background rate or that the bacteria increase the etching by ~230% relative to the background rate.<br />
<br />
<br />
'''Solid Media'''<br />
<br />
In order to achieve controlled etching, liquid media cannot be used because the bacteria is mobile. Therefore, solid media is explored. (Refer to [https://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_Media Solid Media Protocol] for solutions used and how to make solid media.) 15 mL of solid media are poured onto a petri dish and four pieces of 2 cm x 2 cm copper are placed inside the media and allowed to harden. Afterwards, ~ 5 mL of OD 15 bacteria (as well as no bacteria) are placed on top of the solid media, spread evenly using sterile glass beads, and placed in an incubator at approximately room temperature for 12 days. Every 3 days, a petri dish with bacteria and a petri dish without bacteria are taken out and all the copper pieces are massed and thrown out. <br />
[[File:solid_media_only.png|600px|thumb|center|Figure 3]]<br />
<br />
The plot above shows the total average % decrease of copper vs. days. The data here is inconclusive because most of the data points are very close to each other, suggesting that the bacterial etching rate is slow and not faster than the background etching rate. <br />
<br />
<br />
'''Hybrid Media'''<br />
<br />
Since bacteria will not accelerate the etching of copper in solid media alone while bacteria in liquid media does, a combination of liquid and solid media (or hybrid media) will be explored. <br />
<br />
To make sure that hybrid media can work, experiments were done where cubes of solid media enclosed copper pieces were placed in flasks with 100 mL liquid media containing a pellet of bacteria in a shaker. Controls without bacteria were also used. After shaking for several days, and measuring the masses of the copper, it was found that the flasks with bacteria in them had on average ~11.6% copper mass lost since the start while the flasks without bacteria had on average ~1.4% copper mass lost since the start. This shows that bacteria can accelerate the etching of copper in hybrid media. The problem now is to decrease the amount of liquid media used. <br />
<br />
The set-up for the hybrid experiments is the same as the one for solid media except that variable amounts of liquid media are added on top of the solid media before bacteria (if any) were inoculated. <br />
<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
The plot above shows the average % copper lost due solely to the bacteria (bacteria - background) for different amounts of liquid media on solid media. As long as the data points are above zero, the bacteria accelerates the etching of copper in hybrid media using the corresponding amount of liquid media. Thus, volumes of down to 2 mL still work, albeit slow, and we have narrowed the range of liquid media down to between 1 and 2 mL. Note that this doesn't work for the 1 mL case because of the negative percents. <br />
<br />
<br />
<br />
<br />
'''Plasmids Submitted to the Parts Registry:'''<br />
<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in E. Coli:<br />
<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006, we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007, we do not have the additional IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls, we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is to provide information on how sensitive the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab without inducing cell lysis. However, we do not expect this to be the case.<br />
<br />
<br />
'''Depth Etching Rate'''<br />
<br />
As an attempt to obtain a bacterial depth etching rate (the genetically modified A. Ferrooxidans isn't ready yet), hybrid media (15 mL of solid and of liquid media) with four pieces of 2 cm x 2 cm copper in each petri dish were used. In addition, the coppers were painted with nail polish everywhere but a strip down the center on both sides, which we found out prevents etching from occurring. The nail polish simulates the final result with the genetically modified bacteria because it acts as the illuminated spots that trigger cell death and thus no etching in that region. <br />
<br />
[[File:depth_etched.png|600px|thumb|center|Figure 5]]</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-27T03:44:50Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
<br />
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<br />
'''Liquid Media'''<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick ((computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start.<br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. Thus, the data shows that the bacteria can accelerate the etching of copper in liquid media and the following copper consumption rates were obtained:<br />
<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 2]]<br />
<br />
Note that the bacterial rate is ~3x greater than the background rate or that the bacteria increase the etching by ~230% relative to the background rate.<br />
<br />
<br />
'''Solid Media'''<br />
<br />
In order to achieve controlled etching, liquid media cannot be used because the bacteria is mobile. Therefore, solid media is explored. (Refer to [https://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_Media Solid Media Protocol] for solutions used and how to make solid media.) 15 mL of solid media are poured onto a petri dish and four pieces of 2 cm x 2 cm copper are placed inside the media and allowed to harden. Afterwards, ~ 5 mL of OD 15 bacteria (as well as no bacteria) are placed on top of the solid media, spread evenly using sterile glass beads, and placed in an incubator at approximately room temperature for 12 days. Every 3 days, a petri dish with bacteria and a petri dish without bacteria are taken out and all the copper pieces are massed and thrown out. <br />
[[File:solid_media_only.png|600px|thumb|center|Figure 3]]<br />
<br />
The plot above shows the total average % decrease of copper vs. days. The data here is inconclusive because most of the data points are very close to each other, suggesting that the bacterial etching rate is slow and not faster than the background etching rate. <br />
<br />
<br />
'''Hybrid Media'''<br />
<br />
Since bacteria will not accelerate the etching of copper in solid media alone while bacteria in liquid media does, a combination of liquid and solid media (or hybrid media) will be explored. <br />
<br />
To make sure that hybrid media can work, experiments were done where cubes of solid media enclosed copper pieces were placed in flasks with 100 mL liquid media containing a pellet of bacteria in a shaker. Controls without bacteria were also used. After shaking for several days, and measuring the masses of the copper, it was found that the flasks with bacteria in them had on average ~11.6% copper mass lost since the start while the flasks without bacteria had on average ~1.4% copper mass lost since the start. This shows that bacteria can accelerate the etching of copper in hybrid media. The problem now is to decrease the amount of liquid media used. <br />
<br />
The set-up for the hybrid experiments is the same as the one for solid media except that variable amounts of liquid media are added on top of the solid media before bacteria (if any) were inoculated. <br />
<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
The plot above shows the average % copper lost due solely to the bacteria (bacteria - background) for different amounts of liquid media on solid media. As long as the data points are above zero, the bacteria accelerates the etching of copper in hybrid media using the corresponding amount of liquid media. Thus, volumes of down to 2 mL still work, albeit slow, and we have narrowed the range of liquid media down to between 1 and 2 mL. Note that this doesn't work for the 1 mL case because of the negative percents. <br />
<br />
<br />
<br />
<br />
'''Plasmids Submitted to the Parts Registry:'''<br />
<br />
[[File:plasmid01.png|300px|center|Figure 5]]<br />
.<br />
[[File:plasmid02.png|300px|center|Figure 6]]<br />
.<br />
[[File:plasmid03.png|300px|center|Figure 7]]<br />
.<br />
[[File:plasmid04.png|300px|center|Figure 8]]<br />
.<br />
[[File:plasmid05.png|300px|center|Figure 9]]<br />
.<br />
[[File:plasmid06.png|300px|center|Figure 10]]<br />
.<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in E. Coli.<br />
<br />
[[File:plasmid07.png|300px|center|Figure 11]]<br />
<br />
For BBa_K95006, we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center|Figure 12]]<br />
<br />
For BBa_K95007, we do not have the additional IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls, we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is to provide information on how sensitive the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab without inducing cell lysis. However, we do not expect this to be the case.<br />
<br />
<br />
'''Depth Etching Rate'''<br />
<br />
As an attempt to simulate<br />
Here is a plot showing the depth etch rate of copper using nail polish as a mean to control etching:<br />
[[File:depth_etched.png|600px|thumb|center|Figure 13]]</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/AcknowledgementsTeam:Columbia-Cooper-NYC/Acknowledgements2012-10-27T03:43:29Z<p>FourEyeGuy1962: /* Acknowledgements */</p>
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= Acknowledgements =<br />
<br />
Adam Cerini: Copper team, research, Maker Faire<br />
<br />
Marjana Chowdhury: Wiki team, Copper team<br />
<br />
Ciera Lowe: Genetics team, Maker Faire, Wiki team<br />
<br />
Anna Mai: Copper team, Wiki team, Maker Faire<br />
<br />
Yuta Makita: Wiki team, Genetics team, Maker Faire<br />
<br />
Nicholas Mannarino: Genetics team, Maker Faire<br />
<br />
Aakash Mansukhani: Copper team<br />
<br />
Joeseph Mercedes: Copper team, Wiki team<br />
<br />
Steven Neuhaus: Genetics team, research, Wiki team, Maker Faire<br />
<br />
Kirsten Nicassio: Genetics team, research, Wiki team<br />
<br />
Udochukwu (Ud) Okorafor: Copper team, Wiki team, Maker Faire<br />
<br />
Saimon Sharif: Genetics team, research<br />
<br />
Richard Shi: Copper team<br />
<br />
Jeffery Xu: Copper team, Maker Faire<br />
<br />
Vincent Xu: Copper team, Wiki team, Maker Faire<br />
<br />
<br />
<br />
We graciously thank the following parties for helping to fund this year's IGEM project:<br />
<br />
*Columbia University Fu Foundation School of Engineering and Applied Science.<br />
<br />
*The Cooper Union Joint Activities Committee for funding student clubs.<br />
<br />
*The Rose-Sandholm Biology Initiative to help us build up our laboratory offerings for students at The Cooper Union. <br />
<br />
<br />
A special thanks to the following iGEM teams and people:<br />
*Dr. Scott Banta for overseeing our project, providing invaluable advice and allowing us to work in his lab at Columbia.<br />
*Dr. Alan West for his expertise in copper etching.<br />
*Dr. David Orbach for overseeing our project, generating novel ideas and approaches to our goal and allowing us to work in the Kanbar Center at Cooper.<br />
*Dionne Lutz for walking the genetic team through countless protocols, supervising our work in the Kanbar lab, helping organize our Maker Faire table and providing motivation and optimism.<br />
*Sudipta Majumdar for helping us construct plasmids and patiently teaching us new protocols.<br />
*Kevin Dooley for help with expression experiments, providing us with a GFP gene and identifying and removing cut sights within our biobrick and answering questions as we became acquainted with Dr. Banta's lab.<br />
*Tushar Patel for providing us with a GFP gene and answering questions as we became acquainted with Dr. Banta's lab.<br />
*Jason Candreva for being extremely patient with us, teaching us various transformation protocols with ecoli and ferrooxidans and answering every question we threw at him.<br />
*Sara Chuang for initializing the iGEM team. <br />
* iGEM Team Uppsala University for sending us the following parts: BBa_K592004, BBa_K592005, BBa_K592006, BBa_K592009, BBa_K592010, and BBa_K592016<br />
* iGEM Team ETH Zurich for sending us E. coli codon-optimized Pif3 and PhyB<br />
* Dr. Nicole Frankenberg-Dinkel for her advice and for sending plasmids pASK-fphAN753s and pTDho1</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-27T03:37:27Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
<br />
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<br />
'''Liquid Media'''<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick ((computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start.<br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. Thus, the data shows that the bacteria can accelerate the etching of copper in liquid media and the following copper consumption rates were obtained:<br />
<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 2]]<br />
<br />
Note that the bacterial rate is ~3x greater than the background rate or that the bacteria increase the etching by ~230% relative to the background rate.<br />
<br />
<br />
'''Solid Media'''<br />
<br />
In order to achieve controlled etching, liquid media cannot be used because the bacteria is mobile. Therefore, solid media is explored. (Refer to [https://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_Media Solid Media Protocol] for solutions used and how to make solid media.) 15 mL of solid media are poured onto a petri dish and four pieces of 2 cm x 2 cm copper are placed inside the media and allowed to harden. Afterwards, ~ 5 mL of OD 15 bacteria (as well as no bacteria) are placed on top of the solid media, spread evenly using sterile glass beads, and placed in an incubator at approximately room temperature for 12 days. Every 3 days, a petri dish with bacteria and a petri dish without bacteria are taken out and all the copper pieces are massed and thrown out. <br />
[[File:solid_media_only.png|600px|thumb|center|Figure 3]]<br />
<br />
The plot above shows the total average % decrease of copper vs. days. The data here is inconclusive because most of the data points are very close to each other, suggesting that the bacterial etching rate is slow and not faster than the background etching rate. <br />
<br />
<br />
'''Hybrid Media'''<br />
<br />
Since bacteria will not accelerate the etching of copper in solid media alone while bacteria in liquid media does, a combination of liquid and solid media (or hybrid media) will be explored. <br />
<br />
To make sure that hybrid media can work, experiments were done where cubes of solid media enclosed copper pieces were placed in flasks with 100 mL liquid media containing a pellet of bacteria in a shaker. Controls without bacteria were also used. After shaking for several days, and measuring the masses of the copper, it was found that the flasks with bacteria in them had on average ~11.6% copper mass lost since the start while the flasks without bacteria had on average ~1.4% copper mass lost since the start. This shows that bacteria can accelerate the etching of copper in hybrid media. The problem now is to decrease the amount of liquid media used. <br />
<br />
The set-up for the hybrid experiments is the same as the one for solid media except that variable amounts of liquid media are added on top of the solid media before bacteria (if any) were inoculated. <br />
<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
The plot above shows the average % copper lost due solely to the bacteria (bacteria - background) for different amounts of liquid media on solid media. As long as the data points are above zero, the bacteria accelerates the etching of copper in hybrid media using the corresponding amount of liquid media. Thus, volumes of down to 2 mL still work, albeit slow, and we have narrowed the range of liquid media down to between 1 and 2 mL. Note that this doesn't work for the 1 mL case because of the negative percents. <br />
<br />
<br />
<br />
<br />
'''Plasmids Submitted to the Parts Registry:'''<br />
<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in E. Coli.<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006, we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007, we do not have the additional IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls, we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is to provide information on how sensitive the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab without inducing cell lysis. However, we do not expect this to be the case.<br />
<br />
Here is a plot showing the depth etch rate of copper using nail polish as a mean to control etching:<br />
[[File:depth_etched.png|600px|thumb|center|Figure 5]]</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-27T03:36:26Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
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'''Liquid Media'''<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick ((computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start.<br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. Thus, the data shows that the bacteria can accelerate the etching of copper in liquid media and the following copper consumption rates were obtained:<br />
<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 2]]<br />
<br />
Note that the bacterial rate is ~3x greater than the background rate or that the bacteria increase the etching by ~230% relative to the background rate.<br />
<br />
<br />
'''Solid Media'''<br />
<br />
In order to achieve controlled etching, liquid media cannot be used because the bacteria is mobile. Therefore, solid media is explored. (Refer to [https://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_Media Solid Media Protocol] for solutions used and how to make solid media.) 15 mL of solid media are poured onto a petri dish and four pieces of 2 cm x 2 cm copper are placed inside the media and allowed to harden. Afterwards, ~ 5 mL of OD 15 bacteria (as well as no bacteria) are placed on top of the solid media, spread evenly using sterile glass beads, and placed in an incubator at approximately room temperature for 12 days. Every 3 days, a petri dish with bacteria and a petri dish without bacteria are taken out and all the copper pieces are massed and thrown out. <br />
[[File:solid_media_only.png|600px|thumb|center|Figure 3]]<br />
<br />
The plot above shows the total average % decrease of copper vs. days. The data here is inconclusive because most of the data points are very close to each other, suggesting that the bacterial etching rate is slow and not faster than the background etching rate. <br />
<br />
<br />
'''Hybrid Media'''<br />
<br />
Since bacteria will not accelerate the etching of copper in solid media alone while bacteria in liquid media does, a combination of liquid and solid media (or hybrid media) will be explored. <br />
<br />
To make sure that hybrid media can work, experiments were done where cubes of solid media enclosed copper pieces were placed in flasks with 100 mL liquid media containing a pellet of bacteria in a shaker. Controls without bacteria were also used. After shaking for several days, and measuring the masses of the copper, it was found that the flasks with bacteria in them had on average ~11.6% copper mass lost since the start while the flasks without bacteria had on average ~1.4% copper mass lost since the start. This shows that bacteria can accelerate the etching of copper in hybrid media. The problem now is to decrease the amount of liquid media used. <br />
<br />
The set-up for the hybrid experiments is the same as the one for solid media except that variable amounts of liquid media are added on top of the solid media before bacteria (if any) were inoculated. <br />
<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
The plot above shows the average % copper lost due solely to the bacteria (bacteria - background) for different amounts of liquid media on solid media. As long as the data points are above zero, the bacteria accelerates the etching of copper in hybrid media using the corresponding amount of liquid media. Thus, volumes of down to 2 mL still work, albeit slow, and we have narrowed the range of liquid media down to between 1 and 2 mL. Note that this doesn't work for the 1 mL case because of the negative percents. <br />
<br />
<br />
Here is a plot showing the depth etch rate of copper using nail polish as a mean to control etching:<br />
[[File:depth_etched.png|600px|thumb|center|Figure 5]]<br />
<br />
<br />
<br />
'''Plasmids Submitted to the Parts Registry:'''<br />
<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in E. Coli.<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006, we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007, we do not have the additional IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls, we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is to provide information on how sensitive the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab without inducing cell lysis. However, we do not expect this to be the case.</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-27T03:35:05Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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'''Liquid Media'''<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick ((computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start.<br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. Thus, the data shows that the bacteria can accelerate the etching of copper in liquid media and the following copper consumption rates were obtained:<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 2]]<br />
Note that the bacterial rate is ~3x greater than the background rate or that the bacteria increase the etching by ~230% relative to the background rate.<br />
<br />
'''Solid Media'''<br />
<br />
In order to achieve controlled etching, liquid media cannot be used because the bacteria is mobile. Therefore, solid media is explored. (Refer to [https://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_Media Solid Media Protocol] for solutions used and how to make solid media.) 15 mL of solid media are poured onto a petri dish and four pieces of 2 cm x 2 cm copper are placed inside the media and allowed to harden. Afterwards, ~ 5 mL of OD 15 bacteria (as well as no bacteria) are placed on top of the solid media, spread evenly using sterile glass beads, and placed in an incubator at approximately room temperature for 12 days. Every 3 days, a petri dish with bacteria and a petri dish without bacteria are taken out and all the copper pieces are massed and thrown out. <br />
[[File:solid_media_only.png|600px|thumb|center|Figure 3]]<br />
<br />
The plot above shows the total average % decrease of copper vs. days. The data here is inconclusive because most of the data points are very close to each other, suggesting that the bacterial etching rate is slow and not faster than the background etching rate. <br />
<br />
<br />
'''Hybrid Media'''<br />
<br />
Since bacteria will not accelerate the etching of copper in solid media alone while bacteria in liquid media does, a combination of liquid and solid media (or hybrid media) will be explored. <br />
<br />
To make sure that hybrid media can work, experiments were done where cubes of solid media enclosed copper pieces were placed in flasks with 100 mL liquid media containing a pellet of bacteria in a shaker. Controls without bacteria were also used. After shaking for several days, and measuring the masses of the copper, it was found that the flasks with bacteria in them had on average ~11.6% copper mass lost since the start while the flasks without bacteria had on average ~1.4% copper mass lost since the start. This shows that bacteria can accelerate the etching of copper in hybrid media. The problem now is to decrease the amount of liquid media used. <br />
