Team:Stanford/Notebook/Lab Work/Week 3

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__TOC__
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==7/12 Monday==
-
==7/5 Monday==
+
===Planning Meeting Notes===
-
'''Planning Meeting Notes'''
+
*Leader: Alex
-
''Agenda''
+
===Alex's Notebook===
-
*Design Updates
+
Run three gels:
-
**Analog Comparator (Chris & Alex)
+
4A5 (3395- 1069) w/ 2K3 (4425-1069)
-
**Redundancy between the two proposals
+
F2620 (1061-2079) w/ I0500 (1210-4425)
-
**Degree of phosporylation
+
I8 (2093-2079=>936 and 1143) w/ T9 (1945-2157=> 936 and 1221).
-
**Dynamic range and mechanisms
+
Gel extract.
 +
Run diagnostic.
 +
Ligate.
-
**Digital Comparator (Francisco & Karina)
 
-
**RSID; standardizing the design
 
-
**Introducing a PoPs signal output
 
-
*Characteristics between the two Comparators
+
Minipreped inoculations.
-
**What makes the two different?
+
 3C5: 123.5 ng/mL 280: 1.90 230: 2.86
 +
 1K3: 84 ng/mL 280: 1.86 230: 2.58
 +
 I0500: 54.7 ng/mL 280: 1.90 230: 2.32
 +
 I746908: 234.3 ng/mL 280: 1.85 230: 1.90
 +
 +
Ligation/Promoter characterization (2 10X buffer, 1 ligase):
-
*Applications
+
DNA vector 250-500 ng 400 ng
-
**Vaginal Infections/Preterm Birth
+
Insert 5-20x of vector 6 ug
-
*is it really a ratio?
+
Endy’s Promoter
-
*Other ideas: Targeting Cancer Cells, oscillators
+
 F2620 + Superfolded GFP (PCR) + pSB1A2
 +
 F2620 + Superfolded GFP (PCR) + pSB3C5
 +
Bad Promoter
 +
 Testing of I746908 (already in pSB1A2)
 +
 I746908 + pSB3C5 (10, 5)
-
*Administrative Details
+
Endy’s Promoter
-
**Ordering Stuff: Oligos ordering sheet, Digestion and Gel Extraction Kits?
+
 T9002 + 1A2 (10, 5)
-
**Stipend?
+
 T9002 + 3C5 (10, 5)
-
**Sponsorship Updates
+
Bad Promoter
-
**MDV Presentation
+
 I0500 + E0240 + pSB1A2 (5, 5, 5)
 +
 I0500 + E0240 + pSB3C5 (5, 5, 5)
-
''Goals For the Week''
+
Promoter/primer design
 +
20 bp
-
*Chris & Alex
+
===Christopher's Notebook===
-
**need to make 50x TAE
+
*Run Gel of Restricted Digested RBS+GFP+Terminators (I746908 partial)
-
**complete plasmids as far can get w/o kinase and phosphotase
+
*Gel Extract
-
**order DNA sometime this week
+
*Run Gel of Gel Extracted Digest Products from Friday:
-
*Francisco & Karina
+
  3C5    E/P 2738 bp (buffer 3)
-
**Run orginal and new designs by Christina
+
F2620  E/S (on pSB1A2) 1061 bp
-
**design standard sRNA designs and place order by the end of the week
+
*I746908 E/P (on psb1A2) 2093 bp-can’t separate
 +
*B0034 X/P (on psb1A2)  12 bp-do NOT run on gel
 +
 
 +
*J23100 E/S (on psb1A2) 35 bp-do NOT run on gel
 +
 
 +
=== Karina's Notebook ===
 +
 
 +
Goal: We couldn't extract the terminators because they were too small and ran off the gel. After discussing with Laura and Francisco, we decided to clone GFP and RFP into the plasmid in which the terminators come (pSB1AK3). <br/><br/>
 +
 
 +
'''Make BSA'''
 +
*BSA comes as 100x
 +
*made 1 mL of 1x solution by adding 900uL H20 and 100 uL BSA <br/><br/>
 +
 
