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iGEM Leicester Test Page 2012

Attributions

Each team must clearly attribute work done by the team on this page. They must distinguish work done by the team from work done by others, including the host labs, advisors, instructors, graduate students, and postgraduate masters students.

Christopher Morton

3rd July: Morning lab induction, started making CSE kits for Styropack order.
4th July: Prepared lab ready to start work.
10th July: Plated out several of the CSE kits.
11th July: Set up the airing of the pentane polystyrene
12th July: Photographed all of the CSE kits for recording the bacterial growth. Helped with the testing of acetone on polystyrene. Made the 1st plate of dissolved polystrene embedded in the Luria agar as a test to see if the method worked. Made up dilutions of acetone and used methanol to see their effects on polystyrene.
13th July: Learnt how to use the grinder in an attempt to grind the polystyrene. Helped to work out the optimum way to make the "sugar" agar dishes.
16th July: Prepared the minimal media. Worked with the frozen polystyrene (-80oC) in an attempt to grind it down. Worked with the liquid nitrogen in a further attempt to grind the polystyrene down.
18th July: Finished making the control, 5% and 10% polystyrene agar plates and took them to the other lab to be plated with ''Pseudomonas''.
19th July: Shaved EPS to try and recreate our suspension. perfected the method and Plated up some more by sprinkling the polystyrene "sugar" on top of the agar.
23rd July: Went around town looking on the sponsorship drive.
30th July: making control plates, working with Toluene and dissolving polystyrene.

31st July: Helped to produce the minimal media plates for the ''E. coli'' and ''Pseudomonas. sp'' as control plates. Helped to produce the corning tubes for the liquid suspension of ''Pseudomonas sp''.
1st August: Produced the 15ml corning tubes for the suspension of ''Pseudomonas sp'' in rich media.
3rd August: Made the buffers B1 and B2 for the DNA extraction.
6th August - 9th August: Genomic DNA Extraction with QIAGEN Maxi prep.
10th August: Videod a lot of the Rockethub video, to almost have the video complete.
13th August: Worked on the Rockethub site, making it ready to be published. Prepared overnight cultures for the next Genomic tip.
14th August: Worked on the second Genomic extraction, prepared the samples for the gel, worked out how to adapt the tips to allow for pressure to be applied. Previously arranged and met with David the Chairman of the British Plastics Federation EPS division - resulting in a new sponsor of £1500.
15rd August: Loaded, ran and photographed the gel. Started the preperatation for the next tip, made the gel for tomorrow.
16th August: Produced the pellets of DNA, and washed the DNA of salts.
17th August: Went to the Google campus to give a presentation on the iGEM project at the Uk iGEM Meet up 2012 organised by NRP UEA iGEM Team.
21st August: Ran the genomic extraction of ''Pseudomonas''.
22nd August: Ran the nanodrop spectrometry, prepared the CTAB protocol.
23rd August: Started the gel and photographed it when done. Created protocol for the testing of 01#502, as well as made the plates required.
24th August: Made and poured the new gel. Loaded te samples after running a nanodrop to check the DNA concentrations. Made the new plates for the 01#502 for fresh colonies.
28th August: Photographed and Gram stained the 01#502 bacteria. Prepared new 01#502 bacteria for future tests.
29th August: Did the Gram stain againon the 01#502 bacteria. Did an oil immersion as well. Continued the gel at 40 Volts. Made new overnight cultures of 01#502. Photographed the gel.
30th August: Continued to run the overnight gel. Photographed the gel once complete. Made the new gel for the Sau3A1. Made the PCR aliquots and controls.
31st August: Loaded and started the Sau3A1 gel. Loaded the PCR gel. Cut the DNA out of the PCR gel. photographed the Sau3A1 gel. Looked at the 01#502 plates for signs of new growth.
3rd September: Worked out the concentrations for the 16s extraction. Photographed the gel.
4th September: Searched BLAST database for matches. Set up PCR. Re-plated orange, yellow and 01#502 colonies.
5th September: Set up boilate. set up and ran 16S PCR.
6th September: Made, loaded and ran a 2% electrophoresis gel of the PCR samples to run. BLAST searched to find out the Genus of the 16S ribosome of our 01#502. Helped prep for the Sau3A1 digest. Photographed the gel. Set up and ran the QIAGEN gel extraction after extracting the PCR samples from the gel. Set up PCR master mix, took aliquots and added in DNA Set up the PCR machine and ran the PCR.
7th September: Prepared and loaded PCR samples. Photographed gel. Set up PCR master mix.
10th September: Worked on primers using in Silico PCR and BLAST.