<br />
The set-up for the hybrid experiments is the same as the one for solid media except that variable amounts of liquid media are added on top of the solid media before bacteria (if any) were inoculated. <br />
<br />
[[File:depth_etched.png|600px|thumb|center|Figure 4]]<br />
<br />
The plot above shows the average % copper lost due solely to the bacteria (bacteria - background) for different amounts of liquid media on solid media. As long as the data points are above zero, the bacteria accelerates the etching of copper in hybrid media using the corresponding amount of liquid media. Thus, volumes of down to 2 mL still work, albeit slow, and we have narrowed the range of liquid media down to between 1 and 2 mL. Note that this doesn't work for the 1 mL case because of the negative percents. <br />
<br />
<br />
Here is a plot showing the depth etch rate of copper using nail polish as a mean to control etching:<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 5]]<br />
<br />
<br />
<br />
'''Plasmids Submitted to the Parts Registry:'''<br />
<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in E. Coli.<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006, we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007, we do not have the additional IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls, we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is to provide information on how sensitive the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab without inducing cell lysis. However, we do not expect this to be the case.</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-27T03:06:37Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
<br />
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<br />
'''Liquid Media'''<br />
<br />
<p> As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick ((computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start. </p><br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. Thus, the data shows that the bacteria can etch copper in liquid media. <br />
<br />
<br />
'''Solid Media'''<br />
<br />
In order to achieve controlled etching, liquid media cannot be used because the bacteria is mobile. Therefore, solid media is explored. (Refer to [https://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_Media Solid Media Protocol] for solutions used and how to make solid media.) 15 mL of solid media are poured onto a petri dish and a piece of 2 cm x 2 cm copper is placed inside the media and allowed to harden. <br />
[[File:solid_media_only.png|600px|thumb|center|Figure 2]]<br />
<br />
From this data we were able to conclude the following copper consumption rates:<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 3]]<br />
<br />
Here is a plot showing the depth etch rate of copper using nail polish as a mean to control etching:<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
Here is a plot showing the average percent copper lost due solely to the bacteria for different amounts of liquid media on solid media. Note that this doesn't work for the 1 mL case because of the negative %:<br />
[[File:depth_etched.png|600px|thumb|center|Figure 5]]<br />
<br />
The Copper team has further refined their experiments by adding more controls and nuances to the existing experiments in order to collect more refined data which is detailed in the notebook, however the major results are summarized here.<br />
<br />
The genetics group has submitted each of the following plasmids to the parts registry:<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in ecoli.<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006 we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007 we do not have the addition IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is provide information on how sensative the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab with out inducing cell lysis however we do not expect this to be the case.</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-27T03:04:03Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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<br />
= Data and Conclusions =<br />
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<br />
Liquid Media<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick ((computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start. <br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. Thus, the data shows that the bacteria can etch copper in liquid media. <br />
<br />
<br />
Solid Media<br />
<br />
In order to achieve controlled etching, liquid media cannot be used because the bacteria is mobile. Therefore, solid media is explored. (Refer to [https://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_Media Solid Media Protocol] for solutions used and how to make solid media.) 15 mL of solid media are poured onto a petri dish and a piece of 2 cm x 2 cm copper is placed inside the media and allowed to harden. <br />
[[File:solid_media_only.png|600px|thumb|center|Figure 2]]<br />
<br />
From this data we were able to conclude the following copper consumption rates:<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 3]]<br />
<br />
Here is a plot showing the depth etch rate of copper using nail polish as a mean to control etching:<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
Here is a plot showing the average percent copper lost due solely to the bacteria for different amounts of liquid media on solid media. Note that this doesn't work for the 1 mL case because of the negative %:<br />
[[File:depth_etched.png|600px|thumb|center|Figure 5]]<br />
<br />
The Copper team has further refined their experiments by adding more controls and nuances to the existing experiments in order to collect more refined data which is detailed in the notebook, however the major results are summarized here.<br />
<br />
The genetics group has submitted each of the following plasmids to the parts registry:<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in ecoli.<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006 we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007 we do not have the addition IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is provide information on how sensative the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab with out inducing cell lysis however we do not expect this to be the case.</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_MediaTeam:Columbia-Cooper-NYC/Making Solid Media2012-10-27T03:01:32Z<p>FourEyeGuy1962: /* Solid Media Protocol */</p>
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== Solid Media Protocol ==<br />
'''Solution A'''<br />
<BLOCKQUOTE><br />
Sterile filter solution with:<br />
<UL><br />
<LI>2 g of Na2S2O3<br />
<LI>10 mL of H2O<br />
</UL><br />
</BLOCKQUOTE><br />
<br />
'''Solution B'''<br />
<BLOCKQUOTE><br />
Autoclave solution of (2.5% tryptone):<br />
<UL><br />
<LI>2.5g tryptone broth<br />
<LI>100 mL of H2O<br />
</UL><br />
</BLOCKQUOTE><br />
<br />
'''Solution C'''<br />
<BLOCKQUOTE><br />
Sterile filter solution of:<br />
<UL><br />
<LI>500 mL deionized water<br />
<LI>27 g (NH4)2SO4<br />
<LI>0.9 g KCl<br />
<LI>1.605 g leucine<br />
<LI>4.5 g MgSO4<br />
<LI>0.02 g HK2PO4<br />
<LI>0.485 g diaminopimelic acid<br />
<LI> ~0.7 mL H2SO4 (or enough to bring pH down to ~2.0)<br />
<LI>20 g Fe(II)SO4 (after adding everything else above)<br />
</UL><br />
</BLOCKQUOTE><br />
<br />
'''Solution D'''<br />
<BLOCKQUOTE><br />
Autoclave solution containing (4% agarose):<br />
<UL><br />
<LI>20 g Agarose<br />
<LI>500 mL distilled water<br />
</UL><br />
</BLOCKQUOTE><br />
<br />
<OL><br />
<LI>Heat up agarose solution until it becomes liquid<br />
<LI>Pick a volume of solid media to make<br />
<LI>Mix 1% vol A & 50% vol D, and 1% vol B & 48% vol C<br />
<LI>Mix together AD and BC<br />
<LI>Pour into petri dishes and allow to harden<br />
</OL><br />
<br />
<i>Credit for protocol goes to Jason Candreva, Research Associate, Columbia University</i><br />
<br />
Return to [[Team:Columbia-Cooper-NYC/Protocols|Protocols Page]]</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Making_Solid_MediaTeam:Columbia-Cooper-NYC/Making Solid Media2012-10-27T03:00:51Z<p>FourEyeGuy1962: /* Solid Media Protocol */</p>
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== Solid Media Protocol ==<br />
'''Solution A'''<br />
<BLOCKQUOTE><br />
Sterile filter solution with:<br />
<UL><br />
<LI>2 g of Na2S2O3<br />
<LI>10 mL of H2O<br />
</UL><br />
</BLOCKQUOTE><br />
<br />
'''Solution B'''<br />
<BLOCKQUOTE><br />
Autoclave solution of (2.5% tryptone):<br />
<UL><br />
<LI>2.5g tryptone broth<br />
<LI>100 mL of H2O<br />
</UL><br />
</BLOCKQUOTE><br />
<br />
'''Solution C'''<br />
<BLOCKQUOTE><br />
Sterile filter solution of:<br />
<UL><br />
<LI>500 mL deionized water<br />
<LI>27 g (NH4)2SO4<br />
<LI>0.9 g KCl<br />
<LI>1.605 g leucine<br />
<LI>4.5 g MgSO4<br />
<LI>0.02 g HK2PO4<br />
<LI>0.485 g diaminopimelic acid<br />
<LI> ~0.7 mL H2SO4 (or enough to bring pH down to ~2.0)<br />
<LI>10 g Fe(II)SO4 (after adding everything else above)<br />
</UL><br />
</BLOCKQUOTE><br />
<br />
'''Solution D'''<br />
<BLOCKQUOTE><br />
Autoclave solution containing (4% agarose):<br />
<UL><br />
<LI>20 g Agarose<br />
<LI>500 mL distilled water<br />
</UL><br />
</BLOCKQUOTE><br />
<br />
<OL><br />
<LI>Heat up agarose solution until it becomes liquid<br />
<LI>Pick a volume of solid media to make<br />
<LI>Mix 1% vol A & 50% vol D, and 1% vol B & 48% vol C<br />
<LI>Mix together AD and BC<br />
<LI>Pour into petri dishes and allow to harden<br />
</OL><br />
<br />
<i>Credit for protocol goes to Jason Candreva, Research Associate, Columbia University</i><br />
<br />
Return to [[Team:Columbia-Cooper-NYC/Protocols|Protocols Page]]</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-27T02:46:09Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
<br />
<br />
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<br />
Liquid Media<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick ((computer paper thickness), and 99.9% pure. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. Note that A. Ferrooxidans undergo a 20 hour lag phase before growth can start. <br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and it shows that a significant drop in copper mass after Day 1 compared to the bacteria line because of the immediate availability of iron (III) ions. However, the rate of decrease slows down over time because iron (III) ions are depleted. In the case of bacteria, the iron (II) ions present in the media is converted to iron (III) ions from the bacteria's mechanism, the iron (III) reacts with copper and regenerates iron (II), and iron (II) can be converted to iron (III) once again from the bacteria, resulting in a self-sustaining cycle that eventually depletes all of the copper. <br />
<br />
By furthur refining our experiments as described in the copper notebook we were able to show that copper is in fact etched faster in the presence of A. Ferrooxidans than the basal rate of etching by the acidic liquid media (see the work done 7/18-7/23 on [https://2012.igem.org/Team:Columbia-Cooper-NYC/Columbia_notebook_1 Copper Etching] page under Results):<br />
[[File:solid_media_only.png|600px|thumb|center|Figure 2]]<br />
<br />
From this data we were able to conclude the following copper consumption rates:<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 3]]<br />
<br />
Here is a plot showing the depth etch rate of copper using nail polish as a mean to control etching:<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
Here is a plot showing the average percent copper lost due solely to the bacteria for different amounts of liquid media on solid media. Note that this doesn't work for the 1 mL case because of the negative %:<br />
[[File:depth_etched.png|600px|thumb|center|Figure 5]]<br />
<br />
The Copper team has further refined their experiments by adding more controls and nuances to the existing experiments in order to collect more refined data which is detailed in the notebook, however the major results are summarized here.<br />
<br />
The genetics group has submitted each of the following plasmids to the parts registry:<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in ecoli.<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006 we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007 we do not have the addition IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is provide information on how sensative the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab with out inducing cell lysis however we do not expect this to be the case.</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-27T02:36:52Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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<br />
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<br />
Liquid Media<br />
<br />
As mentioned in the [https://2012.igem.org/Team:Columbia-Cooper-NYC/Overview], Acidithiobacillus Ferrooxidans have the ability to oxidize iron (II) to iron (III) and the iron (III) can go through a redox reaction with copper to solubilize copper, which is the goal. But this mechanism only works in aerobic conditions. Therefore, to properly induce mass transfer of oxygen from the media to the bacteria, flasks containing the liquid media and bacteria are placed in a shaker at 220 rpm and room temperature. The copper used in these experiments are 2 cm x 2 cm pieces, 5 mils thick ((computer paper thickness), and 99.9% purity. Individual copper pieces were placed in flasks containing 100 mL of liquid media and either bacteria, no bacteria, or iron (III) sulfate hydrate. These flasks were left in the shaker for four days and copper mass measurements were taken daily in triplicate. The copper piece were massed after cleaning with deionized water and 70% ethanol followed by returning them back to their respective flasks. <br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
The plot above shows the remaining mass of the copper vs. days. The black line represents the data without bacteria and the decrease in copper mass over time indicates that there is some sort of background etching, which is due to side reactions happening such as the oxidation of copper from air. The blue line represents the data with bacteria and it shows that the copper mass decreased to zero after day 3. The red line represents the data with iron (III) sulfate hydrate and<br />
By furthur refining our experiments as described in the copper notebook we were able to show that copper is in fact etched faster in the presence of A. Ferrooxidans than the basal rate of etching by the acidic liquid media (see the work done 7/18-7/23 on [https://2012.igem.org/Team:Columbia-Cooper-NYC/Columbia_notebook_1 Copper Etching] page under Results):<br />
[[File:solid_media_only.png|600px|thumb|center|Figure 2]]<br />
<br />
From this data we were able to conclude the following copper consumption rates:<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 3]]<br />
<br />
Here is a plot showing the depth etch rate of copper using nail polish as a mean to control etching:<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
Here is a plot showing the average percent copper lost due solely to the bacteria for different amounts of liquid media on solid media. Note that this doesn't work for the 1 mL case because of the negative %:<br />
[[File:depth_etched.png|600px|thumb|center|Figure 5]]<br />
<br />
The Copper team has further refined their experiments by adding more controls and nuances to the existing experiments in order to collect more refined data which is detailed in the notebook, however the major results are summarized here.<br />
<br />
The genetics group has submitted each of the following plasmids to the parts registry:<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in ecoli.<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006 we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007 we do not have the addition IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is provide information on how sensative the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab with out inducing cell lysis however we do not expect this to be the case.</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-27T01:54:47Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
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The liquid media that Ferrooxidans thrive in is acidic so the copper team first started working on proving that the bacteria are doing the etching, not just the media. Our initial results were somewhat inconclusive, however the data showed that at certain time intervals the bacteria etched faster than the basal rate (see work from 7/7-7/17 on [https://2012.igem.org/Team:Columbia-Cooper-NYC/Columbia_notebook_1 Copper Etching] page under Results):<br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
By furthur refining our experiments as described in the copper notebook we were able to show that copper is in fact etched faster in the presence of A. Ferrooxidans than the basal rate of etching by the acidic liquid media (see the work done 7/18-7/23 on [https://2012.igem.org/Team:Columbia-Cooper-NYC/Columbia_notebook_1 Copper Etching] page under Results):<br />
[[File:solid_media_only.png|600px|thumb|center|Figure 2]]<br />
<br />
From this data we were able to conclude the following copper consumption rates:<br />
[[File:copper_rate_table.png|600px|thumb|center|Figure 3]]<br />
<br />
Here is a plot showing the depth etch rate of copper using nail polish as a mean to control etching:<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
Here is a plot showing the average percent copper lost due solely to the bacteria for different amounts of liquid media on solid media. Note that this doesn't work for the 1 mL case because of the negative %:<br />
[[File:depth_etched.png|600px|thumb|center|Figure 5]]<br />
<br />
The Copper team has further refined their experiments by adding more controls and nuances to the existing experiments in order to collect more refined data which is detailed in the notebook, however the major results are summarized here.<br />
<br />
The genetics group has submitted each of the following plasmids to the parts registry:<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in ecoli.<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006 we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007 we do not have the addition IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is provide information on how sensative the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab with out inducing cell lysis however we do not expect this to be the case.</div>FourEyeGuy1962http://2012.igem.org/File:Copper_rate_table.pngFile:Copper rate table.png2012-10-27T01:54:16Z<p>FourEyeGuy1962: Table containing copper consumption rates</p>
<hr />
<div>Table containing copper consumption rates</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-27T01:44:00Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
<br />
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The liquid media that Ferrooxidans thrive in is acidic so the copper team first started working on proving that the bacteria are doing the etching, not just the media. Our initial results were somewhat inconclusive, however the data showed that at certain time intervals the bacteria etched faster than the basal rate (see work from 7/7-7/17 on [https://2012.igem.org/Team:Columbia-Cooper-NYC/Columbia_notebook_1 Copper Etching] page under Results):<br />
[[File:liquid_media.png|600px|thumb|center|Figure 1]]<br />
<br />
By furthur refining our experiments as described in the copper notebook we were able to show that copper is in fact etched faster in the presence of A. Ferrooxidans than the basal rate of etching by the acidic liquid media (see the work done 7/18-7/23 on [https://2012.igem.org/Team:Columbia-Cooper-NYC/Columbia_notebook_1 Copper Etching] page under Results):<br />
[[File:solid_media_only.png|600px|thumb|center|Figure 2]]<br />
<br />
From this data we were able to conclude the following copper consumption rates:<br />
[[File:table3.png|600px|thumb|center|Figure 3]]<br />
<br />
Here is a plot showing the depth etch rate of copper using nail polish as a mean to control etching:<br />
[[File:hybrid_media.png|600px|thumb|center|Figure 4]]<br />
<br />
Here is a plot showing the average percent copper lost due solely to the bacteria for different amounts of liquid media on solid media. Note that this doesn't work for the 1 mL case because of the negative %:<br />
[[File:depth_etched.png|600px|thumb|center|Figure 5]]<br />
<br />
The Copper team has further refined their experiments by adding more controls and nuances to the existing experiments in order to collect more refined data which is detailed in the notebook, however the major results are summarized here.<br />
<br />
The genetics group has submitted each of the following plasmids to the parts registry:<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in ecoli.<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006 we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007 we do not have the addition IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is provide information on how sensative the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab with out inducing cell lysis however we do not expect this to be the case.</div>FourEyeGuy1962http://2012.igem.org/File:Depth_etched.pngFile:Depth etched.png2012-10-27T01:24:22Z<p>FourEyeGuy1962: Average depth etched vs. days in solid media</p>
<hr />
<div>Average depth etched vs. days in solid media</div>FourEyeGuy1962http://2012.igem.org/File:Hybrid_media.pngFile:Hybrid media.png2012-10-27T01:23:44Z<p>FourEyeGuy1962: Average bacterial copper etching rate vs. days</p>
<hr />
<div>Average bacterial copper etching rate vs. days</div>FourEyeGuy1962http://2012.igem.org/File:Liquid_media.pngFile:Liquid media.png2012-10-27T01:22:59Z<p>FourEyeGuy1962: Copper mass remaining vs. days in liquid media</p>
<hr />
<div>Copper mass remaining vs. days in liquid media</div>FourEyeGuy1962http://2012.igem.org/File:Solid_media_only.pngFile:Solid media only.png2012-10-27T01:22:11Z<p>FourEyeGuy1962: % decrease of copper vs. days in solid media</p>
<hr />
<div>% decrease of copper vs. days in solid media</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/Data_and_ConclusionsTeam:Columbia-Cooper-NYC/Data and Conclusions2012-10-04T04:07:39Z<p>FourEyeGuy1962: /* Data and Conclusions */</p>
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= Data and Conclusions =<br />
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The liquid media that Ferrooxidans thrive in is acidic so the copper team first started working on proving that the bacteria are doing the etching, not just the media. Our initial results were somewhat inconclusive, however the data showed that at certain time intervals the bacteria etched faster than the basal rate (see work from 7/7-7/17 on [https://2012.igem.org/Team:Columbia-Cooper-NYC/Columbia_notebook_1 Copper Etching] page under Results):<br />
[[File:table2.png|600px|thumb|center|Figure 1]]<br />
<br />
By furthur refining our experiments as described in the cooper notebook we were able to show that copper is in fact etched faster in the presence of A. Ferrooxidans than the basal rate of etching by the acidic liquid media (see the work done 7/18-7/23 on [https://2012.igem.org/Team:Columbia-Cooper-NYC/Columbia_notebook_1 Copper Etching] page under Results):<br />
[[File:table1.png|600px|thumb|center|Figure 2]]<br />
<br />
