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.

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Characterization and expression analysis of an interferon-y2 induced chemokine receptor CXCR3 in common carp (Cyprinus carpio L.)
Chadzinska, M.K. ; Golbach, L.A. ; Pijanowski, L. ; Scheer, M.H. ; Verburg-van Kemenade, B.M.L. - \ 2014
Developmental and Comparative Immunology 47 (2014)1. - ISSN 0145-305X - p. 68 - 76.
central-nervous-system - rheumatoid-arthritis - t-cells - monoclonal-antibodies - molecular evolution - endothelial-cells - phagocytic-cells - teleost fish - b-cells - inflammation
Chemokine and chemokine receptor signalling pairs play a crucial role in regulation of cell migration, morphogenesis, and cell activation. Expressed in mammals on activated T and NK cells, chemokine receptor CXCR3 binds interferon-¿ inducible chemokines CXCL9–11 and CCL21. Here we sequenced the carp CXCR3 chemokine receptor and showed its relationship to CXCR3a receptors found in other teleosts. We found high expression of the CXCR3 gene in most of the organs and tissues of the immune system and in immune-related tissues such as gills and gut, corroborating a predominantly immune-related function. The very high expression in gill and gut moreover indicates a role for CXCR3 in cell recruitment during infection. High in vivo expression of CXCR3 at later stages of inflammation, as well as its in vitro sensitivity to IFN-¿2 stimulation indicate that in carp, CXCR3 is involved in macrophage-mediated responses. Moreover, as expression of the CXCR3 and CXCb genes coincides in the focus of inflammation and as both the CXCb chemokines and the CXCR3 receptor are significantly up-regulated upon IFN-¿ stimulation it is hypothesized that CXCb chemokines may be putative ligands for CXCR3.
Annonaceae substitution rates - a codon model perspective
Chatrou, L.W. ; Pirie, M.D. ; Velzen, R. van; Bakker, F.T. - \ 2014
Revista Brasileira de Fruticultura 36 (2014)edição especial, e.. - ISSN 0100-2945 - p. 108 - 117.
molecular evolution - flowering plants - phylogeny reconstruction - historical biogeography - nucleotide substitution - maximum-likelihood - genera - diversification - characters - patterns
The Annonaceae includes cultivated species of economic interest and represents an important source of information for better understanding the evolution of tropical rainforests. In phylogenetic analyses of DNA sequence data that are used to address evolutionary questions, it is imperative to use appropriate statistical models. Annonaceae are cases in point: Two sister clades, the subfamilies Annonoideae and Malmeoideae, contain the majority of Annonaceae species diversity. The Annonoideae generally show a greater degree of sequence divergence compared to the Malmeoideae, resulting in stark differences in branch lengths in phylogenetic trees. Uncertainty in how to interpret and analyse these differences has led to inconsistent results when estimating the ages of clades in Annonaceae using molecular dating techniques. We ask whether these differences may be attributed to inappropriate modelling assumptions in the phylogenetic analyses. Specifically, we test for (clade-specific) differences in rates of non-synonymous and synonymous substitutions. A high ratio of nonsynonymous to synonymous substitutions may lead to similarity of DNA sequences due to convergence instead of common ancestry, and as a result confound phylogenetic analyses. We use a dataset of three chloroplast genes (rbcL, matK, ndhF) for 129 species representative of the family. We find that differences in branch lengths between major clades are not attributable to different rates of non-synonymous and synonymous substitutions. The differences in evolutionary rate between the major clades of Annonaceae pose a challenge for current molecular dating techniques that should be seen as a warning for the interpretation of such results in other organisms.
Diversification of IFNy-inducible CXCb chemokines in cyprinid fish
Aa, L.M. van der; Chadzinska, M.K. ; Derks, W. ; Scheer, M.H. ; Levraud, J.P. ; Boudinot, P. ; Verburg-van Kemenade, B.M.L. - \ 2012
Developmental and Comparative Immunology 38 (2012)2. - ISSN 0145-305X - p. 243 - 253.
