Difference between revisions of "Team:UBonn HBRS/Description/Notebook/2016"

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{{UBonn_HBRS/header|title=Lab Notebook 2016|Project=active}}
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{{UBonn_HBRS/header|title=Lab Notebook 2016|Project=active|class-main=col-sm-12}}
 
<html><div class="panel notebook-entry"></html>
 
<html><div class="panel notebook-entry"></html>
 
==10KW (7.3-13.3)==
 
==10KW (7.3-13.3)==
−
 
 
transformation of genes bought at genescript: XynA, XynB, LipA, EstC2, CpCel9, CpCel5c, EngB, CelA, BsCel5, Bpul
 
transformation of genes bought at genescript: XynA, XynB, LipA, EstC2, CpCel9, CpCel5c, EngB, CelA, BsCel5, Bpul
−
and Linkers: nprb, SacB
+
and Linkers: nprb, SacB <br />
 
inoculation of liquid cultures and restriction Analysi of linkers (SacB and nprb).
 
inoculation of liquid cultures and restriction Analysi of linkers (SacB and nprb).
  
−
repetition of the transformation for XynB, EngB and linkers.
+
repetition of the transformation for XynB, EngB and linkers. <br />
 
Subsequently inoculation and miniprep of the samples. Preparation of glycerol stock.
 
Subsequently inoculation and miniprep of the samples. Preparation of glycerol stock.
  
Line 14: Line 13:
  
  
 +
<html><div class="panel notebook-entry"></html>
 
==11KW (14.3-20.3)==
 
==11KW (14.3-20.3)==
−
 
 
Repetion of restriction analysis from the genes KW10 and gel clean ups of the linkers.
 
Repetion of restriction analysis from the genes KW10 and gel clean ups of the linkers.
  
−
Deinking:
+
Deinking: <br />
−
*Measurement of inkjet absorbance spectrum
+
* Measurement of inkjet absorbance spectrum
−
*filtration-based method
+
* filtration-based deinking setup
 +
<html></div></html>
  
  
 +
<html><div class="panel notebook-entry"></html>
 
==12KW (21.3-27.3)==
 
==12KW (21.3-27.3)==
−
 
 
repetition of restriction analysis of all genes and gel clean ups of the genes.
 
repetition of restriction analysis of all genes and gel clean ups of the genes.
  
−
==13KW (28.3-3.4)==
+
Deinking: <br />
 +
inkjet ink absorbance spectrum and pulp preparation
 +
<html></div></html>
  
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==13KW (28.3-3.4)==
 
Restrictions and gel clean ups of all genes genes for a new gel clean up, because the ones of KW13 did not works. Ligation of genes from the gel clean ups into C3 and inoculation of cultures and minipreps.
 
Restrictions and gel clean ups of all genes genes for a new gel clean up, because the ones of KW13 did not works. Ligation of genes from the gel clean ups into C3 and inoculation of cultures and minipreps.
 
(1.04.16 :)
 
(1.04.16 :)
−
-> successful ligation of
+
&rarr; successful ligation of
−
*XynA
+
* XynA
−
*CelA
+
* CelA
−
*LipA
+
* LipA
−
*Bpul
+
* Bpul
−
*CpCel5c
+
* CpCel5c
−
*BsCel5
+
* BsCel5
−
*EstC2
+
* EstC2
−
*EngB in C3
+
* EngB in C3
  
−
*nprb + CpCel9
+
* nprb + CpCel9
−
*nprb + BsCel5 in C3
+
* nprb + BsCel5 in C3
  
−
==21KW (23.5-29.5)==
 
  
 +
Deinking: <br />
 +
establishing the set up and starting experiments with different conc of NaOH and Na2SiO3
 +
<html></div></html>
 +
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==14KW (4.4-10.4)==
 +
Deinking: <br />
 +
Experiments with different concentrations of surfactant oleic acid
 +
<html></div></html>
 +
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==15KW (11.4-17.4)==
 +
Deinking: <br />
 +
experiments with different incubation time, vortexing time, temperature
 +
<html></div></html>
 +
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==16KW (18.4-24.4)==
 +
Deinking: <br />
 +
tests with solvents to dissolve ink and fibers
 +
<html></div></html>
 +
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==17KW (25.4-1.5)==
 +
Deinking: <br />
 +
grayscale tests, solvent tests
 +
<html></div></html>
 +
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==18KW (2.5-8.5)==
 +
Deinking: <br />
 +
pulp preparation
 +
<html></div></html>
 +
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==19KW (9.5-15.5)==
 +
Deinking: <br />
 +
establishing water and standard chemical controls
 +
<html></div></html>
 +
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==20KW (16.5-22.5)==
 +
Deinking: <br />
 +
establishing water and standard chemical controls
 +
<html></div></html>
 +
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==21KW (23.5-29.5)==
 
Restriction analysis of genes from the 13KW and mini prep from samples of the 13KW.
 
