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| [[IGEM:Harvard/2006]]
| | =About Me= |
| | | Zachary Zhipeng Sun <br> |
| ==About Me==
| |
| (Zhi)Peng Sun <br>
| |
| Currier House '08 <br> | | Currier House '08 <br> |
| Chemical and Physical Biology <br> | | Chemical and Physical Biology <br> |
| Hometown: Pittsburgh, PA <br> | | Hometown: Pittsburgh, PA <br> |
| | Interests: Synthetic Biology; Public Health <br> |
| Email: zsun --(at)-- fas --.-- harvard --.-- edu <br> | | Email: zsun --(at)-- fas --.-- harvard --.-- edu <br> |
| [http://karma.med.harvard.edu/mcb100/Main_Page Work in MCB100] | | [http://karma.med.harvard.edu/mcb100/Main_Page Work in MCB100, Spring 06]<br> |
| | | [[IGEM:Harvard/2006/cyanobacteria/peng_labbook | Lab notebook from iGEM06, Summer and Fall 06]] <br> |
| ==Notebook==
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| | |
| Below are notes taken during meetings or during lab; they will be either in pdf or below depending on platform used. Let me know if you need a native OneNote copy instead.
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| ===June 12th===
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| '''Morning'''
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| *[[Media:ZS_brainstorm.pdf | Notes from first meeting]] (pdf)
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| '''Afternoon'''
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| *Explained BioBricks Format
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| *Created 1% Agarose Gel
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| *Folding DNA nanostructures
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| *Transformation of R0010, E7104, E0241 into Top-10 Competent E. Coli
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| R0010 - Lac operon promoter
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| E7104 - T7 promoter + GFP
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| E0241 - GFP
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| ===June 13th===
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| '''Morning'''
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| *Brainstorming by presenting previous projects
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| *[[Past_project_notes]]
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| '''Afternoon'''
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| *TF's created a 1% Agarose gel which we ran our DNA scaffold samples on
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| **130V, 45m+, imaged afterwards
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| DNA Scaffold types
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| -both
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| -scaffold only
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| -oligos only
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| *Checked plating of transformant cells; no growth on control
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| *Grew transformant cells in liquid culture (5mL) overnight with 50uL ampicillin
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| *More brainstorming - Perry presented his domain swapping experiment, discussed DNA nanostructure box
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| ===June 14th===
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| '''Morning'''
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| *DNA Miniprep of transformant colonies
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| **Out of 5mL of liquid culture, reserved 1mL for gylcerol+freeze and 4mL other
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| **pelleted E. coli for each sample
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| **followed QIAprep Miniprep Kit for Microcentrifuge directions
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| ***Used warm dH20 for elution
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| ***Put at 40C for ~2 min to evaporate ethanol before elution
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| ***Forgot to label after elution --> don't know what is what
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| ****Sol'n: During digest will have to run PCR, can tell R0010 from rest, but E7104/E0241 is only different by 30bp; if doesn't work can flip and try two experiments.
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| ***Nanodrop demonstration
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| Nanodrop results
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| -1: 31.2ng/uL 260/280:1.75 260/230:1.92
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| -2: 38.5ng/uL 260/280:1.83 260/230:1.87
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| -3: 33.8ng/uL 260/280:1.70 260/230:1.44
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| | |
| '''PROBLEM:''' Messed up labeling of the plasmids! To diagnose, ran a 15min e-Gel to find out which is R0010.
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| *Digestion of vector/insert
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| **Digested R0010 (200bp cutout) as vector at S and P site.
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| ***.5uL Spe1, .5uL Pst1
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| *** 11uL h20
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| *** 2.5uL 10X BSA
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| *** 2.5uL #2 NebBuffer
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| *** 8uL DNA
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| **Digested other 2 (~900bp cutout) as insert at X and P site.
