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.

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    Characterization of B chromosomes in Lilium hybrids through GISH and FISH
    Xie, S.L. ; Marasek-Ciolakowska, A. ; Ramanna, M.S. ; Arens, P.F.P. ; Visser, R.G.F. ; Tuyl, J.M. van - \ 2014
    Plant Systematics and Evolution 300 (2014)8. - ISSN 0378-2697 - p. 1771 - 1777.
    ribosomal-rna genes - in-situ hybridization - nuclear-dna amounts - plants - angiosperms - probe - recombination - isochromosome - misdivision - longiflorum
    Supernumerary (B) chromosomes and small aberrant chromosomes were detected in Lilium hybrids and characterized through genomic in situ hybridization (GISH) and florescence in situ hybridization (FISH). Two small, supernumerary or B chromosomes were detected as extra chromosomes in a tetraploid plant derived from chromosome doubling of a hybrid (2n = 2x = 24) between a cultivar of the Longiflorum (L) and the Trumpet (T) group. When this tetraploid LLTT hybrid was crossed with a triploid LLO hybrid (O = Oriental), the B chromosome was transmitted to 73.4 % of the progenies. Based on GISH and FISH characterization, it was shown that the B chromosome consisted of two identical arms, with 5S rDNA hybridizing to the majority of it, which were flanked by normal telomeres, suggesting that this is an isochromosome. In another population, which is a backcross progeny between a F1 hybrid of Longiflorum x Asiatic (LA) and its Asiatic parent, the former produced functional 2n gametes which resulted in a triploid LAA progeny (2n = 3x = 36), in which three exceptional plants possessed 35 normal chromosomes and a small aberrant chromosome instead of the expected normal number of 36. In all three cases, the small aberrant chromosomes were isochromosomes which had obviously originated during the first backcross generation. These three chromosomes showed normal telomeres and mitosis. In addition, one of the new generated chromosomes possessed two 45S rDNA sites in the proximal positions. These new arisen isochromosomes were proposed to originate from centric breakage and fusion of two short arms of the missing chromosome in three genotypes, respectively, based on the comparison of arm lengths as well as rDNA loci. Their relevance to the origin of Bs is discussed.
    Host-specific microbial communities in three sympatric North Sea sponges
    Naim, M.A. ; Morillo, J.A. ; Sørensen, S.J. ; Waleed, A.A. ; Smidt, H. ; Sipkema, D. - \ 2014
    FEMS microbiology ecology 90 (2014)2. - ISSN 0168-6496 - p. 390 - 403.
    ribosomal-rna genes - marine sponges - halichondria-panicea - bacterial communities - abundance sponges - genomic insights - sequence data - diversity - symbionts - chlamydiae
    The establishment of next-generation technology sequencing has deepened our knowledge of marine sponge-associated microbiota with the identification of at least 32 phyla of Bacteria and Archaea from a large number of sponge species. In this study, we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments. The three sponges harbor species-specific communities each dominated by a different class of Proteobacteria. An a-proteobacterial Rhodobacter-like phylotype was confirmed as the predominant symbiont of Halichondria panicea. The microbial communities of Haliclona xena and H. oculata are described for the first time in this study and are dominated by Gammaproteobacteria and Betaproteobacteria, respectively. Several common phylotypes belonging to Chlamydiae, TM6, Actinobacteria, and Betaproteobacteria were detected in all sponge samples. A number of phylotypes of the phylum Chlamydiae were present at an unprecedentedly high relative abundance of up to 14.4 ± 1.4% of the total reads, which suggests an important ecological role in North Sea sponges. These Chlamydiae-affiliated operational taxonomic units may represent novel lineages at least at the genus level as they are only 86–92% similar to known sequences.
