Team:Bologna/Notebook

From 2008.igem.org

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[[Image:Logo1a.gif|220px]][[Image:Testata_dx.jpg|745px]]
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!align="center"|[[Team:Bologna|HOME]]
!align="center"|[[Team:Bologna|HOME]]
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!align="center"|[[Team:Bologna/Team|TEAM]]
 
!align="center"|[[Team:Bologna/Project|PROJECT]]
!align="center"|[[Team:Bologna/Project|PROJECT]]
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!align="center"|[[Team:Bologna/Modeling|MODELING]]
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!align="center"|[[Team:Bologna/Team|TEAM]]
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!align="center"|[[Team:Bologna/Notebook|WET-LAB]]
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!align="center"|[[Team:Bologna/Software|SOFTWARE]]
!align="center"|[[Team:Bologna/Software|SOFTWARE]]
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!align="center"|[[Team:Bologna/Modeling|MODELING]]
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!align="center"|[[Team:Bologna/Wetlab|WET LAB]]
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!align="center"|[[Team:Bologna/Notebook|LAB-BOOK]]
!align="center"|[[Team:Bologna/Parts|SUBMITTED PARTS]]
!align="center"|[[Team:Bologna/Parts|SUBMITTED PARTS]]
!align="center"|[[Team:Bologna/Biosafety|BIOSAFETY AND PROTOCOLS]]
!align="center"|[[Team:Bologna/Biosafety|BIOSAFETY AND PROTOCOLS]]
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<br>
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[[Image:Collage2.jpg|700px|right]]
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=Notes=
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[[Image:agenda.jpg|right]]
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Here's all our lab work: week by week you can find all the procedures, links to the registry of standard parts and protocols. The chronological structure of this section, organized as a notebook, mirrors the real development of our project and respects the pure iGEM style.
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<br><br><br><br><br><br><br><br><br><br><br><br><br><br>
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= [[Team:Bologna/Biosafety#Protocols|Protocols summary]] =
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[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
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[[Image:SafetyLevels.jpg|thumb|500px|For more information, see [[Team:Bologna/Biosafety|Biosafety page]]]]
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{|
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| '''Protocol'''
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| '''Biosafety level'''
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|-
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| [[Team:Bologna/Biosafety#Plates_preparation|Plates preparation]]
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| <center>1</center>
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|-
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| [[Team:Bologna/Biosafety#Amplification|Amplification]]
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| <center>1</center>
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|-
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| [[Team:Bologna/Biosafety#Transformation|Transformation]]
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| <center>1</center>
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|-
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| [[Team:Bologna/Biosafety#Inoculation|Inoculation]]
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| <center>1</center>
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|-
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| [[Team:Bologna/Biosafety#Miniprep|Miniprep]]
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| <center>1</center>
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|-
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| [[Team:Bologna/Protocols#Digestion_reaction|Digestion reaction]]
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| <center>1</center>
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|-
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| [[Team:Bologna/Protocols#Gel_preparation|Gel preparation]]
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| <center>2</center>
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|-
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| [[Team:Bologna/Protocols#Electrophoretic_run|Electrophoretic run]]
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| <center>2</center>
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|-
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| [[Team:Bologna/Protocols#Gel_extraction|Gel extraction]]
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| <center>2</center>
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|-
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| [[Team:Bologna/Protocols#Ligation_reaction|Ligation reaction]]
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| <center>1</center>
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|-
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| [[Team:Bologna/Protocols#Chemiocompetent_cells|Chemiocompetent cells]]
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| <center>1</center>
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|-
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| [[Team:Bologna/Protocols#Mediums_and_buffers|Mediums and buffers]]
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| <center>1</center>
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|-
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| [[Team:Bologna/Protocols#Antibiotics_stocks_preparation|Antibiotics stocks preparation]]
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| <center>1</center>
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|-
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| [[Team:Bologna/Protocols#IPTG_stocks_preparation|IPTG stocks preparation]]
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| <center>1</center>
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|-
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| [[Team:Bologna/Protocols#Fluorescence_test|Fluorescence test]]
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| <center>1</center>
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|-
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| [[Team:Bologna/Protocols#M9_supplemented_media|M9 supplemented media]]
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| <center>1</center>
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|}
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[https://2008.igem.org/Team:Bologna/Biosafety ''Up'']
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= Week 1: from 07/21/08 to 07/27/08 =
= Week 1: from 07/21/08 to 07/27/08 =
Line 92: Line 36:
# Preparation of antibiotic stocks for Ampicillin and Kanamicin  
# Preparation of antibiotic stocks for Ampicillin and Kanamicin  
# Preparation of LB medium and LB plates for cloning.
# Preparation of LB medium and LB plates for cloning.
 +
 +
 +
 +
[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
= Week 2: from 07/28/08 to 08/03/08 =
= Week 2: from 07/28/08 to 08/03/08 =
-
* Eluition and Amplification from 2008 Registry Collection: [http://partsregistry.org/Part:BBa_R0082 R0082,] [http://partsregistry.org/Part:BBa_R0083, R0083], [http://partsregistry.org/wiki/index.php/Part:BBa_M30109 M30109] in TOP10 strain to build and characterize the Light response system to be our spatial selective trigger. <br>
+
* Eluition and Amplification from 2008 Registry Collection: [http://partsregistry.org/Part:BBa_R0082 R0082], [http://partsregistry.org/Part:BBa_R0083 R0083], [http://partsregistry.org/wiki/index.php/Part:BBa_M30109 M30109] in TOP10 strain to build and characterize the Light response system to be our spatial selective trigger. <br>
* Eluition and Amplification from 2008 Registry Collection: [http://partsregistry.org/Part:BBa_E0240 E0240], [http://partsregistry.org/Part:BBa_P1010 pSB3K3_P1010]in DB3.1 and the Practice Promoter Set ([http://partsregistry.org/wiki/index.php?title=Part:BBa_J23103/ J23150, J23151, J23102]) to test and set up the new [http://partsregistry.org/Measurement Biobrick Standard Measurement Protocol]
* Eluition and Amplification from 2008 Registry Collection: [http://partsregistry.org/Part:BBa_E0240 E0240], [http://partsregistry.org/Part:BBa_P1010 pSB3K3_P1010]in DB3.1 and the Practice Promoter Set ([http://partsregistry.org/wiki/index.php?title=Part:BBa_J23103/ J23150, J23151, J23102]) to test and set up the new [http://partsregistry.org/Measurement Biobrick Standard Measurement Protocol]
-
* Transformation and Amplification from our Lab Stock of [http://partsregistry.org/Part:BBa_S0100 S0100], BBa_I763020, [http://partsregistry.org/wiki/index.php?title=Part:BBa_I763005 I763005] and [http://partsregistry.org/Part:BBa_C0051 C0051]
+
* Transformation and Amplification from our Lab Stock of [http://partsregistry.org/Part:BBa_S0100 S0100],[http://partsregistry.org/Part:BBa_I763020 I763020], [http://partsregistry.org/wiki/index.php?title=Part:BBa_I763005 I763005],[http://partsregistry.org/Part:BBa_C0051 C0051] and [http://partsregistry.org/Part:BBa_C0040 C0040]
* '''Growth Curves of Dh5 Alpha, Top10 and XL1 Blue with Low Medium and High Copy Numbers to assay and define the different kinetics (Further Detail)'''
* '''Growth Curves of Dh5 Alpha, Top10 and XL1 Blue with Low Medium and High Copy Numbers to assay and define the different kinetics (Further Detail)'''
 +
 +
 +
[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
= Week 3: from 08/04/08 to 08/10/08 =
= Week 3: from 08/04/08 to 08/10/08 =
-
'''08/04/08'''
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*In the beginning we decided to use light stimulation. The light-sensitive protein taken from the registry was not consistent, and also the Biobrik sent back from the registry cause us many problems. Finally we opted for [https://2008.igem.org/Team:Bologna/Wetlab#UV_Induction UV stimulation] first for the space selectivity.
 +
 