trout oncorhynchus-mykiss - chemoattractant i-tac - carpio l. - differential expression - molecular evolution - gene-expression - receptor cxcr3 - early-response - cutting edge - cells
We earlier identified two CXCL8-like lineages in cyprinid fish, which are functional homologues of the mammalian CXCL8, but with diverged functions. We here investigated whether the carp IFN-¿-inducible CXCb gene, related to the mammalian CXCL9, -10 and -11 chemokines, was subject to a similar diversification. On the zebrafish genome, a cluster of seven CXCb genes was found on chromosome five. Analysis of the promoter of the zebrafish CXCb genes suggests a partially shared, but differential induction. A second CXCb gene, CXCb2, was identified in common carp by homology cloning. CXCb2 is constitutively expressed in immune-related tissues, predominantly in head kidney lymphocytes/monocytes. Interestingly, an induction of CXCb2 gene expression with recombinant carp IFN-¿2 and LPS was observed in macrophages and granulocytes. Finally, difference in sensitivity to LPS, and kinetics of CXCb1 and CXCb2 gene expression during zymosan-induced peritonitis, was observed. These results indicate a functional diversification for cyprinid CXCb chemokines, with functional homology to mammalian CXCL9–11.
Pro-inflammatory functions of carp CXCL8-like and CXCb chemokines
Aa, L.M. van der; Chadzinska, M.K. ; Golbach, L.A. ; Ribeiro, C.M.S. ; Verburg-van Kemenade, B.M.L. - \ 2012
Developmental and Comparative Immunology 36 (2012)4. - ISSN 0145-305X - p. 741 - 750.
trout oncorhynchus-mykiss - neutrophil chemotactic factor - interleukin-8 receptors - expression analysis - edwardsiella-ictaluri - molecular evolution - sequence-analysis - gene-expression - gro-alpha - tnf-alpha
Numerous CXC chemokines have been identified in fish, however, their role in inflammation is not well established. Here, CXC chemokines of the CXCL8-like (CXCa_L1 and CXCL8_L2) and CXCL9/10/11-like (CXCb) subset were investigated in carp. Recombinant CXCa_L1, CXCL8_L2 and CXCb all stimulated chemotaxis of macrophages and granulocytes in vitro. CXCb also attracted lymphocytes. Distinct effects on phagocyte activation were observed: the CXCL8-like chemokines increase respiratory burst activity, but not nitrite production. The three chemokines differentially induced a moderate increase in IL-1ß, CXCa_L1 and CXCL8_L2 gene expression. Intracellular calcium mobilization in granulocytes upon CXCa_L1 stimulation implies signal transduction through G-protein coupled CXC receptors. Notably, upon intraperitoneal administration, carp CXCL8-like chemokines strongly induced in vivo leukocyte recruitment, including neutrophils and monocytes/macrophages, in contrast to CXCb, for which the number of recruited leukocytes was low. The results indicate functional homology for carp CXCL8-like and CXCb chemokines with mammalian CXCL8 and CXCL9-11, respectively. --------------------------------------------------------------------------------
Effector diversification within compartments of the Leptosphaeria maculans genome affected by repeat induced point mutations
Rouxel, T. ; Grandaubert, J. ; Hane, J.K. ; Hoede, C. ; Wouw, A. ; Couloux, A. ; Dominguez, V. ; Anthouard, V. ; Bally, P. ; Bourras, S. ; Cozijnsen, A.J. ; Ciuffetti, L.M. ; Degrave, A. ; Dilmaghani, A. ; Duret, L. ; Fudal, L. ; Goodwin, S.B. ; Gout, L. ; Glaser, N. ; Linglin, J. ; Kema, G.H.J. ; Lapalu, N. ; Lawrence, C.B. ; May, K. ; Meyer, M. ; Ollivier, B. ; Poulain, J. ; Schoch, C.L. ; Simon, A. ; Spatafora, J.W. ; Stachowiak, A. ; Turgeon, B.G. ; Tyler, B.M. ; Vincent, D. ; Weissenbach, J. ; Amselem, J. ; Quesneville, H. ; Oliver, R.P. ; Wincker, P. ; Balesdent, M.H. ; Howlett, B.J. - \ 2011
Nature Communications 2 (2011). - ISSN 2041-1723 - p. 202 - 202.
