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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    ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins
    Luo, H. ; Lin, K. ; David, A. ; Nijveen, H. ; Leunissen, J.A.M. - \ 2012
    Nucleic acids research 40 (2012)D1. - ISSN 0305-1048 - p. D394 - D399.
    annotation resource - codon usage - sequences - database - evolution - genomes - selection - alanine - algorithm - proteomes
    ProRepeat (http://prorepeat.bioinformatics.nl/) is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together with 85 completely sequenced eukaryotic proteomes contained within the RefSeq collection. It contains non-redundant perfect tandem repeats, approximate tandem repeats and simple, low-complexity sequences, covering the majority of the amino acid tandem repeat patterns found in proteins. The ProRepeat web interface allows querying the repeat database using repeat characteristics like repeat unit and length, number of repetitions of the repeat unit and position of the repeat in the protein. Users can also search for repeats by the characteristics of repeat containing proteins, such as entry ID, protein description, sequence length, gene name and taxon. ProRepeat offers powerful analysis tools for finding biological interesting properties of repeats, such as the strong position bias of leucine repeats in the N-terminus of eukaryotic protein sequences, the differences of repeat abundance among proteomes, the functional classification of repeat containing proteins and GC content constrains of repeats’ corresponding codons.
    Use of rbcL and trnL-F as a two-locus DNA barcode for identification of NW-European ferns: an ecological perspective
    Groot, G.A. de; During, H.J. ; Maas, J.W. ; Schneider, H. ; Erkens, R.H.J. - \ 2011
    PLoS ONE 6 (2011)1. - ISSN 1932-6203
    dryopteris-affinis group - land plants - noncoding regions - chloroplast dna - mononucleotide repeats - sequences - phylogeny - taxonomy - pcr - amplification
    Although consensus has now been reached on a general two-locus DNA barcode for land plants, the selected combination of markers (rbcL + matK) is not applicable for ferns at the moment. Yet especially for ferns, DNA barcoding is potentially of great value since fern gametophytes—while playing an essential role in fern colonization and reproduction—generally lack the morphological complexity for morphology-based identification and have therefore been underappreciated in ecological studies. We evaluated the potential of a combination of rbcL with a noncoding plastid marker, trnL-F, to obtain DNAidentifications for fern species. A regional approach was adopted, by creating a reference database of trusted rbcL and trnL-F sequences for the wild-occurring homosporous ferns of NW-Europe. A combination of parsimony analyses and distancebased analyses was performed to evaluate the discriminatory power of the two-region barcode. DNA was successfully extracted from 86 tiny fern gametophytes and was used as a test case for the performance of DNA-based identification. Primer universality proved high for both markers. Based on the combined rbcL + trnL-F dataset, all genera as well as all species with non-equal chloroplast genomes formed their own well supported monophyletic clade, indicating a high discriminatory power. Interspecific distances were larger than intraspecific distances for all tested taxa. Identification tests on gametophytes showed a comparable result. All test samples could be identified to genus level, species identification was well possible unless they belonged to a pair of Dryopteris species with completely identical chloroplast genomes. Our results suggest a high potential of the combined use of rbcL and trnL-F as a two-locus cpDNA barcode for identification of fern species. A regional approach may be preferred for ecological tests. We here offer such a ready-to-use barcoding approach for ferns, which opens the way for answering a whole range of questions previously unaddressed in fern gametophyte ecology
    First isolation of Hepatitis E virus genotype 4 in Europe through swine surveillance in the Netherlands and Belgium.