* Digestion and Control Gel Run of the previous amplified constructs :
* Digestion and Control Gel Run of the previous amplified constructs :
-
1.''' S0100 E/S''' <br>
+
1.'''[http://partsregistry.org/Part:BBa_S0100 S0100] E/S''' <br>
Consistent Part Length <br>
Consistent Part Length <br>
2. '''PLAC-CI X/P''' <br>
2. '''PLAC-CI X/P''' <br>
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9.'''Pλ GFP X/P''' <br>
9.'''Pλ GFP X/P''' <br>
Consistent Part Length. <br>
Consistent Part Length. <br>
 +
10.'''C0040 X\P''' <br>
 +
Consistent part length. <br>
 +
* Calibration of the fluorescence acquisition system
-
* Ligation of R0082 and R0083 with E0240 to obtain a Reporter for the Light Driven Trigger.
+
 
 +
[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
= Week 4: from 08/11/08 to 08/17/08 =
= Week 4: from 08/11/08 to 08/17/08 =
'''HOLIDAY'''
'''HOLIDAY'''
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 +
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[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
= Week 5: from 08/18/08 to 08/24/08 =
= Week 5: from 08/18/08 to 08/24/08 =
-
Starting development of protein
 
-
construct
 
-
#Ligation of I763020 and B0015, of S0100 and B0015, of TETR and B0015
+
*Problems with restriction enzymes
-
# Trasformation of the ligations in E.coli
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-
#Inoculation and preparation of miniprep
+
 
-
#Digestion and control gel run of the constructs: GFP T x\p, S0100 T x\p, TETR T x\p
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*Eluition and Amplification from 2008 Registry Collection of [http://partsregistry.org/Part:BBa_J22106 J22106]
-
#Gel extraction of the part
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 +
 
 +
*Bacteria growth curves for the following strains:
 +
#TOP10<br>
 +
#DH5ALFA<br>
 +
#XL1BLUE<br>
 +
 
 +
 
 +
[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
= Week 6: from 08/25/08 to 08/31/08 =
= Week 6: from 08/25/08 to 08/31/08 =
 +
Starts the protein construct cloning
-
#Ligation of B0034 and TetR T , B0034 and GFP T,
+
*Digestion and Control Gel Run of the previous amplified part (J22106)
 +
 
 +
#Ligations: [http://partsregistry.org/Part:BBa_I763020 I763020] + [http://partsregistry.org/Part:BBa_B0015 B0015]
 +
# Trasformation of the ligations in E.coli
 +
# Inoculation and miniprep preparation
 +
# Enzymatic digestion and construct gel run: GFP T x\p
 +
# Gel extraction of the parts
 +
 