Anthony Cox

3rd July: Afternoon lab induction.
4th July: preparing lab ready to start work,
10th July: Plated out several of the CSE kits.
13th July: Used the mortar and pestle to try and grind the polystyrene. Learnt how to use the grinder in an attempt to grind the polystyrene.
16th July: Prepared the minimal media. Worked with the frozen polystyrene (-80oC) in an attempt to grind it down. Worked with the liquid nitrogen in a further attempt to grind the polystyrene down.
18th July: Finished making the control, 5% and 10% polystyrene agar plates and took them to the other lab to be plated with ''Pseudomonas''.
19th July: Plated up some more by sprinkling the polystyrene "sugar" on top of the agar.
1st August: Made the protocol for the DNA hybridization.
2nd August: Made the protocol for the DNA extraction test, as well as the growth curves by diluting a broth.
3rd August: Did the CFU colonies and dilutions test with ''E. coli''.
6th August: Altered the protocol for the dilutions experiment.
7th August: Worked for the whole day doing spectrophotometry to finally get the experiment right with a good protocol.
8th August: Repeated the CFU colonies and dilutions test with ''E. coli''.
9th August: Counted colonies from the successful test, and then produced a growth curve for future reference.
14th August: Ran both of the doubling experiments for ''Pseudomonas'' to give a basic time to work with in the dilutions experiment. Melted the agar and poured all the plates required.
16th August: Ran the ''Pseudomonas'' growth curve experiment.
22nd August: Tried counting the colonies for the growth curve experiment. Created new protocol with the plate spinner.
10th September: Photographed gel. Loaded Sau3A1 digest.

