iGEM 2017 — Team UBonn_HBRS

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# Team:UBonn HBRS/Notebook

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TEAM

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[Collaborations](https://2017.igem.org/Team%3AUBonn_HBRS/Collaborations)

PROJECT

[Description](https://2017.igem.org/Team%3AUBonn_HBRS/Description)
[Design](https://2017.igem.org/Team%3AUBonn_HBRS/Design)
[Experiments](https://2017.igem.org/Team%3AUBonn_HBRS/Experiments)
[Notebook](https://2017.igem.org/Team%3AUBonn_HBRS/Notebook)
[InterLab](https://2017.igem.org/Team%3AUBonn_HBRS/InterLab)
[Contribution](https://2017.igem.org/Team%3AUBonn_HBRS/Contribution)
[Model](https://2017.igem.org/Team%3AUBonn_HBRS/Model)
[Results](https://2017.igem.org/Team%3AUBonn_HBRS/Results)
[Demonstrate](https://2017.igem.org/Team%3AUBonn_HBRS/Demonstrate)
[Improve](https://2017.igem.org/Team%3AUBonn_HBRS/Improve)
[Attributions](https://2017.igem.org/Team%3AUBonn_HBRS/Attributions)

PARTS

[Parts](https://2017.igem.org/Team%3AUBonn_HBRS/Parts)
[Basic Parts](https://2017.igem.org/Team%3AUBonn_HBRS/Basic_Part)
[Composite Parts](https://2017.igem.org/Team%3AUBonn_HBRS/Composite_Part)
[Part Collection](https://2017.igem.org/Team%3AUBonn_HBRS/Part_Collection)

[SAFETY](https://2017.igem.org/Team%3AUBonn_HBRS/Safety)

HUMAN PRACTICES

[Silver HP](https://2017.igem.org/Team%3AUBonn_HBRS/HP/Silver)
[Integrated and Gold](https://2017.igem.org/Team%3AUBonn_HBRS/HP/Gold_Integrated)
[Public Engagement](https://2017.igem.org/Team%3AUBonn_HBRS/Engagement)

AWARDS

[Applied Design](https://2017.igem.org/Team%3AUBonn_HBRS/Applied_Design)
[Entrepreneurship](https://2017.igem.org/Team%3AUBonn_HBRS/Entrepreneurship)
[Hardware](https://2017.igem.org/Team%3AUBonn_HBRS/Hardware)
[Measurement](https://2017.igem.org/Team%3AUBonn_HBRS/Measurement)
[Model](https://2017.igem.org/Team%3AUBonn_HBRS/Model)
[Plant](https://2017.igem.org/Team%3AUBonn_HBRS/Plant)
[Software](https://2017.igem.org/Team%3AUBonn_HBRS/Software)

[JUDGING FORM](https://igem.org/2017_Judging_Form?team=UBonn_HBRS)

* [Start](//2017.igem.org/Team%3AUBonn_HBRS)
* Project

  [Description](//2017.igem.org/Team%3AUBonn_HBRS/Description)[Cloning](//2017.igem.org/Team%3AUBonn_HBRS/Description/Cloning)
  [Enzyme Assays](//2017.igem.org/Team%3AUBonn_HBRS/Description/Enzyme_Assays)
  [SELEX](//2017.igem.org/Team%3AUBonn_HBRS/Description/SELEX)
  [Binding Assays](//2017.igem.org/Team%3AUBonn_HBRS/Description/Binding_Assays)[Notebook](//2017.igem.org/Team%3AUBonn_HBRS/Notebook)
* [Human Practices](//2017.igem.org/Team%3AUBonn_HBRS/HP/Silver)
* Team

  [Team](//2017.igem.org/Team%3AUBonn_HBRS/Team)
  [Collaborations](//2017.igem.org/Team%3AUBonn_HBRS/Collaborations)
* [Attributions](//2017.igem.org/Team%3AUBonn_HBRS/Attributions)
* [Parts](//2017.igem.org/Team%3AUBonn_HBRS/Parts)
* [Safety](//2017.igem.org/Team%3AUBonn_HBRS/Safety)