 +
 
 +
#Ligation: [http://partsregistry.org/Part:BBa_B0034 B0034]+ GFP T
 +
#Trasformation of the ligations in E.coli
 +
# Inoculation and miniprep preparation
 +
# Enzymatic digestion and construct gel run: RBS GFP T x\p
 +
# Gel extraction of the parts
 +
 
 +
 
 +
#Ligation: [http://partsregistry.org/Part:BBa_J22106 J22106] and RBS GFP T
 +
#Trasformation of the ligations in E.coli
 +
# Inoculation and miniprep preparation
 +
# Enzymatic digestion and construct gel run: RBS GFP T x\p
 +
# Gel extraction of the parts
 +
 
 +
 
 +
#Ligations: [http://partsregistry.org/Part:BBa_S0100 S0100] + [http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_C0040 C0040] + [http://partsregistry.org/Part:BBa_B0015 B0015] and RBS + C0040 
 +
# Trasformation of the ligations in E.coli
 +
#Inoculation and miniprep preparation
 +
#Enzymatic digestion and construct gel run:S0100 T x\p, C0040 T x\p, RBS C0034 e\s
 +
#Gel extraction of the parts
 +
 
 +
*Fluorescence imaging of the J22106 RBS GFP T construct in different conditions:
 +
#UV irradiation with an exposure time of 5,10,30 seconds and grow in the dark
 +
#UV irradiation with an exposure time of 5,10,30 seconds and grow in presence of light
 +
 
 +
 
 +
[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
 +
 
 +
= Week 7: from 09/01/08 to 09/07/08 =
 +
#Ligations: B0034 + C0040 T
#Trasformation in E.coli  
#Trasformation in E.coli  
-
#Inoculation and preparation of Miniprep
+
#Inoculation and miniprep preparation
-
#Digestion and control gel run of the constructs
+
#Digestion and gel run of the constructs: RBS C0040 T x\p
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RBS TETR T x\p, RBS GFP T x\p
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#Gel extraction of the parts
#Gel extraction of the parts
-
#Ligation of RBS GFP T and S0100, RBS GFP T and RBS TetR
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#Ligations: RBS GFP T + S0100, RBS GFP T + RBS C0040
#Trasformation in E.coli
#Trasformation in E.coli
-
#Inoculation and preparation of Miniprep
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#Inoculation and miniprep preparation
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#Digestion and control gel run of the parts: RBS TETR RBS GFP T x\p, S0100 RBS GFP T x\p
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#Digestion and gel run of: RBS C0040 RBS GFP T x\p, S0100 RBS GFP T x\p
#Gel extraction
#Gel extraction
-
= Week 7: from 09/01/08 to 09/07/08 =
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* Final cloning step:
 +
 
 +
#Ligations: J23118 + RBS GFP T,J23105 + RBS GFP T, J23100 + RBS GFP T
 +
#Trasformation in E.coli
 +
#Inoculation and miniprep preparation
 +
#Digestion and gel run of: [http://partsregistry.org/Part:BBa_K079031 J23118 RBS GFP T], [http://partsregistry.org/Part:BBa_K079030 J23105 RBS GFP T], [http://partsregistry.org/Part:BBa_K079032 J23100 RBS GFP T]
 +
#Gel extraction
 +
 
 +
*Bacteria tracking test on agarose gel
 +
 
 +
*Fluorescence imaging of the construct J22106 RBS GFP T in different conditions:
 +
#UV irradiation with an exposure time of 5,10,30 seconds. Stationary phase of growth and in the dark
 +
#UV irradiation with an exposure time of 5,10,30 seconds. Logaritmic phase of growth and in the dark
 +
 
