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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Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions
Zlotina, A. ; Galkina, S. ; Krasikova, A. ; Crooijmans, R.P.M.A. ; Groenen, M. ; Gaginskaya, E. ; Deryusheva, S. - \ 2012
Chromosome Research 20 (2012)8. - ISSN 0967-3849 - p. 1017 - 1032.
avian lampbrush chromosomes - coturnix-coturnix-japonica - turkey meleagris-gallopavo - karyotype evolution - gallus-domesticus - dna-sequence - molecular characterization - synteny conservation - satellite dna - tandem repeat
Chicken (Gallus gallus domesticus, GGA) and Japanese quail (Coturnix coturnix japonica, CCO) karyotypes are very similar. They have identical chromosome number (2n = 78) and show a high degree of synteny. Centromere positions on the majority of orthologous chromosomes are different in these two species. To explore the nature of this divergence, we used high-resolution comparative fluorescent in situ hybridization mapping on giant lampbrush chromosomes (LBCs) from growing oocytes. We applied 41 BAC clones specific for GGA1, 2, 3, 11, 12, 13, 14, and 15 to chicken and quail LBCs. This approach allowed us to rule out a pericentric inversion earlier proposed to explain the difference between GGA1 and CCO1. In addition to a well-established large-scale pericentric inversion that discriminates GGA2 and CCO2, we identified another, smaller one in the large inverted region. For the first time, we described in detail inversions that distinguish GGA3 from CCO3 and GGA11 from CCO11. Despite the newly identified and confirmed inversions, our data suggest that, in chicken and Japanese quail, the difference in centromere positions is not mainly caused by pericentric inversions but is instead due to centromere repositioning events and the formation of new centromeres. We also consider the formation of short arms of quail microchromosomes by heterochromatin accumulation as a third scenario that could explain the discrepancy in centromeric indexes.
Dynamics of shiga-toxin producing Escherichia coli (STEC) and their virulence factors in cattle
Dopfer, D.D.V. ; Geue, L. ; Schares, S. ; Mintel, B. ; Hoffmann, B. ; Fischer, E.A.J. - \ 2012
Preventive Veterinary Medicine 103 (2012)1. - ISSN 0167-5877 - p. 22 - 30.
hemolytic uremic syndrome - coli o157-h7 - feedlot cattle - epithelial-cells - multiplex pcr - dna-sequence - strains - plasmid - o157h7 - farms
Starting at birth, twenty Holstein calves were housed individually, in groups of five and finally in one large freestall while fecal samples were collected weekly for 25 weeks. From each sample, twenty isolates of Escherichia coli were screened for 6 virulence markers including shiga-toxin 1, 2, intimin, enterohemolysin, the fimbrial antigen efa1 and the adhesin saa. Dynamic models of transmission of E. coli were used to model the transmission of different virulotypes between calves and the loss of the same virulotypes from the calves. It was found that, once E. coli encoding shiga-toxins in combination with enterohemolysin were transmitted and established in a calf, they tended to be eliminated less efficiently compared to E. coli without this combination of virulence markers. It was concluded that the presence of certain combinations of virulence markers coincided with persistence of E. coli in the bovine gastrointestinal tract. In addition, the combinations of stx with either eae or ehxA in E. coli have a greater impact on the loss rates than on the transmission rates.
Regional Regulation of Transcription in the Bovine Genome
Kommadath, A. ; Nie, H. ; Groenen, M.A.M. ; Pas, M.F.W. te; Veerkamp, R.F. ; Smits, M.A. - \ 2011
PLoS One 6 (2011). - ISSN 1932-6203 - 6 p.