Restriction analysis of genes from the 13KW and mini prep from samples of the 13KW.
 
(28.05.16)
 
(28.05.16)
 
successful ligation of:
 
successful ligation of:
  
−
*nprb and sacB in C3
+
* nprb and sacB in C3
  
−
*nprb + EstC2 in C3
+
* nprb + EstC2 in C3
  
−
==22KW (30.6-5.6)==
+
Deinking: <br />
 +
establishing oleic acid and oleic acid + citrate buffer controls
 +
<html></div></html>
  
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==22KW (30.5-5.6)==
 
Restriction analysis of samples of the 21KW
 
Restriction analysis of samples of the 21KW
  
−
==23KW (6.6-12.6)==
+
Deinking: <br />
 +
discovery: paper discs with CB turn red, tests to find the reason
 +
<html></div></html>
  
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==23KW (6.6-12.6)==
 
Inoculation of all genes from glycerol stocks and miniprep. Restriction analysis and gel clean up of the genes, ligation of the missing genes with C3.
 
Inoculation of all genes from glycerol stocks and miniprep. Restriction analysis and gel clean up of the genes, ligation of the missing genes with C3.
  
 +
Deinking: <br />
 +
tests with oleic acid and oleic acid + cb controls
 +
<html></div></html>
 +
 +
 +
<html><div class="panel notebook-entry"></html>
 
==24KW (13.6-19.6)==
 
==24KW (13.6-19.6)==
 +
Restriction of bbMCS and gel clean ups. <br />
 +
Ligations of genes in C5 and C3. <br />
 +
Ligation of genes and tags in C5. <br />
  
−
Restriction of bbMCS and gel clean ups.
 
−
Ligations of genes in C5 and C3
 
−
Ligation of genes and tags in C5.
 
 
Minipreps of all of the samples.
 
Minipreps of all of the samples.
  
−
==25KW (20.6-26.6)==
+
Deinking: <br />
 +
tests with shaking during incubation and different incubation time
 +
<html></div></html>
  
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==25KW (20.6-26.6)==
 
Restriction analysis of the constructs
 
Restriction analysis of the constructs
 +
 
Repetition of ligation of genes in C5 and transformation and preps.
 
Repetition of ligation of genes in C5 and transformation and preps.
  
 +
Deinking: <br />
 +
rotation evaporator concentrating ink
 +
<html></div></html>
 +
 +
 +
<html><div class="panel notebook-entry"></html>
 
==26KW (27.6 - 3.7)==
 
==26KW (27.6 - 3.7)==
 
Restriction analysis of the mini preps.
 
Restriction analysis of the mini preps.
 +
<html></div></html>
  
−
==28KW (11.7-7.17)==
+
 
 +
<html><div class="panel notebook-entry"></html>
 +
==28KW (11.7-17.7)==
 
Repetion of Ligations of genes and C5
 
Repetion of Ligations of genes and C5
  
−
==31KW (1.8-7.8)==
+
''B.subtilis'':
 +
preparing electrocomp cells and transformations
  
−
Ligation of Fragment synthesized at IDT and C3
+
Deinking: <br />
−
Ligation of genes in C3 and genes + tags + C5
+
flotation-based deinking, pulp preparation
 +
<html></div></html>
 +
 
 +
 
 +
<html><div class="panel notebook-entry"></html>
 +
==29KW (18.7-24.7)==
 +
Deinking: <br />
 +
separation of ink from fibers in organic phase of big scale deinking, flotation-based deinking, foam collection, defoaming
 +
<html></div></html>
 +
 
 +
 
 +
<html><div class="panel notebook-entry"></html>
 +
==30KW (25.7-31.7)==
 +
''B.subtilis'': <br />
 +
preparing electrocomp cells and transformations
 +
preparing chemocompetent B. subtilis and transformations
 +
 
 +
Deinking: <br />
 +
tests with toluene flotation-based deinking
 +
<html></div></html>
 +
 
 +
 
 +
<html><div class="panel notebook-entry"></html>
 +
==31KW (1.8-7.8)==
 +
Ligation of Fragment synthesized at IDT and C3. <br />
 +
Ligation of genes in C3 and genes + tags + C5. <br />
 
transformation, and inoculation of liquid cultures of the above.
 
transformation, and inoculation of liquid cultures of the above.
  
 +
''B.subtilis'': <br />
 +
preparing of chemocompetent cells and transformations
 +
<html></div></html>
 +
 +
 +
<html><div class="panel notebook-entry"></html>
 
==32KW (8.8 - 14.8)==
 
==32KW (8.8 - 14.8)==
 +
Ligation of IDT and C3. <br />
 +
Transformation and inoculation. <br />
 +
Minipreps of samples and restriction analysis.
  