From this data we were able to conclude the following copper consumption rates:<br />
[[File:table3.png|600px|thumb|center|Figure 3]]<br />
<br />
Here is a plot showing the depth etch rate of copper using nail polish as a mean to control etching:<br />
[[File:depth.png|600px|thumb|center|Figure 4]]<br />
<br />
Here is a plot showing the average percent copper lost due solely to the bacteria for different amounts of liquid media on solid media. Note that this doesn't work for the 1 mL case because of the negative %:<br />
[[File:liq_media.png|600px|thumb|center|Figure 3]]<br />
<br />
The Copper team has further refined their experiments by adding more controls and nuances to the existing experiments in order to collect more refined data which is detailed in the notebook, however the major results are summarized here.<br />
<br />
The genetics group has submitted each of the following plasmids to the parts registry:<br />
[[File:plasmid01.png|300px|center]]<br />
.<br />
[[File:plasmid02.png|300px|center]]<br />
.<br />
[[File:plasmid03.png|300px|center]]<br />
.<br />
[[File:plasmid04.png|300px|center]]<br />
.<br />
[[File:plasmid05.png|300px|center]]<br />
.<br />
[[File:plasmid06.png|300px|center]]<br />
.<br />
We plan to characterize parts BBa_K952006 and BBa_K952007 in ecoli.<br />
<br />
[[File:plasmid07.png|300px|center]]<br />
<br />
For BBa_K95006 we can grow the cells in the absence of IPTG, then add the IPTG and shine blue light onto the culture to induce expression of the lysis cassette killing the cells. We will run 2 controls, the first we will add IPTG but keep the cells in the dark and the second we will shine blue light on the cells in the absence of IPTG. Neither of the controls should cause apoptosis while the culture with both promotors present should.<br />
<br />
[[File:plasmid08.png|300px|center]]<br />
<br />
For BBa_K95007 we do not have the addition IPTG promotor present so we will grow the cells in the absence of light, then shine blue light on it to cause cell death. As controls we can attempt to grow the cells in the ambient light of the lab, under red light, and then shine blue light on these cultures if they grow. This is provide information on how sensative the system is to blue light. Ideally the cells would be able to grow in the ambient light of the lab with out inducing cell lysis however we do not expect this to be the case.</div>FourEyeGuy1962http://2012.igem.org/File:Depth.pngFile:Depth.png2012-10-04T04:02:35Z<p>FourEyeGuy1962: </p>
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<div></div>FourEyeGuy1962http://2012.igem.org/File:Liq_media.pngFile:Liq media.png2012-10-04T04:02:09Z<p>FourEyeGuy1962: </p>
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<div></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/AcknowledgementsTeam:Columbia-Cooper-NYC/Acknowledgements2012-10-04T01:41:36Z<p>FourEyeGuy1962: /* Acknowledgements */</p>
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= Acknowledgements =<br />
<br />
Adam Cerini: Copper team, research, Maker Faire<br />
<br />
Marjana Chowdhury: Wiki team co-captain, Copper team<br />
<br />
Ciera Lowe: Genetics team, Maker Faire captain, Wiki team<br />
<br />
Anna Mai: Copper team, Maker Faire<br />
<br />
Yuta Makita: Wiki team co-captain, Genetics team<br />
<br />
Nicholas Mannarino: Genetics team<br />
<br />
Aakash Mansukhani: Copper team<br />
<br />
Joeseph Mercedes: Copper team<br />
<br />
Richard Shi: Copper team<br />
<br />
Steven Neuhaus: Genetics team co-captain, research, Wiki team<br />
<br />
Kirsten Nicassio: Genetics team co-captain, wiki team<br />
<br />
Udochukwu (Ud) Okorafor: Copper team, Wiki team, Maker Faire<br />
<br />
Saimon Sharif: Genetics team co-captain, research, liaison<br />
<br />
Jeffery Xu: Copper team<br />
<br />
Vincent Xu: Copper team captain, Wiki team, Maker Faire<br />
<br />
<br />
<br />
A special thanks to the following iGEM teams and people:<br />
*Dr. Scott Banta for over seeing our project, providing invaluable advice and allowing us to work in his lab at Columbia<br />
*Dr. David Orbach for over seeing our project, consistently generating new ideas or approaches to our goal and allowing us to work in the Kanbar lab at Cooper<br />
*Dionne Lutz for walking the genetic team through countless protocols, supervising our work in the Kanbar lab, helping organize our Maker Faire table and providing much needed motivation and optimism throughout the many failures we faced<br />
*Sudipta Majumdar for helping us construct plasmids and patiently teaching us new protocols<br />
*Kevin Dooley for help with expression experiments, providing us with a GFP gene and identifying and removing cut sights within our biobrick and answering questions as we became acquainted with Dr. Banta's lab<br />
*Tushar Patel for providing us with a GFP gene and answering questions as we became acquainted with Dr. Banta's lab<br />
*Jason Candreva for being extremely patient with us, teaching us various transformation protocols with ecoli and ferrooxidans and answering every question we threw at him<br />
* iGEM Team Uppsala University for sending us the following parts: BBa_K592004, BBa_K592005, BBa_K592006, BBa_K592009, BBa_K592010, and BBa_K592016<br />
* iGEM Team ETH Zurich for sending us E. coli codon-optimized Pif3 and PhyB<br />
* Dr. Nicole Frankenberg-Dinkel for her advice and for sending plasmids pASK-fphAN753s and pTDho1</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/SafetyTeam:Columbia-Cooper-NYC/Safety2012-09-08T03:25:32Z<p>FourEyeGuy1962: /* Safety */</p>
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<br />
=='''Safety''' ==<br />
<br />
<div style="text-align:left;"><br />
<h2>Would any of your project ideas raise safety issues in terms of:</h2><br />
<br />
<h3>Researcher Safety?</h3><br />
<br />
<p> To make liquid or solid media for Acidithiobacillus Ferrooxidans, around 1 mL of sulfuric acid is required per batch of media to bring the pH down such that the bacteria can survive. The safety of individuals is greatly minimized with the use of nitrile gloves and safety goggles as well as following lab dress code (shoes that entirely cover the feet and long pants) when dealing with the acid. </p><br />
<br />
<h3>Public Safety?</h3><br />
<br />
<p> Since the liquid media is disposed in labeled waste containers and the solid media in hazardous waste bins, they should not be released to the public. If they are accidentally released, there should not be any public safety issues because the pH of liquid media is around 1.8 and the pH of solid media is around 2.4 (these pH values are around the range of vinegar and orange juice). Also, Acidithiobacillus Ferrooxidans are classified as BSL 1 and are not known to cause any disease in healthy adults. </p> <br />
<br />
<h3>Environmental Safety?</h3><br />
<br />
<p> Since the media and bacteria are disposed in waste containers and waste bins, they should not be released to the environment. But if they are accidentally released, the impact to the environment is minimal because the pH of the media are in the range of common liquids such as vinegar and orange juice. Also, Acidithiobacillus Ferrooxidans can only survive at low pH (about 1.8 - 4.0). Thus, they will degrade if released to the environment since the pH of water is higher. </p><br />
<br />
<h2>Do any of the new BioBrick parts (or devices) that you made this year raise any safety<br />
issues? </h2><br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<h2>Is there a local biosafety group, committee, or review board at your institution?</h2><br />
<br />
<p>The Chemical Engineering Department of Columbia University has an Advisory Board consisting of experts in biosafety, biosecurity, and genetic engineering who hold positions in academia, industry and government. They serve as our Institutional Biosafety Committee. The portions of the project to be carried out at Genspace are strictly BioBrick construction and the construction of plasmids containing metal-binding peptides and other non-pathogenic sequences. This is within the project parameters recommended by our Advisory Board.</p><br />
<br />
<p>[http://genspace.org/page/Advisory%20Board Advisory Board Members]</p><br />
<br />
<p>[https://static.igem.org/mediawiki/2011/2/25/Interim_Safety_Rules.pdf Interim Lab Safety Rules]</p><br />
<br />
<p>Cooper Union does not have an Institutional Biosafety Committee, but the project has been reviewed by David Wootton, Ph.D., Director of The Maurice Kanbar Center for Biomedical Engineering and is being supervised by Jody Grapes, Campus-Wide Safety Officer for Cooper Union.</p><br />
<br />
<p>Students participating in this project received safety training (general/chemical/biological) either at Columbia University or Cooper Union prior to beginning the project. The safety training consisted of a presentation covering the various aspects of safety found in molecular biology laboratories; i.e. proper microbiological techniques, safe disposal of recombinant organisms, etc. Upon completion of the presentation, students were shown the location of all safety equipment i.e. eye wash stations, first aid kits, fire extinguishers and safety exits. Students were also supervised by iGEM instructors at Columbia University or Cooper Union throughout the duration of the project.</p><br />
<br />
<p>Laboratory Safety Guide [https://docs.google.com/presentation/d/1WwrEhIL_cLkcRdZy_loovlCESdAL6CkL606PaGwvL5c/edit#slide=id.p61]</p><br />
<br />
<h2>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2><br />
<br />
<p> Manufacturing processes can be more environmentally friendly by using bacteria, like Acidithiobacillus Ferrooxidans, to manufacture computer technology, such as printed circuit boards, because the current manufacturing processes rely heavily on acids to do the etching on the boards. By switching to bacteria, only a small amount of acid is needed and the acid is used to keep the bacteria alive. The bacteria will accelerate the production of ferric ions and the ferric ions will react with pure copper to solubilize it. In this way, the bacteria is the primarily responsible for an etched PCB and not acid. </p><br />
<br />
<p> The Rio Tinto is a river in Southwest Spain and there is a site along the river that was subjected to mining for copper, silver, and other minerals using acids such as sulfuric acid. This lowered the pH of the river significantly to about 1.7-2.5. Coincidentally, Acidithobacillus Ferrooxidans are found in mines and survive at such low pH. Thus, they live in the river and convert ferrous ions to ferric ions, giving the river a red color that is present to this day. By genetically engineering a kill-switch in the bacteria when subjected to a certain color light, the bacteria can sefl-destruct and not continue to pollute the river. </p></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/SafetyTeam:Columbia-Cooper-NYC/Safety2012-09-08T02:43:28Z<p>FourEyeGuy1962: </p>
<hr />
<div><!--- The Mission, Experiments ---><br />
<!--<br />
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<a href="https://2012.igem.org/Team:Columbia-Cooper-NYC/Columbia_notebook_2">Genetics</a><br />
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<br />
<br />
<br />
=='''Safety''' ==<br />
<br />
<div style="text-align:left;"><br />
<h2>Would any of your project ideas raise safety issues in terms of:</h2><br />
<br />
<h3>researcher safety?</h3><br />
<br />
<p> To make liquid or solid media for Acidithiobacillus Ferrooxidans, around 1 mL of sulfuric acid is required per batch of media to bring the pH down such that the bacteria can survive. The safety of individuals is greatly minimized with the use of nitrile gloves and safety goggles as well as following lab dress code (shoes that entirely cover the feet and long pants) when dealing with the acid. </p><br />
<br />
<h3>public safety?</h3><br />
<br />
<p> Since the liquid media is disposed in labeled waste containers and the solid media in hazardous waste bins, they should not be released to the public. If they are accidentally released, there should not be any public safety issues because the pH of liquid media is around 1.8 and the pH of solid media is around 2.4 (these pH values are around the range of vinegar and orange juice). Also, Acidithiobacillus Ferrooxidans are classified as BSL 1 and are not known to cause any disease in healthy adults. </p> <br />
<br />
<h3>environmental safety?</h3><br />
<br />
<p> Since the media and bacteria are disposed in waste containers and waste bins, they should not be released to the environment. But if they are accidentally released, the impact to the environment is minimal because the pH of the media are in the range of common liquids such as vinegar and orange juice. Also, Acidithiobacillus Ferrooxidans can only survive at low pH (about 1.8 - 4.0). Thus, they will degrade if released to the environment since the pH of water is higher. </p><br />
<br />
<h2>Do any of the new BioBrick parts (or devices) that you made this year raise any safety<br />
issues? <br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<br />
<h2>Is there a local biosafety group, committee, or review board at your institution?</h2><br />
<br />
<p>The Chemical Engineering Department of Columbia University has an Advisory Board consisting of experts in biosafety, biosecurity, and genetic engineering who hold positions in academia, industry and government. They serve as our Institutional Biosafety Committee. The portions of the project to be carried out at Genspace are strictly BioBrick construction and the construction of plasmids containing metal-binding peptides and other non-pathogenic sequences. This is within the project parameters recommended by our Advisory Board.</p><br />
<br />
<p>[http://genspace.org/page/Advisory%20Board Advisory Board Members]</p><br />
<br />
<p>[https://static.igem.org/mediawiki/2011/2/25/Interim_Safety_Rules.pdf Interim Lab Safety Rules]</p><br />
<br />
<p>Cooper Union does not have an Institutional Biosafety Committee, but the project has been reviewed by David Wootton, Ph.D., Director of The Maurice Kanbar Center for Biomedical Engineering and is being supervised by Jody Grapes, Campus-Wide Safety Officer for Cooper Union.</p><br />
<br />
<p>Students participating in this project received safety training (general/chemical/biological) either at Columbia University or Cooper Union prior to beginning the project. The safety training consisted of a presentation covering the various aspects of safety found in molecular biology laboratories; i.e. proper microbiological techniques, safe disposal of recombinant organisms, etc. Upon completion of the presentation, students were shown the location of all safety equipment i.e. eye wash stations, first aid kits, fire extinguishers and safety exits. Students were also supervised by iGEM instructors at Columbia University or Cooper Union throughout the duration of the project.</p><br />
<br />
<p>Laboratory Safety Guide [https://docs.google.com/presentation/d/1WwrEhIL_cLkcRdZy_loovlCESdAL6CkL606PaGwvL5c/edit#slide=id.p61]</p><br />
<br />
<h2>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2><br />
<br />
<p> Manufacturing processes can be more environmentally friendly by using bacteria, like Acidithiobacillus Ferrooxidans, to manufacture computer technology, such as printed circuit boards, because the current manufacturing processes rely heavily on acids to do the etching on the boards. By switching to bacteria, only a small amount of acid is needed and the acid is used to keep the bacteria alive. The bacteria will accelerate the production of ferric ions and the ferric ions will react with pure copper to solubilize it. In this way, the bacteria is the primarily responsible for an etched PCB and not acid. </p><br />
<br />
<p> The Rio Tinto is a river in Southwest Spain and there is a site along the river that was subjected to mining for copper, silver, and other minerals using acids such as sulfuric acid. This lowered the pH significantly to about 1.7-2.5. Coincidentally, Acidithobacillus Ferrooxidans are found in mines and survive at such low pH. Thus, they live in the river and convert ferrous ions to ferric ions, giving the river a red color that is present to this day. By genetically engineering a kill-switch in the bacteria when subjected to a certain color light, the bacteria can sefl-destruct and not continue to pollute the river. </p></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/SafetyTeam:Columbia-Cooper-NYC/Safety2012-09-08T02:42:45Z<p>FourEyeGuy1962: </p>
<hr />
<div><!--- The Mission, Experiments ---><br />
<!--<br />
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<h1>Safety</h1><br />
<br />
<div style="text-align:left;"><br />
<br />
<br />
<h2>Would any of your project ideas raise safety issues in terms of:<h/2><br />
<br />
<h3>Researcher safety?<h/3><br />
<br />
<p>To make liquid or solid media for Acidithiobacillus Ferrooxidans, around 1 mL of sulfuric acid is required per batch of media to bring the pH down such that the bacteria can survive. The safety of individuals is greatly minimized with the use of nitrile gloves and safety goggles as well as following lab dress code (shoes that entirely cover the feet and long pants) when dealing with the acid.</p><br />
<br />
<h3>Public safety?<h3><br />
<br />
Since the liquid media is disposed in labeled waste containers and the solid media in hazardous waste bins, they should not be released to the public. If they are accidentally released, there should not be any public safety issues because the pH of liquid media is around 1.8 and the pH of solid media is around 2.4 (these pH values are around the range of vinegar and orange juice). Also, Acidithiobacillus Ferrooxidans are classified as BSL 1 and are not known to cause any disease in healthy adults. <br />
<br />
'''*Environmental safety''' <br><br />
<br />
Since the media and bacteria are disposed in waste containers and waste bins, they should not be released to the environment. But if they are accidentally released, the impact to the environment is minimal because the pH of the media are in the range of common liquids such as vinegar and orange juice. Also, Acidithiobacillus Ferrooxidans can only survive at low pH (about 1.8 - 4.0). Thus, they will degrade if released to the environment since the pH of water is higher. <br />
<br />
====Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,====<br />
<br />
'''*Did you document these issues in the Registry?''' <br><br />
<br />
None of the parts or devices that we have used during our project will raise any known safety issues.<br />
<br />
'''*How did you manage to handle the safety issue?''' <br><br />
<br />
None of the parts or devices that we have used during our project will raise any known safety issues.<br />
<br />
'''*How could other teams learn from your experience?''' <br><br />
<br />
None of the parts or devices that we have used during our project will raise any known safety issues.<br />
<br />
<br />
====Is there a local biosafety group, committee, or review board at your institution?====<br />
<br />
The Chemical Engineering Department of Columbia University has an Advisory Board consisting of experts in biosafety, biosecurity, and genetic engineering who hold positions in academia, industry and government. They serve as our Institutional Biosafety Committee. The portions of the project to be carried out at Genspace are strictly BioBrick construction and the construction of plasmids containing metal-binding peptides and other non-pathogenic sequences. This is within the project parameters recommended by our Advisory Board.<br />
<br />
<p>[http://genspace.org/page/Advisory%20Board Advisory Board Members]</p><br />
<br />
<p>[https://static.igem.org/mediawiki/2011/2/25/Interim_Safety_Rules.pdf Interim Lab Safety Rules]</p><br />
<br />
<p>Cooper Union does not have an Institutional Biosafety Committee, but the project has been reviewed by David Wootton, Ph.D., Director of The Maurice Kanbar Center for Biomedical Engineering and is being supervised by Jody Grapes, Campus-Wide Safety Officer for Cooper Union.</p><br />
<br />
<p>Students participating in this project received safety training (general/chemical/biological) either at Columbia University or Cooper Union prior to beginning the project. The safety training consisted of a presentation covering the various aspects of safety found in molecular biology laboratories; i.e. proper microbiological techniques, safe disposal of recombinant organisms, etc. Upon completion of the presentation, students were shown the location of all safety equipment i.e. eye wash stations, first aid kits, fire extinguishers and safety exits. Students were also supervised by iGEM instructors at Columbia University or Cooper Union throughout the duration of the project.</p><br />
<br />
<p>Laboratory Safety Guide [https://docs.google.com/presentation/d/1WwrEhIL_cLkcRdZy_loovlCESdAL6CkL606PaGwvL5c/edit#slide=id.p61]</p><br />
<br />
<h2>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2><br />
<br />
<p> Manufacturing processes can be more environmentally friendly by using bacteria, like Acidithiobacillus Ferrooxidans, to manufacture computer technology, such as printed circuit boards, because the current manufacturing processes rely heavily on acids to do the etching on the boards. By switching to bacteria, only a small amount of acid is needed and the acid is used to keep the bacteria alive. The bacteria will accelerate the production of ferric ions and the ferric ions will react with pure copper to solubilize it. In this way, the bacteria is the primarily responsible for an etched PCB and not acid. </p><br />
<br />
<p> The Rio Tinto is a river in Southwest Spain and there is a site along the river that was subjected to mining for copper, silver, and other minerals using acids such as sulfuric acid. This lowered the pH significantly to about 1.7-2.5. Coincidentally, Acidithobacillus Ferrooxidans are found in mines and survive at such low pH. Thus, they live in the river and convert ferrous ions to ferric ions, giving the river a red color that is present to this day. By genetically engineering a kill-switch in the bacteria when subjected to a certain color light, the bacteria can sefl-destruct and not continue to pollute the river. </p></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/SafetyTeam:Columbia-Cooper-NYC/Safety2012-09-08T02:41:42Z<p>FourEyeGuy1962: </p>
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<br />
====1. Would any of your project ideas raise safety issues in terms of:====<br />
'''*Researcher safety?''' <br><br />
<br />
To make liquid or solid media for Acidithiobacillus Ferrooxidans, around 1 mL of sulfuric acid is required per batch of media to bring the pH down such that the bacteria can survive. The safety of individuals is greatly minimized with the use of nitrile gloves and safety goggles as well as following lab dress code (shoes that entirely cover the feet and long pants) when dealing with the acid.<br />
<br />
'''*Public safety?''' <br><br />
<br />
Since the liquid media is disposed in labeled waste containers and the solid media in hazardous waste bins, they should not be released to the public. If they are accidentally released, there should not be any public safety issues because the pH of liquid media is around 1.8 and the pH of solid media is around 2.4 (these pH values are around the range of vinegar and orange juice). Also, Acidithiobacillus Ferrooxidans are classified as BSL 1 and are not known to cause any disease in healthy adults. <br />
<br />
'''*Environmental safety''' <br><br />
<br />
