Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

    We have a manual that explains all the features 

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Get your high-quality low-cost genome sequence
Faino, L. ; Thomma, B.P.H.J. - \ 2014
Trends in Plant Science 19 (2014)5. - ISSN 1360-1385 - p. 288 - 291.
generation - assemblies - alignments - annotation - program - tool
The study of whole-genome sequences has become essential for almost all branches of biological research. Next-generation sequencing (NGS) has revolutionized the scalability, speed, and resolution of sequencing and brought genomic science within reach of academic laboratories that study non-model organisms. Here, we show that a high-quality draft genome of a eukaryote can be obtained at relatively low cost by exploiting a hybrid combination of sequencing strategies.
Metagenomic species profiling using universal phylogenetic marker genes
Sunagawa, S. ; Mende, D.R. ; Zeller, G. ; Izquierdo-Carrasco, F. ; Berger, S.A. ; Kultima, J.R. ; Coelho, L.P. ; Arumugam, M. ; Tap, J. ; Nielsen, H.B. ; Rasmussen, S. ; Brunak, S. ; Pedersen, O. ; Guarner, F. ; Vos, W.M. de; Wang, J. ; Li, J. ; Doré, J. ; Ehrlich, S.D. ; Stamatakis, A. ; Bork, P. - \ 2013
Nature Methods : techniques for life scientists and chemists 10 (2013)12. - ISSN 1548-7091 - p. 1196 - 1199.
maximum-likelihood - human microbiome - gut microbiome - alignments - accurate - catalog - reads - life - tree - ibd
To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome-based methods. An implementation of the method is available at http://www.bork.embl.de/software/mOTU/
Spatial distribution of bacteria associated with the marine sponge Tethya californiana
Sipkema, D. ; Blanch, H.W. - \ 2010
Marine Biology 157 (2010)3. - ISSN 0025-3162 - p. 627 - 638.
microbial community - aplysina-aerophoba - ribosomal-rna - antimicrobial activity - phylogenetic analysis - diversity - demospongiae - alignments - symbionts - porifera
Microbial diversity and spatial distribution of the diversity within tissue of the marine sponge Tethya californiana was analyzed based on 16S rRNA gene sequences. One candidate division and nine bacterial phyla were detected, including members of all five subdivisions of Proteobacteria. Moreover, chloroplast-derived Stramenopiles- and Rhodophyta-affiliated 16S rRNA gene sequences were found and Stramenopiles represented the most abundant clones (30%) in the clone library. On the phylum-level, the microbial fingerprint of T. californiana showed a similar pattern as its Mediterranean relative T. aurantium. An interesting difference was that Cyanobacteria that were abundantly present in T. aurantium were not found in T. californiana, but that the latter sponges harbored phototrophic Stramenopiles instead. Surprisingly, the phototrophic microorganisms were evenly distributed over the inner and outer parts of the sponge tissue, which implies that they also reside in regions without direct light exposure. The other phyla were also present in both the outer cortex and the mesohyl of the sponges. These results were confirmed by analysis on the operational taxonomic unit level. This leads to the conclusion that from a qualitative point of view, spatial distribution of microorganisms in T. californiana tissue is quite homogeneous. Thirty-two percent of the operational taxonomic units shared less than 95% similarity with any other known sequence. This indicates that marine sponges are a rich source of previously undetected microbial life
Calcium-induced tertiary structure modifications of endo-B-1,3-glucanase form Pyrococcus furiosus in 7.9 M guanidinium chloride
Chiaraluce, R. ; Gianese, G. ; Angelaccio, S. ; Florio, R. ; Lieshout, J.F.T. van; Oost, J. van der; Consalvi, V. - \ 2005
Biochemical Journal 386 (2005)3. - ISSN 0264-6021 - p. 515 - 524.
transform infrared-spectroscopy - protein secondary structure - 3-dimensional structures - ftir spectroscopy - free-energy - recognition - database - endo-beta-1,3-glucanase - intermediate - alignments
The family 16 endo-b-1,3 glucanase from the extremophilic archaeon Pyrococcus furiosus is a laminarinase, which in 7.9 M GdmCl (guanidinium chloride) maintains a significant amount of tertiary structure without any change of secondary structure. The addition of calcium to the enzyme in 7.9 M GdmCl causes significant changes to the near-UV CD and fluorescence spectra, suggesting a notable increase in the tertiary structure which leads to a state comparable, but not identical, to the native state. The capability to interact with calcium in 7.9 M GdmCl with a consistent recovery of native tertiary structure is a unique property of this extremely stable endo-b-1,3 glucanase. The effect of calcium on the thermodynamic parameters relative to the GdmCl-induced equilibrium unfolding has been analysed by CD and fluorescence spectroscopy. The interaction of calcium with the native form of the enzyme is studied by Fourier-transform infrared spectroscopy in the absorption region of carboxylate groups and by titration in the presence of a chromophoric chelator. A homology-based model of the enzyme is generated and used to predict the putative binding site(s) for calcium and the structural interactions potentially responsible for the unusual stability of this protein, in comparison with other family 16 glycoside hydrolases
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