−
Ligation of IDT and C3
+
Ligations of genes plus tags in bb_MCS. <br />
−
Transformation and inoculation.
+
Transformation of these samples.
−
Minipreps of samples and restriction analysis
+
  
−
Ligations of genes plus tags in bb_MCS
+
''B.subtilis'': <br />
−
Transformation of these samples
+
preparing of electrocomp and chemocompetent cells and transformations
 +
<html></div></html>
  
−
==33KW (15.8 - 21.8)==
 
  
−
Inoculation and miniprep
+
<html><div class="panel notebook-entry"></html>
−
Repetion of ligation of IDT and C3
+
==33KW (15.8 - 21.8)==
−
Repetion of ligation of bb + nprb + genes
+
Inoculation and miniprep. <br />
−
Midi prep of SacB, bb and nprb
+
Repetion of ligation of IDT and C3. <br />
−
Ligation of Genes + C5 and genes plus tags in C5.
+
Repetion of ligation of bb + nprb + genes. <br />
−
Transformation and inoculation of the samples.
+
Midi prep of SacB, bb and nprb. <br />
 +
Ligation of Genes + C5 and genes plus tags in C5. <br />
 +
Transformation and inoculation of the samples. <br />
 
mini preps
 
mini preps
  
−
==34KW (22.8 - 28.8)==
+
Deinking: <br />
 +
creation of flat paper-like discs
 +
<html></div></html>
  
 +
 +
<html><div class="panel notebook-entry"></html>
 +
==34KW (22.8 - 28.8)==
 
Restrictions of mini prep and repetition of mini prep
 
Restrictions of mini prep and repetition of mini prep
−
{{UBonn_HBRS/footer}}
+
 
 +
''B.subtilis'': <br/>
 +
preparing of chemocompetent cells and transformations
 +
 
 +
Deinking: <br />
 +
grayscale tests with officer scanner and odisey scanner
 +
<html></div></html>
 +
 
 +
 
 +
<html><div class="panel notebook-entry"></html>
 +
==35KW (29.9 - 5.9)==
 +
''B.subtilis'': <br/>
 +
transformations of bb
 +
<html></div></html>
 +
 
 +
 
 +
<html><div class="panel notebook-entry"></html>
 +
==36KW (5.9 - 11.9)==
 +
Deinking: <br />
 +
tests of water controls
 +
<html></div></html>
 +
 
 +
 
 +
<html><div class="panel notebook-entry"></html>
 +
==37KW (12.9 - 18.9)==
 +
''B.subtilis'': <br/>
 +
transformations of bb
 +
 
 +
Deinking: <br />
 +
scanning tests, different conditions tests
 +
<html></div></html>
 +
 
 +
 
 +
<html><div class="panel notebook-entry"></html>
 +
==38KW (19.9 - 25.9)==
 +
''B.subtilis'': <br/>
 +
preparing chemocompetent cells and transformations
 +
<html></div></html>
 +
 
 +
 
 +
<html><div class="panel notebook-entry"></html>
 +
==39KW (26.9 - 2.10)==
 +
Deinking: <br />
 +
establishing water and standard controls into setup with kitchen mixer
 +
<html></div></html>
 +
 
 +
 
 +
<html><div class="panel notebook-entry"></html>
 +
==40KW (3.10 - 9.10)==
 +
Deinking: <br />
 +
xylanase started to test + cb
 +
<html></div></html>
 +
 
 +
 
 +
<html><div class="panel notebook-entry"></html>
 +
==41KW (10.10 - 16.10)==
 +
Deinking: <br />
 +
xyl tests + cb
 +
<html></div></html>
 +
{{UBonn_HBRS/footer|class-sideNav=hidden}}

Latest revision as of 21:47, 19 October 2016

 

Lab Notebook 2016

10KW (7.3-13.3)

transformation of genes bought at genescript: XynA, XynB, LipA, EstC2, CpCel9, CpCel5c, EngB, CelA, BsCel5, Bpul and Linkers: nprb, SacB
inoculation of liquid cultures and restriction Analysi of linkers (SacB and nprb).

repetition of the transformation for XynB, EngB and linkers.
Subsequently inoculation and miniprep of the samples. Preparation of glycerol stock.

restriction analysis of the genes.


11KW (14.3-20.3)

Repetion of restriction analysis from the genes KW10 and gel clean ups of the linkers.

Deinking:

  • Measurement of inkjet absorbance spectrum
  • filtration-based deinking setup


12KW (21.3-27.3)

repetition of restriction analysis of all genes and gel clean ups of the genes.