    Honing-Hakze, R.W. van der; Coillie, E. Van; Antonis, A.F.G. ; Poel, W.H.M. van der - \ 2011
    PLoS ONE 6 (2011)8. - ISSN 1932-6203 - 6 p.
    cross-species infection - united-states - rt-pcr - prevalence - hev - epidemiology - transmission - antibodies - sequences - humans
    Hepatitis E virus (HEV) genotypes 3 and 4 are a cause of human hepatitis and swine are considered the main reservoir. To study the HEV prevalence and characterize circulating HEV strains, fecal samples from swine in the Netherlands and Belgium were tested by RT-PCR. HEV prevalence in swine was 7–15%. The Dutch strains were characterized as genotype 3, subgroups 3a, 3c and 3f, closely related to sequences found in humans and swine earlier. The HEV strains found in Belgium belonged to genotypes 3f and 4b. The HEV genotype 4 strain was the first ever reported in swine in Europe and an experimental infection in pigs was performed to isolate the virus. The genotype 4 strain readily infected piglets and caused fever and virus shedding. Since HEV4 infections have been reported to run a more severe clinical course in humans this observation may have public health implications
    Investigation of Cyprinidherpesvirus-3 genetic diversity by a multi-locus variable number of tandem repeats analysis.
    Avarre, J.C. ; Madeira, J.P. ; Santika, A. ; Zainunb, Z. ; Baud, M. ; Cabon, J. ; Caruso, D. ; Castric, J. ; Bigarré, L. ; Engelsma, M.Y. ; Maskur, M. - \ 2011
    Journal of Virological Methods 173 (2011)2. - ISSN 0166-0934 - p. 320 - 327.
    mediated isothermal amplification - koi-herpesvirus - common carp - r-package - virus - khv - sequences - pcr - dna - mortality
    Cyprinid herpesvirus-3 (CyHV-3), or koi herpesvirus (KHV), is responsible for high mortalities in aquaculture of both common carp (Cyprinus carpio carpio) and koi carp (Cyprinus carpio koi) worldwide. The complete genomes of three CyHV-3 isolates showed more than 99% of DNA sequence identity, with the majority of differences located in short tandem repeats, also called VNTR (variable number of tandem repeats). By targeting these variations, eight loci were selected for genotyping CyHV-3 by multiple locus VNTR analysis (MLVA). CyHV-3 strains obtained after sequential in vivo infections exhibited identical MLVA profiles, whereas samples originating from a single isolate passaged 6 and 82 times in vitro exhibited mutations in two of the eight loci, suggesting a relatively slow genetic evolution rate of the VNTRs. The method was subsequently applied on 38 samples collected in Indonesia, France and the Netherlands. Globally, the isolates grouped in two main genetic clusters, each one divided in two subgroups including either CyHV-3-U/I or CyHV3-J. Interestingly, Indonesian strains were rather distant from CyHV-3-J isolate. The results of the present study indicate that these VNTR molecular markers are efficient in estimating the genetic diversity among CyHV-3 isolates and are therefore suitable for further molecular epidemiological studies.
    DNA damage in plant herbarium tissue.
    Staats, M. ; Cuenca, A. ; Richardson, J.E. ; Ginkel, R.V. ; Petersen, G. ; Seberg, O. ; Bakker, F.T. - \ 2011
    PLoS ONE 6 (2011)12. - ISSN 1932-6203 - 9 p.
    programmed cell-death - ancient dna - miscoding lesions - enzymatic amplification - specimens - repair - preservation - extraction - sequences - reveals
    Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative assessment of DNA post-mortem damage is essential to determine the accuracy of molecular data from herbarium specimens. In this study we present an assessment of DNA damage as miscoding lesions in herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA. In addition, we assess DNA degradation as a result of strand breaks and other types of polymerase non-bypassable damage by quantitative real-time PCR. Comparing four pairs of fresh and herbarium specimens of the same individuals we quantitatively assess post-mortem DNA damage, directly after specimen preparation, as well as after long-term herbarium storage. After specimen preparation we estimate the proportion of gene copy numbers of plastid, mitochondrial, and nuclear DNA to be 2.4–3.8% of fresh control DNA and 1.0–1.3% after long-term herbarium storage, indicating that nearly all DNA damage occurs on specimen preparation. In addition, there is no evidence of preferential degradation of organelle versus nuclear genomes. Increased levels of C¿T/G¿A transitions were observed in old herbarium plastid DNA, representing 21.8% of observed miscoding lesions. We interpret this type of post-mortem DNA damage-derived modification to have arisen from the hydrolytic deamination of cytosine during long-term herbarium storage. Our results suggest that reliable sequence data can be obtained from herbarium specimens.
