From 2012.igem.org

(Difference between revisions)

Revision as of 11:02, 11 September 2012

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

10th July: Plated out several of the CSE kits.
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.
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. Plated up some more by sprinkling the polystyrene "sugar" on top of the agar.
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: 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.
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 Google to give a presentation on the iGEM project.
21st August: Ran the genomic extraction of ''Pseudomonas''.
22nd August: Ran the nanodrop spectrophotometry, prepared the CTAB protocol.

Anthony Cox

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.

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. Produced a new overnight culture of 01#502.
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 was growing and the only carbon source was polystyrene.

William Harrison

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. 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.
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 spectrophotometry, 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 Google to give a presentation on the iGEM project.
21st August: Ran the genomic extraction of ''Pseudomonas''.
22nd August: Prepared the samples for the gel, prepared the CTAB protocol.
27th August: Advertised UOL iGEM project at Aylestone Leisure centre.

Luke Thompson

7th July: started modelling Toluene 2,3-dioxygenase using RASWIN as a potential enzyme that, when modified, could accept and start degrading polystyrene
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.
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 Google to give a presentation on the iGEM project.
22nd August: Loaded the gel, prepared the CTAB protocol.
27th August: Advertised UOL iGEM project at Aylestone Leisure centre.

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.
27th July: Worked on the wiki.
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: Prepeared 5% polystyrene agar plates, took photos of bacteria cultures on plates, worked on wiki.

Nathan Hanna

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.

Reema Naran

10th July: Plated out several of the CSE kits.
17th August: Went to Google to give a presentation on the iGEM project.

Mohammed Idres

10th July: Plated out several of the CSE kits.

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.

Dr. Dalgleish

15th August: Suggested further steps to be taken in the genomic tip, showed Will how to use the Nanodrop spectrophotometer.
22nd August: Showed Chris how to use the Nanodrop spectrophotometer.

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''.

[edit]

@@ Line 126: / Line 126: @@
      <dt>17th August: Went to Google to give a presentation on the iGEM project.</dt>
      <dt>21st August: Ran the genomic extraction of ''Pseudomonas''.</dt>
+    <dt>22nd August: Ran the nanodrop spectrophotometry, prepared the CTAB protocol.</dt>
      <p> 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. </p>
@@ Line 210: / Line 211: @@
      <dt>17th August: Went to Google to give a presentation on the iGEM project.</dt>
      <dt>21st August: Ran the genomic extraction of ''Pseudomonas''.</dt>
+    <dt>22nd August: Prepared the samples for the gel, prepared the CTAB protocol.</dt>
      <dt>27th August: Advertised UOL iGEM project at Aylestone Leisure centre.</dt>
 </dt>
@@ Line 229: / Line 231: @@
      <dt>16th August: Produced the pellets of  DNA, and washed the DNA of salts.</dt>
      <dt>17th August: Went to Google to give a presentation on the iGEM project.</dt>
+    <dt>22nd August: Loaded the gel, prepared the CTAB protocol.</dt>
      <dt>27th August: Advertised UOL iGEM project at Aylestone Leisure centre.</dt>
       </dl>
@@ Line 307: / Line 310: @@
 <div class="day">
 <dl>
-     <dt>15th August: Suggested further steps to be taken in the genomic tip.</dt>
+     <dt>15th August: Suggested further steps to be taken in the genomic tip, showed Will how to use the Nanodrop spectrophotometer.</dt>
+    <dt>22nd August: Showed Chris how to use the Nanodrop spectrophotometer.</dt>
       <dt>&nbsp;</dt>
       </dl>

Team:Leicester/Attributions