 +
 
 +
[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
= Week 8: from 09/08/08 to 09/14/08 =
= Week 8: from 09/08/08 to 09/14/08 =
 +
Arrival of the operator library ([http://partsregistry.org/Part:BBa_K079045 Lac], [http://partsregistry.org/Part:BBa_K079046 Tet], [http://partsregistry.org/Part:BBa_K079048 LexA], [http://partsregistry.org/Part:BBa_K079047 Lambda]) from GeneArt
 +
 +
* Protocol design for isolation of single operators from the library.
 +
#Single digestion with PstI and gel run. In this way we open the plasmid in 3 points,loosing the Lac Operator1 and 2, and keeping the lac Operator 3 into the plasmid.
 +
#Gel extraction of the upper band containing [http://partsregistry.org/Part:BBa_K079017 Lac Operator3].
 +
#Single digestion with XbaI and gel run
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#Gel extraction of the upper band containing [http://partsregistry.org/Part:BBa_K079019 Lac Operator1].
 +
#Single digestion with EcoRI and gel run. In this way we open the plasmid in 2 points,loosing the Lac Operator3, remaining the lac Operator1 and 2 into the plasmid.
 +
#Gel extraction of the upper band containing [http://partsregistry.org/Part:BBa_K079019 Lac Operator1] e [http://partsregistry.org/Part:BBa_K079018 Lac Operator2].
 +
#Further single digestion with PstI and gel run.
 +
#Gel extraction of the upper band containing [http://partsregistry.org/Part:BBa_K079018 Lac Operator2]
 +
 +
This protocol was executed for all of the operator library members, [http://partsregistry.org/Part:BBa_K079046 Tet], [http://partsregistry.org/Part:BBa_K079048 Lex] and [http://partsregistry.org/Part:BBa_K079047 Lambda].
 +
 +
*Fluorescence imaging of the construct J22106 RBS GFP T in different conditions:
 +
#UV irradiation with an exposure time of 1,5,10 seconds. Stationary phase of growth and in the dark
 +
#UV irradiation with an exposure time of 1,5,10 seconds. Logaritmic phase of growth and in the dark
 +
 +
 +
[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
= Week 9: from 09/15/08 to 09/21/08 =
= Week 9: from 09/15/08 to 09/21/08 =
 +
 +
*Execution of protocol design for isolation of single Tet, Lex, Lambda operators from the library.
 +
 +
* Fluorescence imaging of the J22106 RBS GFP T construct in different conditions:
 +
#UV Irradiation with an exposure time of 1,5,10 seconds. Logaritmic phase of growth with different LB volumes and in presence of light
 +
#UV irradiation with an exposure time of 1,5,10 seconds. Logaritmic phase of growth with different LB volumes and in the dark
 +
#UV irradiation with an exposure time of 1,5,10 seconds. Logaritmic phase after different grow times
 +
 +
 +
[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
= Week 10: from 09/22/08 to 09/28/08 =
= Week 10: from 09/22/08 to 09/28/08 =
 +
 +
*Assembly of the constructs
 +
 +
#Ligations: Lac2 operator + S0100 RBS GFP T, Lac2 operator + S0100, Lac1 operator + S0100
 +
#Trasformation in E.coli
 +
#Inoculation and miniprep preparation 
 +
#Digestion and gel run
 +
#Gel extraction of: Lac2 S0100 T x\p, Lac2 S0100 RBS GFP T x\p, Lac1 S0100 T x\p
 +
 +
*Fluorescence imaging of the J22106 RBS GFP T construct in different conditions:
 +
#After anaerobic growth
 +
#After aerobic growth
 +
 +
*Bacterial growth in an environment saturated with nitrogen
 +
 +
 +
[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
= Week 11: from 09/29/08 to 10/05/08 =
= Week 11: from 09/29/08 to 10/05/08 =
-
*Start preparing to LEXA_2 operator reporter construct
+
#Ligation of the previous purified constructs and the promoters J23118, J23100
-
# digestion X/P of BOO34-J04031-B0010-B0012
+
#Trasformation in E.coli
-
# digestion S/P of LEXA_2 operator
+
#Inoculation and miniprep preparation
-
# Control Gel Run of BOO34-J04031-B0010-B0012 digested X/P and LEXA_2 operator digested S/P
+
#Digestion and gel run
-
# Gel extraction of BOO34-J04031-B0010-B0012 digested X/P and LEXA_2 operator digested S/P
+
#Gel extraction of: [http://partsregistry.org/Part:BBa_K079026 J23118 S0100 RBS GFP T], [http://partsregistry.org/Part:BBa_K079020 J23118 Lac2 S0100 RBS GFP T], [http://partsregistry.org/Part:BBa_K079023 J23118 Lac2 S0100 T], [http://partsregistry.org/Part:BBa_K079023 J23118 Lac1 S0100 T]
 +
 
 +
*Fluorescence imaging of the J22106 RBS GFP T construct in different conditions:
 +
#After growth in nitrogen saturated enviroment an UV irradiation for 1,10,15 seconds
 +
#After growth in standard condition, an UV irradiation for 1,10,15 seconds
 +
#After growth in standard condition in a batch
 +
 