    Host status of false brome grass to the leaf rust fungus Puccinia brachypodii and the stripe rust fungus P. Striiformis
    Barbieri, M. ; Marcel, T.C. ; Niks, R.E. - \ 2011
    Plant Disease 95 (2011)11. - ISSN 0191-2917 - p. 1339 - 1345.
    agrobacterium-mediated transformation - model system - distachyon - genome - rice - nonhost - specificity - resistance - morphology - sequences
    Purple false brome grass (Brachypodium distachyon) has recently emerged as a model system for temperate grasses and is also a potential model plant to investigate plant interactions with economically important pathogens such as rust fungi. We determined the host status of five Brachypodium species to three isolates of Puccinia brachypodii, the prevalent rust species on Brachypodium sylvaticum in nature, and to one isolate each of three formae speciales of the stripe rust fungus P. striiformis. Two P. striiformis isolates produced sporulating lesions, both in only one of the tested interactions, suggesting a marginal host status of B. distachyon. P. brachypodii formed sporulating uredinia on the five Brachypodium species tested, and a range of reactions was observed. Surprisingly, the B. sylvaticum–derived rust isolates were more frequently pathogenic to B. distachyon than to their original host species. The B. distachyon diploid inbred lines, developed and distributed as reference material to the Brachypodium research community, include susceptible and resistant genotypes to at least three of the four P. brachypodii isolates tested. This creates the opportunity to use B. distachyon/P. brachypodii as a model pathosystem. In one B. distachyon accession, heavy infection by the loose smut fungus Ustilago bromivora occurred. That pathogen could also serve as a model pathogen of Brachypodium.
    A quantitative account of genomic island acquisitions in prokaryotes
    Roos, T.E. ; Passel, M.W.J. van - \ 2011
    BMC Genomics 12 (2011). - ISSN 1471-2164 - 34 p.
    art. no. 163 - pathogenicity islands - bacterial genomes - signature - sequences - dna - identification - amelioration - evolution - virulence
    BACKGROUND: Microbial genomes do not merely evolve through the slow accumulation of mutations, but also, and often more dramatically, by taking up new DNA in a process called horizontal gene transfer. These innovation leaps in the acquisition of new traits can take place via the introgression of single genes, but also through the acquisition of large gene clusters, which are termed Genomic Islands. Since only a small proportion of all the DNA diversity has been sequenced, it can be hard to find the appropriate donors for acquired genes via sequence alignments from databases. In contrast, relative oligonucleotide frequencies represent a remarkably stable genomic signature in prokaryotes, which facilitates compositional comparisons as an alignment-free alternative for phylogenetic relatedness. In this project, we test whether Genomic Islands identified in individual bacterial genomes have a similar genomic signature, in terms of relative dinucleotide frequencies, and can therefore be expected to originate from a common donor species. RESULTS: When multiple Genomic Islands are present within a single genome, we find that up to 28% of these are compositionally very similar to each other, indicative of frequent recurring acquisitions from the same donor to the same acceptor. CONCLUSIONS: This represents the first quantitative assessment of common directional transfer events in prokaryotic evolutionary history. We suggest that many of the resident Genomic Islands per prokaryotic genome originated from the same source, which may have implications with respect to their regulatory interactions, and for the elucidation of the common origins of these acquired gene clusters
    Base-pairing promotes leader selection to prime in vitro influenza genome transcription
    Geerts-Dimitriadou, C. ; Zwart, M.P. ; Goldbach, R.W. ; Kormelink, R.J.M. - \ 2011
    Virology 409 (2011)1. - ISSN 0042-6822 - p. 17 - 26.