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| ***.5uL Xba1, .5uL Pst1
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| *** 11uL h20
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| *** 2.5uL 10X BSA
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| *** 2.5uL #3 NebBuffer
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| *** 8uL DNA
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| **Incubate @ 37C for 1h
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| *Phosphatase
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| **80C@15min to kill enzyme activity
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| **Used CIP (1 unit) into the R0010, 1h@37C
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| *Run on 1% agarose gel
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| *Image, Cutout, and Purify
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| **Can isolate the three from the gel
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| '''Result'''
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| [[Image:ZS_DR_gelimage_0614.jpg |thumb| "results of PCR"]] | |
| Ladder=1kb+
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| Lane 1=R0010 (#1)
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| Lane 2=E0241 (#2)
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| Lane 3=E7104 (#3)
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| ===June 15th===
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| '''Morning'''
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| *Brainstorming with Pam
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| **Infeasibility of DNA nanostructures
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| **(Linked)
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| *Conduct ligation reaction
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| **6uL insert, 2uL vector, 2uL buffer, 10uL other buffer
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| **5 min incubation @ RT
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| *Conduct transformation
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| **20mL cells for positive, negative, and exp. ea (top 10)
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| '''Afternoon'''
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| *Plate transformant cells on LB-CARB
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| *Brainstorming session in the afternoon
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| **Linked
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| ===June 16th===
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| '''Morning'''
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| *Talk with Prof. Shih about DNA nanostructures and vailidity
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| **Linked
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| '''Afternoon'''
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| *Talks on two papers
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| **[[iGEM:Harvard/2006/Brainstorming_Papers_-_Zhipeng]]
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| *Other talks can be found at [[IGEM:Harvard/2006/Brainstorming]]
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|
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|
| ===June 17th (Sat)===
| | <br> |
| '''Afternoon'''
| | Update: Now in UCLA/Caltech MSTP - see [http://www.its.caltech.edu/~zsun/] |
| *Met up in the evening to conduct research on cyanobacteria with Hetmann, Dave, and Jeff
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|
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|
| ===June 18th (Sun)=== | | =Biophysics 101, Spring 07= |
| '''Afternoon'''
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| *Finalized information and created Powerpoint
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| **[[IGEM:Harvard/2006/Cyanobacteria]] for link to cyanobacteria information
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| **[[Media: Presentation.ppt]] for Powerpoint delievered (requires Beta 2007 to work correctly)
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|
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|
| ===June 19th (Week 2)===
| | ''Note: Go to the due date of the assignment to see the assignment'' |
| '''Morning''' | | *Assignment for 3/15 posted. Please don't look unless your name starts with a G, M, or S. |
| *Presentation of four projects | | <calendar> |
| **DNA nanostructures (Matt Katie Valerie Tiffany)
| | name=Harvard:Biophysics_101/Notebook:ZS |
| **Fusion Proteins (Perry)
| | date=2007/03/01 |
| **Universal Cell Signaling (Lewis)
| | view=threemonths |
| **Cyanobacteria (Peng Hetmann David Jeff)
| | format=%name/%year-%month-%day |
| *Feedback on cyanobacteria
| | weekstart=0 |
| **Found two sources for our plasmids: WHOI and MIT links
| | </calendar> |
| **E. coli link may not work, but should figure out synthesis
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| ***Codon Devices can do it for $0.30/bp
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| **Prof. Alexander van Oudenaarden works with cyanobacteria, [http://web.mit.edu/biophysics/people.html]
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| '''Afternoon'''
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| *Prof. Shih's discussion on the honeycomb lattice
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| *Check plates for GFP expression
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| Two colonies on experimental (R0010+E0241)!
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| Many on +
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| None on control
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| *Grow R0010+E0241 in 5mL LB + 50uL Amp (5mg/uL orig) overnight @37
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| *Further brainstorming
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| *Emailed Eric Webb about Fedex #; Peter Weigele can give us PCC7942 on Thurs.
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|
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| ===June 20th=== | | <calendar> |
| '''Morning'''
| | name=Harvard:Biophysics_101/Notebook:ZS |
| *Ordered culture BC11 by Sigma
| | date=2007/05/01 |
| *Alain ordered PCC7942 and WH8104 strain from WHOI
| | view=threemonths |
| **Need to look up if other strains grow faster / better to culture
| | format=%name/%year-%month-%day |
| *Need to get ahold of Prof. Knoll and vanO lab to ask about cyanobacteria culture
| | weekstart=0 |
| *Make glycerol stocks of R0010+E0241
| | </calendar> |
| **100uL 50% glycerol, 100uL liquid media
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| *DNA Miniprep
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| **Follow handout; had 2 5mL samples, only used one of them
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| **Tubes 0.5mL PCR; labeled in blue on top
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| *Digest for diagnosis
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| **Xba1 and Pst1
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| **#.5uL Xba1, .5uL Pst1
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| **#11uL h20
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| **#2.5uL 10X BSA
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| **#2.5uL #3 NebBuffer
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| **#8uL DNA
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| **#Incubate @ 37C for 1h
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| '''Afternoon'''
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| *Research into cyanobacteria: see [[iGEM:Harvard/2006/cyanobacteria]] for contribution
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| '''Result from digest'''
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| [[Image:Digest_6-20-06.jpg |thumb| "Result from digest. Lane 7 is our reaction, and the ladder is 1kB+. Despite weak signal it looks as if the digest went okay; differences in size probably due to different restriction sites used."]]
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