Since the media and bacteria are disposed in waste containers and waste bins, they should not be released to the environment. But if they are accidentally released, the impact to the environment is minimal because the pH of the media are in the range of common liquids such as vinegar and orange juice. Also, Acidithiobacillus Ferrooxidans can only survive at low pH (about 1.8 - 4.0). Thus, they will degrade if released to the environment since the pH of water is higher. <br />
<br />
====Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,====<br />
<br />
'''*Did you document these issues in the Registry?''' <br><br />
<br />
None of the parts or devices that we have used during our project will raise any known safety issues.<br />
<br />
'''*How did you manage to handle the safety issue?''' <br><br />
<br />
None of the parts or devices that we have used during our project will raise any known safety issues.<br />
<br />
'''*How could other teams learn from your experience?''' <br><br />
<br />
None of the parts or devices that we have used during our project will raise any known safety issues.<br />
<br />
<br />
====Is there a local biosafety group, committee, or review board at your institution?====<br />
<br />
The Chemical Engineering Department of Columbia University has an Advisory Board consisting of experts in biosafety, biosecurity, and genetic engineering who hold positions in academia, industry and government. They serve as our Institutional Biosafety Committee. The portions of the project to be carried out at Genspace are strictly BioBrick construction and the construction of plasmids containing metal-binding peptides and other non-pathogenic sequences. This is within the project parameters recommended by our Advisory Board.<br />
<br />
<p>[http://genspace.org/page/Advisory%20Board Advisory Board Members]</p><br />
<br />
<p>[https://static.igem.org/mediawiki/2011/2/25/Interim_Safety_Rules.pdf Interim Lab Safety Rules]</p><br />
<br />
<p>Cooper Union does not have an Institutional Biosafety Committee, but the project has been reviewed by David Wootton, Ph.D., Director of The Maurice Kanbar Center for Biomedical Engineering and is being supervised by Jody Grapes, Campus-Wide Safety Officer for Cooper Union.</p><br />
<br />
<p>Students participating in this project received safety training (general/chemical/biological) either at Columbia University or Cooper Union prior to beginning the project. The safety training consisted of a presentation covering the various aspects of safety found in molecular biology laboratories; i.e. proper microbiological techniques, safe disposal of recombinant organisms, etc. Upon completion of the presentation, students were shown the location of all safety equipment i.e. eye wash stations, first aid kits, fire extinguishers and safety exits. Students were also supervised by iGEM instructors at Columbia University or Cooper Union throughout the duration of the project.</p><br />
<br />
<p>Laboratory Safety Guide [https://docs.google.com/presentation/d/1WwrEhIL_cLkcRdZy_loovlCESdAL6CkL606PaGwvL5c/edit#slide=id.p61]</p><br />
<br />
<h2>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2><br />
<br />
<p> Manufacturing processes can be more environmentally friendly by using bacteria, like Acidithiobacillus Ferrooxidans, to manufacture computer technology, such as printed circuit boards, because the current manufacturing processes rely heavily on acids to do the etching on the boards. By switching to bacteria, only a small amount of acid is needed and the acid is used to keep the bacteria alive. The bacteria will accelerate the production of ferric ions and the ferric ions will react with pure copper to solubilize it. In this way, the bacteria is the primarily responsible for an etched PCB and not acid. </p><br />
<br />
<p> The Rio Tinto is a river in Southwest Spain and there is a site along the river that was subjected to mining for copper, silver, and other minerals using acids such as sulfuric acid. This lowered the pH significantly to about 1.7-2.5. Coincidentally, Acidithobacillus Ferrooxidans are found in mines and survive at such low pH. Thus, they live in the river and convert ferrous ions to ferric ions, giving the river a red color that is present to this day. By genetically engineering a kill-switch in the bacteria when subjected to a certain color light, the bacteria can sefl-destruct and not continue to pollute the river. </p></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/SafetyTeam:Columbia-Cooper-NYC/Safety2012-09-08T02:39:41Z<p>FourEyeGuy1962: /* Safety */</p>
<hr />
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<br />
<h1>Safety</h1><br />
<br />
<div style="text-align:left;"><br />
====1. Would any of your project ideas raise safety issues in terms of:====<br />
'''*Researcher safety?''' <br><br />
<br />
To make liquid or solid media for Acidithiobacillus Ferrooxidans, around 1 mL of sulfuric acid is required per batch of media to bring the pH down such that the bacteria can survive. The safety of individuals is greatly minimized with the use of nitrile gloves and safety goggles as well as following lab dress code (shoes that entirely cover the feet and long pants) when dealing with the acid.<br />
<br />
'''*Public safety?''' <br><br />
<br />
Since the liquid media is disposed in labeled waste containers and the solid media in hazardous waste bins, they should not be released to the public. If they are accidentally released, there should not be any public safety issues because the pH of liquid media is around 1.8 and the pH of solid media is around 2.4 (these pH values are around the range of vinegar and orange juice). Also, Acidithiobacillus Ferrooxidans are classified as BSL 1 and are not known to cause any disease in healthy adults. <br />
<br />
'''*Environmental safety''' <br><br />
<br />
Since the media and bacteria are disposed in waste containers and waste bins, they should not be released to the environment. But if they are accidentally released, the impact to the environment is minimal because the pH of the media are in the range of common liquids such as vinegar and orange juice. Also, Acidithiobacillus Ferrooxidans can only survive at low pH (about 1.8 - 4.0). Thus, they will degrade if released to the environment since the pH of water is higher. <br />
<br />
====Do any of the new BioBrick parts (or devices) that you made this year raise any safety issues? If yes,====<br />
<br />
'''*Did you document these issues in the Registry?''' <br><br />
<br />
None of the parts or devices that we have used during our project will raise any known safety issues.<br />
<br />
'''*How did you manage to handle the safety issue?''' <br><br />
<br />
None of the parts or devices that we have used during our project will raise any known safety issues.<br />
<br />
'''*How could other teams learn from your experience?''' <br><br />
<br />
None of the parts or devices that we have used during our project will raise any known safety issues.<br />
<br />
<br />
====Is there a local biosafety group, committee, or review board at your institution?====<br />
<br />
The Chemical Engineering Department of Columbia University has an Advisory Board consisting of experts in biosafety, biosecurity, and genetic engineering who hold positions in academia, industry and government. They serve as our Institutional Biosafety Committee. The portions of the project to be carried out at Genspace are strictly BioBrick construction and the construction of plasmids containing metal-binding peptides and other non-pathogenic sequences. This is within the project parameters recommended by our Advisory Board.<br />
<br />
<p>[http://genspace.org/page/Advisory%20Board Advisory Board Members]</p><br />
<br />
<p>[https://static.igem.org/mediawiki/2011/2/25/Interim_Safety_Rules.pdf Interim Lab Safety Rules]</p><br />
<br />
<p>Cooper Union does not have an Institutional Biosafety Committee, but the project has been reviewed by David Wootton, Ph.D., Director of The Maurice Kanbar Center for Biomedical Engineering and is being supervised by Jody Grapes, Campus-Wide Safety Officer for Cooper Union.</p><br />
<br />
<p>Students participating in this project received safety training (general/chemical/biological) either at Columbia University or Cooper Union prior to beginning the project. The safety training consisted of a presentation covering the various aspects of safety found in molecular biology laboratories; i.e. proper microbiological techniques, safe disposal of recombinant organisms, etc. Upon completion of the presentation, students were shown the location of all safety equipment i.e. eye wash stations, first aid kits, fire extinguishers and safety exits. Students were also supervised by iGEM instructors at Columbia University or Cooper Union throughout the duration of the project.</p><br />
<br />
<p>Laboratory Safety Guide [https://docs.google.com/presentation/d/1WwrEhIL_cLkcRdZy_loovlCESdAL6CkL606PaGwvL5c/edit#slide=id.p61]</p><br />
<br />
<h2>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2><br />
<br />
<p> Manufacturing processes can be more environmentally friendly by using bacteria, like Acidithiobacillus Ferrooxidans, to manufacture computer technology, such as printed circuit boards, because the current manufacturing processes rely heavily on acids to do the etching on the boards. By switching to bacteria, only a small amount of acid is needed and the acid is used to keep the bacteria alive. The bacteria will accelerate the production of ferric ions and the ferric ions will react with pure copper to solubilize it. In this way, the bacteria is the primarily responsible for an etched PCB and not acid. </p><br />
<br />
<p> The Rio Tinto is a river in Southwest Spain and there is a site along the river that was subjected to mining for copper, silver, and other minerals using acids such as sulfuric acid. This lowered the pH significantly to about 1.7-2.5. Coincidentally, Acidithobacillus Ferrooxidans are found in mines and survive at such low pH. Thus, they live in the river and convert ferrous ions to ferric ions, giving the river a red color that is present to this day. By genetically engineering a kill-switch in the bacteria when subjected to a certain color light, the bacteria can sefl-destruct and not continue to pollute the river. </p></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/SafetyTeam:Columbia-Cooper-NYC/Safety2012-09-08T02:33:18Z<p>FourEyeGuy1962: /* Safety */</p>
<hr />
<div>{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Columbia-Cooper-NYC|Home]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Columbia-Cooper-NYC Official Team Profile]<br />
!align="center"|[[Tehttps://2012.igem.org/wiki/skins/common/images/button_math.pngam:Columbia-Cooper-NYC/Project|Project]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Modeling|Modeling]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Notebook|Notebook]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Safety|Safety]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Attributions|Attributions]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Sponsor Us|Sponsor Us]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
=='''Safety''' ==<br />
<br />
<div style="text-align:left;"><br />
<h2>Would any of your project ideas raise safety issues in terms of:</h2><br />
<br />
<h3>researcher safety?</h3><br />
<br />
<p> To make liquid or solid media for Acidithiobacillus Ferrooxidans, around 1 mL of sulfuric acid is required per batch of media to bring the pH down such that the bacteria can survive. The safety of individuals is greatly minimized with the use of nitrile gloves and safety goggles as well as following lab dress code (shoes that entirely cover the feet and long pants) when dealing with the acid. </p><br />
<br />
<h3>public safety?</h3><br />
<br />
<p> Since the liquid media is disposed in labeled waste containers and the solid media in hazardous waste bins, they should not be released to the public. If they are accidentally released, there should not be any public safety issues because the pH of liquid media is around 1.8 and the pH of solid media is around 2.4 (these pH values are around the range of vinegar and orange juice). Also, Acidithiobacillus Ferrooxidans are classified as BSL 1 and are not known to cause any disease in healthy adults. </p> <br />
<br />
<h3>environmental safety?</h3><br />
<br />
<p> Since the media and bacteria are disposed in waste containers and waste bins, they should not be released to the environment. But if they are accidentally released, the impact to the environment is minimal because the pH of the media are in the range of common liquids such as vinegar and orange juice. Also, Acidithiobacillus Ferrooxidans can only survive at low pH (about 1.8 - 4.0). Thus, they will degrade if released to the environment since the pH of water is higher. </p><br />
<br />
<h2>Do any of the new BioBrick parts (or devices) that you made this year raise any safety<br />
issues? If yes, <h/2><br />
<br />
<h3>did you document these issues in the Registry?</h3><br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<h3>how did you manage to handle the safety issue?</h3><br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<h3>How could other teams learn from your experience?</h3><br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<br />
<h3>Is there a local biosafety group, committee, or review board at your institution?</h3><br />
<br />
<p>The Chemical Engineering Department of Columbia University has an Advisory Board consisting of experts in biosafety, biosecurity, and genetic engineering who hold positions in academia, industry and government. They serve as our Institutional Biosafety Committee. The portions of the project to be carried out at Genspace are strictly BioBrick construction and the construction of plasmids containing metal-binding peptides and other non-pathogenic sequences. This is within the project parameters recommended by our Advisory Board.</p><br />
<br />
<p>[http://genspace.org/page/Advisory%20Board Advisory Board Members]</p><br />
<br />
<p>[https://static.igem.org/mediawiki/2011/2/25/Interim_Safety_Rules.pdf Interim Lab Safety Rules]</p><br />
<br />
<p>Cooper Union does not have an Institutional Biosafety Committee, but the project has been reviewed by David Wootton, Ph.D., Director of The Maurice Kanbar Center for Biomedical Engineering and is being supervised by Jody Grapes, Campus-Wide Safety Officer for Cooper Union.</p><br />
<br />
<p>Students participating in this project received safety training (general/chemical/biological) either at Columbia University or Cooper Union prior to beginning the project. The safety training consisted of a presentation covering the various aspects of safety found in molecular biology laboratories; i.e. proper microbiological techniques, safe disposal of recombinant organisms, etc. Upon completion of the presentation, students were shown the location of all safety equipment i.e. eye wash stations, first aid kits, fire extinguishers and safety exits. Students were also supervised by iGEM instructors at Columbia University or Cooper Union throughout the duration of the project.</p><br />
<br />
<p>Laboratory Safety Guide [https://docs.google.com/presentation/d/1WwrEhIL_cLkcRdZy_loovlCESdAL6CkL606PaGwvL5c/edit#slide=id.p61]</p><br />
<br />
<h2>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2><br />
<br />
<p> Manufacturing processes can be more environmentally friendly by using bacteria, like Acidithiobacillus Ferrooxidans, to manufacture computer technology, such as printed circuit boards, because the current manufacturing processes rely heavily on acids to do the etching on the boards. By switching to bacteria, only a small amount of acid is needed and the acid is used to keep the bacteria alive. The bacteria will accelerate the production of ferric ions and the ferric ions will react with pure copper to solubilize it. In this way, the bacteria is the primarily responsible for an etched PCB and not acid. </p><br />
<br />
<p> The Rio Tinto is a river in Southwest Spain and there is a site along the river that was subjected to mining for copper, silver, and other minerals using acids such as sulfuric acid. This lowered the pH significantly to about 1.7-2.5. Coincidentally, Acidithobacillus Ferrooxidans are found in mines and survive at such low pH. Thus, they live in the river and convert ferrous ions to ferric ions, giving the river a red color that is present to this day. By genetically engineering a kill-switch in the bacteria when subjected to a certain color light, the bacteria can sefl-destruct and not continue to pollute the river. </p></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/SafetyTeam:Columbia-Cooper-NYC/Safety2012-09-08T02:32:44Z<p>FourEyeGuy1962: /* Safety */</p>
<hr />
<div>{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Columbia-Cooper-NYC|Home]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Columbia-Cooper-NYC Official Team Profile]<br />
!align="center"|[[Tehttps://2012.igem.org/wiki/skins/common/images/button_math.pngam:Columbia-Cooper-NYC/Project|Project]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Modeling|Modeling]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Notebook|Notebook]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Safety|Safety]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Attributions|Attributions]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Sponsor Us|Sponsor Us]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
=='''Safety''' ==<br />
<br />
<div style="text-align:left;"><br />
<h2>Would any of your project ideas raise safety issues in terms of:</h2><br />
<br />
<h3>researcher safety?</h3><br />
<br />
<p> To make liquid or solid media for Acidithiobacillus Ferrooxidans, around 1 mL of sulfuric acid is required per batch of media to bring the pH down such that the bacteria can survive. The safety of individuals is greatly minimized with the use of nitrile gloves and safety goggles as well as following lab dress code (shoes that entirely cover the feet and long pants) when dealing with the acid. </p><br />
<br />
<h3>public safety?</h3><br />
<br />
<p> Since the liquid media is disposed in labeled waste containers and the solid media in hazardous waste bins, they should not be released to the public. If they are accidentally released, there should not be any public safety issues because the pH of liquid media is around 1.8 and the pH of solid media is around 2.4 (these pH values are around the range of vinegar and orange juice). Also, Acidithiobacillus Ferrooxidans are classified as BSL 1 and are not known to cause any disease in healthy adults. </p> <br />
<br />
<h3>environmental safety?</h3><br />
<br />
<p> Since the media and bacteria are disposed in waste containers and waste bins, they should not be released to the environment. But if they are accidentally released, the impact to the environment is minimal because the pH of the media are in the range of common liquids such as vinegar and orange juice. Also, Acidithiobacillus Ferrooxidans can only survive at low pH (about 1.8 - 4.0). Thus, they will degrade if released to the environment since the pH of water is higher. </p><br />
<br />
<h2>Do any of the new BioBrick parts (or devices) that you made this year raise any safety<br />
issues? If yes, <h/2><br />
<br />
<h3>did you document these issues in the Registry?</h3><br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<h3>how did you manage to handle the safety issue?</h3><br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<h3>How could other teams learn from your experience?</h3><br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<br />
<h2>Is there a local biosafety group, committee, or review board at your institution?</h2><br />
<br />
<p>The Chemical Engineering Department of Columbia University has an Advisory Board consisting of experts in biosafety, biosecurity, and genetic engineering who hold positions in academia, industry and government. They serve as our Institutional Biosafety Committee. The portions of the project to be carried out at Genspace are strictly BioBrick construction and the construction of plasmids containing metal-binding peptides and other non-pathogenic sequences. This is within the project parameters recommended by our Advisory Board.</p><br />
<br />
<p>[http://genspace.org/page/Advisory%20Board Advisory Board Members]</p><br />
<br />
<p>[https://static.igem.org/mediawiki/2011/2/25/Interim_Safety_Rules.pdf Interim Lab Safety Rules]</p><br />
<br />
<p>Cooper Union does not have an Institutional Biosafety Committee, but the project has been reviewed by David Wootton, Ph.D., Director of The Maurice Kanbar Center for Biomedical Engineering and is being supervised by Jody Grapes, Campus-Wide Safety Officer for Cooper Union.</p><br />
<br />
<p>Students participating in this project received safety training (general/chemical/biological) either at Columbia University or Cooper Union prior to beginning the project. The safety training consisted of a presentation covering the various aspects of safety found in molecular biology laboratories; i.e. proper microbiological techniques, safe disposal of recombinant organisms, etc. Upon completion of the presentation, students were shown the location of all safety equipment i.e. eye wash stations, first aid kits, fire extinguishers and safety exits. Students were also supervised by iGEM instructors at Columbia University or Cooper Union throughout the duration of the project.</p><br />
<br />
<p>Laboratory Safety Guide [https://docs.google.com/presentation/d/1WwrEhIL_cLkcRdZy_loovlCESdAL6CkL606PaGwvL5c/edit#slide=id.p61]</p><br />
<br />
<h2>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2><br />
<br />
<p> Manufacturing processes can be more environmentally friendly by using bacteria, like Acidithiobacillus Ferrooxidans, to manufacture computer technology, such as printed circuit boards, because the current manufacturing processes rely heavily on acids to do the etching on the boards. By switching to bacteria, only a small amount of acid is needed and the acid is used to keep the bacteria alive. The bacteria will accelerate the production of ferric ions and the ferric ions will react with pure copper to solubilize it. In this way, the bacteria is the primarily responsible for an etched PCB and not acid. </p><br />
<br />
<p> The Rio Tinto is a river in Southwest Spain and there is a site along the river that was subjected to mining for copper, silver, and other minerals using acids such as sulfuric acid. This lowered the pH significantly to about 1.7-2.5. Coincidentally, Acidithobacillus Ferrooxidans are found in mines and survive at such low pH. Thus, they live in the river and convert ferrous ions to ferric ions, giving the river a red color that is present to this day. By genetically engineering a kill-switch in the bacteria when subjected to a certain color light, the bacteria can sefl-destruct and not continue to pollute the river. </p></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/SafetyTeam:Columbia-Cooper-NYC/Safety2012-09-08T02:30:19Z<p>FourEyeGuy1962: /* Safety */</p>
<hr />
<div>{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Columbia-Cooper-NYC|Home]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Columbia-Cooper-NYC Official Team Profile]<br />
!align="center"|[[Tehttps://2012.igem.org/wiki/skins/common/images/button_math.pngam:Columbia-Cooper-NYC/Project|Project]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Modeling|Modeling]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Notebook|Notebook]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Safety|Safety]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Attributions|Attributions]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Sponsor Us|Sponsor Us]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