    messenger-rna synthesis - cap-snatching mechanism - mosaic-virus rnas - viral-rna - 5' ends - complementary rna - a virus - polymerase - endonuclease - sequences
    The requirements for alignment of capped leader sequences along the viral genome during influenza transcription initiation (cap-snatching) have long been an enigma. In this study, competition experiments using an in vitro transcription assay revealed that influenza virus transcriptase prefers leader sequences with base complementarity to the 3'-ultimate residues of the viral template, 10 or 11 nt from the 5' cap. Internal priming at the 3'-penultimate residue, as well as prime-and-realign was observed. The nucleotide identity immediately 5' of the base-pairing residues also affected cap donor usage. Application to the in vitro system of RNA molecules with increased base complementarity to the viral RNA template showed stronger reduction of globin RNA leader initiated influenza transcription compared to those with a single base-pairing possibility. Altogether the results indicated an optimal cap donor consensus sequence of 7mG-(N)7–8-(A/U/G)-(A/U)-AGC-3'.
    Bivariate colour maps for visualizing climate data
    Teuling, A.J. ; Stöckli, R. ; Seneviratne, S.I. - \ 2011
    International Journal of Climatology 31 (2011)9. - ISSN 0899-8418 - p. 1408 - 1412.
    univariate - sequences
    The increasing availability of gridded, high-resolution, multivariate climatological data sets calls for innovative approaches to visualize inter-variable relations. In this study, we present a methodology, based on properties of common colour schemes, to plot two variables in a single colour map by using a two-dimensional colour legend for both sequential and diverging data. This is especially suited for climate data as the spatial distribution of the relation between different variables is often as important as the distribution of variables individually. Two example applications are given to illustrate the use of the method: one that shows the global distribution of climate based on observed temperature and relative humidity, and the other showing the distribution of recent changes in observed temperature and precipitation over Europe. A flexible and easy-to-implement method is provided to construct different colour legends for sequential and diverging data.
    Functional analysis and expression of HcrVf1 and HcrVf2 for development of scab resistant cisgenic and intragenic apples
    Joshi, S.G. ; Schaart, J. ; Groenwold, R. ; Jacobsen, E. ; Schouten, H.J. ; Krens, F.A. - \ 2011
    Plant Molecular Biology 75 (2011)6. - ISSN 0167-4412 - p. 579 - 591.
    receptor-like genes - real-time pcr - venturia-inaequalis - vf gene - plants - sequences - agrobacterium - promoters - linkage - cluster
    Apple scab resistance genes, HcrVf1 and HcrVf2, were isolated including their native promoter, coding and terminator sequences. Two fragment lengths (short and long) of the native gene promoters and the strong apple rubisco gene promoter (PMdRbc) were used for both HcrVf genes to test their effect on expression and phenotype. The scab susceptible cultivar ‘Gala’ was used for plant transformations and after selection of transformants, they were micrografted onto apple seedling rootstocks for scab disease tests. Apple transformants were also tested for HcrVf expression by quantitative RT-PCR (qRTPCR). For HcrVf1 the long native promoter gave significantly higher expression that the short one; in case of HcrVf2 the difference between the two was not significant. The apple rubisco gene promoter proved to give the highest expression of both HcrVf1 and HcrVf2. The top four expanding leaves were used initially for inoculation with monoconidial isolate EU-B05 which belongs to race 1 of V. inaequalis. Later six other V. inaequalis isolates were used to study the resistance spectra of the individual HcrVf genes. The scab disease assays showed that HcrVf1 did not give resistance against any of the isolates tested regardless of the expression level. The HcrVf2 gene appeared to be the only functional gene for resistance against Vf avirulent isolates of V. inaequalis. HcrVf2 did not provide any resistance to Vf virulent strains, even not in case of overexpression. In conclusion, transformants carrying the apple-derived HcrVf2 gene in a cisgenic as well as in an intragenic configuration were able to reach scab resistance levels comparable to the Vf resistant control cultivar obtained by classical breeding, cv. ‘Santana’.