 +
'''Cut the GFP and RFP linearized plasmid (prev. cut at S and P) at EcoRI restriction site '''
 +
*used recipe as described on [[Team:Stanford/Notebook/Lab_Work/Week_2 | July 9, 2010]]
 +
*only used 1 enzyme, therefore used 27 uL H20
 +
*put in waterbath at 10:30 am, and plan to take out after lunch. <br/><br/>
 +
 
 +
'''Results of diagnostic gel''' <br/>
 +
[[Image:071210_gel.jpg | none | frame | left to right: 1 kb ladder, GFP plasmid (cut at S, P),
 +
RFP plasmid (cut at S, P), GFP plasmid (cut at S, P, and cut again at E), RFP plasmid (cut at S, P, and cut again at E)
 +
Note: GFP lanes have no visible bands]]<br/>
 +
 
 +
''Observations/Troubleshooting'':<br/>
 +
*no DNA bands for GFP<br/>
 +
** not enough DNA?<br/>
 +
** will double DNA concentration during digests<br/>
 +
*bands are too large to be RFP
 +
**possible partial digest?
 +
**leave digests overnight
 +
<br/>
 +
 
 +
'''Digests'''<br/>
 +
Digest miniprepped GFP, RFP and Terminators.<br/>
 +
*Cut GFP and RFP at E and S
 +
*Cut terminators at E and X<br/><br/>
 +
''Recipe''<br/>
 +
*25 uL DNA<br/>
 +
*1.0 uL enzyme 1<br/>
 +
*1.0 uL enzyme 2<br/>
 +
*5.0 uL NEB Buffer 2<br/>
 +
*5.0 uL BSA (10x) <br/>
 +
*13 uL H20<br/>
 +
Total Volume: 50 uL<br/>
 +
We used twice as much DNA than the usual protocol because our DNA concentrations from the minipreps were very low. <br/>
 +
Prepared 3 reactions for each RSID; ran 6 PCR reactions total.
 +
Ran digests overnight
 +
 
 +
===Francisco's Notebook===
 +
*Reran the diagnostic gel (see Karina's Notebook):
 +
 
 +
[[Image:071210_gel_2.jpg | none | frame | left to right: 1 kb ladder, GFP and RFP  plasmid (cut at S, P), GFP and RFP plasmid (cut at S, P, and also at E)
 +
Note: GFP lanes now have (faintly) visible bands]]
 +
 
 +
*Lessons learned:
 +
**When loading small volumes, use narrow wells.
 +
**When suspecting there are no bands, increase the exposure time to confirm.
-
==7/6 Tuesday==
 
===Greg's Notebook===
===Greg's Notebook===
-
*During weekly meeting got up to speed with what the team’s been doing while I was away
 
-
*Used heat-shock transformation protocol for DH5alpha to transform with the following genetic material, left to culture overnight:
 
-
{| class="wikitable" style="text-align: center;"
+
*Ran gel with pSB3c5, F2620, I746908
-
|-
+
**I746908 didn't work, extracted pSB3c5 and F2620
-
! Function !! Part # !! Distribution Location !! Resistance
+
*Worked on MDV powerpoint presentation
 +
*Ran diagnostic gel of gel extraction results
 +
**pSB3c5 worked, F2620 left only a faint line
 +
*With Alex, miniprepped pSB1k3, I746908, I0500
 +
*Performed nanodrop on miniprep:
 +
{|
 +
|part #|| 280 || 230 || concentration (ng/uL)
|-
|-
-
| ribosome binding site || B0032 || P1 2I || Amp
+
|I0500r || 1.87 || 1.28 || 62.5
|-
|-
-
| forward double terminator || B0015 || P1 23L || Amp + Kan
+
|pSB1k3 || 1.81 || 1.14 || 67.6
|-
|-
-
| bidirectional double terminator || B0014 || P2 24C || Amp + Kan
+
|I746908 || 1.89 || 1.73 || 175.7
-
|-
+
-
| medium constitutive promoter || J23107 || P1 20A || Amp
+
-
|-
+
-
| strong constitutive promoter || J23100 || P1 18C || Amp
+
-
|-
+
-
| plasmid backbone || pSB1K3 || P1 5A || Kan
+
|}
|}
-
==7/8 Thursday==
+
*Digested more F2620, pSB3c5, and I0500. Also digested 3 superfolded GFP inserts
-
===Christopher's Notebook===
+
-
Running a Gel of F2620, pBAD, and psb4A5:
+
==7/13 Tuesday==
-
*Make a 0.8% agarose gel (0.4 g of agarose in 50 ml of TAE)
+
===Alex's Notebook===
-
*Heat in microwave until agarose is completely dissolved
+
*Streak bacteria
-
*Add 10.0 ul of EtBr to mix (5000x for a 50 ml solution)
+
*Back inoculate bacteria 500 ul
-
*let run for approximately 1 hr
+
-
*refer below for bands 
+
-
      4A5    E/P 3395 bp
+
-
      I0500  E/S (on psb2K3) 1210 bp
+
-
      F2620  E/S (on pSB1A2) 1061 bp
+
-
Gel Extract the Fragments
 