=='''Safety''' ==<br />
<br />
<div style="text-align:left;"><br />
<h2>Would any of your project ideas raise safety issues in terms of:</h2><br />
<br />
<h3>researcher safety?</h3><br />
<br />
<p> To make liquid or solid media for Acidithiobacillus Ferrooxidans, around 1 mL of sulfuric acid is required per batch of media to bring the pH down such that the bacteria can survive. The safety of individuals is greatly minimized with the use of nitrile gloves and safety goggles as well as following lab dress code (shoes that entirely cover the feet and long pants) when dealing with the acid. </p><br />
<br />
<h3>public safety?</h3><br />
<br />
<p> Since the liquid media is disposed in labeled waste containers and the solid media in hazardous waste bins, they should not be released to the public. If they are accidentally released, there should not be any public safety issues because the pH of liquid media is around 1.8 and the pH of solid media is around 2.4 (these pH values are around the range of vinegar and orange juice). Also, Acidithiobacillus Ferrooxidans are classified as BSL 1 and are not known to cause any disease in healthy adults. </p> <br />
<br />
<h3>environmental safety?</h3><br />
<br />
<p> Since the media and bacteria are disposed in waste containers and waste bins, they should not be released to the environment. But if they are accidentally released, the impact to the environment is minimal because the pH of the media are in the range of common liquids such as vinegar and orange juice. Also, Acidithiobacillus Ferrooxidans can only survive at low pH (about 1.8 - 4.0). Thus, they will degrade if released to the environment since the pH of water is higher. </p><br />
<br />
<h2>Do any of the new BioBrick parts (or devices) that you made this year raise any safety<br />
issues? If yes, <h/2><br />
<br />
<h3>did you document these issues in the Registry?</h3><br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<h3>how did you manage to handle the safety issue?</h3><br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<h3>How could other teams learn from your experience?</h3><br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<br />
<br />
<br />
<h2>Is there a local biosafety group, committee, or review board at your institution?</h2><br />
<br />
<p>The Chemical Engineering Department of Columbia University has an Advisory Board consisting of experts in biosafety, biosecurity, and genetic engineering who hold positions in academia, industry and government. They serve as our Institutional Biosafety Committee. The portions of the project to be carried out at Genspace are strictly BioBrick construction and the construction of plasmids containing metal-binding peptides and other non-pathogenic sequences. This is within the project parameters recommended by our Advisory Board.</p><br />
<br />
<p>[http://genspace.org/page/Advisory%20Board Advisory Board Members]</p><br />
<br />
<p>[https://static.igem.org/mediawiki/2011/2/25/Interim_Safety_Rules.pdf Interim Lab Safety Rules]</p><br />
<br />
<p>Cooper Union does not have an Institutional Biosafety Committee, but the project has been reviewed by David Wootton, Ph.D., Director of The Maurice Kanbar Center for Biomedical Engineering and is being supervised by Jody Grapes, Campus-Wide Safety Officer for Cooper Union.</p><br />
<br />
<p>Students participating in this project received safety training (general/chemical/biological) either at Columbia University or Cooper Union prior to beginning the project. The safety training consisted of a presentation covering the various aspects of safety found in molecular biology laboratories; i.e. proper microbiological techniques, safe disposal of recombinant organisms, etc. Upon completion of the presentation, students were shown the location of all safety equipment i.e. eye wash stations, first aid kits, fire extinguishers and safety exits. Students were also supervised by iGEM instructors at Columbia University or Cooper Union throughout the duration of the project.</p><br />
<br />
<p>Laboratory Safety Guide [https://docs.google.com/presentation/d/1WwrEhIL_cLkcRdZy_loovlCESdAL6CkL606PaGwvL5c/edit#slide=id.p61]</p><br />
<br />
<h2>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2><br />
<br />
<p> Manufacturing processes can be more environmentally friendly by using bacteria, like Acidithiobacillus Ferrooxidans, to manufacture computer technology, such as printed circuit boards, because the current manufacturing processes rely heavily on acids to do the etching on the boards. By switching to bacteria, only a small amount of acid is needed and the acid is used to keep the bacteria alive. The bacteria will accelerate the production of ferric ions and the ferric ions will react with pure copper to solubilize it. In this way, the bacteria is the primarily responsible for an etched PCB and not acid. </p><br />
<br />
<p> The Rio Tinto is a river in Southwest Spain and there is a site along the river that was subjected to mining for copper, silver, and other minerals using acids such as sulfuric acid. This lowered the pH significantly to about 1.7-2.5. Coincidentally, Acidithobacillus Ferrooxidans are found in mines and survive at such low pH. Thus, they live in the river and convert ferrous ions to ferric ions, giving the river a red color that is present to this day. By genetically engineering a kill-switch in the bacteria when subjected to a certain color light, the bacteria can sefl-destruct and not continue to pollute the river. </p></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/SafetyTeam:Columbia-Cooper-NYC/Safety2012-09-08T02:28:13Z<p>FourEyeGuy1962: /* Safety */</p>
<hr />
<div>{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Columbia-Cooper-NYC|Home]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Columbia-Cooper-NYC Official Team Profile]<br />
!align="center"|[[Tehttps://2012.igem.org/wiki/skins/common/images/button_math.pngam:Columbia-Cooper-NYC/Project|Project]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Modeling|Modeling]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Notebook|Notebook]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Safety|Safety]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Attributions|Attributions]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Sponsor Us|Sponsor Us]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
=='''Safety''' ==<br />
<br />
<div style="text-align:left;"><br />
<h2>Would any of your project ideas raise safety issues in terms of:</h2><br />
<br />
<h3>researcher safety?</h3><br />
<br />
<p> To make liquid or solid media for Acidithiobacillus Ferrooxidans, around 1 mL of sulfuric acid is required per batch of media to bring the pH down such that the bacteria can survive. The safety of individuals is greatly minimized with the use of nitrile gloves and safety goggles as well as following lab dress code (shoes that entirely cover the feet and long pants) when dealing with the acid. </p><br />
<br />
<h3>public safety?</h3><br />
<br />
<p> Since the liquid media is disposed in labeled waste containers and the solid media in hazardous waste bins, they should not be released to the public. If they are accidentally released, there should not be any public safety issues because the pH of liquid media is around 1.8 and the pH of solid media is around 2.4 (these pH values are around the range of vinegar and orange juice). Also, Acidithiobacillus Ferrooxidans are classified as BSL 1 and are not known to cause any disease in healthy adults. </p> <br />
<br />
<h3>environmental safety?</h3><br />
<br />
<p> Since the media and bacteria are disposed in waste containers and waste bins, they should not be released to the environment. But if they are accidentally released, the impact to the environment is minimal because the pH of the media are in the range of common liquids such as vinegar and orange juice. Also, Acidithiobacillus Ferrooxidans can only survive at low pH (about 1.8 - 4.0). Thus, they will degrade if released to the environment since the pH of water is higher. </p><br />
<br />
<h2>Do any of the new BioBrick parts (or devices) that you made this year raise any safety<br />
issues? <h/2><br />
<br />
<h3> <h/3><br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<br />
<h2>Is there a local biosafety group, committee, or review board at your institution?</h2><br />
<br />
<p>The Chemical Engineering Department of Columbia University has an Advisory Board consisting of experts in biosafety, biosecurity, and genetic engineering who hold positions in academia, industry and government. They serve as our Institutional Biosafety Committee. The portions of the project to be carried out at Genspace are strictly BioBrick construction and the construction of plasmids containing metal-binding peptides and other non-pathogenic sequences. This is within the project parameters recommended by our Advisory Board.</p><br />
<br />
<p>[http://genspace.org/page/Advisory%20Board Advisory Board Members]</p><br />
<br />
<p>[https://static.igem.org/mediawiki/2011/2/25/Interim_Safety_Rules.pdf Interim Lab Safety Rules]</p><br />
<br />
<p>Cooper Union does not have an Institutional Biosafety Committee, but the project has been reviewed by David Wootton, Ph.D., Director of The Maurice Kanbar Center for Biomedical Engineering and is being supervised by Jody Grapes, Campus-Wide Safety Officer for Cooper Union.</p><br />
<br />
<p>Students participating in this project received safety training (general/chemical/biological) either at Columbia University or Cooper Union prior to beginning the project. The safety training consisted of a presentation covering the various aspects of safety found in molecular biology laboratories; i.e. proper microbiological techniques, safe disposal of recombinant organisms, etc. Upon completion of the presentation, students were shown the location of all safety equipment i.e. eye wash stations, first aid kits, fire extinguishers and safety exits. Students were also supervised by iGEM instructors at Columbia University or Cooper Union throughout the duration of the project.</p><br />
<br />
<p>Laboratory Safety Guide [https://docs.google.com/presentation/d/1WwrEhIL_cLkcRdZy_loovlCESdAL6CkL606PaGwvL5c/edit#slide=id.p61]</p><br />
<br />
<h2>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2><br />
<br />
<p> Manufacturing processes can be more environmentally friendly by using bacteria, like Acidithiobacillus Ferrooxidans, to manufacture computer technology, such as printed circuit boards, because the current manufacturing processes rely heavily on acids to do the etching on the boards. By switching to bacteria, only a small amount of acid is needed and the acid is used to keep the bacteria alive. The bacteria will accelerate the production of ferric ions and the ferric ions will react with pure copper to solubilize it. In this way, the bacteria is the primarily responsible for an etched PCB and not acid. </p><br />
<br />
<p> The Rio Tinto is a river in Southwest Spain and there is a site along the river that was subjected to mining for copper, silver, and other minerals using acids such as sulfuric acid. This lowered the pH significantly to about 1.7-2.5. Coincidentally, Acidithobacillus Ferrooxidans are found in mines and survive at such low pH. Thus, they live in the river and convert ferrous ions to ferric ions, giving the river a red color that is present to this day. By genetically engineering a kill-switch in the bacteria when subjected to a certain color light, the bacteria can sefl-destruct and not continue to pollute the river. </p></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/SafetyTeam:Columbia-Cooper-NYC/Safety2012-09-08T02:26:11Z<p>FourEyeGuy1962: /* Safety */</p>
<hr />
<div>{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Columbia-Cooper-NYC|Home]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Columbia-Cooper-NYC Official Team Profile]<br />
!align="center"|[[Tehttps://2012.igem.org/wiki/skins/common/images/button_math.pngam:Columbia-Cooper-NYC/Project|Project]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Modeling|Modeling]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Notebook|Notebook]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Safety|Safety]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Attributions|Attributions]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Sponsor Us|Sponsor Us]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
=='''Safety''' ==<br />
<br />
<div style="text-align:left;"><br />
<h2>Would any of your project ideas raise safety issues in terms of:</h2><br />
<br />
<h3>researcher safety?</h3><br />
<br />
<p> To make liquid or solid media for Acidithiobacillus Ferrooxidans, around 1 mL of sulfuric acid is required per batch of media to bring the pH down such that the bacteria can survive. The safety of individuals is greatly minimized with the use of nitrile gloves and safety goggles as well as following lab dress code (shoes that entirely cover the feet and long pants) when dealing with the acid. </p><br />
<br />
<h3>public safety?</h3><br />
<br />
<p> Since the liquid media is disposed in labeled waste containers and the solid media in hazardous waste bins, they should not be released to the public. If they are accidentally released, there should not be any public safety issues because the pH of liquid media is around 1.8 and the pH of solid media is around 2.4 (these pH values are around the range of vinegar and orange juice). Also, Acidithiobacillus Ferrooxidans are classified as BSL 1 and are not known to cause any disease in healthy adults. </p> <br />
<br />
<h3>environmental safety?</h3><br />
<br />
<p> Since the media and bacteria are disposed in waste containers and waste bins, they should not be released to the environment. But if they are accidentally released, the impact to the environment is minimal because the pH of the media are in the range of common liquids such as vinegar and orange juice. Also, Acidithiobacillus Ferrooxidans can only survive at low pH (about 1.8 - 4.0). Thus, they will degrade if released to the environment since the pH of water is higher. </p><br />
<br />
<h3>Do any of the new BioBrick parts (or devices) that you made this year raise any safety<br />
issues? <h/3><br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<br />
<h2>Is there a local biosafety group, committee, or review board at your institution?</h2><br />
<br />
<p>The Chemical Engineering Department of Columbia University has an Advisory Board consisting of experts in biosafety, biosecurity, and genetic engineering who hold positions in academia, industry and government. They serve as our Institutional Biosafety Committee. The portions of the project to be carried out at Genspace are strictly BioBrick construction and the construction of plasmids containing metal-binding peptides and other non-pathogenic sequences. This is within the project parameters recommended by our Advisory Board.</p><br />
<br />
<p>[http://genspace.org/page/Advisory%20Board Advisory Board Members]</p><br />
<br />
<p>[https://static.igem.org/mediawiki/2011/2/25/Interim_Safety_Rules.pdf Interim Lab Safety Rules]</p><br />
<br />
<p>Cooper Union does not have an Institutional Biosafety Committee, but the project has been reviewed by David Wootton, Ph.D., Director of The Maurice Kanbar Center for Biomedical Engineering and is being supervised by Jody Grapes, Campus-Wide Safety Officer for Cooper Union.</p><br />
<br />
<p>Students participating in this project received safety training (general/chemical/biological) either at Columbia University or Cooper Union prior to beginning the project. The safety training consisted of a presentation covering the various aspects of safety found in molecular biology laboratories; i.e. proper microbiological techniques, safe disposal of recombinant organisms, etc. Upon completion of the presentation, students were shown the location of all safety equipment i.e. eye wash stations, first aid kits, fire extinguishers and safety exits. Students were also supervised by iGEM instructors at Columbia University or Cooper Union throughout the duration of the project.</p><br />
<br />
<p>Laboratory Safety Guide [https://docs.google.com/presentation/d/1WwrEhIL_cLkcRdZy_loovlCESdAL6CkL606PaGwvL5c/edit#slide=id.p61]</p><br />
<br />
<h2>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2><br />
<br />
<p> Manufacturing processes can be more environmentally friendly by using bacteria, like Acidithiobacillus Ferrooxidans, to manufacture computer technology, such as printed circuit boards, because the current manufacturing processes rely heavily on acids to do the etching on the boards. By switching to bacteria, only a small amount of acid is needed and the acid is used to keep the bacteria alive. The bacteria will accelerate the production of ferric ions and the ferric ions will react with pure copper to solubilize it. In this way, the bacteria is the primarily responsible for an etched PCB and not acid. </p><br />
<br />
<p> The Rio Tinto is a river in Southwest Spain and there is a site along the river that was subjected to mining for copper, silver, and other minerals using acids such as sulfuric acid. This lowered the pH significantly to about 1.7-2.5. Coincidentally, Acidithobacillus Ferrooxidans are found in mines and survive at such low pH. Thus, they live in the river and convert ferrous ions to ferric ions, giving the river a red color that is present to this day. By genetically engineering a kill-switch in the bacteria when subjected to a certain color light, the bacteria can sefl-destruct and not continue to pollute the river. </p></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/SafetyTeam:Columbia-Cooper-NYC/Safety2012-09-08T02:25:01Z<p>FourEyeGuy1962: </p>
<hr />
<div>{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Columbia-Cooper-NYC|Home]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Columbia-Cooper-NYC Official Team Profile]<br />
!align="center"|[[Tehttps://2012.igem.org/wiki/skins/common/images/button_math.pngam:Columbia-Cooper-NYC/Project|Project]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Modeling|Modeling]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Notebook|Notebook]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Safety|Safety]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Attributions|Attributions]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Sponsor Us|Sponsor Us]]<br />
|}<br />
<br />
<br />
<br />
<br />
<br />
=='''Safety''' ==<br />
<br />
<div style="text-align:left;"><br />
<h2>Would any of your project ideas raise safety issues in terms of:</h2><br />
<br />
<h3>researcher safety?</h3><br />
<br />
<p> To make liquid or solid media for Acidithiobacillus Ferrooxidans, around 1 mL of sulfuric acid is required per batch of media to bring the pH down such that the bacteria can survive. The safety of individuals is greatly minimized with the use of nitrile gloves and safety goggles as well as following lab dress code (shoes that entirely cover the feet and long pants) when dealing with the acid. </p><br />
<br />
<h3>public safety?</h3><br />
<br />
<p> Since the liquid media is disposed in labeled waste containers and the solid media in hazardous waste bins, they should not be released to the public. If they are accidentally released, there should not be any public safety issues because the pH of liquid media is around 1.8 and the pH of solid media is around 2.4 (these pH values are around the range of vinegar and orange juice). Also, Acidithiobacillus Ferrooxidans are classified as BSL 1 and are not known to cause any disease in healthy adults. </p> <br />
<br />
<h3>environmental safety?</h3><br />
<br />
<p> Since the media and bacteria are disposed in waste containers and waste bins, they should not be released to the environment. But if they are accidentally released, the impact to the environment is minimal because the pH of the media are in the range of common liquids such as vinegar and orange juice. Also, Acidithiobacillus Ferrooxidans can only survive at low pH (about 1.8 - 4.0). Thus, they will degrade if released to the environment since the pH of water is higher. </p><br />
<br />
<h2>Do any of the new BioBrick parts (or devices) that you made this year raise any safety<br />
issues? <br />
<br />
<p> None of the parts or devices that we have used during our project will raise any known safety issues. </p><br />
<br />
<br />
<h2>Is there a local biosafety group, committee, or review board at your institution?</h2><br />
<br />
<p>The Chemical Engineering Department of Columbia University has an Advisory Board consisting of experts in biosafety, biosecurity, and genetic engineering who hold positions in academia, industry and government. They serve as our Institutional Biosafety Committee. The portions of the project to be carried out at Genspace are strictly BioBrick construction and the construction of plasmids containing metal-binding peptides and other non-pathogenic sequences. This is within the project parameters recommended by our Advisory Board.</p><br />
<br />
<p>[http://genspace.org/page/Advisory%20Board Advisory Board Members]</p><br />
<br />
<p>[https://static.igem.org/mediawiki/2011/2/25/Interim_Safety_Rules.pdf Interim Lab Safety Rules]</p><br />
<br />
<p>Cooper Union does not have an Institutional Biosafety Committee, but the project has been reviewed by David Wootton, Ph.D., Director of The Maurice Kanbar Center for Biomedical Engineering and is being supervised by Jody Grapes, Campus-Wide Safety Officer for Cooper Union.</p><br />
<br />
<p>Students participating in this project received safety training (general/chemical/biological) either at Columbia University or Cooper Union prior to beginning the project. The safety training consisted of a presentation covering the various aspects of safety found in molecular biology laboratories; i.e. proper microbiological techniques, safe disposal of recombinant organisms, etc. Upon completion of the presentation, students were shown the location of all safety equipment i.e. eye wash stations, first aid kits, fire extinguishers and safety exits. Students were also supervised by iGEM instructors at Columbia University or Cooper Union throughout the duration of the project.</p><br />
<br />
<p>Laboratory Safety Guide [https://docs.google.com/presentation/d/1WwrEhIL_cLkcRdZy_loovlCESdAL6CkL606PaGwvL5c/edit#slide=id.p61]</p><br />
<br />
<h2>Do you have any other ideas how to deal with safety issues that could be useful for future iGEM competitions? How could parts, devices and systems be made even safer through biosafety engineering?</h2><br />
<br />
<p> Manufacturing processes can be more environmentally friendly by using bacteria, like Acidithiobacillus Ferrooxidans, to manufacture computer technology, such as printed circuit boards, because the current manufacturing processes rely heavily on acids to do the etching on the boards. By switching to bacteria, only a small amount of acid is needed and the acid is used to keep the bacteria alive. The bacteria will accelerate the production of ferric ions and the ferric ions will react with pure copper to solubilize it. In this way, the bacteria is the primarily responsible for an etched PCB and not acid. </p><br />
<br />
