Institute for Biodiversity and Ecosystem Dynamics

Molecular genetic laboratory

Because of the diversity of the research questions that the four research departments of IBED try to answer, our molecular lab is well-equipped and experienced in handling, preparing and analyzing a wide variety of samples. 

PCR

PCR. Photo: IBED

DNA/RNA isolation

Every plant and animal species requires a specific and optimized DNA/RNA isolation protocol. The same applies for tissue types and sample storage conditions. We not only use the popular DNA or RNA isolation kits but also the more old school protocols like 2%CTAB, TES buffers or hot phenol. There is equipment to isolate high quality DNA/RNA in the form of: Precellys24 for cell lysis, different centrifuges (cooled and non-cooled), gel electrophoresis, Nanodrop and Qubit.

qPCR ABI 7500

qPCR ABI 7500. Photo: IBED

Downstream analysis

For downstream analysis we have eight PCR machines and two Quantitative Real-Time PCR Systems (qPCR). To answer population genetic questions we can make use of ALFP (Amplified Fragment Length Polymorphism) or microsatellites. These genetic markers are analysed with the LI-COR 4300 DNA Analysis System or ABI genetic analyzer 3130. Together with SILS we have a well-organized sequence collaboration with Macrogen. Sample preparation for RAD-tag or RNA-seq is possible in our molecular genetics lab. The actual Next Generation Sequencing is outsourced to third party sequencing services. We have two Biological Safety Cabinets and a large amount of climate chambers, climate cabinets and stoves for our genetic transformation and cell cultures.

To keep the molecular lab up-to-date in the fast evolving field of molecular biology we also implement new machines, techniques and protocols. At the moment we are working on CRISPR-cas9.

Bio safety

Biological Safety Cabinet. Photo: IBED

Organization

Three technicians are dedicated to molecular genetic analyses: Peter Kuperus, Betsie Voetdijk and Lin Dong. They assist in conducting molecular-genetic experiments using established protocols together with (and provided by) IBED PhD candidates, Postdoc researchers and staff members. Moreover, they regularly assist in a wide range of projects and courses of Bachelor and Master students.

qPCR  biorad

qPCR Bio-Rad. Photo: IBED

Contact information

If you are a permanent IBED staff member and you or your students are planning to undertake a project for which you need help on conducting molecular genetics, please contact:

Peter Kuperus

IBED-lab-science@uva.nl

Published by  IBED

27 November 2017