|
|
| (14 intermediate revisions not shown) |
| Line 1: |
Line 1: |
| | {{Template:IPN-UNAM-Mexico}} | | {{Template:IPN-UNAM-Mexico}} |
| | | | |
| - | As summer proyect our experimental work began at 07 - july - 2009 using 2008 bioparts catalog, unfurtunly it dosen’t work properly, we had to much troubles to take out DNA and transform, E. Coli for this we had to delay and request 2009 catalog.
| + | =NOTEBOOK= |
| | | | |
| - | Our proyect uses 29 bioparts, 12 ligations and diferent strategys to make it functional as follow:
| |
| | | | |
| - | <h1> [[Image:Month-icon.png | 50px]] June</h1>
| + | |
| | + | As summer proyect our experimental work began at july the 7th 2009 using 2008 bioparts catalog, unfortunately it didn't work properly, so we had a lot of trouble to take out DNA and transform into ''E. coli''. For this reason we had to delay lab work and request the 2009 catalog. |
| | | | |
| - | <h1>[[Image:Month-icon.png | 50px]] July </h1> | + | <h1>[[Image:Month-icon.png | 50px]][[Team:IPN-UNAM-Mexico/Protocols|Protocols]]</h1> |
| | | | |
| - | ==='''''07-July-2009'''''===
| + | <h2>[[Image:Month-icon.png | 50px]][[Team:IPN-UNAM-Mexico/Notebook/July|July]]</h2> |
| | + | <h2>[[Image:Month-icon.png | 50px]][[Team:IPN-UNAM-Mexico/Notebook/August|August]]</h2> |
| | + | <h2>[[Image:Month-icon.png | 50px]][[Team:IPN-UNAM-Mexico/Notebook/September|September]]</h2> |
| | + | <h2>[[Image:Month-icon.png | 50px]][[Team:IPN-UNAM-Mexico/Notebook/October|October]]</h2> |
| | | | |
| - | *Digestion of the follow biobriks with ECORI (E), SPEI (S), and XBAI (X).
| + | <h1>[[Image:Month-icon.png | 50px]][[Team:IPN-UNAM-Mexico/Safety|Safety]]</h1> |
| | + | Our synthetic construction consists of 29 bioparts, which needed 12 ligations and different strategies to make it functional as is described below: |
| | | | |
| - | <center>
| |
| - | {| border="0.5"
| |
| - | ! Biobrick
| |
| - | ! Enzime restriction
| |
| - | |-
| |
| - | |R0079
| |
| - | |E, S
| |
| - | |-
| |
| - | |F1610
| |
| - | |E, X
| |
| - | |-
| |
| - | |B0034
| |
| - | |E, S
| |
| - | |-
| |
| - | |C0078
| |
| - | |E, X
| |
| - | |-
| |
| - | |C0079
| |
| - | |E, X
| |
| - | |-
| |
| - | |B0015
| |
| - | |E, X
| |
| - | |}
| |
| - | </center>
| |
| - |
| |
| - |
| |
| - | *We propose this restrictions for standar assembly for the digest we did a 17 hours incubation at 37ºC.
| |
| - |
| |
| - | *Digest Mix:
| |
| - |
| |
| - | <center>
| |
| - | {| border="0.5"
| |
| - | ! ERCO RI - SPEI
| |
| - | ! Per reaction
| |
| - | |-
| |
| - | |Plasmidic DNA
| |
| - | |align="right" | 3μl
| |
| - | |-
| |
| - | |Enzima ECORI
| |
| - | |align="right" | 2μl
| |
| - | |-
| |
| - | |Enzima SPEI
| |
| - | |align="right" | 2μl
| |
| - | |-
| |
| - | |Buffer NBE
| |
| - | |align="right" | 2μl
| |
| - | |-
| |
| - | |BSA
| |
| - | |align="right" | 0.5μl
| |
| - | |-
| |
| - | |H2O
| |
| - | |align="right" | 10.5μl
| |
| - | |-
| |
| - | !Total
| |
| - | |align="right" | 20μl
| |
| - | |}
| |
| - | </center>
| |
| - |
| |
| - | <center>
| |
| - | {| border="0.5"
| |
| - | ! ECORI - XBAI
| |
| - | !Per reaction
| |
| - | |-
| |
| - | |Plasmidic DNA
| |
| - | |align="right" | 3μl
| |
| - | |-
| |
| - | |Enzime ECORI
| |
| - | |align="right" | 2μl
| |
| - | |-
| |
| - | |Enzime XBAI
| |
| - | |align="right" | 2μl
| |
| - | |-
| |
| - | |Buffer NBE
| |
| - | |align="right" | 2μl
| |
| - | |-
| |
| - | |BSA
| |
| - | |align="right" | 0.5μl
| |
| - | |-
| |
| - | |H20
| |
| - | |align="right" | 10.5μl
| |
| - | |-
| |
| - | !Total
| |
| - | |align="right" | 20μl
| |
| - | |}
| |
| - | </center>
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''08-July-2009'''''===
| |
| - |
| |
| - | *Carry out the restrictions on a 10 wells agarose gel 40 min.
| |
| - | *3μl DNA 2μl Buffer.
| |
| - | *We have not DNA on the Gels maybe the DNA volume is too low. We try again with 20μl DNA 3μl Buffer
| |
| - | *Run on only Plasmidic DNA but we have not DNA.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''09-July-2009'''''===
| |
| - |
| |
| - | *Starting again, and take off DNA from the folder plating R0079, C0178, C0179, C0060, B0034, I739001 biobriks,
| |
| - | *Left 16 hours in 37ºC.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''10-July-2009'''''===
| |
| - |
| |
| - | We don’t have transformed cells in this point we have to delay and request 2009 catalog.