transposable elements - molecular evolution - pathogen effectors - brassica-napus - gene-transfer - oilseed rape - stem canker - avirulence - plant - fungal
Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that are shared by animals and fungi are studied in fungi due to their experimental tractability. Many fungi are pathogens or mutualists and are model systems to analyse effector genes and their mechanisms of diversification. In this study, we report the genome sequence of the phytopathogenic ascomycete Leptosphaeria maculans and characterize its repertoire of protein effectors. The L. maculans genome has an unusual bipartite structure with alternating distinct guanine and cytosine-equilibrated and adenine and thymine (AT)-rich blocks of homogenous nucleotide composition. The AT-rich blocks comprise one-third of the genome and contain effector genes and families of transposable elements, both of which are affected by repeat-induced point mutation, a fungal-specific genome defence mechanism. This genomic environment for effectors promotes rapid sequence diversification and underpins the evolutionary potential of the fungus to adapt rapidly to novel host-derived constraints
The east-west-north colonization history of the Mediterranean and Europe by the coastal plant Carex extensa (Cyperaceae)
Escudero, M. ; Vargas, P. ; Arens, P. ; Ouborg, N.J. ; Luceno, M. - \ 2010
Molecular Ecology 19 (2010)2. - ISSN 0962-1083 - p. 352 - 370.
population genetic-structure - length polymorphism markers - messinian salinity crisis - sedges carex - phylogeographical structure - molecular evolution - microsatellite data - computer-program - chloroplast dna - cakile-maritima
Coastal plants are ideal models for studying the colonization routes of species because of the simple linear distributions of these species. Carex extensa occurs mainly in salt marshes along the Mediterranean and European coasts. Variation in cpDNA sequences, amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs) of 24 populations were analysed to reconstruct its colonization history. Phylogenetic relationships indicate that C. extensa together with the South American Carex vixdentata and the southern African Carex ecklonii form a monophyletic group of halophilic species. Analyses of divergence times suggest that early lineage diversification may have occurred between the late Miocene and the late Pliocene (Messinian crisis). Phylogenetic and network analyses of cpDNA variation revealed the monophyly of the species and an ancestral haplotype contained in populations of the eastern Mediterranean. The AFLP and SSR analyses support a pattern of variation compatible with these two lineages. These analyses also show higher levels of genetic diversity and differentiation in the eastern population group, which underwent an east-to-west Mediterranean colonization. Quaternary climatic oscillations appear to have been responsible for the split between these two lineages. Secondary contacts may have taken place in areas near the Ligurian Sea in agreement with the gene flow detected in Corsican populations. The AFLP and SSR data accord with the 'tabula rasa' hypothesis in which a recent and rapid colonization of northern Europe took place from the western Mediterranean after the Last Glacial Maximum. The unbalanced west-east vs. west-north colonization may be as a result of 'high density blocking' effect
CXCL8 Chemokines in teleost fish: two lineages with distinct expression profiles during early phases of inflammation
Aa, L.M. van der; Chadzinska, M.K. ; Tijhaar, E. ; Boudinot, P. ; Verburg-van Kemenade, B.M.L. - \ 2010
PLoS ONE 5 (2010)8. - ISSN 1932-6203 - 13 p.
neutrophil-activating factor - trout oncorhynchus-mykiss - cyprinus-carpio l. - interleukin-8 receptors - molecular evolution - chemotactic factor - escherichia-coli - gene-expression - gro-alpha - tnf-alpha
Background - During the inflammatory process, chemokine CXCL8 plays a pivotal role in recruitment of human neutrophilic granulocytes. A diversity of sequences similar to CXCL8 was reported in fish, but their evolutionary relationships and functional homology with their human homolog remain unclear. Principal Findings - We screened fish genomes to seek for sequences related to CXCL8. A first lineage was retrieved in all teleosts, while a second CXCL8 lineage was found in zebrafish and carp only. An early inflammatory function for both lineages was indicated by several lines of evidence. The induction of carp CXCL8s, CXCb, and CXC receptor-1 and -2 was analyzed after in vitro stimulation of leukocyte subpopulations and in two in vivo inflammation models. Recombinant proteins of carp CXCL8 proteins were produced and showed significant chemotactic activity for carp leukocytes. Conclusions - While both carp CXCL8s appear to be functional homologs of mammalian CXCL8, their different induction requirements and kinetics evoke a gene-specific sub-functionalization
Genome sequence of the necrotrophic plant pathogen Pythium ultimum reveals original pathogenicity mechanisms and effector repertoire
Lévesque, C.A. ; Brouwer, H. ; Cano, L. ; Hamilton, J.P. ; Holt, C. ; Huitema, E. ; Raffaele, S. ; Robideau, G.P. ; Thines, M. ; Win, J. ; Zerillo, M.M. ; Beakes, G.W. ; Boore, J.L. ; Busam, D. ; Dumas, B. ; Ferriera, S. ; Fuerstenberg, S.I. ; Gachon, C.M.M. ; Gaulin, E. ; Govers, F. ; Grenville-Briggs, L. ; Horner, N. ; Hostetler, J. ; Jiang, R.H.Y. ; Johnson, J. ; Krajaejun, T. ; Lin, H. ; Meijer, H.J.G. ; Moore, B. ; Morris, P. ; Phuntmart, V. ; Puiu, D. ; Shetty, J. ; Stajich, J.E. ; Tripathy, S. ; Wawra, S. ; West, P. van; Whitty, B.R. ; Coutinho, P.M. ; Henrissat, B. ; Martin, F. ; Thomas, P.D. ; Tyler, B.M. ; Vries, R.P. de; Kamoun, S. ; Yandell, M. ; Tisserat, N. ; Buell, C.R. - \ 2010
Genome Biology 11 (2010)7. - ISSN 1474-7596 - 22 p.