    Ercella succinigenes gen. nov., sp. nov., an anaerobic succinate-producing bacterium
    Gelder, A.H. van; Sousa, D.Z. ; Rijpstra, W.I. ; Damsté, J.S. ; Stams, A.J.M. ; Sanchez Andrea, I. - \ 2014
    International Journal of Systematic and Evolutionary Microbiology 64 (2014)7. - ISSN 1466-5026 - p. 2449 - 2454.
    ribosomal-rna genes - acid - heterogeneity - fermentation - sequences - biofuels - glycerol - industry - operons - genomes
    A novel anaerobic succinate-producing bacterium, strain ZWBT, was isolated from sludge collected from a biogas desulfurization bioreactor (Eerbeek, the Netherlands). Cells were non-spore-forming, motile, slightly curved rods (0.4–0.5 µm in diameter and 2–3 µm in length), and stained Gram-negative. The temperature range for growth was 25–40 °C, with an optimum at 37 °C. The pH range for growth was 7.0–9.0, with an optimum at pH 7.5. Strain ZWBT was able to ferment glycerol and several carbohydrates mainly to H2, succinate and acetate. Sulfur and fumarate could be used as electron acceptors by strain ZWBT. The G+C content of the genomic DNA was 37.6 mol%. The most abundant fatty acids were iso-C14¿:¿0 and iso-C16¿:¿0 DMA. On the basis of 16S rRNA gene sequence similarity, strain ZWBT belongs to the family Ruminococcaceae and it is distantly related to Saccharofermentans acetigenes JCM 14006T (92.1¿%). Based on the physiological features and phylogenetic analysis, strain ZWBT represents a novel species of a new genus, for which the name Ercella succinigenes gen. nov., sp. nov. is proposed. The type strain of Ercella succinigenes is ZWBT (¿=¿DSM 27333T¿=¿JCM 19283T).
    Characterization of Romboutsia ilealis gen. nov., sp. nov., isolated from the gastro-intestinal tract of a rat and proposal for the reclassification of five closely related members of the genus Clostridium into the genera Romboutsia gen. nov., Intestinibacter gen. nov., Terrisporobacter gen. nov. and Asaccharospora gen. nov.
    Gerritsen, J. ; Fuentes Enriquez de Salamanca, S. ; Grievink, W. ; Niftrik, L. van; Tindall, B.J. ; Timmerman, H.M. ; Rijkers, G.T. ; Smidt, H. - \ 2014
    International Journal of Systematic and Evolutionary Microbiology 64 (2014)Pt. 5. - ISSN 1466-5026 - p. 1600 - 1616.
    ribosomal-rna genes - acid methyl-esters - lipid-composition - deoxyribonucleic-acid - electron microscopy - renaturation rates - dna hybridization - polar lipids - bacteria - chromatography
    A Gram-positive staining, rod-shaped, non-motile, spore-forming obligately anaerobic bacterium, designated CRIBT, was isolated from the gastro-intestinal tract of a rat and characterized. The major cellular fatty acids of strain CRIBT were saturated and unsaturated straight chain C12-C19 fatty acids, with C16:0 being the predominant fatty acid. The polar lipid profile comprised six glycolipids, four phospholipids and one lipid that did not stain with any of the specific spray reagents used. The only quinone was MK-6. The predominating cell wall sugars were glucose and galactose. The peptidoglycan type of strain CRIBT was A1d lanthionine-direct. The genomic DNA G+C content of strain CRIBT was 28.1 mol %. On the basis of 16S rRNA gene sequence similarity, strain CRIBT was most closely related to a number of Clostridium species, including C. lituseburense (97.2 %), C. glycolicum (96.2 %), C. mayombei (96.2 %), C. bartlettii (96.0 %) and C. irregulare (95.5 %). All these species show very low 16S rRNA gene sequence similarity (
    Microarray analysis and barcoded pyrosequencing provide consistent microbial profiles depending on the source of human intestinal samples
    Bogert, B. van den; Vos, W.M. de; Zoetendal, E.G. ; Kleerebezem, M. - \ 2011
    Applied and Environmental Microbiology 77 (2011)6. - ISSN 0099-2240 - p. 2071 - 2080.