    Hoe ver en hoeveel? Verspreiding en infecties van koolluis in Nederland, Thema: Functionele biodiversiteit BO-12.03-004-001a
    Belder, E. den; Smulders, M.J.M. ; Esselink, D. ; Elderson, J. - \ 2011
    S.n.
    brevicoryne brassicae - gewasbescherming - verkeerde liggingen - volgorden - gewasmengsels - gewassen - koolsoorten - brevicoryne brassicae - plant protection - malpositions - sequences - crop mixtures - crops - cabbages
    Informatieposter met de titel "Hoe ver en hoeveel? Verspreiding en infecties van koolluis in Nederland", thema functionele biodiversiteit. De frequenties van bladluisinfecties worden beïnvloed door de ruimtelijke ligging en de opvolging van gewassen. Kan er door wijzigingen in bouwplan en gewasrotatie worden bijgedragen aan bladluisbeheersing?
    SLIDER: A Generic Metaheuristic for the Discovery of Correlated Motifs in Protein-Protein Interaction Networks
    Boyen, P. ; Dyck, D. van; Neven, F. ; Ham, R.C.H.J. van; Dijk, A.D.J. van - \ 2011
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 8 (2011)5. - ISSN 1545-5963 - p. 1344 - 1357.
    sequences - scale - pairs
    Correlated motif mining (CMM) is the problem of finding overrepresented pairs of patterns, called motifs, in sequences of interacting proteins. Algorithmic solutions for CMM thereby provide a computational method for predicting binding sites for protein interaction. In this paper, we adopt a motif-driven approach where the support of candidate motif pairs is evaluated in the network. We experimentally establish the superiority of the Chi-square-based support measure over other support measures. Furthermore, we obtain that CMM is an NP-hard problem for a large class of support measures (including Chi-square) and reformulate the search for correlated motifs as a combinatorial optimization problem. We then present the generic metaheuristic SLIDER which uses steepest ascent with a neighborhood function based on sliding motifs and employs the Chi-square-based support measure. We show that SLIDER outperforms existing motif-driven CMM methods and scales to large protein-protein interaction networks. The SLIDER-implementation and the data used in the experiments are available on http://bioinformatics.uhasselt.be.
    Genetic Basis of Tetracycline Resistance in Bifidobacterium animalis subsp lactis
    Gueimonde, M. ; Florez, A.B. ; Hoek, A.H.A.M. van; Stuer-Lauridsen, B. ; Stroman, P. ; Reyes-Gavilan, C.G. de los; Margolles, A. - \ 2010
    Applied and Environmental Microbiology 76 (2010)10. - ISSN 0099-2240 - p. 3364 - 3369.
    antibiotic susceptibility - probiotic products - tet(w) - bacteria - bile - lactobacillus - sequences - strains - humans - thermophilum
    All strains of Bifidobacterium animalis subsp. lactis described to date show medium level resistance to tetracycline. Screening of 26 strains from a variety of sources revealed the presence of tet(W) in all isolates. A transposase gene upstream of tet(W) was found in all strains, and both genes were cotranscribed in strain IPLAIC4. Mutants with increased tetracycline resistance as well as tetracycline-sensitive mutants of IPLAIC4 were isolated and genetically characterized. The native tet(W) gene was able to restore the resistance phenotype to a mutant with an alteration in tet(W) by functional complementation, indicating that tet(W) is necessary and sufficient for the tetracycline resistance seen in B. animalis subsp. lactis.