<p> The Rio Tinto is a river in Southwest Spain and there is a site along the river that was subjected to mining for copper, silver, and other minerals using acids such as sulfuric acid. This lowered the pH significantly to about 1.7-2.5. Coincidentally, Acidithobacillus Ferrooxidans are found in mines and survive at such low pH. Thus, they live in the river and convert ferrous ions to ferric ions, giving the river a red color that is present to this day. By genetically engineering a kill-switch in the bacteria when subjected to a certain color light, the bacteria can sefl-destruct and not continue to pollute the river. </p></div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYCTeam:Columbia-Cooper-NYC2012-07-17T16:47:52Z<p>FourEyeGuy1962: </p>
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<div><!-- *** What falls between these lines is the Alert Box! You can remove it from your pages once you have read and understood the alert *** --><br />
<br />
<html><br />
<div id="box" style="width: 700px; margin-left: 137px; padding: 5px; border: 3px solid #000; background-color: #fe2b33;"><br />
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This is a template page. READ THESE INSTRUCTIONS.<br />
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You are provided with this team page template with which to start the iGEM season. You may choose to personalize it to fit your team but keep the same "look." Or you may choose to take your team wiki to a different level and design your own wiki. You can find some examples <a href="https://2009.igem.org/Help:Template/Examples">HERE</a>.<br />
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<!-- *** End of the alert box *** --><br />
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<br />
<br />
{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Columbia-Cooper-NYC_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
''The Columbia-Cooper iGEM team is working with Acidithiobacillus ferrooxidans to create a light-controlled printed circuit board manufacturing process. This bacteria’s metabolism relies on its ability to oxidize iron; the iron can then be used to oxidize, and in turn solubilize, copper. By genetically altering the bacteria, we intend to install a light sensitive mechanism which will enable us to etch copper in a desired pattern, leaving a finished circuit board.''<br />
<br />
|[[Image:Columbia-Cooper-NYC_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Columbia-Cooper-NYC | Team Columbia-Cooper-NYC]]<br />
|}<br />
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<!--- The Mission, Experiments ---><br />
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Columbia-Cooper-NYC|Home]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Columbia-Cooper-NYC Official Team Profile]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Project|Project]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Modeling|Modeling]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Notebook|Notebook]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Safety|Safety]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Attributions|Attributions]]<br />
|}</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/TeamTeam:Columbia-Cooper-NYC/Team2012-05-31T20:29:20Z<p>FourEyeGuy1962: </p>
<hr />
<div>{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Columbia-Cooper-NYC_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
|[[Image:Columbia-Cooper-NYC_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Columbia-Cooper-NYC | Team Columbia-Cooper-NYC]]<br />
|}<br />
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<!--- The Mission, Experiments ---><br />
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Columbia-Cooper-NYC|Home]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Columbia-Cooper-NYC Official Team Profile]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Project|Project]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Modeling|Modeling]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Notebook|Notebook]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Safety|Safety]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Attributions|Attributions]]<br />
|}<br />
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<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
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<br />
<br />
<br />
<h2>'''Advisors'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Advisor_1.png|200px|right|frame]]<br />
'''David Orbach''': <br />
<p>David Orbach joined Cooper Union in the summer of 2008 with a BS in Agricultural and Biological Engineering from Cornell University and a MS in Biomedical Engineering from the University of Rochester. Before joining Cooper he also earned an MD, did an intern year, and developed an interest in improving efficiency and patient throughput in the Emergency Room setting. He teaches several biology and biomedical engineering courses, including cell and molecular biology, physiology, and microbiology; helps direct the Kanbar Center for Biomedical Engineering; and serves as the college’s pre-medical advisor. Outside of Cooper, David now helps create iPhone apps and workbooks for children. See www.Brain-go.com.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Advisor_2.png|200px|right|frame]]<br />
'''Scott A. Banta''': <br />
<br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Grad_Student_1.png|200px|right|frame]]<br />
'''Grad Student 1''': <br />
<p>Our leader</p><br />
<br />
<br />
<br />
<br />
<br />
<h2>'''Undergraduates'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_1.png|200px|right|frame]]<br />
'''Aakash Mansukhani''': <p>When he’s not obsessively watching American Idol videos or playing tunes on his guitar, Aakash Mansukhani studies chemical engineering at Columbia University. As a rising sophomore, Aakash hopes that participating in IGEM will help him learn more about how principles from chemical engineering and synthetic biology can be combined to program bacteria. In his free time, Aakash loves to sing and reinvent pop songs by putting his own acoustic spin on them.</p> <br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_2.png|200px|right|frame]]<br />
'''Akachi Ukwu''': <p>Akachi is a rising Sophomore at Columbia University. Her potential major is Chemical Engineering. She was interested in IGEM because she wanted to learn about the many ways she can apply what she is being taught in school to real world problems. Akachi also enjoys watching soap operas.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_3.png|200px|right|frame]]<br />
'''Pnina Grossman''': <p>Pnina is a rising sophomore at The Cooper Union. She is currently in the BSE track there (with a possibility of switching to mechanical engineering), and hopes to specialize in biomedical engineering. IGEM seemed like a great opportunity to get some real hands-on experience in study of biology and problem-solving combined.</p><br />
<br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_4.png|200px|right|frame]]<br />
'''Naimun Siraj''': <p>Naimun is a rising Sophomore at Columbia University. He began the year as a Physics major and changed to Biomedical Engineering followed up by a change to Electrical Engineering to Applied Physics and finally, to Chemical Engineering. IGEM seemed like an opportunity for him to learn more about some of the applications of engineering and its consequences. Naimun loves reading about theoretical physics and hopes to die in a black hole one day.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_5.png|200px|right|frame]]<br />
'''Sara Chuang''': <p>Sara just finished her third year as a Chemical Engineer at Columbia University. She is interested in pharmaceuticals and protein engineering. IGEM was particularly appealing, because she wanted a chance to pursue a fun application of synthetic biology. Sara also enjoys super hero movies.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_6.png|200px|right|frame]]<br />
'''Roshan Ramkeesoon''': <p>Roshan is a rising sophomore majoring in chemical engineering at Columbia University. He is interested in working in alternative energy. He joined the IGEM team because it was a great opportunity to apply engineering principles to solve real world problems while gaining invaluable hands-on experience.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_7.png|200px|right|frame]]<br />
'''Nicholas Mannarino''': <p>Nicholas Mannarino is a rising sophomore at The Cooper Union. He is studying chemical engineering, with a hope to specialize in biomedical engineering and biotechnology. He joined IGEM because it seemed like a great way to spend a summer getting acquainted with a field he is interested in. In his spare time, Nicholas enjoys playing the guitar and long-distance running.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_8.png|200px|right|frame]]<br />
'''Anna Mai''': <p>Anna Mai is a rising junior majoring in chemical engineering at Columbia University, with a minor in environmental engineering. She joined IGEM because it presented an interesting medium for interacting with engineers around the world and providing hands on experience in the highly applicable field of synthetic biology. In her spare time she enjoys playing ultimate Frisbee, building paper crafts, and serenading her neighbors (not well).</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_9.png|200px|right|frame]]<br />
'''Udochukwu (Ud) Okorafor''': <p>Ud Okorafor is a rising senior at Columbia University. He is majoring in chemical engineering and has interests in protein engineering and pharmaceuticals. He joined IGEM because he enjoyed the research he had done previously on genetic engineering of E. coli. In his spare time, he enjoys playing various sports, reading science fiction books, and watching movies.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_10.png|200px|right|frame]]<br />
'''Saimon Sharif''': <p>Saimon is a rising sophomore at The Cooper Union. He is studying Chemical Engineering and intends to minor in Mathematics. He joined IGEM because it gives him the opportunity to apply engineering and creativity to biology. In his spare time, Saimon enjoys listening to alternative rock and watching science fiction television shows.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_11.png|200px|right|frame]]<br />
'''Kirsten Nicassio''': <p>Kirsten Nicassio just finished her freshman year at The Cooper Union. She is majoring in chemical engineering, with an intended math minor. She joined IGEM because of interest in the field of biomedical engineering. In her spare time, Kirsten enjoys reading, knitting, and swimming.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_12.png|200px|right|frame]]<br />
'''Marjana Chowdhury''': <p>Despite being from the bustling streets of New York City, Marjana was born to live in the wild. This nature lover and rising sophomore intends to major in Environmental Biology at Columbia University. In the past, Marjana's research has scaled a size spectrum ranging from immense invasive species to minuscule endangered species. As part of the Columbia-Cooper iGEM team, she is excited about her newest and smallest challenge yet, microorganisms.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_13.png|200px|right|frame]]<br />
'''Jackie Song''': <p>Jackie Song is a rising sophomore studying mechanical engineering at The Cooper Union. She joined iGEM out of curiosity about the processes and techniques used in synthetic biology. Jackie enjoys playing the flute and meshing gears. </p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_14.png|200px|right|frame]]<br />
'''Peter Liu''': <p>Peter Liu is a rising senior at The Cooper Union majoring in Chemical Engineering with a minor in biomedical engineering. He joined the igem team this year to further his knowledge and lab skills in the field of synthetic and microbiology.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_15.png|200px|right|frame]]<br />
'''Jang suk Roh''': <p>Jang suk Roh is a rising Junior at the Cooper Union majoring in Chemical Engineering. He likes doing lab work related to microbiology. He is also a front page featured redditor.</p><br />
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<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_16.png|200px|right|frame]]<br />
'''Swetha Chandrasekar''': <p>Swetha Chandrasekar is a rising Sophomore studying Chemical Engineering with a Biomedical Minor. Her avid interests and research done in biomedical device design, biorobotics, virology and bacterial chemistry drew her to be a part of iGEM. She hopes to apply her interests in working as a member of the Cooper-Columbia team to create something novel and inspiring! Outside of academics, Swetha loves singing, dancing and drawing.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_17.png|200px|right|frame]]<br />
'''Chauncy Yin''': <p>Chauncy Yin is a rising senior majoring in chemical engineering and minoring in materials & science at Columbia University. His research focuses on developing multifunctional magnetic nanoparticles as delivery platforms for therapeutic and diagnostic agents. He joins IGEM because he wants to apply the biology knowledge he learns in IGEM to the research and development of new pharmaceutical vehicles.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_18.png|200px|right|frame]]<br />
'''Vincent Xu''': <p>Vincent is a rising senior at Columbia University majoring in chemical engineering and minoring in applied mathematics. He is more interested in computational modeling than lab work and has been doing research in the applied math department since the summer of his freshman year. He decided to join IGEM because he thinks that it’s a good chance to learn something about biology, which is a subject he hasn’t studied since high school, and to get involved in any computational or modeling work. In addition to enjoying popular activities that college students engage in, such as eating and sleeping, Vincent does ballroom dancing.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_19.png|200px|right|frame]]<br />
'''Yuta Makita''': <p>Yuta Makita is a rising sophomore studying chemical engineering at the Cooper Union. Yuta joined the iGEM team with an interest in research based study and process of synthetic biology and the microscopic world. In addition to academic studies, he enjoys taking part in orchestra related activities by playing the viola.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_20.png|200px|right|frame]]<br />
'''Ciera Lowe''': <p>Ciera is a rising junior at The Cooper Union majoring in chemical engineering with a minor in biomedical engineering. She joined the iGEM team because this competition provides an amazing opportunity to gain hands on experience in synthetic biology, an exciting field full of potential to improve the world we live in. In addition to her studies, Ciera keeps busy by playing foosball on Cooper’s newly acquired table, playing basketball with Cooper’s women’s team or organizing events with the engineering student council and Cooper’s National Society of Black Engineers chapter.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_21.png|200px|right|frame]]<br />
'''Steven Neuhaus''': <p>Steven Neuhaus is a rising sophomore who studies chemical engineering at The Cooper Union for the Advancement of Science and Art. He’s quite fond of the idea of using little things to solve big problems, and joined iGEM because it provides a tremendous opportunity to do just that (and also time to play in the lab!). Steven also enjoys pointing out that writing about oneself in the third person is extremely awkward, is interested in most things that are interesting, and if you show him something cool, he’s usually more than glad to run with it.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_22.png|200px|right|frame]]<br />
'''Shivrat Chhabra''': <p>Shivrat Chhabra is a rising junior at Columbia University, majoring in Chemical Engineering and minoring in Biomedical Engineering. He’s always been interested in bioengineering on the micro-scale, and joined the iGEM team to further that interest. Outside of the academic sphere, he is also involved in ballroom dance.</p><br />
<br />
<br />
<br />
<h2>'''High School Students'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_23.png|200px|right|frame]]<br />
'''Richard Shi''': <p>Richard Shi is a high school research student at Jericho High School. He had previously studied and written a paper based on the Dye Sensitized Solar Cell at Farmingdale University. He joined iGEM to vary his exposure to different sciences (moving from the engineering sciences to synthetic biology) and hopes to collect data for the upcoming Intel STS competition. He hopes to bring much to the table, despite being in high school.</p><br />
<br />
|}<br />
<br />
== '''What we did''' ==<br />
<br />
(Provide proper attribution for all work)<br />
<br />
== '''Where we're from''' ==<br />
<br />
Everywhere, =]</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/TeamTeam:Columbia-Cooper-NYC/Team2012-05-31T20:28:24Z<p>FourEyeGuy1962: </p>
<hr />
<div>{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Columbia-Cooper-NYC_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
|[[Image:Columbia-Cooper-NYC_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Columbia-Cooper-NYC | Team Columbia-Cooper-NYC]]<br />
|}<br />
<br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Columbia-Cooper-NYC|Home]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Columbia-Cooper-NYC Official Team Profile]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Project|Project]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Modeling|Modeling]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Notebook|Notebook]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Safety|Safety]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
<br />
<br />
<br />
<h2>'''Advisors'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Advisor_1.png|right|frame]]<br />
'''David Orbach''': <br />
<p>David Orbach joined Cooper Union in the summer of 2008 with a BS in Agricultural and Biological Engineering from Cornell University and a MS in Biomedical Engineering from the University of Rochester. Before joining Cooper he also earned an MD, did an intern year, and developed an interest in improving efficiency and patient throughput in the Emergency Room setting. He teaches several biology and biomedical engineering courses, including cell and molecular biology, physiology, and microbiology; helps direct the Kanbar Center for Biomedical Engineering; and serves as the college’s pre-medical advisor. Outside of Cooper, David now helps create iPhone apps and workbooks for children. See www.Brain-go.com.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Advisor_2.png|200px|right|frame]]<br />
'''Scott A. Banta''': <br />
<br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Grad_Student_1.png|200px|right|frame]]<br />
'''Grad Student 1''': <br />
<p>Our leader</p><br />
<br />
<br />
<br />
<h2>'''Undergraduates'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_1.png|200px|right|frame]]<br />
'''Aakash Mansukhani''': <p>When he’s not obsessively watching American Idol videos or playing tunes on his guitar, Aakash Mansukhani studies chemical engineering at Columbia University. As a rising sophomore, Aakash hopes that participating in IGEM will help him learn more about how principles from chemical engineering and synthetic biology can be combined to program bacteria. In his free time, Aakash loves to sing and reinvent pop songs by putting his own acoustic spin on them.</p> <br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_2.png|200px|right|frame]]<br />
'''Akachi Ukwu''': <p>Akachi is a rising Sophomore at Columbia University. Her potential major is Chemical Engineering. She was interested in IGEM because she wanted to learn about the many ways she can apply what she is being taught in school to real world problems. Akachi also enjoys watching soap operas.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_3.png|200px|right|frame]]<br />
'''Pnina Grossman''': <p>Pnina is a rising sophomore at The Cooper Union. She is currently in the BSE track there (with a possibility of switching to mechanical engineering), and hopes to specialize in biomedical engineering. IGEM seemed like a great opportunity to get some real hands-on experience in study of biology and problem-solving combined.</p><br />
<br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_4.png|200px|right|frame]]<br />
'''Naimun Siraj''': <p>Naimun is a rising Sophomore at Columbia University. He began the year as a Physics major and changed to Biomedical Engineering followed up by a change to Electrical Engineering to Applied Physics and finally, to Chemical Engineering. IGEM seemed like an opportunity for him to learn more about some of the applications of engineering and its consequences. Naimun loves reading about theoretical physics and hopes to die in a black hole one day.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_5.png|200px|right|frame]]<br />
'''Sara Chuang''': <p>Sara just finished her third year as a Chemical Engineer at Columbia University. She is interested in pharmaceuticals and protein engineering. IGEM was particularly appealing, because she wanted a chance to pursue a fun application of synthetic biology. Sara also enjoys super hero movies.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_6.png|200px|right|frame]]<br />
'''Roshan Ramkeesoon''': <p>Roshan is a rising sophomore majoring in chemical engineering at Columbia University. He is interested in working in alternative energy. He joined the IGEM team because it was a great opportunity to apply engineering principles to solve real world problems while gaining invaluable hands-on experience.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_7.png|200px|right|frame]]<br />
'''Nicholas Mannarino''': <p>Nicholas Mannarino is a rising sophomore at The Cooper Union. He is studying chemical engineering, with a hope to specialize in biomedical engineering and biotechnology. He joined IGEM because it seemed like a great way to spend a summer getting acquainted with a field he is interested in. In his spare time, Nicholas enjoys playing the guitar and long-distance running.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_8.png|200px|right|frame]]<br />
'''Anna Mai''': <p>Anna Mai is a rising junior majoring in chemical engineering at Columbia University, with a minor in environmental engineering. She joined IGEM because it presented an interesting medium for interacting with engineers around the world and providing hands on experience in the highly applicable field of synthetic biology. In her spare time she enjoys playing ultimate Frisbee, building paper crafts, and serenading her neighbors (not well).</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_9.png|200px|right|frame]]<br />
'''Udochukwu (Ud) Okorafor''': <p>Ud Okorafor is a rising senior at Columbia University. He is majoring in chemical engineering and has interests in protein engineering and pharmaceuticals. He joined IGEM because he enjoyed the research he had done previously on genetic engineering of E. coli. In his spare time, he enjoys playing various sports, reading science fiction books, and watching movies.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_10.png|200px|right|frame]]<br />
'''Saimon Sharif''': <p>Saimon is a rising sophomore at The Cooper Union. He is studying Chemical Engineering and intends to minor in Mathematics. He joined IGEM because it gives him the opportunity to apply engineering and creativity to biology. In his spare time, Saimon enjoys listening to alternative rock and watching science fiction television shows.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_11.png|200px|right|frame]]<br />
'''Kirsten Nicassio''': <p>Kirsten Nicassio just finished her freshman year at The Cooper Union. She is majoring in chemical engineering, with an intended math minor. She joined IGEM because of interest in the field of biomedical engineering. In her spare time, Kirsten enjoys reading, knitting, and swimming.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_12.png|200px|right|frame]]<br />