 +
 
 +
[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
= Week 12: from 10/06/08 to 10/12/08 =
= Week 12: from 10/06/08 to 10/12/08 =
 +
 +
*Start preparing to [http://partsregistry.org/Part:BBa_K079040 LEXA_2] operator reporter construct:
 +
 +
# X/P digestion of B0034-J04031-B0010-B0012
 +
# S/P digestion of [http://partsregistry.org/Part:BBa_K079040 LEXA_2] operator
 +
# gel run of B0034-J04031-B0010-B0012 X/P digested and LEXA_2 operator S/P digested
 +
# gel extraction of B0034-J04031-B0010-B0012 X/P digested and LEXA_2 operator S/P digested
 +
# ligation: B0034-J04031-B0010-B0012 X/P digested + LEXA_2 operator S/P digested
 +
# trasformation in E.coli
 +
# inoculation of LEXA_2-B0034-J04031-B0010-B0012
 +
# miniprep of LEXA_2-B0034-J04031-B0010-B0012
 +
# X/P digestion of LEXA_2-B0034-J04031-B0010-B0012
 +
# S/P digestion of J23118
 +
# gel run of LEXA_2-B0034-J04031-B0010-B0012 X/P digested and J23118 S/P digested
 +
# gel extraction of LEXA_2-B0034-J04031-B0010-B0012 X/P digested and J23118 S/P digested
 +
# ligation: LEXA_2-B0034-J04031-B0010-B0012 X/P digested + J23118 S/P digested
 +
# trasformation of J23118-LEXA_2-B0034-J04031-B0010-B0012
 +
# inoculation of J23118-LEXA_2-B0034-J04031-B0010-B0012
 +
# miniprep of [http://partsregistry.org/Part:BBa_K079049 J23118-LEXA_2-B0034-J04031-B0010-B0012]
 +
# UV testing of J23118-LEXA_2-B0034-J04031-B0010-B0012
 +
 +
* since test construct  was successfully working, we planned to clone the same construct for the other two [http://partsregistry.org/Part:BBa_K079048 LEXA operators] to test the repressor- operator binding affinity, in order to choose the one that better suites the implementation of the bistable toggle switch.
 +
 +
*Fluorescence imaging of the J22106 RBS GFP T construct in different conditions:
 +
#After overnight anaerobic growth in a nitrogen saturated enviroment, an UV  irradiation for 1,5,10,15,30 seconds was performed, interposing different water thicknesses between the sample and the UV lamp
 +
#After overnight anaerobic growth in a nitrogen saturated enviroment, an  UV irradiation for 1,5,10,15,20 minutes was performed
 +
 +
 +
[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
= Week 13: from 10/13/08 to 10/19/08 =
= Week 13: from 10/13/08 to 10/19/08 =
 +
 +
# Ligation: J23100 + LexA2 RBS GFP T
 +
# Trasformation in E.coli
 +
# Inoculation and miniprep preparation
 +
# Digestion and gel run
 +
# Gel extraction of: [http://partsregistry.org/Part:BBa_K079050 J23100-LEXA_2-B0034-J04031-B0010-B0012]
 +
 +
*Fluorescence imaging of the [http://partsregistry.org/Part:BBa_K079050 J23100-LEXA_2-B0034-J04031-B0010-B0012] construct in different conditions:
 +
#UV irradiation with an exposure time of 10,15,20 minutes. Logaritmic phase of growth and in persence of light
 +
#UV irradiation with an exposure time of 10,15,20 minutes. Logaritmic phase of growth and in the dark
 +
#UV irradiation with an exposure time of 10,15,20 minutes. Logaritmic phase of growth with different LB volumes
 +
 +
 +
[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
= Week 14: from 10/20/08 to 10/26/08 =
= Week 14: from 10/20/08 to 10/26/08 =
 +
*Starting from our operator library, we need to extract every single operator to insert these in standard plasmids.
-
= Week 15: from 10/27/08 to 10/29/08 =
+
To achieve that we try some methods:
 +
#Agarose gel 3% for electrophoresis run: no results, the bands are too feeble and yield problem with [https://2008.igem.org/Team:Bologna/Biosafety#Protocols QIA quick gel extraction kit]. The spin columns are optimized for  parts ≥ 60bp.
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#Low melting gel 3% and extraction with Phenol Clorophorm: no results, complicated method and high toxicity.
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<br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br><br>
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Developed of a [https://2008.igem.org/Team:Bologna/Wetlab#Operator_site_cloning_in_standard_plasmids new experimental protocol] in course of study at our laboratory
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<!---
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*Fluorescence imaging of the [http://partsregistry.org/Part:BBa_K079049 J23118-LEXA_2-B0034-J04031-B0010-B0012] construct in different conditions:
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{|align="justify"
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#UV irradiation with an exposure time of 12 minutes. Logaritmic phase of growth in a LB volume of 1 ml and in the dark
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|You can write a background of your team here. Give us a background of your team, the members, etc.  Or tell us more about something of your choosing.
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|[[Image:Example_logo.png|200px|right|frame]]
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*Sample UV irradiation in different media:
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#Petri dish
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#15ml tube
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''Tell us more about your project. Give us background. Use this is the abstract of your project.  Be descriptive but concise (1-2 paragraphs)''
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#Agarose gel matrix
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|[[Image:Team.png|right|frame|Your team picture]]
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[https://2008.igem.org/Team:Bologna/Notebook ''Up'']
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|align="center"|[[Team:Bologna | Team Example 2]]
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= Week 15: from 10/27/08 to 10/29/08 =
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--->
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*Fluorescence imaging of the [http://partsregistry.org/Part:BBa_K079049 J23118-LEXA_2-B0034-J04031-B0010-B0012] construct in different conditions:
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<!--- The Mission, Experiments --->
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#UV irradiation with an exposure time of 10,20,30 seconds. Logaritmic phase of growth in a LB volume of 1 ml and in the dark
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#UV irradiation with an exposure time of 1,5 seconds. Logaritmic phase of growth in a LB volume of 1 ml and in the dark
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==Notebook==
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You should make use of the calendar feature on the wiki and start a lab notebook.  This may be looked at by the judges to see how your work progressed throughout the summer.  It is a very useful organizational tool as well. 
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Working on our wiki!!!
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Find more information on how to use the calendar feature by going to the [[Help:Calendar | general calendar page]].
 
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[https://2008.igem.org/Team:Bologna/Notebook ''Up'']

Latest revision as of 01:13, 30 October 2008

Logo1a.gifTestata dx.jpg
HOME PROJECT TEAM SOFTWARE MODELING WET LAB LAB-BOOK SUBMITTED PARTS BIOSAFETY AND PROTOCOLS


Contents

Notes

Agenda.jpg


Here's all our lab work: week by week you can find all the procedures, links to the registry of standard parts and protocols. The chronological structure of this section, organized as a notebook, mirrors the real development of our project and respects the pure iGEM style.