-
Running a Gel of PCR Product:
 
-
*first need to PCR cleanup
 
-
*then run on 1.4% agarose gel (0.7 g of agarose in 50 ml of TAE)
 
-
*this is necessary because of the 800 bp size of the fragment
 
-
Miniprep
+
===Christopher's Notebook===
-
Ligations
+
*Run Gels (0.8%) of Restriction Digests:
-
*F2620+E0240+psb1A2
+
  1M, 2M, 2J (X/P)
-
*pBAD+E0240+psb1A2
+
  F2620 (E/S)
-
 
+
  3C5 (E/P)
-
Restriction Digests
+
  I0500 (E/S)
-
PCR product
+
-
F2620
+
 +
'''Note: for PCR of I746908: after first  gel of PCR product, gel extract, and then do a restriction digest. After restriction digest, do a reaction cleanup; pieces are ready for ligation'''.
===Laura's Notebook===
===Laura's Notebook===
 +
*restreaked plates from 7/1/10 (with Karina)
 +
*for each plate, pick 8 colonies and streak, starting at the center of the "pie piece," and working towards the perimeter of the plate
 +
*plate ID's:
-
miniprepped Alex's/Chris' liquid cultures, using Promega kit
+
===Greg's Notebook===
-
*2 each of:
+
*Made gel, ran digests from yesterday
-
**psb1K3
+
*Extracted pBAD (I0500) and pSB3c5
-
**J23107
+
*Practiced primer design
-
**B0032
+
*Inventoried my box
-
*eluted in 100 uL H2O
+
 +
==7/14 Wednesday==
 +
===Alex's Notebook===
 +
*Order oligos/primers
 +
*Ligate remaining sets
 +
*Streak new bacteria
 +
*Plate old bacteria
 +
*PPT presentation
 +
 +
 +
===Laura's Notebook===
 +
*plates restreaked yesterday look good- bacteria grew well, some individual colonies
 +
*helped Francisco with minipreps (Promega kit) of : terminator, GFP, RFP
 +
**Francisco set up liquid cultures yesterday afternoon
 +
*Francisco poured, ran 0.8% gel
 +
**yesterday's digestions, with today's minipreps as controls
 +
*gel extraction: (I cut out bands, Francisco and Karina extracted)
{|
{|
-
!Nanodrop Data
+
|part || tube mass (g) || tube + gel (g) || gel (g) || volume QG (uL)
|-
|-
-
| tube ID || 260/280 || 260/230 || ng/uL
+
|terminator || 1.03 || 1.14 || 0.11 || 330
|-
|-
-
|psB1K3-1 || 1.77 || 1.08 || 71.3
+
|RFP || 1.11 || 1.18 || 0.07 || 210
|-
|-
-
|psB1K3-2 || 1.73 || 1.01 || 77.8
+
|GFP || 1.03 || 1.13 || 0.10 || 300
 +
|}
 +
 
 +
===Francisco's Notebook===
 +
*We've decided to cut out GFP and RFP inserts and ligate them into a linearized terminator plasmid. GFP and RFP inserts are fairly large (~700 bp) and would be easier to gel extract than a terminator insert. The terminator we are using is B1006.
 +
 
