Molecular Biology Laboratory

The Molecular Biology laboratory facilitates work on DNA and RNA of marine organisms. Scientists from all NIOZ departments as well as from other institutions and companies are welcome to cooperate or to join proposals. We develop diagnostic tools for species identification and offer assistance and advice on:

Taking and storing samples for DNA/RNA analyses
Processing samples in our lab
Analyzing sequences, (meta)genomes and transcriptomes
Statistics

Facilities

To avoid contamination of samples, the Molecular Biology Laboratory is divided in compartments:

Clean room for reagent preparation
DNA extraction laboratory
RNA extraction laboratory
Cycler room with 4 gradient cyclers and 1 Quantitative-PCR machine (Biorad CFX)
Measurement room with Biorad Experion, Nanodrop and capillary DNA sequencer (ABI310).
Post-PCR laboratory with digital imaging system (UVP)
Agarose and DGGE gel electrophoresis room
Cloning room of class ML-II
Computer room (Linux systems)

Current research topics and activities

Which organisms survive the treatment of ballast water
Quantification of viruses of eukaryote algae and cyanobacteria
Nitrification in sponges by bacteria and archaea
Aerobic and anaerobic ammonium oxidation in sediments of the North Sea
Expression of genes related to calcification in corals
Identification of bivalve larvae: monitoring of six bivalve species in the Wadden Sea
Identification of larvae of Lutraria lutraria and Spisula subtruncata in the North Sea
Sexing of birds
Population genetics of the bivalve Scrobicularia plana
Population genetics of the bivalve Loripes lacteus
Cryptic species of Arenicola marina
Genetic diversity of Nanochloropsis in relation to biomarker studies

Techniques

DNA and RNA extraction
PCR and Quantitative PCR
TRFLP and ARISA
DGGE and Cloning
Sanger Sequencing and Next generation Sequencing
Microsatellite analyses and AFLPs
Primer design
Sequence analyses
Taxonomic profiling

Selected publications

Cardoso JFMF, van Bleijswijk JDL, Witte H, van Duyl FC (2013) Diversity and abundance of ammonia-oxidizing Archaea and Bacteria in tropical and cold-water coral reef sponges. Aquat Microb Ecol 68:215-230.

Philippart CJM, A Amaral, R Asmus, J van Bleijswijk, J Bremner, F Buchholz, M Cabanellas-Reboredo, D Catarino, A Cattrijsse, F Charles, T Comtet, A Cunha, S Deudero, J-C Duchêne, S Fraschetti, F Gentil, A Gittenberger, JS Gray, K Guizien, JM Gonçalves, G Guarnieri, I Hendriks, B Hussel, R Pinheiro Vieira, B Reijnen, I Sampaio, E Serrao, I Sousa Pinto, E Thiebaut, F Viard, AF Zuur (2012) Spatial synchronies in the seasonal occurrence of larvae of oysters (Crassostrea gigas) and mussels (Mytilus edulis/galloprovincialis) in European coastal waters. Estuarine, Coastal and Shelf Science 108: 52-63

Stefan Schouten S, A Pitcher, EC Hopmans, L Villanueva, J van Bleijswijk, JS Sinninghe Damsté (2012) Intact polar and core glycerol dibiphytanyl glycerol tetraether lipids in the Arabian Sea oxygen minimum zone: I. Selective preservation and degradation in the water column and consequences for the TEX86. Geochimica et Cosmochimica Acta 98: 228-243

Luttikhuizen PC, A Bol, H Witte, J van Bleijswijk, O Haddrath, AJ Baker, T Piersma, J Reneerkens (2011) Novel and cross-species microsatellite markers for parentage analysis in sanderling Calidris alba. Journal of Ornithology DOI 10.1007/s10336-011-0681-6

Rampen SW, S Schouten, EC Hopmans, B Abbas, AAM Noordeloos, JDL van Bleijswijk, JAJ Geenevasen, JS Sinninghe Damsté (2009) Diatoms as a source for 4-desmethyl-23,24-dimethyl steroids in sediments and petroleum. Geochimica et Cosmochimica Acta 73(2):377-387

Weijers JWH, E Panoto, J van Bleijswijk, S Schouten, WIC Rijpstra, M Balk, AJM Stams, JS Sinninghe Damsté (2009) Constraints on the Biological Source(s) of the Orphan Branched Tetraether Membrane Lipids. Geomicrobiology Journal 26(6):402-414

Luttikhuizen PC, J Campos, J van Bleijswijk, KT Peijnenburg, HW van der Veer (2008) Phylogeography of the common shrimp, Crangon crangon (L.) across its distribution range. Molecular Phylogenetics and Evolution 46:1015–1030

Frade PR, F de Jongh, F Vermeulen, J van Bleijswijk, RPM Bak (2008) Variation in symbiont distribution between closely related coral species over large depth ranges. Molecular Ecology 17:691-703

Coolen, MJL, B Abbas, J van Bleijswijk, EC Hopmans, MMM Kuypers, SG Wakeham, JS Sinninghe Damsté (2007).Putative ammonia-oxidizing Crenarchaeota thrive in suboxic waters of the Black Sea: A basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids. Environmental Microbiology 9(4):1001-1016

Wuchter C, B Abbas, MJL Coolen, L Herfort, J van Bleijswijk, P Timmers, M Strous, E Teira, GJ Herndl, JJ Middelburg, S Schouten, JS Sinninghe Damste (2006) Archaeal nitrification in the ocean. Proc. Natl. Acad. Sci. USA 103:12317–12322