Philip Higgs

12th July: Photographed all of the CSE kits for recording the bacterial growth. Helped with the testing of acetone on polystyrene. Made the 1st plate of dissolved polystrene embedded in the Luria agar as a test to see if the method worked. Made up dilutions of acetone and used methanol to see their effects on polystyrene.
13th July: Used the mortar and pestle to try and grind the polystyrene. Learnt how to use the grinder in an attempt to grind the polystyrene.
16th July: Prepared the minimal media. Worked with the frozen polystyrene (-80oC) in an attempt to grind it down. Worked with the liquid nitrogen in a further attempt to grind the polystyrene down.
19th July: Spent almost the whole day researching methods of transport to Amsterdam and hotels for the stay at the Jamboree to find the best deal both pricewise and comfort.
20th July: Produced the nutrient broth for the liquid suspension plates.
23rd July: Went around town looking on the sponsorship drive.
31st July: Helped to produce the minimal media plates for the ''E. coli'' and ''Pseudomonas. sp'' as control plates. Helped to produce the corning tubes for the liquid suspension of ''Pseudomonas sp''.
1st August: Sorted out all the information needed to pick the correct DNA extraction kit. Produced the 15ml corning tubes for the suspension of ''Pseudomonas sp'' in rich media.
2nd August: Innoculated tshe 15ml corning tube with ''E. coli'' for the DNA extraction test.
3rd August: Did the CFU colonies and dilutions test with ''E. coli''.
6th August: Altered the protocol for the dilutions experiment. Used the spectrophotometer to give the DNA digest the starting value. Innoculated the 3ml of luria broth for the final ''E. coli'' test.
7th August: Worked for the whole day doing spectrophotometry to finally get the experiment right with a good protocol.
8th August: Repeated the CFU colonies and dilutions test with ''E. coli''.
9th August: Counted colonies from the successful test.
10th August: Videod a lot of the Rockethub video, to almost have the video complete.
13th August: Plated out all the CSE kits onto 5% polystyrene on minimal agar.
14th August: Ran both of the doubling experiments for ''Pseudomonas'' to give a basic time to work with in the dilutions experiment. Labelled up all the plates and eppendorfs ready for the next day.
15th August: Produced the overnight culture ready for the growth curve experiment.
16th August: Ran the ''Pseudomonas'' growth curve experiment.
17th August: Counted colonies for the experiment, created the gel, then ran the gel for the DNA digestion experiment.
20th August: Checked and edited the Rockethub site to work out most of the errors and got it ready for publishing after the weekly meeting. Created the overnight culture to rerun the growth curve experiment.
21st August: Edited the protocol, then reran the ''Pseudomonas'' growth curve experiment.
22nd August: Reran ''Pseudomonas'' growth curve experiment using the plate spinner.
23rd August: Streaked out the plates to see if the growth curve experiment failed due to agar or the bacteria. Created new overnight culture.
24th August: Did final run of ''Pseudomonas'' growth curve experiment.
27th August: Advertised UOL iGEM project at Aylestone Leisure centre.
28th August: Counted the colonies on yesterdays plates, tabulated the data then made a graph using excel to show the growth curve. Did some administration for the iGEM team (general sorting out of everything). Wrote the equiz into word, and the answers into excel ready for publishing.
29th August: Made the minimal media. Produced lots of plates for the next few experiments. Produced the overnight culture of 01#502 for tomorrow.
30th August: Ran the doubling experiment of 01#502 in the morning to work out doubling time. Ran the first growth curve experiment for 01#502.
31th August: Reran growth curve experiment with a greater starting dilution.
3rd September: Worked on the wiki for most of the day sorting out spelling and our half of the groups past 3 weeks of work.
4th September: Made up a load more plates, and plated out the colonies for the test. Took spec readings of the minimal media broth, that indicated bacteria it was growing and the only carbon source was polystyrene.
6th September: Worked on tasks set in the meeting on the 5th.
7th September: Produced a rough poster for the lecture the team intends to give before going to Amsterdam.
11th September: Looked over and edited the entire wiki for August, correcting grammar and changing it to the required format.

William Harrison

3rd July: Morning lab induction, started making CSE kits for Styropack order.
4th July: Prepared lab ready to start work.
10th July: Wrote the wiki entries for all of the plating and details.
16th July: Prepared the minimal media. Worked with the liquid nitrogen in a further attempt to grind the polystyrene down.
18th July: Finished making the control, 5% and 10% polystyrene agar plates and took them to the other lab to be plated with ''Pseudomonas''.
19th July: Shaved EPS to try and recreate our suspension.Made the method and tested it worked to sprinkle the polystyrene "sugar" on top of the agar. Plated up some more by sprinkling the polystyrene "sugar" on top of the agar.
20th July: Produced the nutrient broth for the liquid suspension plates.
23rd July: Filled out the COSHH form. Went around town looking on the sponsorship drive.
24th July: Filled out new COSHH form. Called the potential sponsors found on the 23rd.
30th July: making control plates, working with Toluene and dissolving polystyrene