Contents

# Notebook

## Week 19 (09.10-13.10)

## Contents

* [1 Day 1](#Day_1)
* [2 Day 1](#Day_1_2)
* [3 Day 1](#Day_1_3)
* [4 Day 2](#Day_2)
* [5 Day 3](#Day_3)
* [6 Day 4](#Day_4)
* [7 Day 1](#Day_1_4)
* [8 Day 2](#Day_2_2)
* [9 Day 3](#Day_3_2)
* [10 Day 1](#Day_1_5)
* [11 Day 2](#Day_2_3)
* [12 Day 3](#Day_3_3)
* [13 Day 4](#Day_4_2)
* [14 Day 1](#Day_1_6)
* [15 Day 2](#Day_2_4)
* [16 Day 3](#Day_3_4)
* [17 Day 4](#Day_4_3)
* [18 Day 5](#Day_5)
* [19 Day 1](#Day_1_7)
* [20 Day 2](#Day_2_5)
* [21 Day 3](#Day_3_5)
* [22 Day 4](#Day_4_4)
* [23 Day 1](#Day_1_8)
* [24 Day 2](#Day_2_6)
* [25 Day 3](#Day_3_6)
* [26 Day 4](#Day_4_5)
* [27 Day 1](#Day_1_9)
* [28 Day 2](#Day_2_7)
* [29 Day 3](#Day_3_7)
* [30 Day 4](#Day_4_6)
* [31 Day 1](#Day_1_10)
* [32 Day 2](#Day_2_8)
* [33 Day 1](#Day_1_11)
* [34 Day 2](#Day_2_9)
* [35 Day 3](#Day_3_8)
* [36 Day 4](#Day_4_7)
* [37 Day 1](#Day_1_12)
* [38 Day 2](#Day_2_10)
* [39 Day 3](#Day_3_9)
* [40 Day 4](#Day_4_8)
* [41 Day 5](#Day_5_2)
* [42 Day 1](#Day_1_13)
* [43 Day 2](#Day_2_11)
* [44 Day 3](#Day_3_10)
* [45 Day 4](#Day_4_9)
* [46 Day 1](#Day_1_14)
* [47 Day 2](#Day_2_12)
* [48 Day 3](#Day_3_11)
* [49 Day 1](#Day_1_15)
* [50 Day 2](#Day_2_13)
* [51 Day 3](#Day_3_12)
* [52 Day 4](#Day_4_10)
* [53 Day 5](#Day_5_3)
* [54 Day 1](#Day_1_16)
* [55 Day 2](#Day_2_14)
* [56 Day 3](#Day_3_13)
* [57 Day 4](#Day_4_11)
* [58 Day 5](#Day_5_4)
* [59 Day 1](#Day_1_17)
* [60 Day 2](#Day_2_15)
* [61 Day 1](#Day_1_18)
* [62 Day 2](#Day_2_16)
* [63 Day 3](#Day_3_14)
* [64 Day 1](#Day_1_19)
* [65 Day 2](#Day_2_17)
* [66 Day 3](#Day_3_15)
* [67 Day 4](#Day_4_12)

#### Day 1

* Binding assay of gtfC to dynabeads
* Inhibition study of D3 PCR
* Dephosphorylation of gtfC2 + psB1C3
* Gel electrophoreis, gel extraction, ligation

## Week 18 (02.10-06.10)

#### Day 1

* Miniprep of gtfC part 2
* Ligation of gtfC part 2 + gtfC part 1
* Ligation of gtfC part 1 + gtfC part 2

## Week 17 (28.09-01.10)

#### Day 1

* Checked sequencing results
* Checked buffer's composition

#### Day 2

* Restriction analysis of gtfC 2 + 1
* Enzyme assay with Miller reagents
* Picked 4 more colonies of Spap1 and 1 pick gtfC2+1

