Team:Mexico-UNAM-CINVESTAV/Notebook/Week Four

From 2010.igem.org

(Difference between revisions)
(→Wenesday)
 
(24 intermediate revisions not shown)
Line 1: Line 1:
{{Mexico-UNAM-CINVESTAV-HEADER}}
{{Mexico-UNAM-CINVESTAV-HEADER}}
 +
__NOTOC__
-
= Week #4       27th  September - 01 October  2010 =
+
 
 +
= Week #4= 
 +
   
 +
=27th  September - 01 October  2010 =
==''Monday''==
==''Monday''==
-
==='''Well we are stuck with the vector this week we have to get vector is our main objetive.'''===  
+
==='''Well...we are stuck with the vector. This week we have to get it.'''===  
-
*'''We have achived a nanodrop readings as below'''
+
*'''We have achieved a nano spectrophotometer and readings are below:'''
Line 69: Line 73:
-
*'''Yep our trouble is the lisis alcaline method to do the mini prep'''
+
*'''Yep, our trouble is the miniprep method'''
-
'''we have a low concentration of vector’s plasmid DNA.'''
+
'''we have a low concentration of vector plasmid.'''
-
'''We have to work an try to get more plasmid and make dilutions of PCR’s'''
+
'''We have to work an try to get more plasmid and used diluted PCR products'''
-
'''is not posible to do ligations with this ratio betwen vector an insert.'''
+
'''is not possible achieve ligations with this vector an insert ratio.'''
-
'''On this step we advisor has proposed a method via Low Meelting agarose'''
+
'''Our advisor proposed use low Melting agarose'''
-
'''to geting out plasmid from the band.'''
+
'''to extract the plasmid from the gel.'''
==''Tuesday''==
==''Tuesday''==
-
==='''We run with a low meelting's agarose prove to extract band tomorrow'''===   
+
==='''We ran with a low meelting agarose and cut off the band '''===   
-
==='''we do a protocol to precipit with alchol an salts our objetive is do it all'''===  
+
==='''we precipitated using alchol and salts in order '''===  
-
==='''to get vector and do the ligations.'''===
+
==='''to get enough vector to do the ligations.'''===
Line 93: Line 97:
-
==''Wensday''==
+
==''Wednesday''==
==='''Plan'''===
==='''Plan'''===
-
*'''We prepared all to do ligations PsB1C3 with our Pcr's.'''
+
*'''We set up all to do the ligations.'''
-
*'''For this we going to cut with EcoRI and PstI both vector and insert.'''
+
*'''We digested both vector and insert with ''EcoR''I and ''Pst''I .'''
-
*'''We'll run a low melting gel slow 2 hours then purified from the band.'''
+
*'''We ran a low melting agarose gel 1 hour at 80 volts, then cut off the band from gel.'''
-
'''At Claudia's lab we cut tree bands of which two of them where purified by Axigen kit'''
+
'''At Claudia's lab we tried three two different kits to recover DNA from gel.'''
-
'''The third one by a diferent kit'''
+
*'''Mobio ultra clean Microbial DNA kit'''
 +
*'''Axygen.....'''
 +
*'''
-
'''The digestion was done with following amounts'''
+
'''The digestions were done with following amounts.'''
{| border="1"
{| border="1"
-
 