31st July: Helped to produce the minimal media plates for the ''E. coli'' and ''Pseudomonas. sp'' as control plates.
2nd August: Found all the ingredients needed for the experiments on the 3rd.
3rd August: Worked around with other labs to find all the ingredients for the buffers B1 and B2 for the DNA extraction test.
6th August - 9th August: Genomic DNA Extraction with QIAGEN Maxi prep.
14th August: Worked on the second Genomic extraction, prepared the samples for the gel, prepared the agarose and made the gel ready.
15rd August: Nano drop spectrometry, ran the lysate to try and get pure DNA. Started the preparation for the next tip.
16th August: Produced the pellets of DNA, and washed the DNA of salts.
17th August: Went to the Google campus to give a presentation on the iGEM project at the Uk iGEM Meet up 2012 organised by NRP UEA iGEM Team.
21st August: Ran the genomic extraction of ''Pseudomonas''.
22nd August: Prepared the samples for the gel, prepared the CTAB protocol.
23rd August: Made the spectrophotometry reading of the overnight culture. Created the new lysate.
24th August: Prepared the 1ml culutres for the robot and CTAB. Ran the CTAB for the 6 tubes.
27th August: Advertised UOL iGEM project at Aylestone Leisure centre.
28th August: Made and prepared the gel.
29th August: Organised the PCR and antibiotic test plates. Made the overnight gel. Loaded the Sau3A1 gel.
30th August: Photographed the overnight gel. Found the OD for the overnight culture. Ran the boilate and serial dilutions of 01#502.
31st August: Made a 2% gel for the PCR to be run on. Made more TBE buffer. Took over the gel extraction once the samples were removed. Made another 2% gel.
5th September: Made the minimal broth. Ran the boilate.

7th September: Made several new gels.
10th September: Found the DNA markers used. Got Pseudomonas putida strains from Sarah Glenn. Then inocculated them into luria broth and onto luria agar and moved into 30 degree incubator in MSB. Restreaked 01#502 onto new plates. Made multiple 2% gels. Assisted in the gel extraction. Photographed gels.

Luke Thompson

3rd July: Afternoon lab induction.
4th July: Preparing lab ready to start work.
7th July: Started modelling on Toluene 2,3-dioxygenase.
9th July: Determined the protocol for plating out all the CSE kits coming back.
10th July: Plated out several of the CSE kits.
12th July: Helped with the testing of acetone on polystyrene. Made up dilutions of acetone and used methanol to see their effects on polystyrene.
13th July: Learnt how to use the grinder in an attempt to grind the polystyrene. helped work out the optimum way to make the "sugar" agar dishes
19th July: Made the method and tested it worked to sprinkle the polystyrene "sugar" on top of the agar.
3rd August: Made the buffers B1 and B2 for the DNA extraction.
6th August - 9th August: Genomic DNA Extraction with QIAGEN Maxi prep.
9th August: Started using Pymol to model mutations that could potentially allow the terminal phenyl side chains of polystyrene to fit into its active site.
14th August: Worked on the second Genomic extraction.
16th August: Produced the pellets of DNA, and washed the DNA of salts.
17th August: Went to the Google campus to give a presentation on the iGEM project at the Uk iGEM Meet up 2012 organised by NRP UEA iGEM Team.
22nd August: Loaded the gel, prepared the CTAB protocol.
23rd August: Worked on modelling mutagenesis of toluene 2,3-dioxygenase, found the base mutations for polystyrene. Created the 2nd and 3rd lysates.
24th August: Remade the slow gel. Loaded the slow gel.
27th August: Advertised UOL iGEM project at Aylestone Leisure centre.
28th August: Loaded the gel to be ran.
29th August: Continued to model on toluene 2,3-dioxygenase. Created then ran the Sau3A1 prep.
30th August: Photographed the overnight gel. Reran the Sau3A1 experiment. Thought of a new method for plating out the bacteria, with a strip left bare down the middle showing that no contamination was there.
4th September: Searched BLAST database for matches.
5th September: Made MMP plates.
7th September: Performed the Sau3A1 digest. Designed primers. Photographed gel. Helped set up the PCR samples.
10th September: Found the DNA markers used. Loaded DNA digest from last week. Photographed DNA digest. Finished the work on primers. Photogrpahed Sau3A1 digest.