Up

Week 1: from 07/21/08 to 07/27/08

General Preparations

  1. Preparation of chemiocompetent cells from E. Coli DH5α, Top10 and DB 3.1
  2. Preparation of antibiotic stocks for Ampicillin and Kanamicin
  3. Preparation of LB medium and LB plates for cloning.


Up

Week 2: from 07/28/08 to 08/03/08

  • Eluition and Amplification from 2008 Registry Collection: [http://partsregistry.org/Part:BBa_R0082 R0082], [http://partsregistry.org/Part:BBa_R0083 R0083], [http://partsregistry.org/wiki/index.php/Part:BBa_M30109 M30109] in TOP10 strain to build and characterize the Light response system to be our spatial selective trigger.
  • Eluition and Amplification from 2008 Registry Collection: [http://partsregistry.org/Part:BBa_E0240 E0240], [http://partsregistry.org/Part:BBa_P1010 pSB3K3_P1010]in DB3.1 and the Practice Promoter Set ([http://partsregistry.org/wiki/index.php?title=Part:BBa_J23103/ J23150, J23151, J23102]) to test and set up the new [http://partsregistry.org/Measurement Biobrick Standard Measurement Protocol]
  • Transformation and Amplification from our Lab Stock of [http://partsregistry.org/Part:BBa_S0100 S0100],[http://partsregistry.org/Part:BBa_I763020 I763020], [http://partsregistry.org/wiki/index.php?title=Part:BBa_I763005 I763005],[http://partsregistry.org/Part:BBa_C0051 C0051] and [http://partsregistry.org/Part:BBa_C0040 C0040]
  • Growth Curves of Dh5 Alpha, Top10 and XL1 Blue with Low Medium and High Copy Numbers to assay and define the different kinetics (Further Detail)


Up

Week 3: from 08/04/08 to 08/10/08

  • In the beginning we decided to use light stimulation. The light-sensitive protein taken from the registry was not consistent, and also the Biobrik sent back from the registry cause us many problems. Finally we opted for UV stimulation first for the space selectivity.


  • Digestion and Control Gel Run of the previous amplified constructs :

1.[http://partsregistry.org/Part:BBa_S0100 S0100] E/S
Consistent Part Length
2. PLAC-CI X/P
Consistent Part Length
3. R0083 S/P
Single Vector Band as Expexted. Is Hard to verify the Part length correctness given the small size
4. R0082 S/P
Single Vector Band as Expexted. Is Hard to verify the Part length correctness given the small size
5. C0051 X/P
Consistent Part Length.
7. M30105 E/S
The Part appears not consistent. The Gel has unexpected multiple bands.
8. RBS GFP TAG X/P
Consistent Part Length
9.Pλ GFP X/P
Consistent Part Length.
10.C0040 X\P
Consistent part length.

  • Calibration of the fluorescence acquisition system


Up

Week 4: from 08/11/08 to 08/17/08

HOLIDAY


Up

Week 5: from 08/18/08 to 08/24/08

  • Problems with restriction enzymes


  • Eluition and Amplification from 2008 Registry Collection of [http://partsregistry.org/Part:BBa_J22106 J22106]


  • Bacteria growth curves for the following strains:
  1. TOP10
  2. DH5ALFA
  3. XL1BLUE


Up

Week 6: from 08/25/08 to 08/31/08

Starts the protein construct cloning

  • Digestion and Control Gel Run of the previous amplified part (J22106)
  1. Ligations: [http://partsregistry.org/Part:BBa_I763020 I763020] + [http://partsregistry.org/Part:BBa_B0015 B0015]
  2. Trasformation of the ligations in E.coli
  3. Inoculation and miniprep preparation
  4. Enzymatic digestion and construct gel run: GFP T x\p
  5. Gel extraction of the parts


  1. Ligation: [http://partsregistry.org/Part:BBa_B0034 B0034]+ GFP T
  2. Trasformation of the ligations in E.coli
  3. Inoculation and miniprep preparation
  4. Enzymatic digestion and construct gel run: RBS GFP T x\p
  5. Gel extraction of the parts


  1. Ligation: [http://partsregistry.org/Part:BBa_J22106 J22106] and RBS GFP T
  2. Trasformation of the ligations in E.coli
  3. Inoculation and miniprep preparation
  4. Enzymatic digestion and construct gel run: RBS GFP T x\p
  5. Gel extraction of the parts


  1. Ligations: [http://partsregistry.org/Part:BBa_S0100 S0100] + [http://partsregistry.org/Part:BBa_B0015 B0015], [http://partsregistry.org/Part:BBa_C0040 C0040] + [http://partsregistry.org/Part:BBa_B0015 B0015] and RBS + C0040
  2. Trasformation of the ligations in E.coli
  3. Inoculation and miniprep preparation
  4. Enzymatic digestion and construct gel run:S0100 T x\p, C0040 T x\p, RBS C0034 e\s
  5. Gel extraction of the parts
  • Fluorescence imaging of the J22106 RBS GFP T construct in different conditions:
  1. UV irradiation with an exposure time of 5,10,30 seconds and grow in the dark
  2. UV irradiation with an exposure time of 5,10,30 seconds and grow in presence of light