    gastrointestinal-tract microbiota - ribosomal-rna genes - real-time pcr - phylogenetic microarray - quantitative-analysis - bacterial community - gut microbiome - fecal samples - extensive set - sequence data
    Large-scale and in-depth characterization of the intestinal microbiota necessitates application of high-throughput 16S rRNA gene-based technologies, such as barcoded pyrosequencing and phylogenetic microarray analysis. In this study, the two techniques were compared and contrasted for analysis of the bacterial composition in three fecal and three small intestinal samples from human individuals. As PCR remains a crucial step in sample preparation for both techniques, different forward primers were used for amplification to assess their impact on microbial profiling results. An average of 7,944 pyrosequences, spanning the V1 and V2 region of 16S rRNA genes, was obtained per sample. Although primer choice in barcoded pyrosequencing did not affect species richness and diversity estimates, detection of Actinobacteria strongly depended on the selected primer. Microbial profiles obtained by pyrosequencing and phylogenetic microarray analysis (HITChip) correlated strongly for fecal and ileal lumen samples but were less concordant for ileostomy effluent. Quantitative PCR was employed to investigate the deviations in profiling between pyrosequencing and HITChip analysis. Since cloning and sequencing of random 16S rRNA genes from ileostomy effluent confirmed the presence of novel intestinal phylotypes detected by pyrosequencing, especially those belonging to the Veillonella group, the divergence between pyrosequencing and the HITChip is likely due to the relatively low number of available 16S rRNA gene sequences of small intestinal origin in the DNA databases that were used for HITChip probe design. Overall, this study demonstrated that equivalent biological conclusions are obtained by high-throughput profiling of microbial communities, independent of technology or primer choice
    The origin of a selfish B chromosome triggering paternal sex ratio in the parasitoid wasp Trichogramma kaykai
    Vugt, J.J.F.A. van; Jong, J.H.S.G.M. de; Stouthamer, R. - \ 2009
    Proceedings of the Royal Society. B: Biological Sciences 276 (2009)1676. - ISSN 0962-8452 - p. 4149 - 4154.
    ribosomal-rna genes - nasonia-vitripennis - brachycome-dichromosomatica - insitu hybridization - crepis-capillaris - dna-sequences - evolution - parthenogenesis - hymenoptera - psr
    This study uses molecular and cytogenetic methods to determine the origin of a B chromosome in some males of the wasp Trichogramma kaykai. This so-called paternal sex ratio (PSR) chromosome transmits only through sperm and shortly after fertilization triggers degeneration of the paternal genome, while keeping itself intact. The resulting embryos develop into haploid B-chromosome-carrying males. Another PSR chromosome with a very similar mode of action is found in the distantly related wasp Nasonia vitripennis and its origin was traced by transposon similarity to the genus Trichomalopsis, which is closely related to Nasonia. To determine whether both PSR chromosomes have a similar origin we aimed to reveal the origin of the Trichogramma PSR chromosome. Using fluorescent in situ hybridization, we discovered a major satellite repeat on the PSR chromosome, the 45S ribosomal DNA. Analysis of the internal transcribed spacer 2 (ITS2) of this repeat showed the presence of multiple ITS2 sequences on the PSR chromosome resembling either the ITS2 of T. oleae or of T. kaykai. We therefore conclude that the Trichogramma PSR chromosome originates from T. oleae or a T. oleae-like species. Our results are consistent with different origins for the PSR chromosomes in Trichogramma and Nasonia
    Finding the needles in the meta-genome haystack
    Kowalchuk, G.A. ; Speksnijder, A.G.C.L. ; Zhang, K. ; Goodman, R.M. ; Veen, J.A. van - \ 2007
    Microbial Ecology 53 (2007)3. - ISSN 0095-3628 - p. 475 - 485.