#### Day 3

* Miniprep
* Restriction digest, gelelectrophoresis

#### Day 4

* Restriction analysis of gtfC 2+1 with EcoRI, HindIII, PstI
* Restriction analysis of gtfC 2+1 with EcoRI, HindIII
* Sent in Pick 8 of SpaP 1+2
* Sent in Pick 1 of gtfC 1+2

## Week 16 (18.09-22.09)

#### Day 1

* Restriction digest
* Gel extraction
* Ligation over night of gtfC part 2 in psB1C3
* PCR of amplified gtfC part 1

#### Day 2

* D3 library amplification
* D3 library inhibition assay
* Poured new agar plates
* PCR amplification

#### Day 3

* Enzyme assay

## Week 15 (11.09-15.09)

#### Day 1

* Restriction
* Gel extraction
* Over night ligation of gtfc2 in psB1C3 and PCR amplified gtfC1

#### Day 2

* Transformation of NEB with ligates
* Miller assay
* Beads coupling assay

#### Day 3

* Prepared cultures for miniprep
* Checked if protein inhibits the D3 library’s PCR

#### Day 4

* Miniprep
* Restriction analysis
* Sent in DNA
* PCR for Spap 1 and 2

## Week 14 (04.09-08.09)

#### Day 1

* PCR for amplification of the parts
* Changed the buffer of enzyme with the Mondelli buffer

#### Day 2

* Miniprep of gtfC part 2
* Ligation of gtfC part 2 + gtfC part 1
* Ligation of gtfC part 1 + gtfC part 2

#### Day 3

* PCR
* SDS-Page

#### Day 4

* Performing restriction of each part with EcoRI and PstI
* Restriction of psB1C3 plasmid
* Restriction of each SpaP part with NheI, PCR clean up and subsequent ligation
* Restriction of each gtfC part with HindIII, PCR clean up and subsequent ligation
* Ligation on higher concentrations

#### Day 5

* Picking colonies
* Binding assay in Mondelli buffer without BSA and tween
* PCR of gtfC part 1

## Week 13 (28.08-01.09)

#### Day 1

* Adding SDS into the Miller-reagent
* Measuring the pH of the Mondelli-buffer
* Glucan assay with new concentrations
* Checking the pH of the Mondelli-buffer

#### Day 2

* Miller assay with Mondelli buffer
* Preculture for IPTG induction
* PCR of parts
* Binding Enzyme to Ni-NTA-beads
* Calibrating pipettes

#### Day 3

* IPTG Induction
* Ligations and transformations with a higher concentration in DNA
* Running a gel of d3 library

#### Day 4

* PCR amplfication of IDT parts with newly arrived primers
* Evaluating IPTG induction and gel of D3 library
* Testing Ni-NTA-beads’ binding capacity for our enzyme

## Week 12 (21.08-25.08)

#### Day 1

* Testing the Miller-reagent
* Gel electrophoresis

#### Day 2

* Redid restriction of pick 1, 2, 3, 4 of gtfC part 2+1

#### Day 3

* Miniprep of gtfC part 2
* Miniprep of amplified parts

#### Day 4

* IPTG Induction of BL21 promoter construct
* Enzyme assay

## Week 11 (14.08-18.08)

#### Day 1

* Minipreps of 5 Spap2-picks
* Dephosphorylation of gtfC2 + psB1C3
* Ligation of gtfC 1 + 2
* Restriction of:
  + Picks 5 - 9 of SpaP part 2 (for Restriction-Analysis)
  + GTFc I and II (only HindIII)
  + validated (GTFc II + psB1C3) & GTFc II (EcoRI & HindIII)

#### Day 2

* Ligation and transformation of gtfC1 into vector+gtfC2
* Restriction analysis of SpaP 2

#### Day 3

* Picking of colonies (gtfC1+2)
* Inoculation in LB-media

#### Day 4

* Miniprep and restriction for later restriction analysis

## Week 10 (07.08-11.08)

#### Day 1

* Picking and inoculating miniprep results
* Restriction analysis
* Inoculating LB medium with validated gtfC part 2 bacteria

#### Day 2

* Miniprep of gtfC part 2
* Ligation of gtfC part 2 + gtfC part 1
* Ligation of gtfC part 1 + gtfC part 2