Up

Week 7: from 09/01/08 to 09/07/08

  1. Ligations: B0034 + C0040 T
  2. Trasformation in E.coli
  3. Inoculation and miniprep preparation
  4. Digestion and gel run of the constructs: RBS C0040 T x\p
  5. Gel extraction of the parts
  6. Ligations: RBS GFP T + S0100, RBS GFP T + RBS C0040
  7. Trasformation in E.coli
  8. Inoculation and miniprep preparation
  9. Digestion and gel run of: RBS C0040 RBS GFP T x\p, S0100 RBS GFP T x\p
  10. Gel extraction
  • Final cloning step:
  1. Ligations: J23118 + RBS GFP T,J23105 + RBS GFP T, J23100 + RBS GFP T
  2. Trasformation in E.coli
  3. Inoculation and miniprep preparation
  4. Digestion and gel run of: [http://partsregistry.org/Part:BBa_K079031 J23118 RBS GFP T], [http://partsregistry.org/Part:BBa_K079030 J23105 RBS GFP T], [http://partsregistry.org/Part:BBa_K079032 J23100 RBS GFP T]
  5. Gel extraction
  • Bacteria tracking test on agarose gel
  • Fluorescence imaging of the construct J22106 RBS GFP T in different conditions:
  1. UV irradiation with an exposure time of 5,10,30 seconds. Stationary phase of growth and in the dark
  2. UV irradiation with an exposure time of 5,10,30 seconds. Logaritmic phase of growth and in the dark


Up

Week 8: from 09/08/08 to 09/14/08

Arrival of the operator library ([http://partsregistry.org/Part:BBa_K079045 Lac], [http://partsregistry.org/Part:BBa_K079046 Tet], [http://partsregistry.org/Part:BBa_K079048 LexA], [http://partsregistry.org/Part:BBa_K079047 Lambda]) from GeneArt

  • Protocol design for isolation of single operators from the library.
  1. Single digestion with PstI and gel run. In this way we open the plasmid in 3 points,loosing the Lac Operator1 and 2, and keeping the lac Operator 3 into the plasmid.
  2. Gel extraction of the upper band containing [http://partsregistry.org/Part:BBa_K079017 Lac Operator3].
  3. Single digestion with XbaI and gel run
  4. Gel extraction of the upper band containing [http://partsregistry.org/Part:BBa_K079019 Lac Operator1].
  5. Single digestion with EcoRI and gel run. In this way we open the plasmid in 2 points,loosing the Lac Operator3, remaining the lac Operator1 and 2 into the plasmid.
  6. Gel extraction of the upper band containing [http://partsregistry.org/Part:BBa_K079019 Lac Operator1] e [http://partsregistry.org/Part:BBa_K079018 Lac Operator2].
  7. Further single digestion with PstI and gel run.
  8. Gel extraction of the upper band containing [http://partsregistry.org/Part:BBa_K079018 Lac Operator2]

This protocol was executed for all of the operator library members, [http://partsregistry.org/Part:BBa_K079046 Tet], [http://partsregistry.org/Part:BBa_K079048 Lex] and [http://partsregistry.org/Part:BBa_K079047 Lambda].

  • Fluorescence imaging of the construct J22106 RBS GFP T in different conditions:
  1. UV irradiation with an exposure time of 1,5,10 seconds. Stationary phase of growth and in the dark
  2. UV irradiation with an exposure time of 1,5,10 seconds. Logaritmic phase of growth and in the dark


Up

Week 9: from 09/15/08 to 09/21/08

  • Execution of protocol design for isolation of single Tet, Lex, Lambda operators from the library.
  • Fluorescence imaging of the J22106 RBS GFP T construct in different conditions:
  1. UV Irradiation with an exposure time of 1,5,10 seconds. Logaritmic phase of growth with different LB volumes and in presence of light
  2. UV irradiation with an exposure time of 1,5,10 seconds. Logaritmic phase of growth with different LB volumes and in the dark
  3. UV irradiation with an exposure time of 1,5,10 seconds. Logaritmic phase after different grow times


Up

Week 10: from 09/22/08 to 09/28/08

  • Assembly of the constructs
  1. Ligations: Lac2 operator + S0100 RBS GFP T, Lac2 operator + S0100, Lac1 operator + S0100
  2. Trasformation in E.coli
  3. Inoculation and miniprep preparation
  4. Digestion and gel run
  5. Gel extraction of: Lac2 S0100 T x\p, Lac2 S0100 RBS GFP T x\p, Lac1 S0100 T x\p
  • Fluorescence imaging of the J22106 RBS GFP T construct in different conditions:
  1. After anaerobic growth
  2. After aerobic growth
  • Bacterial growth in an environment saturated with nitrogen


Up

Week 11: from 09/29/08 to 10/05/08

  1. Ligation of the previous purified constructs and the promoters J23118, J23100
  2. Trasformation in E.coli
  3. Inoculation and miniprep preparation
  4. Digestion and gel run
  5. Gel extraction of: [http://partsregistry.org/Part:BBa_K079026 J23118 S0100 RBS GFP T], [http://partsregistry.org/Part:BBa_K079020 J23118 Lac2 S0100 RBS GFP T], [http://partsregistry.org/Part:BBa_K079023 J23118 Lac2 S0100 T], [http://partsregistry.org/Part:BBa_K079023 J23118 Lac1 S0100 T]
  • Fluorescence imaging of the J22106 RBS GFP T construct in different conditions:
  1. After growth in nitrogen saturated enviroment an UV irradiation for 1,10,15 seconds
  2. After growth in standard condition, an UV irradiation for 1,10,15 seconds
  3. After growth in standard condition in a batch