    whole-genome amplification - ribosomal-rna genes - soil dna libraries - wide host-range - enrichment cultures - uncultured microorganisms - microbial diversity - escherichia-coli - natural-products - messenger-rna
    In the collective genomes (the metagenome) of the microorganisms inhabiting the Earth's diverse environments is written the history of life on this planet. New molecular tools developed and used for the past 15 years by microbial ecologists are facilitating the extraction, cloning, screening, and sequencing of these genomes. This approach allows microbial ecologists to access and study the full range of microbial diversity, regardless of our ability to culture organisms, and provides an unprecedented access to the breadth of natural products that these genomes encode. However, there is no way that the mere collection of sequences, no matter how expansive, can provide full coverage of the complex world of microbial metagenomes within the foreseeable future. Furthermore, although it is possible to fish out highly informative and useful genes from the sea of gene diversity in the environment, this can be a highly tedious and inefficient procedure. Microbial ecologists must be clever in their pursuit of ecologically relevant, valuable, and niche-defining genomic information within the vast haystack of microbial diversity. In this report, we seek to describe advances and prospects that will help microbial ecologists glean more knowledge from investigations into metagenomes. These include technological advances in sequencing and cloning methodologies, as well as improvements in annotation and comparative sequence analysis. More significant, however, will be ways to focus in on various subsets of the metagenome that may be of particular relevance, either by limiting the target community under study or improving the focus or speed of screening procedures. Lastly, given the cost and infrastructure necessary for large metagenome projects, and the almost inexhaustible amount of data they can produce, trends toward broader use of metagenome data across the research community coupled with the needed investment in bioinformatics infrastructure devoted to metagenomics will no doubt further increase the value of metagenomic studies in various environments.
    Microvariation Artifacts Introduced by PCR and Cloning of Closely Related 16S rRNA Gene Sequences
    Speksnijder, A.G.C.L. ; Kowalchuk, G.A. ; Jong, S. de; Kline, E. ; Stephen, J.R. ; Laanbroek, H.J. - \ 2001
    Applied and Environmental Microbiology 67 (2001)1. - ISSN 0099-2240 - p. 469 - 472.
    ribosomal-rna genes - polymerase chain-reaction - chimeric molecules - dna amplification - escherichia-coli - heteroduplexes - populations - coamplification - consequence - diversity
    A defined template mixture of seven closely related 16S-rDNA clones was used in a PCR-cloning experiment to assess and track sources of artifactual sequence variation in 16S rDNA clone libraries. At least 14% of the recovered clones contained aberrations. Artifact sources were polymerase errors, a mutational hot spot, and cloning of heteroduplexes and chimeras. These data may partially explain the high degree of microheterogeneity typical of sequence clusters detected in environmental clone libraries
    Karyotype analysis of Lilium longiflorum and Lilium rubellum by chromosome banding and fluorescence in situ hybridisation
    Lim, K.B. ; Wennekes, J. ; Jong, J.H.S.G.M. de; Jacobsen, E. ; Tuyl, J.M. van - \ 2001
    Genome 44 (2001)5. - ISSN 0831-2796 - p. 911 - 918.
    ribosomal-rna genes - nuclear-dna amounts - sequence - barley - genome - hybridization - wheat - organization - angiosperms - regions
    Detailed karyotypes of Lilium longiflorum and L. rubellum were constructed on the basis of chromosome arm lengths, C-banding, AgNO3 staining, and PI-DAPI banding, together with fluorescence in situ hybridisation (FISH) with the 5S and 45S rDNA sequences as probes. The C-banding patterns that were obtained with the standard BSG technique revealed only few minor bands on heterologous positions of the L. longiflorum and L. rubellum chromosomes. FISH of the 5S and 45S rDNA probes on L. longiflorum metaphase complements showed overlapping signals at proximal positions of the short arms of chromosomes 4 and 7, a single 5S rDNA signal on the secondary constriction of chromosome 3, and one 45S rDNA signal adjacent to the 5S rDNA signal on the subdistal part of the long arm of chromosome 3. In L. rubellum, we observed co-localisation of the 5S and 45S rDNA sequences on the short arm of chromosomes 2 and 4 and on the long arms of chromosomes 2 and 3, and two adjacent bands on chromosome 12. Silver staining (Ag-NOR) of the nucleoli and NORs in L. longiflorum and L. rubellum yielded a highly variable number of signals in interphase nuclei and only a few faint silver deposits on the NORs of mitotic metaphase chromosomes. In preparations stained with PI and DAPI, we observed both red- and blue-fluorescing bands at different positions on the L. longiflorum and L. rubellum chromosomes. The red-fluorescing or so-called reverse PI-DAPI bands always coincided with rDNA sites, whereas the blue-fluorescing DAPI bands corresponded to C-bands. Based on these techniques, we could identify most of chromosomes of the L. longiflorum and L. rubellum karyotypes.
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