Emily Halsey

12th July: Photographed all of the CSE kits for recording the bacterial growth.
13th July: Started to design the wiki on paper.
16th July: Leant how to use the Matlab programming language.
17th July: Starts work design wiki in html.
18th July: Worked on the wiki.
19th July: Worked on the wiki.
23rd July: Worked on the wiki, making cartoons and animations.
24th July: Learns more Matlab.
25th July: Worked on the wiki.
26th July: Worked on the wiki – creating the notebook pages. Helped organise and run cake sale

27th July: Worked on the wiki. Helped organise and run the cake sale
28th July: Worked on the wiki.
17th August: Helped team attend UK iGEM UK meetup.
20th August: Created animation for the homepage of wiki.
26th August: Wrote up some of the modelling page on the wiki.
28th August: Worked on the wiki and researched the Michaelis-Menton equation.
29th August: Came into labs, took photos of bacteria on plates, worked on the model.
30th August: Took photos of bacteria cultures on plates. Prepeared 5% polystyrene agar plates. Worked on wiki.
7th September: Photographed gel.

Nathan Hanna

3rd July: Morning lab induction, started making CSE kits for Styropack order.
16th July: Wrote and edited the Rockethub script.
17th-31st July: Did editing/stitching together of the current Rockethub video, as it was produced.
1st August: Tested the cooling for our hybridization in the DNA extraction and isolation processes.
2nd-4th August: Worked on the outtake reel for the video.
5th-7th August: Narration of the video and trimming of the introduction and attempting to fix Chris' sections together to make them flow.
8th-9th August: Trimming and sound quality check of Rockethub video.
10th August: Videod a lot of the Rockethub video, to almost have the video complete.
11th August: Checked and edited Phil's section of Rockethub video.
13th-14th August: Trimming and sound quality check of Luke's section as well as the normalisation of the narration (as it was far too loud in comparation to other segments) and the addition of Anthony's Layman terms explanation.
14th August: Ran both of the doubling experiments for ''Pseudomonas'' to give a basic time to work with in the dilutions experiment.
15th-17th August: On the 15th and in gaps of experiment, did the video revamp of the prize section as well as an attempt to remove wind from other segments, especially the park.
16th August: Ran the ''Pseudomonas'' growth curve experiment.
17th August: Counted colonies for the experiment, ran the gel for the DNA digestion experiment.
18th-20th August: Finalisation of all segments as well as adding Will's section, the prizes and Nathan's section, and smoothed out the audio more.
20th August: Corrected the entire wiki, spelling errors, grammatical errors and punctuation errors.
21st August: Had to fix the video after a minor frame glitch froze the video at the funding segment. Then edited the protocol, then reran the ''Pseudomonas'' growth curve experiment.
31st August: Cleared the iGEM email and sorted out data onto the Google map. Sent emails to get CSE kits returned to us. Readied materials for autoclaving and tidied the lab. Advertised the Rockethub to try and get more funds. Worked on some of the deadline tasks for the competition. Made the minimal media broth.
3rd September: Worked out the concentrations for the 16s extraction. loaded the extraction gel.
10th September: Photographed DNA digest then again later after it had been run longer.

Reema Naran

3rd July: Produced a mechanism, then checked the route with Mohammed.
5th July: Researched organic mechanisms.
9th July: Made notes and drafted mechanisms on polystyrene degredation.
10th July: Lab induction. Plated out several of the CSE kits.
11th July: Looked over Idres' 1st mechanism and made some adjustments.
12th July: Looked through a polymer chemistry booklet.
19th July: Confirmed retrosynthesis in mechanism pathway.
23rd July: Found more retrosynthesis processes.
26th July: Worked on the cyanide route as products are hard to identify, and the process would probably be too dangerous.
27th July: Continued work on the cyanide process.
30th July: Created a hazards list, ready to be checked and gone through.
13th August: Edited and completed the hazards list.
16th August: Checked the final version of the 1st mechanism.
17th August: Went to the Google campus to give a presentation on the iGEM project at the Uk iGEM Meet up 2012 organised by NRP UEA iGEM Team.
22nd August: Drafted new mechanism to produce hydroxy polymer.
23rd August: Continued work on the new mechanism.
24th August: The new mechanism needed editing but it looked promising, so finished the mechanism.
28th August: Researched organometallic chemistry as a possible route.
30th August: Started work on the 3rd mechanism using TMS as a solvent.
31st August: The 3rd mechanism using is drawn, and forms the desired product by focusing on the acid anhydride chain.
5th September: Looked at a 4th mechanism invloving the dehyrdration of the H-C bond in mechanism 3.
11th September: Created hazards for the 2nd and 3rd mechanisms.
12th September: Looked over Mohammed's rate laws. Looked how to dehydrate the proton from the hydrocarbon.