'''Marjana Chowdhury''': <p>Despite being from the bustling streets of New York City, Marjana was born to live in the wild. This nature lover and rising sophomore intends to major in Environmental Biology at Columbia University. In the past, Marjana's research has scaled a size spectrum ranging from immense invasive species to minuscule endangered species. As part of the Columbia-Cooper iGEM team, she is excited about her newest and smallest challenge yet, microorganisms.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_13.png|200px|right|frame]]<br />
'''Jackie Song''': <p>Jackie Song is a rising sophomore studying mechanical engineering at The Cooper Union. She joined iGEM out of curiosity about the processes and techniques used in synthetic biology. Jackie enjoys playing the flute and meshing gears. </p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_14.png|200px|right|frame]]<br />
'''Peter Liu''': <p>Peter Liu is a rising senior at The Cooper Union majoring in Chemical Engineering with a minor in biomedical engineering. He joined the igem team this year to further his knowledge and lab skills in the field of synthetic and microbiology.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_15.png|200px|right|frame]]<br />
'''Jang suk Roh''': <p>Jang suk Roh is a rising Junior at the Cooper Union majoring in Chemical Engineering. He likes doing lab work related to microbiology. He is also a front page featured redditor.</p><br />
<br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_16.png|200px|right|frame]]<br />
'''Swetha Chandrasekar''': <p>Swetha Chandrasekar is a rising Sophomore studying Chemical Engineering with a Biomedical Minor. Her avid interests and research done in biomedical device design, biorobotics, virology and bacterial chemistry drew her to be a part of iGEM. She hopes to apply her interests in working as a member of the Cooper-Columbia team to create something novel and inspiring! Outside of academics, Swetha loves singing, dancing and drawing.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_17.png|200px|right|frame]]<br />
'''Chauncy Yin''': <p>Chauncy Yin is a rising senior majoring in chemical engineering and minoring in materials & science at Columbia University. His research focuses on developing multifunctional magnetic nanoparticles as delivery platforms for therapeutic and diagnostic agents. He joins IGEM because he wants to apply the biology knowledge he learns in IGEM to the research and development of new pharmaceutical vehicles.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_18.png|200px|right|frame]]<br />
'''Vincent Xu''': <p>Vincent is a rising senior at Columbia University majoring in chemical engineering and minoring in applied mathematics. He is more interested in computational modeling than lab work and has been doing research in the applied math department since the summer of his freshman year. He decided to join IGEM because he thinks that it’s a good chance to learn something about biology, which is a subject he hasn’t studied since high school, and to get involved in any computational or modeling work. In addition to enjoying popular activities that college students engage in, such as eating and sleeping, Vincent does ballroom dancing.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_19.png|200px|right|frame]]<br />
'''Yuta Makita''': <p>Yuta Makita is a rising sophomore studying chemical engineering at the Cooper Union. Yuta joined the iGEM team with an interest in research based study and process of synthetic biology and the microscopic world. In addition to academic studies, he enjoys taking part in orchestra related activities by playing the viola.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_20.png|200px|right|frame]]<br />
'''Ciera Lowe''': <p>Ciera is a rising junior at The Cooper Union majoring in chemical engineering with a minor in biomedical engineering. She joined the iGEM team because this competition provides an amazing opportunity to gain hands on experience in synthetic biology, an exciting field full of potential to improve the world we live in. In addition to her studies, Ciera keeps busy by playing foosball on Cooper’s newly acquired table, playing basketball with Cooper’s women’s team or organizing events with the engineering student council and Cooper’s National Society of Black Engineers chapter.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_21.png|200px|right|frame]]<br />
'''Steven Neuhaus''': <p>Steven Neuhaus is a rising sophomore who studies chemical engineering at The Cooper Union for the Advancement of Science and Art. He’s quite fond of the idea of using little things to solve big problems, and joined iGEM because it provides a tremendous opportunity to do just that (and also time to play in the lab!). Steven also enjoys pointing out that writing about oneself in the third person is extremely awkward, is interested in most things that are interesting, and if you show him something cool, he’s usually more than glad to run with it.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_22.png|200px|right|frame]]<br />
'''Shivrat Chhabra''': <p>Shivrat Chhabra is a rising junior at Columbia University, majoring in Chemical Engineering and minoring in Biomedical Engineering. He’s always been interested in bioengineering on the micro-scale, and joined the iGEM team to further that interest. Outside of the academic sphere, he is also involved in ballroom dance.</p><br />
<br />
<br />
<br />
<h2>'''High School Students'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_23.png|200px|right|frame]]<br />
'''Richard Shi''': <p>Richard Shi is a high school research student at Jericho High School. He had previously studied and written a paper based on the Dye Sensitized Solar Cell at Farmingdale University. He joined iGEM to vary his exposure to different sciences (moving from the engineering sciences to synthetic biology) and hopes to collect data for the upcoming Intel STS competition. He hopes to bring much to the table, despite being in high school.</p><br />
<br />
|}<br />
<br />
== '''What we did''' ==<br />
<br />
(Provide proper attribution for all work)<br />
<br />
== '''Where we're from''' ==<br />
<br />
Everywhere, =]</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/TeamTeam:Columbia-Cooper-NYC/Team2012-05-31T20:01:53Z<p>FourEyeGuy1962: </p>
<hr />
<div>{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Columbia-Cooper-NYC_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
|[[Image:Columbia-Cooper-NYC_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Columbia-Cooper-NYC | Team Columbia-Cooper-NYC]]<br />
|}<br />
<br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Columbia-Cooper-NYC|Home]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Columbia-Cooper-NYC Official Team Profile]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Project|Project]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Modeling|Modeling]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Notebook|Notebook]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Safety|Safety]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
<br />
<br />
<br />
<h2>'''Advisors'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Advisor_1.png|left|frame]]<br />
'''David Orbach''': <br />
<p>David Orbach joined Cooper Union in the summer of 2008 with a BS in Agricultural and Biological Engineering from Cornell University and a MS in Biomedical Engineering from the University of Rochester. Before joining Cooper he also earned an MD, did an intern year, and developed an interest in improving efficiency and patient throughput in the Emergency Room setting. He teaches several biology and biomedical engineering courses, including cell and molecular biology, physiology, and microbiology; helps direct the Kanbar Center for Biomedical Engineering; and serves as the college’s pre-medical advisor. Outside of Cooper, David now helps create iPhone apps and workbooks for children. See www.Brain-go.com.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Advisor_2.png|200px|left|frame]]<br />
'''Scott A. Banta''': <br />
<br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Grad_Student_1.png|200px|left|frame]]<br />
'''Grad Student 1''': <br />
<p>Our leader</p><br />
<br />
<br />
<h2>'''Undergraduates'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_1.png|200px|left|frame]]<br />
'''Aakash Mansukhani''': <p>When he’s not obsessively watching American Idol videos or playing tunes on his guitar, Aakash Mansukhani studies chemical engineering at Columbia University. As a rising sophomore, Aakash hopes that participating in IGEM will help him learn more about how principles from chemical engineering and synthetic biology can be combined to program bacteria. In his free time, Aakash loves to sing and reinvent pop songs by putting his own acoustic spin on them.</p> <br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_2.png|200px|left|frame]]<br />
'''Akachi Ukwu''': <p>Akachi is a rising Sophomore at Columbia University. Her potential major is Chemical Engineering. She was interested in IGEM because she wanted to learn about the many ways she can apply what she is being taught in school to real world problems. Akachi also enjoys watching soap operas.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_3.png|200px|left|frame]]<br />
'''Pnina Grossman''': <p>Pnina is a rising sophomore at The Cooper Union. She is currently in the BSE track there (with a possibility of switching to mechanical engineering), and hopes to specialize in biomedical engineering. IGEM seemed like a great opportunity to get some real hands-on experience in study of biology and problem-solving combined.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_4.png|200px|left|frame]]<br />
'''Naimun Siraj''': <p>Naimun is a rising Sophomore at Columbia University. He began the year as a Physics major and changed to Biomedical Engineering followed up by a change to Electrical Engineering to Applied Physics and finally, to Chemical Engineering. IGEM seemed like an opportunity for him to learn more about some of the applications of engineering and its consequences. Naimun loves reading about theoretical physics and hopes to die in a black hole one day.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_5.png|200px|left|frame]]<br />
'''Sara Chuang''': <p>Sara just finished her third year as a Chemical Engineer at Columbia University. She is interested in pharmaceuticals and protein engineering. IGEM was particularly appealing, because she wanted a chance to pursue a fun application of synthetic biology. Sara also enjoys super hero movies.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_6.png|200px|left|frame]]<br />
'''Roshan Ramkeesoon''': <p>Roshan is a rising sophomore majoring in chemical engineering at Columbia University. He is interested in working in alternative energy. He joined the IGEM team because it was a great opportunity to apply engineering principles to solve real world problems while gaining invaluable hands-on experience.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_7.png|200px|left|frame]]<br />
'''Nicholas Mannarino''': <p>Nicholas Mannarino is a rising sophomore at The Cooper Union. He is studying chemical engineering, with a hope to specialize in biomedical engineering and biotechnology. He joined IGEM because it seemed like a great way to spend a summer getting acquainted with a field he is interested in. In his spare time, Nicholas enjoys playing the guitar and long-distance running.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_8.png|200px|left|frame]]<br />
'''Anna Mai''': <p>Anna Mai is a rising junior majoring in chemical engineering at Columbia University, with a minor in environmental engineering. She joined IGEM because it presented an interesting medium for interacting with engineers around the world and providing hands on experience in the highly applicable field of synthetic biology. In her spare time she enjoys playing ultimate Frisbee, building paper crafts, and serenading her neighbors (not well).</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_9.png|200px|left|frame]]<br />
'''Udochukwu (Ud) Okorafor''': <p>Ud Okorafor is a rising senior at Columbia University. He is majoring in chemical engineering and has interests in protein engineering and pharmaceuticals. He joined IGEM because he enjoyed the research he had done previously on genetic engineering of E. coli. In his spare time, he enjoys playing various sports, reading science fiction books, and watching movies.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_10.png|200px|left|frame]]<br />
'''Saimon Sharif''': <p>Saimon is a rising sophomore at The Cooper Union. He is studying Chemical Engineering and intends to minor in Mathematics. He joined IGEM because it gives him the opportunity to apply engineering and creativity to biology. In his spare time, Saimon enjoys listening to alternative rock and watching science fiction television shows.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_11.png|200px|left|frame]]<br />
'''Kirsten Nicassio''': <p>Kirsten Nicassio just finished her freshman year at The Cooper Union. She is majoring in chemical engineering, with an intended math minor. She joined IGEM because of interest in the field of biomedical engineering. In her spare time, Kirsten enjoys reading, knitting, and swimming.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_12.png|200px|left|frame]]<br />
'''Marjana Chowdhury''': <p>Despite being from the bustling streets of New York City, Marjana was born to live in the wild. This nature lover and rising sophomore intends to major in Environmental Biology at Columbia University. In the past, Marjana's research has scaled a size spectrum ranging from immense invasive species to minuscule endangered species. As part of the Columbia-Cooper iGEM team, she is excited about her newest and smallest challenge yet, microorganisms.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_13.png|200px|left|frame]]<br />
'''Jackie Song''': <p>Jackie Song is a rising sophomore studying mechanical engineering at The Cooper Union. She joined iGEM out of curiosity about the processes and techniques used in synthetic biology. Jackie enjoys playing the flute and meshing gears. </p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_14.png|200px|left|frame]]<br />
'''Peter Liu''': <p>Peter Liu is a rising senior at The Cooper Union majoring in Chemical Engineering with a minor in biomedical engineering. He joined the igem team this year to further his knowledge and lab skills in the field of synthetic and microbiology.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_15.png|200px|left|frame]]<br />
'''Jang suk Roh''': <p>Jang suk Roh is a rising Junior at the Cooper Union majoring in Chemical Engineering. He likes doing lab work related to microbiology. He is also a front page featured redditor.</p><br />
<br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_16.png|200px|left|frame]]<br />
'''Swetha Chandrasekar''': <p>Swetha Chandrasekar is a rising Sophomore studying Chemical Engineering with a Biomedical Minor. Her avid interests and research done in biomedical device design, biorobotics, virology and bacterial chemistry drew her to be a part of iGEM. She hopes to apply her interests in working as a member of the Cooper-Columbia team to create something novel and inspiring! Outside of academics, Swetha loves singing, dancing and drawing.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_17.png|200px|left|frame]]<br />
'''Chauncy Yin''': <p>Chauncy Yin is a rising senior majoring in chemical engineering and minoring in materials & science at Columbia University. His research focuses on developing multifunctional magnetic nanoparticles as delivery platforms for therapeutic and diagnostic agents. He joins IGEM because he wants to apply the biology knowledge he learns in IGEM to the research and development of new pharmaceutical vehicles.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_18.png|200px|left|frame]]<br />
'''Vincent Xu''': <p>Vincent is a rising senior at Columbia University majoring in chemical engineering and minoring in applied mathematics. He is more interested in computational modeling than lab work and has been doing research in the applied math department since the summer of his freshman year. He decided to join IGEM because he thinks that it’s a good chance to learn something about biology, which is a subject he hasn’t studied since high school, and to get involved in any computational or modeling work. In addition to enjoying popular activities that college students engage in, such as eating and sleeping, Vincent does ballroom dancing.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_19.png|200px|left|frame]]<br />
'''Yuta Makita''': <p>Yuta Makita is a rising sophomore studying chemical engineering at the Cooper Union. Yuta joined the iGEM team with an interest in research based study and process of synthetic biology and the microscopic world. In addition to academic studies, he enjoys taking part in orchestra related activities by playing the viola.</p><br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_20.png|200px|left|frame]]<br />
'''Ciera Lowe''': <p>Ciera is a rising junior at The Cooper Union majoring in chemical engineering with a minor in biomedical engineering. She joined the iGEM team because this competition provides an amazing opportunity to gain hands on experience in synthetic biology, an exciting field full of potential to improve the world we live in. In addition to her studies, Ciera keeps busy by playing foosball on Cooper’s newly acquired table, playing basketball with Cooper’s women’s team or organizing events with the engineering student council and Cooper’s National Society of Black Engineers chapter.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_21.png|200px|left|frame]]<br />
'''Steven Neuhaus''': <p>Steven Neuhaus is a rising sophomore who studies chemical engineering at The Cooper Union for the Advancement of Science and Art. He’s quite fond of the idea of using little things to solve big problems, and joined iGEM because it provides a tremendous opportunity to do just that (and also time to play in the lab!). Steven also enjoys pointing out that writing about oneself in the third person is extremely awkward, is interested in most things that are interesting, and if you show him something cool, he’s usually more than glad to run with it.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_22.png|200px|left|frame]]<br />
'''Shivrat Chhabra''': <p>Shivrat Chhabra is a rising junior at Columbia University, majoring in Chemical Engineering and minoring in Biomedical Engineering. He’s always been interested in bioengineering on the micro-scale, and joined the iGEM team to further that interest. Outside of the academic sphere, he is also involved in ballroom dance.</p><br />
<br />
<br />
<br />
<h2>'''High School Students'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_23.png|200px|left|frame]]<br />
'''Richard Shi''': <p>Richard Shi is a high school research student at Jericho High School. He had previously studied and written a paper based on the Dye Sensitized Solar Cell at Farmingdale University. He joined iGEM to vary his exposure to different sciences (moving from the engineering sciences to synthetic biology) and hopes to collect data for the upcoming Intel STS competition. He hopes to bring much to the table, despite being in high school.</p><br />
<br />
|}<br />
<br />
== '''What we did''' ==<br />
<br />
(Provide proper attribution for all work)<br />
<br />
== '''Where we're from''' ==<br />
<br />
Everywhere, =]</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/TeamTeam:Columbia-Cooper-NYC/Team2012-05-31T19:59:02Z<p>FourEyeGuy1962: </p>
<hr />
<div>{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Columbia-Cooper-NYC_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
|[[Image:Columbia-Cooper-NYC_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Columbia-Cooper-NYC | Team Columbia-Cooper-NYC]]<br />
|}<br />
<br />
<br />
<!--- The Mission, Experiments ---><br />
<br />
{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Columbia-Cooper-NYC|Home]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Columbia-Cooper-NYC Official Team Profile]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Project|Project]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Modeling|Modeling]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Notebook|Notebook]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Safety|Safety]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
<br />
<br />
<br />
<h2>'''Advisors'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Advisor_1.png|left|frame]]<br />
'''David Orbach''': <br />
<p>David Orbach joined Cooper Union in the summer of 2008 with a BS in Agricultural and Biological Engineering from Cornell University and a MS in Biomedical Engineering from the University of Rochester. Before joining Cooper he also earned an MD, did an intern year, and developed an interest in improving efficiency and patient throughput in the Emergency Room setting. He teaches several biology and biomedical engineering courses, including cell and molecular biology, physiology, and microbiology; helps direct the Kanbar Center for Biomedical Engineering; and serves as the college’s pre-medical advisor. Outside of Cooper, David now helps create iPhone apps and workbooks for children. See www.Brain-go.com.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Advisor_2.png|200px|left|frame]]<br />
'''Scott A. Banta''': <br />
<br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Grad_Student_1.png|200px|left|frame]]<br />
'''Grad Student 1''': <br />
<p>Our leader</p><br />
<br />
<br />
<h2>'''Undergraduates'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_1.png|200px|left|frame]]<br />
'''Aakash Mansukhani''': <p>When he’s not obsessively watching American Idol videos or playing tunes on his guitar, Aakash Mansukhani studies chemical engineering at Columbia University. As a rising sophomore, Aakash hopes that participating in IGEM will help him learn more about how principles from chemical engineering and synthetic biology can be combined to program bacteria. In his free time, Aakash loves to sing and reinvent pop songs by putting his own acoustic spin on them.</p> <br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_2.png|200px|left|frame]]<br />
'''Akachi Ukwu''': <p>Akachi is a rising Sophomore at Columbia University. Her potential major is Chemical Engineering. She was interested in IGEM because she wanted to learn about the many ways she can apply what she is being taught in school to real world problems. Akachi also enjoys watching soap operas.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_3.png|200px|left|frame]]<br />
'''Pnina Grossman''': <p>Pnina is a rising sophomore at The Cooper Union. She is currently in the BSE track there (with a possibility of switching to mechanical engineering), and hopes to specialize in biomedical engineering. IGEM seemed like a great opportunity to get some real hands-on experience in study of biology and problem-solving combined.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_4.png|200px|left|frame]]<br />
'''Naimun Siraj''': <p>Naimun is a rising Sophomore at Columbia University. He began the year as a Physics major and changed to Biomedical Engineering followed up by a change to Electrical Engineering to Applied Physics and finally, to Chemical Engineering. IGEM seemed like an opportunity for him to learn more about some of the applications of engineering and its consequences. Naimun loves reading about theoretical physics and hopes to die in a black hole one day.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_5.png|200px|left|frame]]<br />