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''28-July-2009'''''===
| |
| - |
| |
| - | With the 2009 catalog we retake the work and take on the biobriks we need. First of all we test them to be sure that the biobriks worked properly, for this we take a biobrik with RFP reporter (BBa_I3522), plate and incubate 17 hours in 37ºC.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''29-July-2009'''''===
| |
| - |
| |
| - | The transformation was successful we are sure the biobricks and method works and we proceed to take off our biobricks as next chart.
| |
| - |
| |
| - | <center>
| |
| - | {| border="0.5"
| |
| - | !Number
| |
| - | !Biobrick
| |
| - | |-
| |
| - | |2
| |
| - | |BBa_R0079
| |
| - | |-
| |
| - | |3
| |
| - | |BBa_F1610
| |
| - | |-
| |
| - | |4
| |
| - | |BBa_K091146
| |
| - | |-
| |
| - | |5
| |
| - | |BBa_K093005
| |
| - | |-
| |
| - | |6
| |
| - | |BBa_K081016
| |
| - | |-
| |
| - | |7
| |
| - | |BBa_EC840
| |
| - | |-
| |
| - | |8
| |
| - | |BBa_K081009
| |
| - | |-
| |
| - | |9
| |
| - | |BBa_R0051
| |
| - | |-
| |
| - | |10
| |
| - | |BBa_J06800
| |
| - | |-
| |
| - | |11
| |
| - | |BBa_Q04121
| |
| - | |-
| |
| - | |12
| |
| - | |BBa_B0034
| |
| - | |-
| |
| - | |13
| |
| - | |BBa_C0079
| |
| - | |-
| |
| - | |14
| |
| - | |BBa_C0179
| |
| - | |-
| |
| - | |15
| |
| - | |BBa_B0015
| |
| - | |-
| |
| - | |16
| |
| - | |BBa_K081018
| |
| - | |-
| |
| - | |17
| |
| - | |BBa_K116640
| |
| - | |}
| |
| - | </center>
| |
| - |
| |
| - | For transformation we use the same method as follow.
| |
| - |
| |
| - | *Elusion: 3μl DNA from the well.
| |
| - | *Put it on a Eppendorf Vial 1.5 ml with competent cells.
| |
| - | *Electoporate shock to transform and recovery in LB ampr 1 hour and a half.
| |
| - | *Plate on petri dishes and incubate 17 hours.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''31-July-2009'''''===
| |
| - |
| |
| - | * Plated Top 10 biobricks F1610, K091146, K081016, K081009, R0051, K081018 and incubate during 17 hours
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | <h1>[[Image:Month-icon.png | 50px]] August </h1>
| |
| - |
| |
| - | ==='''''01-Agust-2009'''''===
| |
| - |
| |
| - | Yesterday’s transformations were successful, continued to incubate it will ready for tomorrow’s mini prepped.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - |
| |
| - | ==='''''02-Agust-2009'''''===
| |
| - |
| |
| - |
| |
| - | We made mini preped (protocol) and did the follow restrictions:
| |
| | | | |
| | <center> | | <center> |
| - | {| border="0.5" | + | {| border="2" |
| | !Number | | !Number |
| | !Biobrick | | !Biobrick |
| Line 304: |
Line 98: |
| | </center> | | </center> |
| | | | |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''03-Agust-2009'''''===
| |
| - |
| |
| - | * Prepared falcon tubes with 5ml agar liquid Ampr and inoculate.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''04-Agust-2009'''''===
| |
| - |
| |
| - | *Miniprep next clones: #16, #8, #23, #24, and prepare glycerol stocks.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''05-Agust-2009'''''===
| |
| - |
| |
| - | *Digest wit ECORI we use this method to check out if is the plasmid correct and begin ligations.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''08-Agust-2009'''''===
| |
| - |
| |
| - | We start with ligations 15-13 (BBa_K266002) and 2-3 (BBa_K266000).