## Week 9 (31.07-04.08)

#### Day 1

* Ligation of gtfC part 2 into psB1C3
* Ligation of gtfC part 1+2 int psB1C3

#### Day 2

* Transformation in NEB Turbo (part 2)
* Transformation in NEB Turbo and BL21 (part 1+2)

#### Day 3

* Picking clones (4-5 each plate, 10 from part 1+2) in TB+Kanamycin
* Miniprep of cultures

#### Day 4

* Restriction analysis of the results from miniprep
* Sending in the results for sequencing

## Week 8 (24.07-28.07)

#### Day 1

* Restriction analysis of SpaP2 and gtfC2

#### Day 2

* Ligation ans transformation of IDT genes (part1 of SpaP)

#### Day 3

* Miniprep of five picks of SpaP fragment and SpaP part 2
* Miniprep of the other colonies
* Transformation of BL21 with pick 4 of promoter B1C3 construct

#### Day 4

* Transformation of promoter B1C3 construct into BL21
* Ligation and transformation of SpaP part 2 and 1 into NEB Turbo bacteria

#### Day 5

* Preparation of Glycerol stocks
* Restriction digest
* Sent DNA for sequencing

## Week 7 (17.07-21.07)

#### Day 1

* Cutting, ligating and transformation of IDT genes (fragment of SpaP)
* Added canamycin to the agar LB and poured plates

#### Day 2

* Miniprep of three picks of SpaP fragment
* Cutting, ligating and transformation of SpaP part2 and gtfC

#### Day 3

* Miniprep of three picks of each SpaP and gtfC
* Restriction analysis of SpaP fragment's picks and sending to sequencing
* Competent BL21 bacteria prepared

#### Day 4

* Restriction analysis of part 2 of SpaP and gtfC
* Results sent to sequencing

## Week 6 (10.07-14.07)

#### Day 1

* Preparing LB medium and CaCl₂ buffer
* Making new plates
* Starting pre-culture of BL21 bacteria

#### Day 2

* Preparing competent bacteria

#### Day 3

* Testing the competence of the bacteria
* Preparing agar plates

## Week 5 (03.07-07.07)

#### Day 1

* Starting a pre-culture with BL21 bacteria in non-validate box

#### Day 2

* Production of competent bacteria
* Transformation of BL21 bacteria with the promoter construct and with the standard C1B3-Plac-mRFP1 as a positive control

#### Day 3

* Picking colonies of our construct and the positive control into TB medium

#### Day 4

* Ligation

#### Day 5

* Picking colonies and inoculating
* Making glycerol stocks
* Gel electrophoresis
* Sending DNA for sequencing

## Week 4 (26.06-30.06)

#### Day 1

* Transformation of NEB Turbo bacteria

#### Day 2

* Picking colonies and inoculating
* Making glycerol stocks
* Gel electrophoresis
* Sending DNA for sequencing

#### Day 3

* Planning IPTG induction
* Starting a pre-culture

#### Day 4

* IPTG induction at OD600 ~ 0.4

#### Day 5

* Picking colonies and inoculating
* Making glycerol stocks
* Gelelectrophoresis
* Sending DNA for sequencing

## Week 3 (19.06-23.06)

#### Day 1

* IDT DNA suspension

#### Day 2

* Digest
* DNA extraction
* Dephosphorylation of the backbone
* Ligation
* Making INOUE buffer for new competent bacteria
* Making SOB

## Week 2 (05.06-09.06)

#### Day 1

* Sequencing sample 1.2
* Transformation with and without IPTG

#### Day 2

* Checking TB transformation

#### Day 3

* IPTG assay

## Week 1 (29.05-02.06)

#### Day 1

* Inoculation of the promoter construct
* Miniprep

#### Day 2

* Restriction analysis

#### Day 3

* Re-Measurement of C3-IDT-RFP
* Restriction analysis
* Inoculation of plate 1 and 2

#### Day 4

* Making glycerol stocks
* Miniprep
* Restriction analysis

© iGEM Team Bonn 2017
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# Team:UBonn HBRS/Experiments