    Novel fungal genera and species associated with the sooty blotch and flyspeck complex on apple in China and the USA
    Yang, H.L. ; Sun, G.Y. ; Batzer, J.C. ; Crous, P.W. ; Groenewald, J.Z. ; Gleason, M.L. - \ 2010
    Persoonia (2010)24. - ISSN 0031-5850 - p. 29 - 37.
    ribosomal dna - sp-nov - sporidesmium - sequences - disease
    Fungi in the sooty blotch and flyspeck (SBFS) complex cause blemishes on apple and pear fruit that result in economic losses for growers. The SBFS fungi colonise the epicuticular wax layer of pomaceous fruit but do not invade the cuticle. Fungi causing fuliginous and punctate mycelial types on apple are particularly difficult to identify based on morphological criteria because many species in the SBFS complex share the same mycelial phenotypes. We compared the morphology and nuclear ribosomal DNA phylogeny (ITS, LSU) of 11 fungal strains isolated from SBFS blemishes on apple obtained from two provinces in China and five states in the USA. Parsimony analysis, supported by cultural characteristics and morphology in vitro, provided support to delimit the isolates into three novel genera, representing five new species. Phaeothecoidiella, with two species, P. missouriensis and P. illinoisensis, is introduced as a new genus with pigmented endoconidia in the Dothideomycetes. Houjia (Capnodiales) is introduced for H. pomigena and H. yanglingensis. Although morphologically similar to Stanjehughesia (Chaetosphaeriaceae), Houjia is distinct in having solitary conidiogenous cells. Sporidesmajora (Capnodiales), based on S. pennsylvaniensis, is distinguished from Sporidesmium (Sordariomycetes) in having long, multiseptate conidiophores that frequently have a subconical, darkly pigmented apical cell, and very long, multi-euseptate conidia
    Microcyclospora and Microcyclosporella: novel genera accommodating epiphytic fungi causing sooty blotch on apple
    Frank, J. ; Crous, P.W. ; Groenewald, J.Z. ; Oertel, B. ; Hyde, K.D. ; Phengsintham, P. ; Schroers, H.J. - \ 2010
    Persoonia 24 (2010). - ISSN 0031-5850 - p. 93 - 105.
    flyspeck complex - ribosomal dna - mycosphaerella - anamorphs - phylogeny - disease - teratosphaeria - proteaceae - morphology - sequences
    Recent studies have found a wide range of ascomycetes to be associated with sooty blotch and flyspeck (SBFS) blemishes on the surfaces of pomaceous fruits, specifically apples. Based on collections of such fungi from apple orchards in Germany and Slovenia we introduce two novel genera according to analyses of morphological characters and nuclear ribosomal DNA sequences (large subunit and internal transcribed spacer regions). Microcyclosporella is represented by a single species, M. mali, and is presently known from Germany and Slovenia. Microcyclosporella is Pseudocercosporella-like in morphology, but genetically and morphologically distinct from Pseudocercosporella s.str., for which an epitype is designated based on a fresh collection of P. bakeri from Laos. Furthermore, Pseudocercosporella is shown to be paraphyletic within the Capnodiales. Microcyclospora gen. nov. is Pseudocercospora-like in morphology, but is genetically and morphologically distinct from Pseudocercospora s.str., which is based on P. vitis. Three species, Microcyclospora malicola, M. pomicola (both collected in Germany), and M. tardicrescens (collected in Slovenia) are described. Finally, a new species of Devriesia, D. pseudoamericana, is described from pome fruit surfaces collected in Germany. Devriesia is shown to be paraphyletic, and to represent several lineages of which only Devriesia s.str. is thermotolerant. Further collections are required, however, before the latter generic complex can be resolved.
