User:Kfifer

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<h3> Lab Notebook </h3>
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<div class="tabs-blue">
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June 12, 2006
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<ul>
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<h4> Transformation </h4>
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<li >[[IGEM:Harvard/2006/DNA nanostructures|Home]]</li>
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#Add DNA to TOP 10 competent cells from the -80 freezer.
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<li id="current">[[IGEM:Harvard/2006/DNA_nanostructures/Designs|Scoping]]</li>
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#20 minutes on ice.
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<li>[[IGEM:Harvard/2006/DNA_nanostructures/Notebook|Evaluating]]</li>
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#Heat shock in 42 degree water for 30 seconds (exactly).
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<li>[[IGEM:Harvard/2006/DNA_nanostructures/Protocols|Implementation]]</li>
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#2 minutes on ice.
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<li>[[IGEM:Harvard/2006/DNA_nanostructures/Presentations|Monitoring]]</li>
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#Add 200ul S.O.C. to each tube.
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<li>[[IGEM:Harvard/2006/DNA_nanostructures/Literature|Resources]]</li>
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#Shake on the warm shaker 1 hr.
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</ul>
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#Plate on carb plates and grow at 37 degrees o/n.
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</div>
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#Grow up colonies in LB next.
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<br style="clear:both">
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<h4> Growth of transformant colonies </h4>
 
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# Fill a number of glass tubes (labeled with tape) with 5ml LB each.
 
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# Add 50ul of ampcillin to each tube.
 
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# Pick one colony with a sterile plastic pick and swirl it around in the LB. Repeat for each of the colonies you want with a different tube each time. (We did two colonies per plate, so 6 total because nothing grew on our negative control, as expected).
 
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# Place in lager glass tubes in the warm shaker. Shake o/n.
 
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# Do a plasmid miniprep next.
 
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June 14, 2006
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==Geographic Rationalization==
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Short introduction
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*[http://parts2.mit.edu/wiki/index.php/Main_Page  Example 1]
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*[http://parts2.mit.edu/wiki/index.php/Main_Page Example 2]
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<h4> Plasmid Miniprep </h4>
 
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Samples
 
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*lac operon promoter
 
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**R0010-1
 
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**R0010-2
 
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*promoter and GFP
 
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**E0241-1
 
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**E0241-2
 
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* GFP
 
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**E7104-1
 
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**E7104-2
 
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<h5> Qiagen Miniprep Protocol </h5> (from kit essentially)
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==Lead Generation==
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*Blurb
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*List of examples
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#Remove growing LB cultures from warm shaker.
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==Compensation==
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#Set aside 1mL of each sample for later glycerol storage at -80 if the transformation worked.
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*Short Blurb
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#Use an eppendorf tube to spin down the rest of the LB culture (probably in about 3 spins each - keep the pellet each time and remove  the supernatant by just pouring it off. The final time, pipet the supernatant away so that there's nothing left but pellet.)
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*List of examples
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#Resuspend pelleted bacterial cells in 250 µl Buffer P1 (kept at 4 °C) and transfer to a microcentrifuge tube. Ensure that RNase A has been added to Buffer P1. Pipet up and down. No cell clumps should be visible after resuspension of the pellet.
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#Add 250 μl Buffer P2 and gently invert the tube 4–6 times to mix. Mix gently by inverting the tube. Do not vortex, as this will result in shearing of genomic DNA. If necessary, continue inverting the tube until the solution becomes viscous and slightly clear. Do not allow the lysis reaction to proceed for more than 5 min.
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#Add 350 μl Buffer N3 and invert the tube immediately but gently 4–6 times. To avoid localized precipitation, mix the solution gently but thoroughly, immediately after addition of Buffer N3. The solution should become cloudy.
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#Centrifuge for 10 min at 13,000 rpm (~17,900 x g) in a table-top microcentrifuge.  A compact white pellet will form.
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#Apply the supernatants from step 4 to the QIAprep spin column by decanting or pipetting.
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#Centrifuge for 30–60 s. Discard the flow-through. Spinning for 60 seconds produces good results.
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#(Optional): Wash the QIAprep spin column by adding 0.5 ml Buffer PB and centrifuging for 30–60 s. Discard the flow-through.
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#Wash QIAprep spin column by adding 0.75 ml Buffer PE and centrifuging for 60 s.
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#Discard the flow-through, and centrifuge for an additional 1 min to remove residual wash buffer. IMPORTANT: Residual wash buffer will not be completely removed unless the flow-through is discarded before this additional centrifugation. Residual ethanol from Buffer PE may inhibit subsequent enzymatic reactions.
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#Place the QIAprep column in a clean 1.5 ml microcentrifuge tube. To elute DNA, add 50 μl Buffer EB (10 mM Tris·Cl, pH 8.5) or water to the center of each QIAprep spin column, let stand for 1 min, and centrifuge for 1 min.
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#Use the nanodrop to determine the concentration of the DNA.
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<h5> Nanodrop Protocol </h5>
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==Topic 4==
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The nanodrop is used to measure the concentration of DNA in a tiny sample (1ul).  The machine is located in the back of the larger lab.
 