oomycete phytophthora-infestans - potato famine pathogen - protein families - mitochondrial genome - pleiotropic drug - gene family - arabidopsis-thaliana - cadherin superfamily - microbe interactions - molecular evolution
Background - Pythium ultimum is a ubiquitous oomycete plant pathogen responsible for a variety of diseases on a broad range of crop and ornamental species. Results -The P. ultimum genome (42.8 Mb) encodes 15,290 genes and has extensive sequence similarity and synteny with related Phytophthora species, including the potato blight pathogen Phytophthora infestans. Whole transcriptome sequencing revealed expression of 86% of genes, with detectable differential expression of suites of genes under abiotic stress and in the presence of a host. The predicted proteome includes a large repertoire of proteins involved in plant pathogen interactions, although, surprisingly, the P. ultimum genome does not encode any classical RXLR effectors and relatively few Crinkler genes in comparison to related phytopathogenic oomycetes. A lower number of enzymes involved in carbohydrate metabolism were present compared to Phytophthora species, with the notable absence of cutinases, suggesting a significant difference in virulence mechanisms between P. ultimum and more host-specific oomycete species. Although we observed a high degree of orthology with Phytophthora genomes, there were novel features of the P. ultimum proteome, including an expansion of genes involved in proteolysis and genes unique to Pythium. We identified a small gene family of cadherins, proteins involved in cell adhesion, the first report of these in a genome outside the metazoans. Conclusions - Access to the P. ultimum genome has revealed not only core pathogenic mechanisms within the oomycetes but also lineage-specific genes associated with the alternative virulence and lifestyles found within the pythiaceous lineages compared to the Peronosporaceae.
Vertical transmission as the key to the colonization of Madagascar by fungus-growing termites?
Nobre, T. ; Eggleton, P. ; Aanen, D.K. - \ 2010
Proceedings of the Royal Society. B: Biological Sciences 277 (2010)1680. - ISSN 0962-8452 - p. 359 - 365.
multiple sequence alignment - molecular evolution - macrotermitinae - dispersal - isoptera - termitomyces - symbionts - africa - comb - inoculation
The mutualism between fungus-growing termites (Macrotermitinae) and their mutualistic fungi (Termitomyces) began in Africa. The fungus-growing termites have secondarily colonized Madagascar and only a subset of the genera found in Africa is found on this isolated island. Successful long-distance colonization may have been severely constrained by the obligate interaction of the termites with fungal symbionts and the need to acquire these symbionts secondarily from the environment for most species (horizontal symbiont transmission). Consistent with this hypothesis, we show that all extant species of fungus-growing termites of Madagascar are the result of a single colonization event of termites belonging to one of the only two groups with vertical symbiont transmission, and we date this event at approximately 13 Mya (Middle/Upper Miocene). Vertical symbiont transmission may therefore have facilitated long-distance dispersal since both partners disperse together. In contrast to their termite hosts, the fungal symbionts have colonized Madagascar multiple times, suggesting that the presence of fungus-growing termites may have facilitated secondary colonizations of the symbiont. Our findings indicate that the absence of the right symbionts in a new environment can prevent long-distance dispersal of symbioses relying on horizontal symbiont acquisition
Flanking regions of monomorphic microsatellite loci provide a new source of data for plant species-level phylogenetics
Chatrou, L.W. ; Escribano, M.P. ; Viruel, M.A. ; Maas, J.W. ; Richardson, J.E. ; Hormaza, J.I. - \ 2009
Molecular Phylogenetics and Evolution 53 (2009)3. - ISSN 1055-7903 - p. 726 - 733.