human housekeeping genes - highly expressed genes - coexpressed genes - dna-sequence - selection - biology - clusters - bioconductor - unification - domains
Eukaryotic genes are distributed along chromosomes as clusters of highly expressed genes termed RIDGEs (Regions of IncreaseD Gene Expression) and lowly expressed genes termed anti-RIDGEs, interspersed among genes expressed at intermediate levels or not expressed. Previous studies based on this observation suggested a dual mechanism of gene regulation, where, in addition to transcription factors, the chromosomal domain influences the expression level of their embedded genes. The objectives here were to provide evidence for the existence of chromosomal regional regulation of transcription in the bovine genome, to analyse the genomic features of genes located within RIDGEs versus anti-RIDGEs and tissue-specific genes versus housekeeping and to examine the genomic distribution of genes subject to positive selection in bovines. Gene expression analysis of four brain tissues and the anterior pituitary of 28 cows identified 70 RIDGEs and 41 anti-RIDGEs (harbouring 3735 and 1793 bovine genes respectively) across the bovine genome which are significantly higher than expected by chance. Housekeeping genes (defined here as genes expressed in all five tissues) were over-represented within RIDGEs but tissue-specific genes (genes expressed in only one of the five tissues) were not. Housekeeping genes and genes within RIDGEs had, in general, higher expression levels and GC content but shorter gene lengths and intron lengths than tissue-specific genes and genes within anti-RIDGES. Our findings suggest the existence of chromosomal regional regulation of transcription in the bovine genome. The genomic features observed for genes within RIDGEs and housekeeping genes in bovines agree with previous studies in several other species further strengthening the hypothesis of selective pressure to keep the highly and widely expressed genes short and compact for transcriptional efficiency. Further, positively selected genes were found non-randomly distributed on the genome with a preference for RIDGEs and regions of intermediate gene expression compared to anti-RIDGEs.
Mitochondrial recombination increases with age in Podospora anserina
Diepeningen, A.D. van; Goedbloed, D.J. ; Slakhorst, S.M. ; Koopmanschap-Memelink, A.B. ; Maas, M.F.P.M. ; Hoekstra, R.F. ; Debets, A.J.M. - \ 2010
Mechanisms of Ageing and Development 131 (2010)5. - ISSN 0047-6374 - p. 315 - 322.
group-ii introns - life-span - excision-amplification - sexual reproduction - sequence-analysis - plasmid pal2-1 - dna-sequence - wild-type - senescence - selection
With uniparental inheritance of mitochondria, there seems little reason for homologous recombination in mitochondria, but the machinery for mitochondrial recombination is quite well-conserved in many eukaryote species. In fungi and yeasts heteroplasmons may be formed when strains fuse and transfer of organelles takes place, making it possible to study mitochondrial recombination when introduced mitochondria contain different markers. A survey of wild-type isolates from a local population of the filamentous fungus Podospora anserina for the presence of seven optional mitochondrial introns indicated that mitochondrial recombination does take place in nature. Moreover the recombination frequency appeared to be correlated with age: the more rapidly ageing fraction of the population had a significantly lower linkage disequilibrium indicating more recombination. Direct confrontation experiments with heterokaryon incompatible strains with different mitochondrial markers at different (relative) age confirmed that mitochondrial recombination increases with age. We propose that with increasing mitochondrial damage over time, mitochondrial recombination – even within a homoplasmic population of mitochondria – is a mechanism that may restore mitochondrial function
Fish on avian lampbrush chromosomes produces higher resolution gene mapping
Galkina, S.A. ; Deryusheva, S. ; Fillon, V. ; Vignal, A. ; Crooijmans, R.P.M.A. ; Groenen, M.A.M. ; Rodionov, A.V. ; Gaginskaya, E. - \ 2006
Genetica 128 (2006)1-3. - ISSN 0016-6707 - p. 241 - 251.
coturnix-coturnix-japonica - japanese-quail - dna-sequence - chicken chromosomes - gallus-domesticus - cytological map - crossing-over - w-chromosome - evolution - homology
Giant lampbrush chromosomes, which are characteristic of the diplotene stage of prophase I during avian oogenesis, represent a very promising system for precise physical gene mapping. We applied 35 chicken BAC and 4 PAC clones to both mitotic metaphase chromosomes and meiotic lampbrush chromosomes of chicken (Gallus gallus domesticus) and Japanese quail (Coturnix coturnix japonica). Fluorescence in situ hybridization (FISH) mapping on lampbrush chromosomes allowed us to distinguish closely located probes and revealed gene order more precisely. Our data extended the data earlier obtained using FISH to chicken and quail metaphase chromosomes 1¿6 and Z. Extremely low levels of inter- and intra-chromosomal rearrangements in the chicken and Japanese quail were demonstrated again. Moreover, we did not confirm the presence of a pericentric inversion in Japanese quail chromosome 4 as compared to chicken chromosome 4. Twelve BAC clones specific for chicken chromosome 4p and 4q showed the same order in quail as in chicken when FISH was performed on lampbrush chromosomes. The centromeres of chicken and quail chromosomes 4 seem to have formed independently after centric fusion of ancestral chromosome 4 and a microchromosome
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