Mohammed Idres

2nd July: Started pitching ideas about mechanisms.
3rd July: Drafted and established 1st mechanism.
5th July: Researched organic mechanisms.
9th July: Made notes and drafted mechanisms on polystyrene degredation.
10th July: Lab induction. Plated out several of the CSE kits.
11th July: Researched current methods or recycling polystyrene.
12th July: Looked through a polymer chemistry booklet.
19th July: Confirmed retrosynthesis in mechanism pathway.
26th July: Reworked 1st mechanism and fixed errors. Worked on the cyanide route as products are hard to identify, and the process would probably be too dangerous.
3rd August: Checked the hazards list made by Reema.
9th August: Looked through a large polymer chemistry textbook for more detailed mechanisms.
15th August: Finalized 1st mechanism.
22nd August: Drafted new mechanism to produce hydroxy polymer.
23rd August: Continued work on the new mechanism.
24th August: The new mechanism needed editing but it looked promising, so finished the mechanism.
28th August: Researched organometallic chemistry as a possible route.
30th August: Started work on the 3rd mechanism using TMS as a solvent.
5th September: Looked at a 4th mechanism invloving the dehyrdration of the H-C bond in mechanism 3.
11th September: Worked on the rate laws for the mechanisms.
13th September: Looked into using radiation to break individual bonds, until realized the full mechanism needed to be finalized. Continued to work through and finish the 3rd mechanism so the gas phase kinetics could be applied for the radiation.

Dr. Badge

14th August: Worked on the second Genomic extraction, prepared the samples for the gel, worked out how to adapt the tips to allow for pressure to be applied.
23rd August: Suggested experiment to run and see what caused the failed growth experiment. Created two new plates of the 01#502 for definite fresh single colonies.
24th August: Vacuum dried the precipitated DNA ready for the slow gel.
30th August: Produced some dNTP's. Made the master mix for the PCR. Programmed the PCR block.
31st August: Cut the DNA out of the PCR gel. Looked at the 01#502 plates for signs of new growth.
4th September: Discussed options for engineering a BioBrick. Set up PCR.
10th September: Checked the primers from Friday.

Dr. Dalgleish

15th August: Suggested further steps to be taken in the genomic tip, showed Will how to use the Nanodrop spectrometer.
22nd August: Showed Chris how to use the Nanodrop spectrometer.
31st August: Suggested changes to the Sau3A1 for a better gel.
4th September: Discussed options for engineering a BioBrick.

Dr. Bayliss

Sue Hardy (Lab technician)

29th July: Plated up some ''E. coli'' for the team to use.
5th August: Produced the overnight cultures of ''E. coli'' for the team to use.

Alex (Researcher)

Carlo (Researcher)

16th July: Brought the team liquid nitrogen and showed us how to use it safely.

Pseudomonas researcher - Jaspreet Sahota

18th July: Plated out the control, 5% and 10% polystyrene plates with 5 strains of ''Pseudomonas''.

Sarah Curtis

[edit]

@@ Line 395: / Line 395: @@
      <dt>31st August: Cut the DNA out of the PCR gel. Looked at the 01#502 plates for signs of new growth.</dt>
 <dt>4th September: Discussed options for engineering a BioBrick. Set up PCR.</dt>
+<dt>10th September: Checked the primers from Friday.</dt>
       </dl>
 </div>

Team:Leicester/Attributions