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Team:TU-Munich/Notebook/Methods
From 2013.igem.org
Molecular-biological Methods
Preparation of Nucleotide fragments
Digestion, Dephosphorylation
Hybridization of Oligonucleotides
Polymerase Chain Reaction
Site-directed Mutagenesis
Agarose Gel Electrophoresis
TAE-Buffer | |
| Reagent | Amount |
Ligation of DNA-Fragments
Microbiological Methods
Preparation of LB-Media
LB-Media | |
| Reagent | Amount |
Transformation of E. coli
Cultivation of E. coli
Protein-biochemical Methods
Physcomitrella Methods
The techniques used for the cultivation and manipulation of Physcomitrella patens are based on the knowledge of the chair for Plantbiotechnology of Prof. Dr. Reski at Freiburg University which are availible at [http://www.plant-biotech.net Plant-Biotech.net].
Preparation of Knob-Media
Knob-Media | |
| Reagent | Amount |
Cultivation of P. patens
Homogenization
Bioinformatical Methods
Generation of Annimated GIFs
- The structure was opened with Pymol
- The approach was adapted from a PyMol-Tutorial http://ihome.cuhk.edu.hk/~b102142/pymol/pymol_tutorial.html Wong
- The following commands were entered into the command line:
PyMOL> orient
PyMOL> hide everything, all
PyMOL> show cartoon, all
PyMol> bg_color white
PyMOL> color lime, ss h; color yelloworange, ss s; color limon, ss ""
PyMOL> mset 1 x180
PyMOL> util.mroll 1,180
PyMOL> mpng frame
- Afterward the *.png files were automatically converted to *.tif files using xxx
- The program xxx was used to generate the annimated GIFs
- A new working folder was generated and the *.gif files were imported
- The background was set to white
- The range of colors was set to 256
- Finally the annimated Gif was computed
The result is the following:
References:
http://www.ncbi.nlm.nih.gov/pubmed/6327079 Edens et al., 1984
- http://www.ncbi.nlm.nih.gov/pubmed/6327079 Edens et al., 1984 Edens, L., Bom, I., Ledeboer, A. M., Maat, J., Toonen, M. Y., Visser, C., and Verrips, C. T. (1984). Synthesis and processing of the plant protein thaumatin in yeast. Cell, 37(2):629–33.
- http://ihome.cuhk.edu.hk/~b102142/pymol/pymol_tutorial.html Wong A tutorial on using PyMOL to generate publication quality figures. http://ihome.cuhk.edu.hk/~b102142/pymol/pymol_tutorial.html]]
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