plastid dna regions - rain-forest trees - rapid diversification - nicotiana solanaceae - molecular evolution - chloroplast genes - potential utility - sequence loci - nuclear - annonaceae
Well-resolved phylogenetic trees are essential for us to understand evolutionary processes at the level of species. The degree of species-level resolution in the plant phylogenetic literature is poor, however, largely due to the dearth of sufficiently variable molecular markers. Unlike the common genic approach to marker development, we generated DNA sequences of monomorphic nuclear microsatellite flanking regions in a phylogenetic study of Annona species (Annonaceae). The resulting data showed no evidence of paralogy or allelic diversity that would confound attempts to reconstruct the species tree. Microsatellite flanking regions are short, making them practical to use, yet have astounding proportions of variable characters. They have 3.5- to 10-fold higher substitution rates compared to two commonly used chloroplast markers, have no rate heterogeneity among nucleotide positions, evolve in a clock-like fashion, and show no evidence of saturation. These advantages are offset by the short length of the flanking regions, resulting in similar numbers of parsimony informative characters to the chloroplast markers. The neutral evolution and high variability of flanking regions, together with the wide availability of monomorphic microsatellite loci in angiosperms, are useful qualities for species-level phylogenetics. The general methodology we present here facilitates to find phylogenetic markers in groups where microsatellites have been developed
The utility of NBS profiling for plant systematics: a first study in tuber-bearing Solanum species
Wang, M. ; Berg, R.G. van den; Linden, G. van der; Vosman, B. - \ 2008
Plant Systematics and Evolution 276 (2008)1-2. - ISSN 0378-2697 - p. 137 - 148.
late blight resistance - broad-spectrum resistance - length difference test - disease resistance - chloroplast dna - sect. petota - phytophthora-infestans - molecular evolution - cultivated potato - r-gene
Systematic relationships are important criteria for researchers and breeders to select materials. We evaluated a novel molecular technique, nucleotide binding site (NBS) profiling, for its potential in phylogeny reconstruction. NBS profiling produces multiple markers in resistance genes and their analogs (RGAs). Potato (Solanum tuberosum L.) is a crop with a large secondary genepool, which contains many important traits that can be exploited in breeding programs. In this study we used a set of over 100 genebank accessions, representing 49 tuber-bearing wild and cultivated Solanum species. NBS profiling was compared to amplified fragment length polymorphism (AFLP). Cladistic and phenetic analyses showed that the two techniques had similar resolving power and delivered trees with a similar topology. However, the different statistical tests used to demonstrate congruency of the trees were inconclusive. Visual inspection of the trees showed that, especially at the lower level, many accessions grouped together in the same way in both trees; at the higher level, when looking at the more basal nodes, only a few groups were well supported. Again this was similar for both techniques. The observation that higher level groups were poorly supported might be due to the nature of the material and the way the species evolved. The similarity of the NBS and AFLP results indicate that the role of disease resistance in speciation is limited
Evolution and genetic population structure of prickly lettuce (Lactuca serriola) and its RGC2 resistance gene cluster
Kuang, H. ; Eck, H.J. van; Sicard, D. ; Michelmore, R. ; Nevo, E. - \ 2008
Genetics 178 (2008)3. - ISSN 0016-6731 - p. 1547 - 1558.
mildew bremia-lactucae - arabidopsis-thaliana - natural-populations - wild lactuca - cultivated lettuce - molecular evolution - statistical tests - encoding genes - major cluster - diversity
Genetic structure and diversity of natural populations of prickly lettuce (Lactuca serriola) were studied using AFLP markers and then compared with the diversity of the RGC2 disease resistance gene cluster. Screening of 696 accessions from 41 populations using 319 AFLP markers showed that eastern Turkish and Armenian populations were the most diverse populations and might be located in the origin and center of diversity of L. serriola. Screening 709 accessions using the microsatellite MSATE6 that is located in the coding region of most RGC2 homologs detected 366 different haplotypes. Again, the eastern Turkish and Armenian populations had the highest diversities at the RGC2 cluster. The diversities at the RGC2 cluster in different populations were significantly correlated with their genomewide diversities. There was significant variation of copy number of RGC2 homologs in different populations, ranging from 12 to 22 copies per genome. The nucleotide diversities of two conserved lineages (type II) of RGC2 genes (K and L) were not correlated with diversities calculated using the MSATE6 or AFLP data. We hypothesize that the high genomewide diversity and diversity of the RGC2 cluster in eastern Turkish and Armenian populations resulted from high abiotic and biotic stresses in the regions of origin of L. serriola.