    Biochemical and genetical analysis reveal a new clade of biovar 3 Dickeya spp. strains isolated from potato in Europe
    Slawiak, M. ; Beckhoven, J.R.C.M. van; Speksnijder, A.G.C.L. ; Czajkowski, R.L. ; Grabe, G. ; Wolf, J.M. van der - \ 2009
    European Journal of Plant Pathology 125 (2009)2. - ISSN 0929-1873 - p. 245 - 261.
    erwinia-chrysanthemi - xanthomonas - pcr - sequences - hosts - water - fingerprints - genomes - plants
    Sixty-five potato strains of the soft rot-causing plant pathogenic bacterium Dickeya spp., and two strains from hyacinth, were characterised using biochemical assays, REP-PCR genomic finger printing, 16S rDNA and dnaX sequence analysis. These methods were compared with nineteen strains representing six Dickeya species which included the type strains. A group of twenty-two potato strains isolated between 2005-2007 in the Netherlands, Poland, Finland and Israel were characterised as belonging to biovar 3. They were 100% identical in REP-PCR, dnaX and 16S rDNA sequence analysis. In a polyphasic analysis they formed a new clade different from the six Dickeya species previously described, and may therefore constitute a new species. The strains were very similar to a Dutch strain from hyacinth. On the basis of dnaX sequences and biochemical assays, all other potato strains isolated in Europe between 1979 and 1994 were identified as D. dianthicola (biovar 1 and 7), with the exception of two German strains classified as D. dieffenbachia (biovar 2) and D. dadantii (biovar 3), respectively. Potato strains from Peru were classified as D. dadantii, from Australia as D. zeae and from Taiwan as D. chrysanthemi bv. parthenii, indicating that different Dickeya species are found in association with potato.
    Base composition, selection, and phylogenetic significance of indels in the recombination activating gene-1 in vertebrates
    Chiari, Y. ; Meijden, A. van der; Madsen, O. ; Vences, M. ; Meyer, A. - \ 2009
    Frontiers in Zoology 6 (2009). - ISSN 1742-9994 - 15 p.
    nuclear rag-1 gene - v(d)j recombination - mitochondrial-dna - evolution - sequences - diversification - patterns - frogs - amphibians - inference
    Background: The Recombination Activating Proteins, RAG1 and RAG2, play a crucial role in the immune response in vertebrates. Among the nuclear markers currently used for phylogenetic purposes, Rag1 has especially enjoyed enormous popularity, since it successfully contributed to elucidating the relationships among and within a large variety of vertebrate lineages. We here report on a comparative investigation of the genetic variation, base composition, presence of indels, and selection in Rag1 in different vertebrate lineages (Actinopterygii, Amphibia, Aves, Chondrichthyes, Crocodylia, Lepidosauria, Mammalia, and Testudines) through the analysis of 582 sequences obtained from Genbank. We also analyze possible differences between distinct parts of the gene with different type of protein functions. Results: In the vertebrate lineages studied, Rag1 is over 3 kb long. We observed a high level of heterogeneity in base composition at the 3(rd) codon position in some of the studied vertebrate lineages and in some specific taxa. This result is also paralleled by taxonomic differences in the GC content at the same codon position. Moreover, positive selection occurs at some sites in Aves, Lepidosauria and Testudines. Indels, which are often used as phylogenetic characters, are more informative across vertebrates in the 5' than in the 3'-end of the gene. When the entire gene is considered, the use of indels as phylogenetic character only recovers one major vertebrate clade, the Actinopterygii. However, in numerous cases insertions or deletions are specific to a monophyletic group. Conclusions: Rag1 is a phylogenetic marker of undoubted quality. Our study points to the need of carrying out a preliminary investigation on the base composition and the possible existence of sites under selection of this gene within the groups studied to avoid misleading resolution. The gene shows highly heterogeneous base composition, which affects some taxa in particular and contains sites under positive selection in some vertebrate lineages in the 5'-end. The first part of the gene (5'-end) is more variable than the second (3'-end), and less affected by a heterogeneous base composition. However, in some vertebrate lineages the 5'-end of the gene is not yet widely used for phylogenetic studies
    Eukaryotic transcriptomics in silico: Optimizing cDNA-AFLP efficiency
    Stölting, K.N. ; Gort, G. ; Wüst, C. ; Wilson, A.B. - \ 2009
    BMC Genomics 10 (2009). - ISSN 1471-2164 - 15 p.