|-
|-
|DNA
|DNA
Line 130: Line 135:
|Total
|Total
|30μl
|30μl
 +
|}
 +
 +
==''Thursday''==
 +
 +
==='''Plan'''===
 +
 +
'''We then proceed  to diluted PCR fragments'''
 +
 +
'''For this we did the following operations:'''
 +
 +
'''Poner las fórmulas usadas en un formato bonito'''
 +
 +
'''We did the ligations using the following amounts:'''
 +
 +
{| border="1"
 +
|-
 +
|Insert [20ng/μl]
 +
|5μl
 +
|-
 +
|Vector
 +
|1μl
 +
|-
 +
|Reaction buffer
 +
|1μl
 +
|-
 +
|T4 DNA Ligase
 +
|1μl
 +
|-
 +
|H2O
 +
|2μl
 +
|-
 +
|Total
 +
|10μl
 +
|}
 +
 +
 +
'''We used the follow denomination.'''
 +
*'''Band purified vector :                              Pu'''
 +
*'''iGEM's vector (Vial with green cover):  P'''
 +
*'''Digested vector:                                      S'''
 +
 +
'''After one hour ligation we transformed by heat shock'''
 +
 +
'''and kept overnight the plates at 37ºC'''
 +
 +
 +
 +
 +
==''Friday''==
 +
 +
'''Today we discussed what we going to do with the AFP (anti freeze protein),'''
 +
 +
'''We decided transform by heat shock and plating it on kanamicina medium, then prepare'''
 +
 +
'''miniprep plasmid and cut it with ''Xba''I and ''Pst''I.  We have to ligate it to the backbone  J13002'''
 +
 +
'''the backbone had to be  cut with ''Spe''I and ''Pst''I.'''
 +
 +
'''Meanwhile, here are the  previous day ligations.'''
 +
 +
*'''PCR1 Lig S Positive!!!!!!!'''
 +
*'''PCR2 Lig S Positive!!!!'''
 +
*'''PCR3 Lig S Positive!!!!'''
 +
*'''PCR4 Lig Pu Positive!!!!'''
 +
*'''PCR4 Lig S Positive!!!!'''
 +
 +
[[Image:Labo_254.JPG|400px]]

Latest revision as of 06:41, 27 October 2010



Week #4

27th September - 01 October 2010

Monday

Well...we are stuck with the vector. This week we have to get it.

  • We have achieved a nano spectrophotometer and readings are below:


ng/μl 260/280 260/230
PsB1C3 0.60 -0.73 -0.0
PCR 1 red 427.70 1.71 1.71
PCR 2 red 483.20 1.74 1.71
PCR 3 red 410.70 1.76 2.02
PCR 4 red 431.05 1.61 1.88
PCR 1 blue 533.35 1.71 1.75
PCR 2 blue 536.00 1.72 1.82
PCR 3 blue 577.50 1.69 1.59
PCR 4 blue 627.55 1.70 1.56
PsB1C3 4.10 2.62 1.01


  • Yep, our trouble is the miniprep method

we have a low concentration of vector plasmid.

We have to work an try to get more plasmid and used diluted PCR products

is not possible achieve ligations with this vector an insert ratio.

Our advisor proposed use low Melting agarose

to extract the plasmid from the gel.


Tuesday

We ran with a low meelting agarose and cut off the band

we precipitated using alchol and salts in order

to get enough vector to do the ligations.

Imagen5.gif


Wednesday

Plan

  • We set up all to do the ligations.
  • We digested both vector and insert with EcoRI and PstI .
  • We ran a low melting agarose gel 1 hour at 80 volts, then cut off the band from gel.

At Claudia's lab we tried three two different kits to recover DNA from gel.

  • Mobio ultra clean Microbial DNA kit
  • Axygen.....

The digestions were done with following amounts.

DNA 20μl
Buffer NB2 3μl
EcoRI 2μl
PstI 2μl
H2O 2.4μl
BSA 0.6μl
Total 30μl

Thursday

Plan

We then proceed to diluted PCR fragments

For this we did the following operations:

Poner las fórmulas usadas en un formato bonito

We did the ligations using the following amounts:

Insert [20ng/μl] 5μl
Vector 1μl
Reaction buffer 1μl
T4 DNA Ligase 1μl
H2O 2μl
Total 10μl


We used the follow denomination.

  • Band purified vector : Pu
  • iGEM's vector (Vial with green cover): P
  • Digested vector: S

After one hour ligation we transformed by heat shock

and kept overnight the plates at 37ºC



Friday

Today we discussed what we going to do with the AFP (anti freeze protein),

We decided transform by heat shock and plating it on kanamicina medium, then prepare

miniprep plasmid and cut it with XbaI and PstI. We have to ligate it to the backbone J13002

the backbone had to be cut with SpeI and PstI.

Meanwhile, here are the previous day ligations.

  • PCR1 Lig S Positive!!!!!!!
  • PCR2 Lig S Positive!!!!
  • PCR3 Lig S Positive!!!!
  • PCR4 Lig Pu Positive!!!!
  • PCR4 Lig S Positive!!!!

Labo 254.JPG

Retrieved from "http://2010.igem.org/Team:Mexico-UNAM-CINVESTAV/Notebook/Week_Four"