 +
*Mini-prepped GFP, RFP and terminator plasmids. Mini-prep results:
 +
{| border = "1" |  align = center
 +
! Part !! 260/280 !! 260/230 !! ng/uL
|-
|-
-
|J23107-1 || 1.87 || 1.60 || 116.3
+
| Term  || 1.84 || 0.87 || 62.9
|-
|-
-
|J23107-2 || 1.90 || 1.74 || 142.0
+
| RFP  || 1.87 || 1.65 || 235.5
|-
|-
-
|B0032-1 || 1.81 || 1.20 || 68.1
+
| GFP || 1.85 || 1.05 || 121.7
-
|-
+
-
|B0032-2 || 1.83 || 1.32 || 72.5
+
|}
|}
-
==7/9 Friday==
+
*Digested RFP and GFP plasmids  with EcoR1 and Spe1; terminator plamids with EcoR1 and Xba1.
 +
*Gel extracted the RFP and GFP inserts and the linearized terminator plasmid.
-
===Friday Recap Meeting===
+
===Greg's Notebook===
-
Weekly Presentation: Karina PPT
+
*Worked on MDV presentation
-
Analog Comparator update: Chris
 
-
MDV Presentation Updates & Planning
 
-
*July 16, 2010 11:00 am
 
-
*Separate Meeting for planning, Tuesday 4:00 pm, Green Atrium
 
-
*Grad Students: Ryan
 
-
Administrative Details
+
==7/15 Thursday==
 +
===Alex's Notebook===
-
Stipend?
+
Check plates; streak new ones; back dilute for a third time.
-
*Check on Axess for Billing statements
+
Practice PPT for MDV
-
Sponsorship Updates
+
-
Christina’s announcements:
+
==7/16 Friday==
-
*Start talking about Medal Requirements
+
===Recap Meeting Notes===
-
*Keep in mind the wiki!
+
*No recap meeting- presented at MDV this morning.
-
*Digitized Cloning Scheme
+
-
Medal Requirements- Presentation next week how we’re addressing those
 
-
*Collaborative, Improving Standard, Human Practice
 
-
*Idea: improving promoter database on Parts Registry
 
-
*Need to get access to parts registry to edit  e-mail Drew to e-mail them
 
-
*Gold Medal Meeting Meeting Wed Morning at 9:00 am? Send out the Doodle (Anusuya)
 
-
Next Weeks Leader: Alex  
+
===Alex's Notebook===
 +
Due Monday morning:
 +
Cloning scheme; check list on wiki for Christina and Drew.
 +
Create a timeline for our own use. Deadlines as well.
-
=== Karina's Notebook ===
+
===Francisco's Notebook===
-
Today's Goal: Digest GFP, RFP, and Terminators. Will do (GFP + T) and  (RFP + T) ligations on monday. <br/><br/>
+
-
'''Part #'s:''' <br/>
+
-
*GFP: E0040 (cut at S and P) <br/>
+
-
*RFP: E1010 (cut at S and P) <br/>
+
-
*Term: B1006 (cut at X and P) <br/><br/>
+
-
'''Recipe''' <br/>
+
*Ran a diagnostic gel of the digestion done on Wednesday
-
*12.0 uL DNA<br/>
+
**GFP and RFP plasmids (cut at E, S); Term plasmid (cut at E, X):
-
*1.0 uL each enzyme<br/>
+
-
*5.0 uL NEB buffer 2<br/>
+
-
*5 uL BSA (10x) <br/>
+
-
*Sterile H20 to fill up to 50 uL<br/><br/>
+
-
Mix and put 37º waterbath for 2 or more hours. <br/><br/>
+
[[Image: 071310_gel.jpg | none | frame | left to right: 1 kb ladder, RFP (cut at E, S), GFP (cut at E, S), Term (cut at E, X). Notes: Loaded every other lane, RFP lane has extremely faint band (but not visible in this image). Ran at 95V for 45 min.]]
-
'''Making Gel'''<br/>
+
*Results: the terminator backbone has a bright band, but the gel extracted GFP and RFP inserts had very faint bands (low concentrations). When we ligate, we may need to use larger volumes of the inserts.
-
To make 50 mL of  0.8% agarose gel, add: <br/>
+
-
*.4 g agarose <br/>
+
-
*50 mL TAE (1x)<br/>
+
-
*10 uL EtBr<br/><br/>
+
-
'''Loading the Gel''' <br/>
+
===Chris's Notebook===
-
*add 10 uL loading dye (6x) to digests <br/>
+
-
*add 40 uL of dye + digests to wells <br/>
+
-
*don't forget to include wells with controls! (uncut plasmids) <br/>
+
-
*load 10 uL ladder <br/>
+
-
*run at 95 V for about an hour <br/>
+
-
!!note sizes of plasmids/inserts <br/>
+
====Ligations:====
-
GFP plasmid (pSB1A2) --> 2079 bp <br/>
+
  F2620+sfGFP+psb1A2
-
GFP insert --> 720 bp<br/>
+
  pBAD+sfGFP+psb1A2
-
RFP plasmid (pSB2K3) --> 4425 bp <br/>
+
  F2620+sfGFP+psb3C5
-
RFP insert --> 681 bp <br/>
+
  pBAD+sfGFP+psb3C5
-
Terminator plasmid (pSB1AK3) --> 3189 bp
+
-
Terminator insert --> 39 bp
+
-
'''Gel Results'''<br/>
+
====Ligation (20 μl reaction volume):====
-
[add link to gel picture here] <br/>
+
-
All bands look fine except for, there were no bands for the terminators. They were so small they ran off the gel. We are considering using PCR purification to isolate these parts.  <br/><br/>
+
*DNA vector 250-500 ng (5 ul of vector)
 +
*Insert 5-20x of vector (equal amounts 5 ul of each insert)
 +
*10x buffer 2 μl
 +
*Ligase 1 μl
 +
*ATP (optional) 1 μl of 10 mM stock (4°C)
 +
*NP water Bring to 20 μl total volume
-
'''Gel Extraction'''<br/>
+
Ligate at RT for 2 hr (sticky end) or 2 hr (blunt end)
-
[http://molecool.wustl.edu/krolllab/Kroll_Lab_Protocols/Molecular%20Biology%20protocols/Cloning%20protocols%20folder/Gel%20extraction-Qiagen.pdf Follow QIAquick Gel Extraction Kit Protocol], skip isopropanol step and elute in 50 uL H20.
+
Transform 0.5 and 1.0 ul
 +
 