'''Sara Chuang''': <p>Sara just finished her third year as a Chemical Engineer at Columbia University. She is interested in pharmaceuticals and protein engineering. IGEM was particularly appealing, because she wanted a chance to pursue a fun application of synthetic biology. Sara also enjoys super hero movies.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_6.png|200px|left|frame]]<br />
'''Roshan Ramkeesoon''': <p>Roshan is a rising sophomore majoring in chemical engineering at Columbia University. He is interested in working in alternative energy. He joined the IGEM team because it was a great opportunity to apply engineering principles to solve real world problems while gaining invaluable hands-on experience.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_7.png|200px|left|frame]]<br />
'''Nicholas Mannarino''': <p>Nicholas Mannarino is a rising sophomore at The Cooper Union. He is studying chemical engineering, with a hope to specialize in biomedical engineering and biotechnology. He joined IGEM because it seemed like a great way to spend a summer getting acquainted with a field he is interested in. In his spare time, Nicholas enjoys playing the guitar and long-distance running.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_8.png|200px|left|frame]]<br />
'''Anna Mai''': <p>Anna Mai is a rising junior majoring in chemical engineering at Columbia University, with a minor in environmental engineering. She joined IGEM because it presented an interesting medium for interacting with engineers around the world and providing hands on experience in the highly applicable field of synthetic biology. In her spare time she enjoys playing ultimate Frisbee, building paper crafts, and serenading her neighbors (not well).</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_9.png|200px|left|frame]]<br />
'''Udochukwu (Ud) Okorafor''': <p>Ud Okorafor is a rising senior at Columbia University. He is majoring in chemical engineering and has interests in protein engineering and pharmaceuticals. He joined IGEM because he enjoyed the research he had done previously on genetic engineering of E. coli. In his spare time, he enjoys playing various sports, reading science fiction books, and watching movies.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_10.png|200px|left|frame]]<br />
'''Saimon Sharif''': <p>Saimon is a rising sophomore at The Cooper Union. He is studying Chemical Engineering and intends to minor in Mathematics. He joined IGEM because it gives him the opportunity to apply engineering and creativity to biology. In his spare time, Saimon enjoys listening to alternative rock and watching science fiction television shows.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_11.png|200px|left|frame]]<br />
'''Kirsten Nicassio''': <p>Kirsten Nicassio just finished her freshman year at The Cooper Union. She is majoring in chemical engineering, with an intended math minor. She joined IGEM because of interest in the field of biomedical engineering. In her spare time, Kirsten enjoys reading, knitting, and swimming.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_12.png|200px|left|frame]]<br />
'''Marjana Chowdhury''': <p>Despite being from the bustling streets of New York City, Marjana was born to live in the wild. This nature lover and rising sophomore intends to major in Environmental Biology at Columbia University. In the past, Marjana's research has scaled a size spectrum ranging from immense invasive species to minuscule endangered species. As part of the Columbia-Cooper iGEM team, she is excited about her newest and smallest challenge yet, microorganisms.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_13.png|200px|left|frame]]<br />
'''Jackie Song''': <p>Jackie Song is a rising sophomore studying mechanical engineering at The Cooper Union. She joined iGEM out of curiosity about the processes and techniques used in synthetic biology. Jackie enjoys playing the flute and meshing gears. </p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_14.png|200px|left|frame]]<br />
'''Peter Liu''': <p>Peter Liu is a rising senior at The Cooper Union majoring in Chemical Engineering with a minor in biomedical engineering. He joined the igem team this year to further his knowledge and lab skills in the field of synthetic and microbiology.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_15.png|200px|left|frame]]<br />
'''Jang suk Roh''': <p>Jang suk Roh is a rising Junior at the Cooper Union majoring in Chemical Engineering. He likes doing lab work related to microbiology. He is also a front page featured redditor.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_16.png|200px|left|frame]]<br />
'''Swetha Chandrasekar''': <p>Swetha Chandrasekar is a rising Sophomore studying Chemical Engineering with a Biomedical Minor. Her avid interests and research done in biomedical device design, biorobotics, virology and bacterial chemistry drew her to be a part of iGEM. She hopes to apply her interests in working as a member of the Cooper-Columbia team to create something novel and inspiring! Outside of academics, Swetha loves singing, dancing and drawing.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_17.png|200px|left|frame]]<br />
'''Chauncy Yin''': <p>Chauncy Yin is a rising senior majoring in chemical engineering and minoring in materials & science at Columbia University. His research focuses on developing multifunctional magnetic nanoparticles as delivery platforms for therapeutic and diagnostic agents. He joins IGEM because he wants to apply the biology knowledge he learns in IGEM to the research and development of new pharmaceutical vehicles.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_18.png|200px|left|frame]]<br />
'''Vincent Xu''': <p>Vincent is a rising senior at Columbia University majoring in chemical engineering and minoring in applied mathematics. He is more interested in computational modeling than lab work and has been doing research in the applied math department since the summer of his freshman year. He decided to join IGEM because he thinks that it’s a good chance to learn something about biology, which is a subject he hasn’t studied since high school, and to get involved in any computational or modeling work. In addition to enjoying popular activities that college students engage in, such as eating and sleeping, Vincent does ballroom dancing.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_19.png|200px|left|frame]]<br />
'''Yuta Makita''': <p>Yuta Makita is a rising sophomore studying chemical engineering at the Cooper Union. Yuta joined the iGEM team with an interest in research based study and process of synthetic biology and the microscopic world. In addition to academic studies, he enjoys taking part in orchestra related activities by playing the viola.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_20.png|200px|left|frame]]<br />
'''Ciera Lowe''': <p>Ciera is a rising junior at The Cooper Union majoring in chemical engineering with a minor in biomedical engineering. She joined the iGEM team because this competition provides an amazing opportunity to gain hands on experience in synthetic biology, an exciting field full of potential to improve the world we live in. In addition to her studies, Ciera keeps busy by playing foosball on Cooper’s newly acquired table, playing basketball with Cooper’s women’s team or organizing events with the engineering student council and Cooper’s National Society of Black Engineers chapter.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_21.png|200px|left|frame]]<br />
'''Steven Neuhaus''': <p>Steven Neuhaus is a rising sophomore who studies chemical engineering at The Cooper Union for the Advancement of Science and Art. He’s quite fond of the idea of using little things to solve big problems, and joined iGEM because it provides a tremendous opportunity to do just that (and also time to play in the lab!). Steven also enjoys pointing out that writing about oneself in the third person is extremely awkward, is interested in most things that are interesting, and if you show him something cool, he’s usually more than glad to run with it.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_22.png|200px|left|frame]]<br />
'''Shivrat Chhabra''': <p>Shivrat Chhabra is a rising junior at Columbia University, majoring in Chemical Engineering and minoring in Biomedical Engineering. He’s always been interested in bioengineering on the micro-scale, and joined the iGEM team to further that interest. Outside of the academic sphere, he is also involved in ballroom dance.</p><br />
<br />
<br />
<h2>'''High School Students'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_23.png|200px|left|frame]]<br />
'''Richard Shi''': <p>Richard Shi is a high school research student at Jericho High School. He had previously studied and written a paper based on the Dye Sensitized Solar Cell at Farmingdale University. He joined iGEM to vary his exposure to different sciences (moving from the engineering sciences to synthetic biology) and hopes to collect data for the upcoming Intel STS competition. He hopes to bring much to the table, despite being in high school.</p><br />
<br />
|}<br />
<br />
== '''What we did''' ==<br />
<br />
(Provide proper attribution for all work)<br />
<br />
== '''Where we're from''' ==<br />
<br />
Everywhere, =]</div>FourEyeGuy1962http://2012.igem.org/Team:Columbia-Cooper-NYC/TeamTeam:Columbia-Cooper-NYC/Team2012-05-31T19:58:50Z<p>FourEyeGuy1962: </p>
<hr />
<div>{|align="justify"<br />
|You can write a background of your team here. Give us a background of your team, the members, etc. Or tell us more about something of your choosing.<br />
|[[Image:Columbia-Cooper-NYC_logo.png|200px|right|frame]]<br />
|-<br />
|<br />
|[[Image:Columbia-Cooper-NYC_team.png|right|frame|Your team picture]]<br />
|-<br />
|<br />
|align="center"|[[Team:Columbia-Cooper-NYC | Team Columbia-Cooper-NYC]]<br />
|}<br />
<br />
<br />
<!--- The Mission, Experiments ---><br />
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{| style="color:#1b2c8a;background-color:#0c6;" cellpadding="3" cellspacing="1" border="1" bordercolor="#fff" width="62%" align="center"<br />
!align="center"|[[Team:Columbia-Cooper-NYC|Home]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Team|Team]]<br />
!align="center"|[https://igem.org/Team.cgi?year=2012&team_name=Columbia-Cooper-NYC Official Team Profile]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Project|Project]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Parts|Parts Submitted to the Registry]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Modeling|Modeling]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Notebook|Notebook]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Safety|Safety]]<br />
!align="center"|[[Team:Columbia-Cooper-NYC/Attributions|Attributions]]<br />
|}<br />
<br />
<br />
<br />
== '''Who we are''' ==<br />
{|border = "0"<br />
|-<br />
|rowspan="3"|<br />
<br />
<br />
<br />
<br />
<br />
<h2>'''Advisors:'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Advisor_1.png|left|frame]]<br />
'''David Orbach''': <br />
<p>David Orbach joined Cooper Union in the summer of 2008 with a BS in Agricultural and Biological Engineering from Cornell University and a MS in Biomedical Engineering from the University of Rochester. Before joining Cooper he also earned an MD, did an intern year, and developed an interest in improving efficiency and patient throughput in the Emergency Room setting. He teaches several biology and biomedical engineering courses, including cell and molecular biology, physiology, and microbiology; helps direct the Kanbar Center for Biomedical Engineering; and serves as the college’s pre-medical advisor. Outside of Cooper, David now helps create iPhone apps and workbooks for children. See www.Brain-go.com.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Advisor_2.png|200px|left|frame]]<br />
'''Scott A. Banta''': <br />
<br />
<br />
<br />
[[Image:Columbia-Cooper-NYC_Grad_Student_1.png|200px|left|frame]]<br />
'''Grad Student 1''': <br />
<p>Our leader</p><br />
<br />
<br />
<h2>'''Undergraduates'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_1.png|200px|left|frame]]<br />
'''Aakash Mansukhani''': <p>When he’s not obsessively watching American Idol videos or playing tunes on his guitar, Aakash Mansukhani studies chemical engineering at Columbia University. As a rising sophomore, Aakash hopes that participating in IGEM will help him learn more about how principles from chemical engineering and synthetic biology can be combined to program bacteria. In his free time, Aakash loves to sing and reinvent pop songs by putting his own acoustic spin on them.</p> <br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_2.png|200px|left|frame]]<br />
'''Akachi Ukwu''': <p>Akachi is a rising Sophomore at Columbia University. Her potential major is Chemical Engineering. She was interested in IGEM because she wanted to learn about the many ways she can apply what she is being taught in school to real world problems. Akachi also enjoys watching soap operas.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_3.png|200px|left|frame]]<br />
'''Pnina Grossman''': <p>Pnina is a rising sophomore at The Cooper Union. She is currently in the BSE track there (with a possibility of switching to mechanical engineering), and hopes to specialize in biomedical engineering. IGEM seemed like a great opportunity to get some real hands-on experience in study of biology and problem-solving combined.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_4.png|200px|left|frame]]<br />
'''Naimun Siraj''': <p>Naimun is a rising Sophomore at Columbia University. He began the year as a Physics major and changed to Biomedical Engineering followed up by a change to Electrical Engineering to Applied Physics and finally, to Chemical Engineering. IGEM seemed like an opportunity for him to learn more about some of the applications of engineering and its consequences. Naimun loves reading about theoretical physics and hopes to die in a black hole one day.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_5.png|200px|left|frame]]<br />
'''Sara Chuang''': <p>Sara just finished her third year as a Chemical Engineer at Columbia University. She is interested in pharmaceuticals and protein engineering. IGEM was particularly appealing, because she wanted a chance to pursue a fun application of synthetic biology. Sara also enjoys super hero movies.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_6.png|200px|left|frame]]<br />
'''Roshan Ramkeesoon''': <p>Roshan is a rising sophomore majoring in chemical engineering at Columbia University. He is interested in working in alternative energy. He joined the IGEM team because it was a great opportunity to apply engineering principles to solve real world problems while gaining invaluable hands-on experience.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_7.png|200px|left|frame]]<br />
'''Nicholas Mannarino''': <p>Nicholas Mannarino is a rising sophomore at The Cooper Union. He is studying chemical engineering, with a hope to specialize in biomedical engineering and biotechnology. He joined IGEM because it seemed like a great way to spend a summer getting acquainted with a field he is interested in. In his spare time, Nicholas enjoys playing the guitar and long-distance running.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_8.png|200px|left|frame]]<br />
'''Anna Mai''': <p>Anna Mai is a rising junior majoring in chemical engineering at Columbia University, with a minor in environmental engineering. She joined IGEM because it presented an interesting medium for interacting with engineers around the world and providing hands on experience in the highly applicable field of synthetic biology. In her spare time she enjoys playing ultimate Frisbee, building paper crafts, and serenading her neighbors (not well).</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_9.png|200px|left|frame]]<br />
'''Udochukwu (Ud) Okorafor''': <p>Ud Okorafor is a rising senior at Columbia University. He is majoring in chemical engineering and has interests in protein engineering and pharmaceuticals. He joined IGEM because he enjoyed the research he had done previously on genetic engineering of E. coli. In his spare time, he enjoys playing various sports, reading science fiction books, and watching movies.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_10.png|200px|left|frame]]<br />
'''Saimon Sharif''': <p>Saimon is a rising sophomore at The Cooper Union. He is studying Chemical Engineering and intends to minor in Mathematics. He joined IGEM because it gives him the opportunity to apply engineering and creativity to biology. In his spare time, Saimon enjoys listening to alternative rock and watching science fiction television shows.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_11.png|200px|left|frame]]<br />
'''Kirsten Nicassio''': <p>Kirsten Nicassio just finished her freshman year at The Cooper Union. She is majoring in chemical engineering, with an intended math minor. She joined IGEM because of interest in the field of biomedical engineering. In her spare time, Kirsten enjoys reading, knitting, and swimming.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_12.png|200px|left|frame]]<br />
'''Marjana Chowdhury''': <p>Despite being from the bustling streets of New York City, Marjana was born to live in the wild. This nature lover and rising sophomore intends to major in Environmental Biology at Columbia University. In the past, Marjana's research has scaled a size spectrum ranging from immense invasive species to minuscule endangered species. As part of the Columbia-Cooper iGEM team, she is excited about her newest and smallest challenge yet, microorganisms.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_13.png|200px|left|frame]]<br />
'''Jackie Song''': <p>Jackie Song is a rising sophomore studying mechanical engineering at The Cooper Union. She joined iGEM out of curiosity about the processes and techniques used in synthetic biology. Jackie enjoys playing the flute and meshing gears. </p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_14.png|200px|left|frame]]<br />
'''Peter Liu''': <p>Peter Liu is a rising senior at The Cooper Union majoring in Chemical Engineering with a minor in biomedical engineering. He joined the igem team this year to further his knowledge and lab skills in the field of synthetic and microbiology.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_15.png|200px|left|frame]]<br />
'''Jang suk Roh''': <p>Jang suk Roh is a rising Junior at the Cooper Union majoring in Chemical Engineering. He likes doing lab work related to microbiology. He is also a front page featured redditor.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_16.png|200px|left|frame]]<br />
'''Swetha Chandrasekar''': <p>Swetha Chandrasekar is a rising Sophomore studying Chemical Engineering with a Biomedical Minor. Her avid interests and research done in biomedical device design, biorobotics, virology and bacterial chemistry drew her to be a part of iGEM. She hopes to apply her interests in working as a member of the Cooper-Columbia team to create something novel and inspiring! Outside of academics, Swetha loves singing, dancing and drawing.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_17.png|200px|left|frame]]<br />
'''Chauncy Yin''': <p>Chauncy Yin is a rising senior majoring in chemical engineering and minoring in materials & science at Columbia University. His research focuses on developing multifunctional magnetic nanoparticles as delivery platforms for therapeutic and diagnostic agents. He joins IGEM because he wants to apply the biology knowledge he learns in IGEM to the research and development of new pharmaceutical vehicles.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_18.png|200px|left|frame]]<br />
'''Vincent Xu''': <p>Vincent is a rising senior at Columbia University majoring in chemical engineering and minoring in applied mathematics. He is more interested in computational modeling than lab work and has been doing research in the applied math department since the summer of his freshman year. He decided to join IGEM because he thinks that it’s a good chance to learn something about biology, which is a subject he hasn’t studied since high school, and to get involved in any computational or modeling work. In addition to enjoying popular activities that college students engage in, such as eating and sleeping, Vincent does ballroom dancing.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_19.png|200px|left|frame]]<br />
'''Yuta Makita''': <p>Yuta Makita is a rising sophomore studying chemical engineering at the Cooper Union. Yuta joined the iGEM team with an interest in research based study and process of synthetic biology and the microscopic world. In addition to academic studies, he enjoys taking part in orchestra related activities by playing the viola.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_20.png|200px|left|frame]]<br />
'''Ciera Lowe''': <p>Ciera is a rising junior at The Cooper Union majoring in chemical engineering with a minor in biomedical engineering. She joined the iGEM team because this competition provides an amazing opportunity to gain hands on experience in synthetic biology, an exciting field full of potential to improve the world we live in. In addition to her studies, Ciera keeps busy by playing foosball on Cooper’s newly acquired table, playing basketball with Cooper’s women’s team or organizing events with the engineering student council and Cooper’s National Society of Black Engineers chapter.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_21.png|200px|left|frame]]<br />
'''Steven Neuhaus''': <p>Steven Neuhaus is a rising sophomore who studies chemical engineering at The Cooper Union for the Advancement of Science and Art. He’s quite fond of the idea of using little things to solve big problems, and joined iGEM because it provides a tremendous opportunity to do just that (and also time to play in the lab!). Steven also enjoys pointing out that writing about oneself in the third person is extremely awkward, is interested in most things that are interesting, and if you show him something cool, he’s usually more than glad to run with it.</p><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_22.png|200px|left|frame]]<br />
'''Shivrat Chhabra''': <p>Shivrat Chhabra is a rising junior at Columbia University, majoring in Chemical Engineering and minoring in Biomedical Engineering. He’s always been interested in bioengineering on the micro-scale, and joined the iGEM team to further that interest. Outside of the academic sphere, he is also involved in ballroom dance.</p><br />
<br />
<br />
<h2>'''High School Students'''</h2><br />
<br />
[[Image:Columbia-Cooper-NYC_Team_member_23.png|200px|left|frame]]<br />
'''Richard Shi''': <p>Richard Shi is a high school research student at Jericho High School. He had previously studied and written a paper based on the Dye Sensitized Solar Cell at Farmingdale University. He joined iGEM to vary his exposure to different sciences (moving from the engineering sciences to synthetic biology) and hopes to collect data for the upcoming Intel STS competition. He hopes to bring much to the table, despite being in high school.</p><br />
<br />
|}<br />
<br />
== '''What we did''' ==<br />
<br />
(Provide proper attribution for all work)<br />
<br />
== '''Where we're from''' ==<br />
<br />
Everywhere, =]</div>FourEyeGuy1962