Team:TU-Munich/Notebook/Methods

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Revision as of 12:18, 29 August 2013


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

PyMOL> orient
PyMOL> hide everything, all
PyMOL> show cartoon, all
PyMol> bg_color white
click> Settings>Rendering>Shadows>Occlusion
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:

File:TUM13 Annimated Gif test.gif
Description

References:

http://www.ncbi.nlm.nih.gov/pubmed/6327079 Edens et al., 1984

  1. 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.
  2. 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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