 +
==7/17 Saturday==
 +
===Alex's Notebook===
 +
 
 +
Check plates again for no growth.
 +
Restreaked again.
 +
 
 +
Run gels for restriction digest products; 120 ul each plasmid type, 240 total.
 +
Ten wells minimum total, 4 more lanes for space.
 +
Gel extract (partial).
 +
Minipreped B0014.
-
{| border="1"
 
-
!colspan="6"|Gel Extraction
 
-
|-
 
-
|Part || Tubes (g) || Gel Extract + tube (g) || Gel Extract (g)   
 
-
|-
 
-
| GFP  || 1.06 || 1.11 || .05       
 
-
|-
 
-
| RFP || 1.09 || 1.22 || .13
 
-
|}
 
 +
==7/18 Sunday==
 +
===Alex's Notebook===
 +
 +
Gel extract (complete).
 +
Streak, possible success.
 +
Digested B0014 (X/P).
-
===Laura's Lab Notebook===
 
-
*worked with Karina and Francisco on digestions, gel, gel extraction (see Karina's notebook for details)
 
-
*for digestion: Francisco set up RFP, Karina set up terminator, I set up GFP
 
</div>
</div>

Latest revision as of 17:12, 14 September 2010

Home Project Applications Modeling Parts Team Notebook Twitter

Contents

7/12 Monday

Planning Meeting Notes

  • Leader: Alex

Alex's Notebook

Run three gels: 4A5 (3395- 1069) w/ 2K3 (4425-1069) F2620 (1061-2079) w/ I0500 (1210-4425) I8 (2093-2079=>936 and 1143) w/ T9 (1945-2157=> 936 and 1221). Gel extract. Run diagnostic. Ligate.