Up

Week 12: from 10/06/08 to 10/12/08

  • Start preparing to [http://partsregistry.org/Part:BBa_K079040 LEXA_2] operator reporter construct:
  1. X/P digestion of B0034-J04031-B0010-B0012
  2. S/P digestion of [http://partsregistry.org/Part:BBa_K079040 LEXA_2] operator
  3. gel run of B0034-J04031-B0010-B0012 X/P digested and LEXA_2 operator S/P digested
  4. gel extraction of B0034-J04031-B0010-B0012 X/P digested and LEXA_2 operator S/P digested
  5. ligation: B0034-J04031-B0010-B0012 X/P digested + LEXA_2 operator S/P digested
  6. trasformation in E.coli
  7. inoculation of LEXA_2-B0034-J04031-B0010-B0012
  8. miniprep of LEXA_2-B0034-J04031-B0010-B0012
  9. X/P digestion of LEXA_2-B0034-J04031-B0010-B0012
  10. S/P digestion of J23118
  11. gel run of LEXA_2-B0034-J04031-B0010-B0012 X/P digested and J23118 S/P digested
  12. gel extraction of LEXA_2-B0034-J04031-B0010-B0012 X/P digested and J23118 S/P digested
  13. ligation: LEXA_2-B0034-J04031-B0010-B0012 X/P digested + J23118 S/P digested
  14. trasformation of J23118-LEXA_2-B0034-J04031-B0010-B0012
  15. inoculation of J23118-LEXA_2-B0034-J04031-B0010-B0012
  16. miniprep of [http://partsregistry.org/Part:BBa_K079049 J23118-LEXA_2-B0034-J04031-B0010-B0012]
  17. UV testing of J23118-LEXA_2-B0034-J04031-B0010-B0012
  • since test construct was successfully working, we planned to clone the same construct for the other two [http://partsregistry.org/Part:BBa_K079048 LEXA operators] to test the repressor- operator binding affinity, in order to choose the one that better suites the implementation of the bistable toggle switch.
  • Fluorescence imaging of the J22106 RBS GFP T construct in different conditions:
  1. After overnight anaerobic growth in a nitrogen saturated enviroment, an UV irradiation for 1,5,10,15,30 seconds was performed, interposing different water thicknesses between the sample and the UV lamp
  2. After overnight anaerobic growth in a nitrogen saturated enviroment, an UV irradiation for 1,5,10,15,20 minutes was performed


Up

Week 13: from 10/13/08 to 10/19/08

  1. Ligation: J23100 + LexA2 RBS GFP T
  2. Trasformation in E.coli
  3. Inoculation and miniprep preparation
  4. Digestion and gel run
  5. Gel extraction of: [http://partsregistry.org/Part:BBa_K079050 J23100-LEXA_2-B0034-J04031-B0010-B0012]
  • Fluorescence imaging of the [http://partsregistry.org/Part:BBa_K079050 J23100-LEXA_2-B0034-J04031-B0010-B0012] construct in different conditions:
  1. UV irradiation with an exposure time of 10,15,20 minutes. Logaritmic phase of growth and in persence of light
  2. UV irradiation with an exposure time of 10,15,20 minutes. Logaritmic phase of growth and in the dark
  3. UV irradiation with an exposure time of 10,15,20 minutes. Logaritmic phase of growth with different LB volumes


Up

Week 14: from 10/20/08 to 10/26/08

  • Starting from our operator library, we need to extract every single operator to insert these in standard plasmids.

To achieve that we try some methods:

  1. Agarose gel 3% for electrophoresis run: no results, the bands are too feeble and yield problem with QIA quick gel extraction kit. The spin columns are optimized for parts ≥ 60bp.
  2. Low melting gel 3% and extraction with Phenol Clorophorm: no results, complicated method and high toxicity.

Developed of a new experimental protocol in course of study at our laboratory

  • Fluorescence imaging of the [http://partsregistry.org/Part:BBa_K079049 J23118-LEXA_2-B0034-J04031-B0010-B0012] construct in different conditions:
  1. UV irradiation with an exposure time of 12 minutes. Logaritmic phase of growth in a LB volume of 1 ml and in the dark
  • Sample UV irradiation in different media:
  1. Petri dish
  2. 15ml tube
  3. Agarose gel matrix


Up

Week 15: from 10/27/08 to 10/29/08

  • Fluorescence imaging of the [http://partsregistry.org/Part:BBa_K079049 J23118-LEXA_2-B0034-J04031-B0010-B0012] construct in different conditions:
  1. UV irradiation with an exposure time of 10,20,30 seconds. Logaritmic phase of growth in a LB volume of 1 ml and in the dark
  2. UV irradiation with an exposure time of 1,5 seconds. Logaritmic phase of growth in a LB volume of 1 ml and in the dark

Working on our wiki!!!


Up