Team:Northwestern/Notebook/Week1

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Notebook  <div style="margin: -40px 0px 0px 420px;font:35px helvetica; color:#444444;">    &nbsp; Week 1</div>
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==Day 6 - Monday, June 20th 2011==
 
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*Prepared all relevant buffers for competency procedure
 
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*Started growing our seed stock over night so that we could perform the competency procedure in the morning.
 
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*Obtained the 2011 distribution kit complete with DNA, plasmid backbones, pins and stickers!
 
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*Started a new transformation procedure with Part BBa_R0061 from the 2011 kit. We are mostly testing our transformation technique to make sure we are doing everything correctly.
 
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*Made a lot of progress finalizing the design of our project. We figured out what parts our project will need and determined where we will obtain each part.
 
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==Day 7 - Tuesday, June 21st 2011==
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*The transformations from yesterday appeared successful.
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*The TOP10 cells we started growing last night were already at an OD600 level above 0.3, so we immediately proceeded to the next steps in the competency procedure. After a couple of centrifuging and resuspending cycles, we stored the competent cells in the -80 freezer.
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*We held a meeting with our advisers and presented our idea for a quorum-sensing based Psuedomonas aeruginosa detector. The advisers seemed to like the idea, and we are moving forward with it. We may also integrate sensing of other bacteria such as salmonella and staph depending on how the project goes.
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*Investigated the process of planning our parts. We explored the sandbox tool on the registry and began to use tools like restriction enzyme mappers to make sure the parts would work properly.
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==Day 8 - Wednesday, June 22nd 2011==
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*Spent the morning making plates. We made 20 plates with each of the four main antibiotics.  
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*Started another round of transformation procedures, this time with actual parts that we will use in our project.
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<div style="margin: -40px 0px 18px 20px;font:24px helvetica;font-weight:550; color:#ffffff;"> Day 1 - Monday, June 13, 2011
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*Mapped the restriction sites and enzymes that we will need to use in order to get the final project up and running.  
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*Held a meeting to determine the different administrative roles and tasks that each team member will perform.
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*Took inventory of all the supplies in the lab and began organizing our benches.
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*Visited a graduate student in Professor Leonard's lab and learned the procedure to make chemically competent cells, which will allow us to begin the transformation process.
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*Most of the day was spent on various tasks to get the project up and running, such as setting up the wiki and learning how to autoclave.
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==Day 9 - Thursday, June 23rd 2011==
 
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*The transformations from last night appeared successful. There were many transformed colonies, although still slightly less than you would expect from fully competent colonies for our positive controls.
 
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*The promoter/RFP plasmid colonies were clearly red by lunchtime.
 
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*Finished analysis of the restriction sites, codon usage, and mRNA folding for the genes from P. Aeruginosa we may use.
 
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*Finished cataloging and inventory of parts that may be useful to our project.
 
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*Began transformations of parts we may use that came in the 2011 distribution kit.
 
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*Started overnight cultures with our transformed bacteria.
 
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*Began to store DNA from the used wells in the distribution kit in microcentrifuge tubes to ensure preservation.
 
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*Started another batch of competent cells
 
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==Day 10 - Friday, June 24th 2011==
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*The transformations appeared successful. All of the plates except one had colonies.
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*The competent cells once again grew faster than we were expect and had OD600 levels above 0.3 by the morning. We diluted the cells in order to lower their OD closer to the target level before proceeding with the rest of the procedure. We’ve also learned to aliquot smaller volumes of the cells because we only use 25 microliters per transformation.  
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<div style="margin: -40px 0px 18px 20px;font:24px helvetica;font-weight:550; color:#ffffff;"> Day 2 - Tuesday, June 14 2011
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*We began making a glycerol stock so that we can store our transformed bacteria.
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*We miniprepped the parts that we overnighted last night. When we were done, we tested the DNA concentration. The positive controls were both around 200-300 ng/uL and the part was about 65 ng/uL.
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*Obtained some TOP10 cells and plated them to begin the process of producing a stock solution, which will give us a continuous supply of chemically competent cells.  
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*We started overnight cultures from the 5 successful transformations from yesterday.
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*Used competent cells to begin the transformation process
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*On Saturday, we came in to transfer the overnight cultures into long-term glycerol stocks.
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*Finalized primary idea for project definition and created a timeline
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*Continued website design process
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<div class='right-heading'>Calendar</div><br><center>
 
