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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    We will mail you new results for this query: keywords==pcr amplification
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Detection of bacterial DNA in bile of cats with lymphocytic cholangitis
Otte, C.M.A. ; Pérez, O.N. ; Favier, R.P. ; Rothuizen, J. ; Penning, L.C. - \ 2012
Veterinary Microbiology 156 (2012)1-2. - ISSN 0378-1135 - p. 217 - 221.
16s ribosomal-rna - gradient gel-electrophoresis - polymerase-chain-reaction - helicobacter-pylori - pcr amplification - sp-nov. - jeotgalicoccus - disease - liver - populations
In this study, we have successfully used molecular methods based on the amplification of the 16S ribosomal RNA gene on feline bile samples to show that bile of cats with LC is not sterile. This is probably due to the fact that the inflammatory process in the biliary tree causes dilatations. As a result, bacteria can easily migrate from the intestines via the common bile duct. The diversity of species identified and the presence of Helicobacter spp. DNA in both patients and controls suggests that bacteriobilia is secondary to the disease and is not the cause of LC.
Phytophthora infestans isolates from Northern China show high virulence diversity but low genotypic diversity
Guo, J. ; Lee, T. van der; Qu, D.Y. ; Yao, Y.Q. ; Gong, X.F. ; Liang, D.L. ; Xie, K.Y. ; Wang, X.W. ; Govers, F. - \ 2009
Plant Biology 11 (2009)1. - ISSN 1435-8603 - p. 57 - 67.
pcr amplification - mating-type - potato - populations - netherlands - resistance - metalaxyl - dna - aggressiveness - polymorphisms
Phenotypic and genotypic characteristics of 48 Phytophthora infestans isolates, collected in five provinces in Northern China between 1997 and 2003, were determined and compared with reference isolates. Characterisation included mating type, virulence, mitochondrial DNA (mtDNA) haplotype and DNA fingerprinting patterns based on simple sequence repeats (SSR) and amplified fragment length polymorphisms (AFLP). All isolates had the A1 mating type, mtDNA haplotype IIa and an identical SSR genotype (designated as SG-01-01) that differed from SSR genotypes found in the reference isolates, including those representing the 'old' US-1 lineage that dominated the P. infestans population worldwide prior to 1980. In contrast, the virulence spectra were highly variable and virulence to all resistance genes present in the standard differential set (R1 to R11) was found. AFLP analysis revealed some diversity; eight different AFLP genotypes were found that could be grouped into two major clusters. This study shows that there is very little genotypic diversity in the P. infestans population in Northern China. The occurrence of many different races within this rather uniform population is discussed in the framework of recent insights into the molecular determinants of avirulence in potato¿P. infestans'gene-for-gene' interactions
Genetic diversity of Phytophthora infestans sensu lato in Ecuador provides new insight into the origin of this important plant pathogen
Adler, N.E. ; Erselius, L.J. ; Chacón, G.M. ; Flier, W.G. ; Ordonez, M.E. ; Kroon, L.P.N.M. ; Forbes, G.A. - \ 2004
Phytopathology 94 (2004)2. - ISSN 0031-949X - p. 154 - 162.
toluca valley - central mexico - population-structure - pcr amplification - wild solanum - mating-type - pear melon - potato - host - dna
The metapopulation structure of Phytophthora infestans sensu lato is genetically diverse in the highlands of Ecuador. Previous reports documented the diversity associated with four putative clonal lineages of the pathogen collected from various hosts in the genus Solanum. This paper simultaneously analyzes diversity of the complete collection of isolates, including a large number that had not yet been reported. This analysis confirmed the existence of three pathogen populations, which all appear to be clonal lineages, and that correspond to those previously reported as US-1, EC-1. and EC-3. No evidence was found from the analyses of recently collected isolates that would contradict earlier reports about these three lineages. In contrast, new data from a group of isolates from several similar hosts caused us to modify the previous description of clonal lineage EC-2 and its previously proposed hosts, S. brevifolium and S. tetrapetalum. Given the uncertainty associated with the identification of these hosts, which all belong to the section Anarrhichomenum, we refer to them as the Anarrhichomenum complex, pending further taxonomic clarification. New pathogen genotypes associated with the Anarrhichomenum complex were isolated recently that are A I mating type and la mitochondrial DNA (mtDNA) haplotype, and therefore differ from the previously described EC-2 lineage, which is A2 and Ic, respectively. Because of uncertainty on host identification. we do not know if the new genotypes are limited to one host species and therefore represent yet another host-adapted clonal lineage. For now, we refer to the new genotypes and previously described EC-2 genotypes, together, as the pathogen group attacking the Anarrhichomenum complex. Two A2 isolates identical to the previously described EC-2 archetype were collected from severely infected plants of pear melon (S. muricatum). Pear melon is generally attacked by US-1. and this is the first clear case we have documented in which two distinct pathogen genotypes have caused severe epidemics on the same host. Based on presence of unique marker alleles (restriction fragment length polymorphism [RFLP] and mtDNA) and genetic similarity analysis using RFLP and amplified fragment length polymorphism data, EC-3 and isolates from the Anarrhichomenum complex are genetically distinct from all genotypes of P. infestans that have been reported previously. No current theory of historical migrations for this pathogen can adequately Support a Mexican origin for EC-3 and genotypes of the Anarrhichomenum complex and they may, therefore. be palaeoendemic to the Andean highlands. To date. we have identified 15 hosts in the genus Solanum, in addition to the Anarrhichomenum complex, and some unidentified species of P. infestans sensu lato in Ecuador. Five of the Solanum hosts are cultivated. One isolate was collected from Brugmansia sanguinea, which represents the first report from Ecuador of a host of this pathogen that is not in the genus Solanum. However, P infestans sensu lato was only found on flower petals of B. sanguinea. This study provides new insights into the Population structure of highly specialized genotypes of infestans sensu lato in the Andean highlands. The results are discussed in light of previous hypotheses regarding the geographic origin of the pathogen.