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MENU

[HOME](https://2017.igem.org/Team%3AUBonn_HBRS)

TEAM

[Team](https://2017.igem.org/Team%3AUBonn_HBRS/Team)
[Collaborations](https://2017.igem.org/Team%3AUBonn_HBRS/Collaborations)

PROJECT

[Description](https://2017.igem.org/Team%3AUBonn_HBRS/Description)
[Design](https://2017.igem.org/Team%3AUBonn_HBRS/Design)
[Experiments](https://2017.igem.org/Team%3AUBonn_HBRS/Experiments)
[Notebook](https://2017.igem.org/Team%3AUBonn_HBRS/Notebook)
[InterLab](https://2017.igem.org/Team%3AUBonn_HBRS/InterLab)
[Contribution](https://2017.igem.org/Team%3AUBonn_HBRS/Contribution)
[Model](https://2017.igem.org/Team%3AUBonn_HBRS/Model)
[Results](https://2017.igem.org/Team%3AUBonn_HBRS/Results)
[Demonstrate](https://2017.igem.org/Team%3AUBonn_HBRS/Demonstrate)
[Improve](https://2017.igem.org/Team%3AUBonn_HBRS/Improve)
[Attributions](https://2017.igem.org/Team%3AUBonn_HBRS/Attributions)

PARTS

[Parts](https://2017.igem.org/Team%3AUBonn_HBRS/Parts)
[Basic Parts](https://2017.igem.org/Team%3AUBonn_HBRS/Basic_Part)
[Composite Parts](https://2017.igem.org/Team%3AUBonn_HBRS/Composite_Part)
[Part Collection](https://2017.igem.org/Team%3AUBonn_HBRS/Part_Collection)

[SAFETY](https://2017.igem.org/Team%3AUBonn_HBRS/Safety)

HUMAN PRACTICES

[Silver HP](https://2017.igem.org/Team%3AUBonn_HBRS/HP/Silver)
[Integrated and Gold](https://2017.igem.org/Team%3AUBonn_HBRS/HP/Gold_Integrated)
[Public Engagement](https://2017.igem.org/Team%3AUBonn_HBRS/Engagement)

AWARDS

[Applied Design](https://2017.igem.org/Team%3AUBonn_HBRS/Applied_Design)
[Entrepreneurship](https://2017.igem.org/Team%3AUBonn_HBRS/Entrepreneurship)
[Hardware](https://2017.igem.org/Team%3AUBonn_HBRS/Hardware)
[Measurement](https://2017.igem.org/Team%3AUBonn_HBRS/Measurement)
[Model](https://2017.igem.org/Team%3AUBonn_HBRS/Model)
[Plant](https://2017.igem.org/Team%3AUBonn_HBRS/Plant)
[Software](https://2017.igem.org/Team%3AUBonn_HBRS/Software)

[JUDGING FORM](https://igem.org/2017_Judging_Form?team=UBonn_HBRS)

# Experiments

Describe the research, experiments, and protocols you used in your iGEM project. These should be detailed enough for another team to repeat your experiments.

Please remember to put all characterization and measurement data for your parts on the corresponding Registry part pages.

##### What should this page contain?

* Protocols
* Experiments
* Documentation of the development of your project

##### Inspiration

* [2014 Colombia](https://2014.igem.org/Team%3AColombia/Protocols)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Protocols)
* [2014 Caltech](https://2014.igem.org/Team%3ACaltech/Project/Experiments)

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[![](https://static.igem.org/mediawiki/2017/8/8b/HQ_page_logo.jpg)](https://2017.igem.org)

# Team:UBonn HBRS/Results

[![](//2017.igem.org/wiki/images/6/66/T--UBonn_HBRS--sidemenu_logo.png)](https://2017.igem.org/Team%3AUBonn_HBRS)

MENU

[HOME](https://2017.igem.org/Team%3AUBonn_HBRS)