| |
| - |
| |
| - | In this step we use 2 as backbone and 3 as insert, on the same 15 as backbone and 13 as insert, for 2-3 (BBa_K266000) we expect 3034 bp band as shown below, for 15-13 4074 bp
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''09-Agust-2009'''''===
| |
| - |
| |
| - | "Check plasmid and gel picutre below"
| |
| - |
| |
| - | We carried out ligation 4-23 (BBa_K2660059) and consider unsuccessful, we proceed to repeat the transformation.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''11-Agust-2009'''''===
| |
| - |
| |
| - | We did ECORI 3 hours restriction for 3, L 4-23 (BBa_K266005), 17, 3, 7 we see an inespecific band on 17 maybe a sobredigestion, we proceede to repeat this one.
| |
| - |
| |
| - | "Check plasmid and gel picutre below"
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''12 -Agust-2009'''''===
| |
| - |
| |
| - | We procede with 17_24 (Bba_K266001) ligation on this we going to use 17 as backbone and 24 as insert, we leave a 16 hours ligation in 14º camera.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''13-Agust-2009'''''===
| |
| - |
| |
| - | We did transformation using heat shock then plate.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''14-Agust-2009'''''===
| |
| - |
| |
| - | The transformation was successful and proceed to incubate tree colonys 17 hours in liquid LB medium.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''15-Agust-2009'''''===
| |
| - |
| |
| - | We did midi prep for the ligation and carried out the plasmid is successful.
| |
| - |
| |
| - | "Check plasmid and gel picutre below"
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''17-Agust-2009'''''===
| |
| - |
| |
| - | We going to proceed with J23100 – 11 (Bba_K266008) J23100 is a constitutive promoter and we going to use as backbone 11 as insert. We leave overnight ligation in 14º camera.
| |
| - |
| |
| - | "Check plasmid and gel picutre below"
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''18-Agust-2009'''''===
| |
| - |
| |
| - | We did a transformation for thermic shock and plate, we expect colonys for midi
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''19-Agust-2009'''''===
| |
| - |
| |
| - | The transformation was unsuccessful we dont get colonys we going to try again.
| |
| - |
| |
| - | ----
| |
| - | ----
| |
| - |
| |
| - | ==='''''20-Agust-2009.'''''===
| |
| - |
| |
| - | We get Amplicon – L15-13 (BBa_K266003): Restriction digest 16 hours at 14º (overnight) then we will use thermic shock for cells transform.
| |
| - |
| |
| - | L 2-3 (BBa_K266000) we’re doing ECORI 3 hours digest at 37º.
| |
| - |
| |
| - | For BBa P1010 we take off the ccdB gene for this use PSTI and ECORI double restriction we going to use this part as chloramphenicol resistance vector .
| |
| - |
| |
| - | For 24-17 BBa_K266001 we get this ligation and proceed to double digest
| |
| - |
| |
| - | #1
| |
| - |
| |
| - | <h1>[[Image:Month-icon.png | 50px]] September </h1>
| |
| - |
| |
| - | <h1>[[Image:Month-icon.png | 50px]] October </h1>
| |
| | | | |
| | + | <center> |
| | + | {| border="2" |
| | + | ! Ligation |
| | + | ! Nickname |
| | + | ! Biobrick |
| | + | |- |
| | + | |4-23 |
| | + | |Ciencias I |
| | + | |BBa_K226005 |
| | + | |- |
| | + | |13-15 |
| | + | |Ciencias II |
| | + | |BBa_K266002 |
| | + | |- |
| | + | |Ciencias I-7 |
| | + | |Ciencias III |
| | + | |BBa_K266006 |
| | + | |- |
| | + | |24-17 |
| | + | |Ciencias IV |
| | + | |BBa_K266001 |
| | + | |- |
| | + | |2-3 |
| | + | |Ciencias V |
| | + | |BBa_K266000 |
| | + | |- |
| | + | |J231000-11 |
| | + | |Ciencias VI |
| | + | |BBa_K266008 |
| | + | |- |
| | + | |Amplicon - Ciencias II |
| | + | |Ciencias VII |
| | + | |BBa_K266003 |
| | + | |- |
| | + | |Ciencias VI - 12 |
| | + | |Ciencias VIII |
| | + | |BBa_K266009 |
| | + | |- |
| | + | |Ciencias III - 19 |
| | + | |Ciencias IX |
| | + | |BBa_K266006 |
| | + | |- |
| | + | |J23100 – Ciencias VII |
| | + | |Ciencias X |
| | + | |BBa_K266004 |
| | + | |- |
| | + | |Ciencias III - Ciencias V |
| | + | |Ciencias XI |
| | + | |BBa_K266007 |
| | + | |- |
| | + | |Ciencias X - Ciencias IV |
| | + | |Ciencias XII |
| | + | |BBa_K266010 |
| | + | |}</center> |
| | | | |
| | {{Template:IPN-UNAM-Mexico-footer}} | | {{Template:IPN-UNAM-Mexico-footer}} |
As summer proyect our experimental work began at july the 7th 2009 using 2008 bioparts catalog, unfortunately it didn't work properly, so we had a lot of trouble to take out DNA and transform into E. coli. For this reason we had to delay lab work and request the 2009 catalog.
Our synthetic construction consists of 29 bioparts, which needed 12 ligations and different strategies to make it functional as is described below:
"
Protocols