The presence of multiple and differentially regulated interleukin-12p40 genes in bony fishes signifies an expansion of the vertebrate heterodimeric cytokine family
Huising, M.O. ; Schijndel, J. van; Kruiswijk, C.P. ; Nabuurs, S.B. ; Savelkoul, H.F.J. ; Flik, G. ; Verburg-van Kemenade, B.M.L. - \ 2006
Molecular Immunology 43 (2006)10. - ISSN 0161-5890 - p. 1519 - 1533.
cell stimulatory factor - il-12 p40 homodimer - cyprinus-carpio l - cd4(+) t-cells - in-vitro - molecular evolution - immune-responses - th1 responses - teleost fish - common carp
Interleukin-12 (IL-12) is the founding member of a rapidly growing family of heterodimeric cytokines. It consists of two subunits, designated p35 and p40 that together constitute a disulphide-linked heterodimeric cytokine. IL-12 is well known for its prominent role in both the early innate immune response and the skewing of the ensuing acquired immune response towards Th1. Here, we report the presence of IL-12p35 and three highly distinct IL-12p40 genes in common carp (Cyprinus carpio). The carp is a bony fish species genetically similar to the zebrafish, but its substantially larger body size facilitates immunological studies. A comparison of IL-12p35 genes of mammalian and non-mammalian species reveals the presence of a duplicated exon that is unique to the mammalian lineage. The organisation of the three carp IL-12p40 genes is similar to that of higher vertebrates. Phylogenetic analyses that include the p40-related subunits of other composite cytokines confirm the presence of three genuine IL-12p40 genes in carp and indicate that they are evolutionary ancient and possibly not restricted to bony fishes. The orthology of the different carp p40 subunits to mammalian IL-12p40 is further evident from the conservation of key residues involved in the formation of intra- and interchain disulphide bridges and the tight interlocking topology between p35 and p40. The expression of each of the carp IL-12p40 genes differs profoundly, constitutively as well as in response to in vitro stimulation of carp macrophages. Collectively, the presence of multiple and substantially different IL-12 genes signifies a considerable expansion of the vertebrate heterodimeric cytokine family
Central and peripheral interleukin-1ß and interleukin-1 receptor I expression and their role in the acute stress response of common carp, Cyprinus carpio L.
Metz, J.R. ; Huising, M.O. ; Leon, K.M. ; Verburg-van Kemenade, B.M.L. ; Flik, G. - \ 2006
Journal of Endocrinology 191 (2006)1. - ISSN 0022-0795 - p. 25 - 35.
corticotropin-releasing hormone - pituitary-adrenal axis - tumor necrosis factors - pomc-derived peptides - growth-hormone - adrenocorticotropic hormone - molecular evolution - oncorhynchus-mykiss - gene-expression - rainbow-trout
In fish, the hypothalamus-pituitary-interrenal axis (HPI-axis), the equivalent of the hypothalamus-pituitary-adrenal axis (HPA-axis) in mammals, is activated during stress and leads to production and release of cortisol by the interregnal cells in the head kidney. In mammals, the cytokine interleukin-1ß (IL-1ß) takes a key position in the innate immune and inflammatory responses and influences the HPA-axis. In fish, studies that address the effects of cytokines on HPI-axis activation are limited. We quantitatively assessed expression of IL-1ß and its receptor, IL-1RI (the latter was cloned and sequenced), in an acute restraint stress paradigm in common carp, Cyprinus carpio. We also considered expression of the pituitary hormones prolactin (PRL) and GH that have been shown to be structurally related to cytokines and have immunomodulatory actions. Pituitary PRL expression increased fourfold during stress; GH mRNA levels were unaffected. Following restraint, hypothalamic IL-1ß expression was upregulated; in head kidney and pituitary pars intermedia, IL-1RI expression significantly increased. We suggest that during acute stress IL-1ß signalling in the HPI-axis becomes more sensitive, since both ligand and receptor expressions are enhanced. In vitro, recombinant carp IL-1ß stimulates release of ¿-MSH and N-Ac ß-endorphin from the pituitary gland. This observation concurs with increased in vivo plasma levels of ¿-MSH and N-Ac ß-endorphin following restraint. Our findings combined lead us to conclude that IL-1ß affects the activity of the HPI-axis and, in turn, expression profiles of genes encoding IL-1ß and its receptor are modified during acute stress. Our study provides convincing evidence for bi-directional communication of the HPI-axis and the immune system in fish
Gene function beyond the single trait: natural variation, gene effects, and evolutionary ecology in Arabidopsis thaliana
Tonsor, S.J. ; Alonso-Blanco, C. ; Koornneef, M. - \ 2005
Plant, Cell & Environment 28 (2005)1. - ISSN 0140-7791 - p. 2 - 20.