    full-length cdnas - differential gene-expression - identification - distributions - resistance - sequences - resources - markers - library - plant
    Background - Complementary-DNA based amplified fragment length polymorphism (cDNA-AFLP) is a commonly used tool for assessing the genetic regulation of traits through the correlation of trait expression with cDNA expression profiles. In spite of the frequent application of this method, studies on the optimization of the cDNA-AFLP assay design are rare and have typically been taxonomically restricted. Here, we model cDNA-AFLPs on all 92 eukaryotic species for which cDNA pools are currently available, using all combinations of eight restriction enzymes standard in cDNA-AFLP screens. Results - In silco simulations reveal that cDNA pool coverage is largely determined by the choice of individual restriction enzymes and that, through the choice of optimal enzyme combinations, coverage can be increased from
    Towards a phylogenetic clarification of Lophiostoma / Massarina and morphologically similar genera in the Pleosporales
    Zhang, Y. ; Wang, H.K. ; Fournier, J. ; Crous, P.W. ; Jeewon, R. ; Pointing, S.B. ; Hyde, K.D. - \ 2009
    Fungal Diversity 38 (2009). - ISSN 1560-2745 - p. 225 - 251.
    submerged wood - ribosomal dna - fresh-water - hong-kong - fungi - ascomycota - revision - epitypification - teleomorph - sequences
    Lophiostoma, Lophiotrema and Massarina are similar genera that are difficult to distinguish morphologically. In order to obtain a better understanding of these genera, lectotype material of the generic types, Lophiostoma macrostomun, Lophiotrema nucula and Massarina eburnea were examined and are re-described. The phylogeny of these genera is investigated based oil the analysis of 26 Lophiostoma- and Massarina-like taxa and three genes - 18S, 28S rDNA and RPB2. These taxa formed five well-supported sub-clades in Pleosporales. This Study confirms that both Lophiostoma and Massarina are polyphyletic. Massarina-like taxa can presently be differentiated into two groups - the Lentithecium group and the Massarina group. Of these, the type species M. eburnea together with the Massarina group represents Massarina sensu stricto. Lophiostoma taxa Clustered in two groups - one group, including the type species L. macrostomum, is characterized by fusiform, hyaline one-septate ascospores which are pigmented and 3-septate when senescent, clavate asci, and apical structures which are highly variable, being crest-like in L. macrostomum, all umbilicate pore surrounded by 4-6 radial ridges in L. rugulosum, or papillate in L. glabrotunicatum. The second group comprises Lophiostoma species with heavily pigmented multi-septate ascospores and compressed crests. Lophiotrema species including the type species L. nucula form a monophyletic group. One new genus - Lentithecium with five new species - Lentithecium aquaticum, Lophiostoma glabrotunicatum, L. rugulosum, Lophiotrema brunneosporum and L. lignicola and three new combinations - Lentithecium arundinaceum, L. fluviatile and L. lineare are introduced in this paper.
    Quest for ion–ion correlations in electric double layers and overcharging phenomena
    Lyklema, J. - \ 2009
    Advances in Colloid and Interface Science 147-148 (2009). - ISSN 0001-8686 - p. 205 - 213.
    charge inversion - silver-iodide - adsorption - interface - sequences - stability - reversal - systems - anatase - water
    A discussion is given of the experimental evidence for overcharging, also known as charge reversal. The phenomenon is very common. The most general explanation is specific chemical adsorption. However, overcharging can also be explained on the basis of ion-ion correlations, which is rather a physical type of interpretation, and which can also be specific. Several theories have been developed for that. So, there is the luxury problem that two alternative explanations are available for the same observation. The purpose of this paper is to consider the various approaches critically and try to devise experimental options to discriminate between the two interpretations
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