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[[Team:Northwestern/Notebook/Week1|Week 1 - 6/12 to 6/18]]
 
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[[Team:Northwestern/Notebook/Week2|Week 2 - 6/19 to 6/25]]
 
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<div style="margin: -40px 0px 18px 20px;font:24px helvetica;font-weight:550; color:#ffffff;"> Day 3 - Wednesday, June 15 2011
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*Neither the transformation nor the stock solution plates showed any growth in the morning. We suspected the LB broth might be the problem  because it was the only thing common to both procedures.
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*Made new LB Broth and LB plates. After the plates were ready, we attempted the TOP10 stock solution procedure again.
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*Lots of brainstorming for secondary project ideas
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*Designed biosynthetic mechanism for primary project proposal.
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<div style="margin: -40px 0px 18px 20px;font:24px helvetica;font-weight:550; color:#ffffff;"> Day 4 - Thursday, June 16 2011
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*To our surprise, the original now 2 day old plate was filled with TOP10 colonies. One of the new plates from yesterday was in the incubator overnight and also had growth. Apparently the process just takes longer than we expected and nothing was wrong!
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*This allowed us to proceed with making the seed stock. Later in the day, we transferred several single colonies from the plates into LB broth and put them in the shaker overnight.
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*The team also continued researching our project and determining an exact method to achieve our goals.
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<div style="margin: -40px 0px 18px 20px;font:24px helvetica;font-weight:550; color:#ffffff;"> Day 5 - Friday, June 17 2011
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*We took the seed stock tubes out of the shaker, added gylcerol, aliquoted and stored them in the -80 freezer. We now have a supply of cells ready to be made competent at any time.
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*Also continued to finalize the project definition.
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Latest revision as of 03:40, 23 September 2011

RETURN TO IGEM 2010



day banner
Day 1 - Monday, June 13, 2011

  • Held a meeting to determine the different administrative roles and tasks that each team member will perform.
  • Took inventory of all the supplies in the lab and began organizing our benches.
  • Visited a graduate student in Professor Leonard's lab and learned the procedure to make chemically competent cells, which will allow us to begin the transformation process.
  • Most of the day was spent on various tasks to get the project up and running, such as setting up the wiki and learning how to autoclave.


day banner
Day 2 - Tuesday, June 14 2011

  • Obtained some TOP10 cells and plated them to begin the process of producing a stock solution, which will give us a continuous supply of chemically competent cells.
  • Used competent cells to begin the transformation process
  • Finalized primary idea for project definition and created a timeline
  • Continued website design process


day banner
Day 3 - Wednesday, June 15 2011

  • Neither the transformation nor the stock solution plates showed any growth in the morning. We suspected the LB broth might be the problem because it was the only thing common to both procedures.
  • Made new LB Broth and LB plates. After the plates were ready, we attempted the TOP10 stock solution procedure again.
  • Lots of brainstorming for secondary project ideas
  • Designed biosynthetic mechanism for primary project proposal.


day banner
Day 4 - Thursday, June 16 2011

  • To our surprise, the original now 2 day old plate was filled with TOP10 colonies. One of the new plates from yesterday was in the incubator overnight and also had growth. Apparently the process just takes longer than we expected and nothing was wrong!
  • This allowed us to proceed with making the seed stock. Later in the day, we transferred several single colonies from the plates into LB broth and put them in the shaker overnight.
  • The team also continued researching our project and determining an exact method to achieve our goals.


day banner
Day 5 - Friday, June 17 2011

  • We took the seed stock tubes out of the shaker, added gylcerol, aliquoted and stored them in the -80 freezer. We now have a supply of cells ready to be made competent at any time.
  • Also continued to finalize the project definition.
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