recombinant inbred lines - mediated shade-avoidance - heat-shock-protein - flowering time - allelic variation - resistance gene - loci analysis - pseudomonas-syringae - molecular evolution - escherichia-coli
The purpose of plant functional genomics is to describe the patterns of gene expression and internal plant function underlying the ecological functions that sustain plant growth and reproduction. Plants function as integrated systems in which metabolic and developmental pathways draw on common resource pools and respond to a relatively small number of signal/response systems. Plants are also integrated with their environment, exchanging energy and matter with their surroundings and are consequently sensitive to changes in energy and resource fluxes. These two levels of integration complicate the description of gene function. Internal integration results in single genes often affecting multiple characteristics (pleiotropy) and interacting with multiple other genes (epistasis). Integration with the external environment leads to gene expression and the genes' phenotypic effects varying across environmental backgrounds (gene-environment interaction). An accurate description of the function of all genes requires an augmentation, already underway, of the study of isolated developmental and metabolic pathways to a more integrated approach involving the study of genetic effects across scales of variation usually regarded as the purview of ecological and evolutionary research. Since the evolution of gene function also depends on this complex of gene effects, progress in evolutionary genetics will also require understanding the nature of gene interactions and pleiotropy and the constraints and patterns they impose on adaptive evolution. Studying gene function in the context of the integrated organism is a major challenge, best met by developing co-ordinated research efforts in model systems. This review highlights natural variation in A. thaliana as a system for understanding integrated gene function in an ecological and evolutionary context. The current state of this research integration in A. thaliana is described by summarizing relevant approaches, current knowledge, and some potentially fruitful future studies. By introducing some of the fundamental questions of ecological and evolutionary research, experimental approaches and systems that can reveal new facets of gene function and gene effect are also described. A glossary is included in the Appendix.
Historical biogeography of two cosmopolitan families of flowering plants: Annonaceae and Rhamnaceae
Richardson, J.E. ; Chatrou, L.W. ; Mols, J.B. ; Erkens, R.H.J. ; Pirie, M.D. - \ 2004
Philosophical Transactions of the Royal Society B. Biological sciences 359 (2004)1450. - ISSN 0962-8436 - p. 1495 - 1508.
phylogenetic analysis - molecular evolution - divergence times - dna-sequences - north-america - cape flora - dispersal - tertiary - diversification - forest
Annonaceae are a pantropically distributed family found predominantly in rainforests, so they are megathermal taxa, whereas Rhamnaceae are a cosmopolitan family that tend to be found in xeric regions and may be classified as mesothermal. Phylogenetic analyses of these families are presented based on rbcL and trnL-F plastid DNA sequences. Likelihood ratio tests revealed rate heterogeneity in both phylogenetic trees and they were therefore made ultrametric using non-parametric rate smoothing and penalized likelihood. Divergence times were then estimated using fossil calibration points. The historical biogeography of these families that are species rich in different biomes is discussed and compared with other published reconstructions. Rhamnaceae and most lineages within Annonaceae are too young to have had their distribution patterns influenced by break-up of previously connected Gondwanan landmasses. Contrasts in the degree of geographical structure between these two families may be explained by differences in age and dispersal capability. In both groups, long-distance dispersal appears to have played a more significant role in establishing modern patterns than had previously been assumed. Both families also contain examples of recent diversification of species-rich lineages. An understanding of the processes responsible for shaping the distribution patterns of these families has contributed to our understanding of the historical assembly of the biomes that they occupy
Introduction and synthesis: plant phylogeny and the origin of major biomes
Pennington, R.T. ; Cronk, Q.C.B. ; Richardson, J.E. - \ 2004
Philosophical Transactions of the Royal Society B. Biological sciences 359 (2004)1450. - ISSN 0962-8436 - p. 1455 - 1464.