Minipreped inoculations.  3C5: 123.5 ng/mL 280: 1.90 230: 2.86  1K3: 84 ng/mL 280: 1.86 230: 2.58  I0500: 54.7 ng/mL 280: 1.90 230: 2.32  I746908: 234.3 ng/mL 280: 1.85 230: 1.90

Ligation/Promoter characterization (2 10X buffer, 1 ligase):

DNA vector 250-500 ng 400 ng Insert 5-20x of vector 6 ug

Endy’s Promoter  F2620 + Superfolded GFP (PCR) + pSB1A2  F2620 + Superfolded GFP (PCR) + pSB3C5 Bad Promoter  Testing of I746908 (already in pSB1A2)  I746908 + pSB3C5 (10, 5)

Endy’s Promoter  T9002 + 1A2 (10, 5)  T9002 + 3C5 (10, 5) Bad Promoter  I0500 + E0240 + pSB1A2 (5, 5, 5)  I0500 + E0240 + pSB3C5 (5, 5, 5)

Promoter/primer design 20 bp

Christopher's Notebook

  • Run Gel of Restricted Digested RBS+GFP+Terminators (I746908 partial)
  • Gel Extract
  • Run Gel of Gel Extracted Digest Products from Friday: 
 3C5     E/P 2738 bp (buffer 3)
F2620   E/S (on pSB1A2) 1061 bp
  • I746908 E/P (on psb1A2) 2093 bp-can’t separate
  • B0034 X/P (on psb1A2) 12 bp-do NOT run on gel
  • J23100 E/S (on psb1A2) 35 bp-do NOT run on gel

Karina's Notebook

Goal: We couldn't extract the terminators because they were too small and ran off the gel. After discussing with Laura and Francisco, we decided to clone GFP and RFP into the plasmid in which the terminators come (pSB1AK3).

Make BSA

  • BSA comes as 100x
  • made 1 mL of 1x solution by adding 900uL H20 and 100 uL BSA

Cut the GFP and RFP linearized plasmid (prev. cut at S and P) at EcoRI restriction site

  • used recipe as described on July 9, 2010
  • only used 1 enzyme, therefore used 27 uL H20
  • put in waterbath at 10:30 am, and plan to take out after lunch.

Results of diagnostic gel

left to right: 1 kb ladder, GFP plasmid (cut at S, P), RFP plasmid (cut at S, P), GFP plasmid (cut at S, P, and cut again at E), RFP plasmid (cut at S, P, and cut again at E) Note: GFP lanes have no visible bands

Observations/Troubleshooting:

  • no DNA bands for GFP
    • not enough DNA?
    • will double DNA concentration during digests
  • bands are too large to be RFP
    • possible partial digest?
    • leave digests overnight


Digests
Digest miniprepped GFP, RFP and Terminators.

  • Cut GFP and RFP at E and S
  • Cut terminators at E and X

Recipe

  • 25 uL DNA
  • 1.0 uL enzyme 1
  • 1.0 uL enzyme 2
  • 5.0 uL NEB Buffer 2
  • 5.0 uL BSA (10x)
  • 13 uL H20

Total Volume: 50 uL
We used twice as much DNA than the usual protocol because our DNA concentrations from the minipreps were very low.
Prepared 3 reactions for each RSID; ran 6 PCR reactions total. Ran digests overnight

Francisco's Notebook

  • Reran the diagnostic gel (see Karina's Notebook):
left to right: 1 kb ladder, GFP and RFP plasmid (cut at S, P), GFP and RFP plasmid (cut at S, P, and also at E) Note: GFP lanes now have (faintly) visible bands
  • Lessons learned:
    • When loading small volumes, use narrow wells.
    • When suspecting there are no bands, increase the exposure time to confirm.

Greg's Notebook

  • Ran gel with pSB3c5, F2620, I746908
    • I746908 didn't work, extracted pSB3c5 and F2620
  • Worked on MDV powerpoint presentation
  • Ran diagnostic gel of gel extraction results
    • pSB3c5 worked, F2620 left only a faint line
  • With Alex, miniprepped pSB1k3, I746908, I0500
  • Performed nanodrop on miniprep:
part # 280 230 concentration (ng/uL)
I0500r 1.87 1.28 62.5
pSB1k3 1.81 1.14 67.6
I746908 1.89 1.73 175.7
  • Digested more F2620, pSB3c5, and I0500. Also digested 3 superfolded GFP inserts

7/13 Tuesday

Alex's Notebook

  • Streak bacteria
  • Back inoculate bacteria 500 ul


Christopher's Notebook

  • Run Gels (0.8%) of Restriction Digests: 
 1M, 2M, 2J (X/P)
 F2620 (E/S)
 3C5 (E/P)
 I0500 (E/S)

Note: for PCR of I746908: after first gel of PCR product, gel extract, and then do a restriction digest. After restriction digest, do a reaction cleanup; pieces are ready for ligation.

