I am looking for a thesis student (spring 2019 for 6 months) that is interested in metabolic engineering of secondary metabolites by CRISPR, RNAi, and/or overexpression of target genes. Background with biotechnology, and/or molecular biology and cloning is essential. You will clone, transform plants, analyse transgene expression and measure metabolites.
If you are interested, please send a short CV with motivation to julian.verdonk@wur.nl
The 5th edition of the Postharvest Technology course was held in Wageningen last week. Course leaders Ernst Woltering and Julian Verdonk, lecturers, Rob Schouten, Eelke Westra, Leo Lukasse, Jan van Kan, Marcel Wenneker, Jan Verschoor, and guest course leader Mary Lu Arpaia, were put together in four days of lectures, demo’s and pitches, and and excursion. We hosted participants from industry and education from all over the world, to teach them about product physiology and the cold chain of a large variety of fruits, vegetables and ornamental plant products. Continue reading
The isolation of plasmids from bacteria, is one of the simplest biochemical excersize in a molecular biological lab. It is a beautiful illustartion where the pH and differences in solubility of molecules are used to separate them from each other. The wole procedure can be done in about 30 min, quick and clean. The method is desribed in Birnboim and Doly, (1979) and also on wikipedia. Continue reading
Orange GMO Petunia. Photo credit Teemu Teeri
Nov 2017: In the 5th round of the Graduate School Tuinbouw & Uitgangsmaterialen, the proposal of Sara Abdou and Julian Verdonk was granted.
It is a collaboration with Francesca Quattrocchio of the University of Amsterdam and Teemu Teeri from the university of Helsinki, and industry partners from Deliflor, Dümmen Orange, Florensis, Gene Twister and Hudson River Biotechnology. Continue reading
introduction
plant RNA isolations often requires the of use unhealthy organic solutions like phenol or beta-mercaptoethanol, and although I still prefer the TriZOL method or the SDS-TriZOL combo for when I need large quantities of great RNA, you have to wonder if it will ever be needed for me to do a northern blot. This method described here is for when you dont need that much RNA, for example because you’re going to do qRT-PCR. Here is a method to quickly and more importantly cheaply isolate good RNA from relatively small amounts of tissue (30-50 mg/a few 0.5 cm leaf discs) using only a low pH from citric acid to inactivate the RNAses. The method is described by Oñate-Sánchez and Vicente-Carbajosa (2008).
Update 2022: Luis Oñate-Sanchez and me have published an updated version of this protocol in Current Protocols. We also renamed the method to CiAR: Citrate-Citric Acid RNA Isolation. Now you can cite the method if you use it! Here is the link.
Introduction
For simple tissues, I prefer to isolate RNA with the Citrate-Citric Acid method, but the isolation of good quality RNA of fruits and other plant tissue with a lot of sugars and/or other inhibiting crap in it can be quite a challenge. The TRIzol method is not always the best option because these compounds sometimes have similar biochemical characteristics as the nucleic acids we try to isolate. This method was used on maize aleurones (Reyes et al., 2011) based on Holding et al., (2007). You can do it all in eppendorf tubes, use about 0.2 g/sample, which is enough for a high enough yield and quality for RNA seq. Continue reading
H-index: 10. Google Scholar profile
My all time favorite RNA isolation, and most used protocol is the TRIzol method. Here I give you the basic protocol, including the recipe to make it yourself, which will save you a lot of money.
Update 2022: Balta and me have published this protocol in Current Protocols. It is open access, and now you can cite the method if you use it! Here is the link.
composition:
38% Phenol (pure phenol from crystals, i.e. SIGMA P1037-500G)
0.8 M Guanidine Thiocyanate (118.16 g/mol)
0.4 M Ammonium Thiocyanate (79.12 g/mol)
0.1 M Sodium Acetate (82.03 g/mol)
5 % Glycerol
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