Deinking:
inkjet ink absorbance spectrum and pulp preparation


13KW (28.3-3.4)

Restrictions and gel clean ups of all genes genes for a new gel clean up, because the ones of KW13 did not works. Ligation of genes from the gel clean ups into C3 and inoculation of cultures and minipreps. (1.04.16 :) → successful ligation of

  • XynA
  • CelA
  • LipA
  • Bpul
  • CpCel5c
  • BsCel5
  • EstC2
  • EngB in C3
  • nprb + CpCel9
  • nprb + BsCel5 in C3


Deinking:
establishing the set up and starting experiments with different conc of NaOH and Na2SiO3


14KW (4.4-10.4)

Deinking:
Experiments with different concentrations of surfactant oleic acid


15KW (11.4-17.4)

Deinking:
experiments with different incubation time, vortexing time, temperature


16KW (18.4-24.4)

Deinking:
tests with solvents to dissolve ink and fibers


17KW (25.4-1.5)

Deinking:
grayscale tests, solvent tests


18KW (2.5-8.5)

Deinking:
pulp preparation


19KW (9.5-15.5)

Deinking:
establishing water and standard chemical controls


20KW (16.5-22.5)

Deinking:
establishing water and standard chemical controls


21KW (23.5-29.5)

Restriction analysis of genes from the 13KW and mini prep from samples of the 13KW. (28.05.16) successful ligation of:

  • nprb and sacB in C3
  • nprb + EstC2 in C3

Deinking:
establishing oleic acid and oleic acid + citrate buffer controls


22KW (30.5-5.6)

Restriction analysis of samples of the 21KW

Deinking:
discovery: paper discs with CB turn red, tests to find the reason


23KW (6.6-12.6)

Inoculation of all genes from glycerol stocks and miniprep. Restriction analysis and gel clean up of the genes, ligation of the missing genes with C3.

Deinking:
tests with oleic acid and oleic acid + cb controls


24KW (13.6-19.6)

Restriction of bbMCS and gel clean ups.
Ligations of genes in C5 and C3.
Ligation of genes and tags in C5.

Minipreps of all of the samples.

Deinking:
tests with shaking during incubation and different incubation time


25KW (20.6-26.6)

Restriction analysis of the constructs

Repetition of ligation of genes in C5 and transformation and preps.

Deinking:
rotation evaporator concentrating ink


26KW (27.6 - 3.7)

Restriction analysis of the mini preps.


28KW (11.7-17.7)

Repetion of Ligations of genes and C5

B.subtilis: preparing electrocomp cells and transformations

Deinking:
flotation-based deinking, pulp preparation


29KW (18.7-24.7)

Deinking:
separation of ink from fibers in organic phase of big scale deinking, flotation-based deinking, foam collection, defoaming


30KW (25.7-31.7)

B.subtilis:
preparing electrocomp cells and transformations preparing chemocompetent B. subtilis and transformations

Deinking:
tests with toluene flotation-based deinking


31KW (1.8-7.8)

Ligation of Fragment synthesized at IDT and C3.
Ligation of genes in C3 and genes + tags + C5.
transformation, and inoculation of liquid cultures of the above.

B.subtilis:
preparing of chemocompetent cells and transformations


32KW (8.8 - 14.8)

Ligation of IDT and C3.
Transformation and inoculation.
Minipreps of samples and restriction analysis.

Ligations of genes plus tags in bb_MCS.
Transformation of these samples.

B.subtilis:
preparing of electrocomp and chemocompetent cells and transformations


33KW (15.8 - 21.8)

Inoculation and miniprep.
Repetion of ligation of IDT and C3.
Repetion of ligation of bb + nprb + genes.
Midi prep of SacB, bb and nprb.
Ligation of Genes + C5 and genes plus tags in C5.
Transformation and inoculation of the samples.
mini preps

Deinking:
creation of flat paper-like discs


34KW (22.8 - 28.8)

Restrictions of mini prep and repetition of mini prep

B.subtilis:
preparing of chemocompetent cells and transformations

Deinking:
grayscale tests with officer scanner and odisey scanner


35KW (29.9 - 5.9)

B.subtilis:
transformations of bb


36KW (5.9 - 11.9)

Deinking:
tests of water controls


37KW (12.9 - 18.9)

B.subtilis:
transformations of bb

Deinking:
scanning tests, different conditions tests


38KW (19.9 - 25.9)

B.subtilis:
preparing chemocompetent cells and transformations


39KW (26.9 - 2.10)

Deinking:
establishing water and standard controls into setup with kitchen mixer


40KW (3.10 - 9.10)

Deinking:
xylanase started to test + cb


41KW (10.10 - 16.10)

Deinking:
xyl tests + cb

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