Paraconiothyrium, a new genus to accommodate the mycoparasite Coniothyrium minitans, anamorphs of Paraphaeosphaeria, and four new species
Verkley, G.J.M. ; Silva, M. da; Wicklow, D.T. ; Crous, P.W. - \ 2004
Studies in Mycology 50 (2004). - ISSN 0166-0616 - p. 323 - 335.
ribosomal dna-sequences - microsphaeropsis-ochracea - aromatic-hydrocarbons - estuarine sediments - pcr amplification - apple scab - fungi - identification - germination - biocontrol
Coniothyrium-like coelomycetes are drawing attention as biological control agents, potential bioremediators, and producers of antibiotics. Four genera are currently used to classify such anamorphs, namely, Coniothyrium, Microsphaeropsis, Cyclothyrium, and Cytoplea. The morphological plasticity of these fungi, however, makes it difficult to ascertain their best generic disposition in many cases. A new genus, Paraconiothyrium is here proposed to accommodate four new species, P. estuarinum, P. brasiliense, P. cyclothyrioides, and P. fungicola. Their formal descriptions are based on anamorphic characters as seen in vitro. The teleomorphs of these species are unknown, but maximum parsimony analysis of ITS and partial SSU nrDNA sequences showed that they belong in the Pleosporales and group in a clade including Paraphaeosphaeria s. str., the biocontrol agent Coniothyrium minitans, and the ubiquitous soil fungus Coniothyrium sporulosum. Coniothyrium minitans and C. sporulosum are therefore also combined into the genus Paraconiothyrium. The anamorphs of Paraphaeosphaeria michotii and Paraphaeosphaeria pilleata are regarded representative of Paraconiothyrium, but remain formally unnamed. Paraconiothyrium species are phylogenetically distant from typical members of the other coelomycete genera mentioned above
The population structure of Phytophthora infestans from the Toluca Valley of Central Mexico suggests genetic differentiation between populations from cultivated potato and wild Solanum spp.
Flier, W.G. ; Grünwald, N.J. ; Kroon, L.P.N.M. ; Sturbaum, A.K. ; Bosch, G.B.M. van den; Garay-Serrano, E. ; Lozoya-Saldaña, H. ; Fry, W.E. ; Turkensteen, L.J. - \ 2003
Phytopathology 93 (2003)4. - ISSN 0031-949X - p. 382 - 390.
nevado-de-toluca - western slopes - mont debary - sympatric speciation - pcr amplification - p-infestans - flow - resistance - diversity - oospores
The Population structure of Phytophthora infestans in the Toluca Valley of central Mexico was assessed using 170 isolates collected front cultivated potatoes and the native wild Solanum spp., S. demissum and S. xedinense. All isolates were analyzed for mitochondrial DNA (mtDNA) haplotype and amplified fragment length polymorphism (AFLP) multi-locus fingerprint genotype. Isolate samples were monomorphic for mtDNA haplotype because all isolates tested were of the la haplotype. A total of 158 multilocus AFLP genotypes were identified among the 170 P. infestans isolates included in this study. P. infestans populations sampled in the Toluca Valley in 1997 were highly variable and almost every single isolate represented a unique genotype based on the analysis of 165 AFLP marker loci. Populations of P infestans collected from the commercial potato-growing region in the valley, the subsistence potato production area along the slopes of the Nevado de Toluca, and the native Solanum spp. on the forested slopes of the volcano showed a high degree of genetic diversity. The number of polymorphic loci varied from 20.0 to 62.4% for isolates collected from the field station and wild Solanum spp. On average, 81.8% (135) of the AFLP loci were polymorphic. Heterozygosity varied between 7.7 and 19.4%. Significant differentiation was found at the population level between strains originating from cultivated potatoes and wild Solanum spp. (P = 0.001 to 0.022). Private alleles were observed in individual isolates collected from all three populations, with numbers of unique dominant alleles varying from 9 to 16 for isolates collected from commercial potato crops and native Solanum spp.. respectively. Four AFLP markets were exclusively found present in isolates collected from S. demissum. Indirect estimation of gene flow between populations indicated restricted gene flow between both P. infestans populations front cultivated potatoes and wild Solanum hosts. There was no evidence found for the presence of substructuring at the subpopulation (field) level. We hypothesize that population differentiation and genetic isolation of P infestans in the Toluca Valley is driven by host-specific factors (i.e., R-genes) widely distributed in wild Solanum spp. and random genetic drift.
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