Team:TU-Munich/Notebook/Methods

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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> color lime, ss h; color yelloworange, ss s; color limon, ss "" PyMOL> mset 1 x180 PyMOL> util.mroll 1,180 PyMOL> mpng frame

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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@@ Line 76: / Line 76: @@
 PyMOL> hide everything, all<br>
 PyMOL> show cartoon, all<br>
-PyMOL> color purple, ss h; color yellow, ss s; color green, ss ""<br>
+PyMOL> color lime, ss h; color yelloworange, ss s; color limon, ss ""<br>
 PyMOL> mset 1 x180<br>
 PyMOL> util.mroll 1,180<br>