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#Turn on machine and computer.
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#Clean silver platform top and bottom with ethanol on kimwipe.
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#Click ND 1000 on the desktop to open the program.
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==About Me==
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#Load a water sample (1ul) directly onto bottom part of silver platform and press 0K on the computer to make sure it's clean.
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* I'm a computer science concentrator also interested in biology. I also enjoy teaching and currently am tfing [http://www.fas.harvard.edu/~lib51 cs51].
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#Wipe it off and load another sample of water to get the background. Press blank on the screen so that it calibrates.
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* Harvard College '08
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#Wipe again. Load first sample and type in the Sample ID and press measure.  
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* contact: kfifer --at-- fas.harvard.edu
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#Repeat this clean, load, measure process for each sample.
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#Press show report to see all the results.
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==Biophysics 101==
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Please click on the date homework is due to see the assignment.
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<calendar>
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name=Harvard:Biophysics_101/2007/Notebook:Katie_Fifer
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date=2007/03/01
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view=threemonths
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format=%name/%year-%month-%day
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weekstart=0
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</calendar>
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<calendar>
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name=Harvard:Biophysics_101/2007/Notebook:Katie_Fifer
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date=2007/05/01
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view=month
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format=%name/%year-%month-%day
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weekstart=0
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</calendar>
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==Summer 2006==
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* I really enjoyed working with the Harvard iGEM team last summer. You can find the group wiki [http://openwetware.org/wiki/IGEM:Harvard/2006 here].
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* I primarily focused my work on DNA nanostructures. You can find our wiki [http://openwetware.org/wiki/IGEM:Harvard/2006/DNA_nanostructures here].  
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* Also you can read about our work covered in [http://www.technologyreview.com/Biotech/17790/ Technology Review.]
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* We participated in the iGEM jamboree. If you're interested in iGEM you can find more information [http://parts2.mit.edu/wiki/index.php/Main_Page here].
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* Useful DNA Nanostructures [[IGEM:Harvard/2006/Container_Design_4/Python_Code|scripts]].
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==Misc==
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[[Katie_Fifer/Design_Docs|Graphic Design Work]]<br>
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[[Media:IGEM_Harv_Katie_pres_final.ppt|PRISE Presentation]]<br>
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[[Media:IGEM_Harvard_Katie_aug_27_final.ppt|iGEM final presentation]]<br>
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[[Media:IGEM_elisa.ppt|Elisa Presentation]]<br>

Current revision



Contents

Geographic Rationalization

Short introduction


Lead Generation

  • Blurb
  • List of examples

Compensation

  • Short Blurb
  • List of examples

Topic 4

About Me

  • I'm a computer science concentrator also interested in biology. I also enjoy teaching and currently am tfing cs51.
  • Harvard College '08
  • contact: kfifer --at-- fas.harvard.edu

Biophysics 101

Please click on the date homework is due to see the assignment.

February
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Summer 2006

  • I really enjoyed working with the Harvard iGEM team last summer. You can find the group wiki here.
  • I primarily focused my work on DNA nanostructures. You can find our wiki here.
  • Also you can read about our work covered in Technology Review.
  • We participated in the iGEM jamboree. If you're interested in iGEM you can find more information here.
  • Useful DNA Nanostructures scripts.

Misc

Graphic Design Work
PRISE Presentation
iGEM final presentation
Elisa Presentation

Personal tools