TEAM

[Team](https://2017.igem.org/Team%3AUBonn_HBRS/Team)
[Collaborations](https://2017.igem.org/Team%3AUBonn_HBRS/Collaborations)

PROJECT

[Description](https://2017.igem.org/Team%3AUBonn_HBRS/Description)
[Design](https://2017.igem.org/Team%3AUBonn_HBRS/Design)
[Experiments](https://2017.igem.org/Team%3AUBonn_HBRS/Experiments)
[Notebook](https://2017.igem.org/Team%3AUBonn_HBRS/Notebook)
[InterLab](https://2017.igem.org/Team%3AUBonn_HBRS/InterLab)
[Contribution](https://2017.igem.org/Team%3AUBonn_HBRS/Contribution)
[Model](https://2017.igem.org/Team%3AUBonn_HBRS/Model)
[Results](https://2017.igem.org/Team%3AUBonn_HBRS/Results)
[Demonstrate](https://2017.igem.org/Team%3AUBonn_HBRS/Demonstrate)
[Improve](https://2017.igem.org/Team%3AUBonn_HBRS/Improve)
[Attributions](https://2017.igem.org/Team%3AUBonn_HBRS/Attributions)

PARTS

[Parts](https://2017.igem.org/Team%3AUBonn_HBRS/Parts)
[Basic Parts](https://2017.igem.org/Team%3AUBonn_HBRS/Basic_Part)
[Composite Parts](https://2017.igem.org/Team%3AUBonn_HBRS/Composite_Part)
[Part Collection](https://2017.igem.org/Team%3AUBonn_HBRS/Part_Collection)

[SAFETY](https://2017.igem.org/Team%3AUBonn_HBRS/Safety)

HUMAN PRACTICES

[Silver HP](https://2017.igem.org/Team%3AUBonn_HBRS/HP/Silver)
[Integrated and Gold](https://2017.igem.org/Team%3AUBonn_HBRS/HP/Gold_Integrated)
[Public Engagement](https://2017.igem.org/Team%3AUBonn_HBRS/Engagement)

AWARDS

[Applied Design](https://2017.igem.org/Team%3AUBonn_HBRS/Applied_Design)
[Entrepreneurship](https://2017.igem.org/Team%3AUBonn_HBRS/Entrepreneurship)
[Hardware](https://2017.igem.org/Team%3AUBonn_HBRS/Hardware)
[Measurement](https://2017.igem.org/Team%3AUBonn_HBRS/Measurement)
[Model](https://2017.igem.org/Team%3AUBonn_HBRS/Model)
[Plant](https://2017.igem.org/Team%3AUBonn_HBRS/Plant)
[Software](https://2017.igem.org/Team%3AUBonn_HBRS/Software)

[JUDGING FORM](https://igem.org/2017_Judging_Form?team=UBonn_HBRS)

# Results

Here you can describe the results of your project and your future plans.

##### What should this page contain?

* Clearly and objectively describe the results of your work.
* Future plans for the project.
* Considerations for replicating the experiments.

##### You should also describe what your results mean:

* Interpretation of the results obtained during your project. Don't just show a plot/figure/graph/other, tell us what you think the data means. This is an important part of your project that the judges will look for.
* Show data, but remember all measurement and characterization data must be on part pages in the Registry.
* Consider including an analysis summary section to discuss what your results mean. Judges like to read what you think your data means, beyond all the data you have acquired during your project.

##### Project Achievements

You can also include a list of bullet points (and links) of the successes and failures you have had over your summer. It is a quick reference page for the judges to see what you achieved during your summer.

* A list of linked bullet points of the successful results during your project
* A list of linked bullet points of the unsuccessful results during your project. This is about being scientifically honest. If you worked on an area for a long time with no success, tell us so we know where you put your effort.

##### Inspiration

See how other teams presented their results.

* [2014 TU Darmstadt](https://2014.igem.org/Team%3ATU_Darmstadt/Results/Pathway)
* [2014 Imperial](https://2014.igem.org/Team%3AImperial/Results)
* [2014 Paris Bettencourt](https://2014.igem.org/Team%3AParis_Bettencourt/Results)

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