Laura's Notebook

  • restreaked plates from 7/1/10 (with Karina)
  • for each plate, pick 8 colonies and streak, starting at the center of the "pie piece," and working towards the perimeter of the plate
  • plate ID's:

Greg's Notebook

  • Made gel, ran digests from yesterday
  • Extracted pBAD (I0500) and pSB3c5
  • Practiced primer design
  • Inventoried my box

7/14 Wednesday

Alex's Notebook

  • Order oligos/primers
  • Ligate remaining sets
  • Streak new bacteria
  • Plate old bacteria
  • PPT presentation


Laura's Notebook

  • plates restreaked yesterday look good- bacteria grew well, some individual colonies
  • helped Francisco with minipreps (Promega kit) of : terminator, GFP, RFP
    • Francisco set up liquid cultures yesterday afternoon
  • Francisco poured, ran 0.8% gel
    • yesterday's digestions, with today's minipreps as controls
  • gel extraction: (I cut out bands, Francisco and Karina extracted)
part tube mass (g) tube + gel (g) gel (g) volume QG (uL)
terminator 1.03 1.14 0.11 330
RFP 1.11 1.18 0.07 210
GFP 1.03 1.13 0.10 300

Francisco's Notebook

  • We've decided to cut out GFP and RFP inserts and ligate them into a linearized terminator plasmid. GFP and RFP inserts are fairly large (~700 bp) and would be easier to gel extract than a terminator insert. The terminator we are using is B1006.
  • Mini-prepped GFP, RFP and terminator plasmids. Mini-prep results:
Part 260/280 260/230 ng/uL
Term 1.84 0.87 62.9
RFP 1.87 1.65 235.5
GFP 1.85 1.05 121.7
  • Digested RFP and GFP plasmids with EcoR1 and Spe1; terminator plamids with EcoR1 and Xba1.
  • Gel extracted the RFP and GFP inserts and the linearized terminator plasmid.

Greg's Notebook

  • Worked on MDV presentation


7/15 Thursday

Alex's Notebook

Check plates; streak new ones; back dilute for a third time. Practice PPT for MDV

7/16 Friday

Recap Meeting Notes

  • No recap meeting- presented at MDV this morning.


Alex's Notebook

Due Monday morning: Cloning scheme; check list on wiki for Christina and Drew. Create a timeline for our own use. Deadlines as well.

Francisco's Notebook

  • Ran a diagnostic gel of the digestion done on Wednesday
    • GFP and RFP plasmids (cut at E, S); Term plasmid (cut at E, X):
left to right: 1 kb ladder, RFP (cut at E, S), GFP (cut at E, S), Term (cut at E, X). Notes: Loaded every other lane, RFP lane has extremely faint band (but not visible in this image). Ran at 95V for 45 min.
  • Results: the terminator backbone has a bright band, but the gel extracted GFP and RFP inserts had very faint bands (low concentrations). When we ligate, we may need to use larger volumes of the inserts.

Chris's Notebook

Ligations:

  F2620+sfGFP+psb1A2
  pBAD+sfGFP+psb1A2
  F2620+sfGFP+psb3C5
  pBAD+sfGFP+psb3C5

Ligation (20 μl reaction volume):

  • DNA vector 250-500 ng (5 ul of vector)
  • Insert 5-20x of vector (equal amounts 5 ul of each insert)
  • 10x buffer 2 μl
  • Ligase 1 μl
  • ATP (optional) 1 μl of 10 mM stock (4°C)
  • NP water Bring to 20 μl total volume

Ligate at RT for 2 hr (sticky end) or 2 hr (blunt end) Transform 0.5 and 1.0 ul

7/17 Saturday

Alex's Notebook

Check plates again for no growth. Restreaked again.

Run gels for restriction digest products; 120 ul each plasmid type, 240 total. Ten wells minimum total, 4 more lanes for space. Gel extract (partial). Minipreped B0014.


7/18 Sunday

Alex's Notebook

Gel extract (complete). Streak, possible success. Digested B0014 (X/P).


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