estimating divergence times - cape-flora - floristic diversity - molecular evolution - south-america - global 200 - forest - biogeography - speciation - africa
Phylogenetic trees based upon DNA sequence data, when calibrated with a dimension of time, allow inference of: (i) the pattern of accumulation of lineages through time; (ii) the time of origin of monophyletic groups; (iii) when lineages arrived in different geographical areas; (iv) the time of origin of biome-specific morphologies. This gives a powerful new view of the history of biomes that in many cases is not provided by the incomplete plant fossil record. Dated plant phylogenies for angiosperm families such as Leguminoaceae (Fabaceae), Melastomataceae sensu stricto, Annonaceae and Rhamnaceae indicate that long-distance, transoceanic dispersal has played an important role in shaping their distributions, and that this can obscure any effect of tectonic history, previously assumed to have been the major cause of their biogeographic patterns. Dispersal from other continents has also been i mportant in the assembly of the Amazonian rainforest flora and the Australian flora. Comparison of dated biogeographic patterns of plants and animals suggests that recent long-distance dispersal might be more prevalent in plants, which has major implications for community assembly and coevolution. Dated plant phylogenies also reveal the role of past environmental changes on the evolution of lineages in species-rich biomes, and show that recent Plio-Pleistocene diversification has contributed substantially to their current species richness. Because of the critical role of fossils and morphological characters in assigning ages to nodes in phylogenetic trees, future studies must include careful morphological consideration of fossils and their extant relatives in a phylogenetic context. Ideal study systems will be based upon DNA sequence data from multiple loci and multiple fossil calibrations. This allows cross-validation both of age estimates from different loci, and from different fossil calibrations. For a more complete view of biome history, future studies should emphasize full taxon sampling in ecologically important groups, and should focus on geographical areas for which few species-level phylogenies are available, such as tropical Africa and Asia. These studies are urgent because understanding the history of biomes can both inform conservation decisions, and help predict the effects of future environmental changes at a time when biodiversity is being impacted on an unprecedented scale
Effect of fusion protein cleavage site mutations on virulence of Newcastle disease virus: non-virulent cleavage site mutants revert to virulence after one passage in chicken brain.
Leeuw, O.S. de; Hartog, L. ; Koch, G. ; Peeters, B.P.H. - \ 2003
Journal of General Virology 84 (2003)2. - ISSN 0022-1317 - p. 475 - 484.
phylogenetic-relationships - proteolytic cleavage - nucleotide-sequence - molecular evolution - avirulent strains - mammalian-cells - activation site - factor-x - glycoprotein - pathogenicity
Virulence of Newcastle disease virus (NDV) is mainly determined by the amino acid sequence of the fusion (F0) protein cleavage site. Full-length NDV cDNA clone pNDFL was used to generate infectious NDV with defined mutations in the F0 cleavage site (RRQRR downward arrow L, GRQGR downward arrow F, RRQGR downward arrow F, RGQRR downward arrow F and RKQKR downward arrow F). All the mutants were viable and the mutations were maintained after virus propagation in embryonated eggs. The mutants showed single-cell infections on chicken embryo fibroblasts, which suggested that they were non-virulent. However, virulence tests in 1-day-old chickens resulted in an intracerebral pathogenicity index (ICPI) between 0 and 1.3. Moreover, virulent virus was isolated from chickens that had died in the virulence tests. Subsequent sequence analysis showed that the mutants RRQRR downward arrow L, RRQGR downward arrow F, RGQRR downward arrow F and RKQKR downward arrow F gave rise to the appearance of revertants containing the virulent cleavage site RRQ(K/R)R downward arrow F and an ICPI of 1.4 or higher. This indicated that reversion to virulence was caused by alteration of the amino acid sequence of the F0 cleavage site from a non-virulent to a virulent type. Furthermore, the ICPI of the revertants was higher than that of cDNA-derived strain NDFLtag, which has the same cleavage site, RRQRR downward arrow F (ICPI=1.3). NDFLtag(Pass), which was isolated from dead chickens after intracerebral inoculation of NDFLtag, also showed an increase in the ICPI from 1.3 to 1.5. This study proves that reversion to virulence occurs within non-virulent NDV populations and that the virulence may increase after one passage in chicken brain
Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology.
Belkum, A. van; Struelens, M. ; Visser, J.A.G.M. de; Verburgh, H. ; Tibayrenc., M. - \ 2001
Clinical Microbiology Reviews 14 (2001)3. - ISSN 0893-8512 - p. 547 - 560.
resistant staphylococcus-aureus - field gel-electrophoresis - escherichia-coli k-12 - commercial software packages - term experimental evolution - adaptive evolution - molecular evolution - hemorrhagic colitis - infectious-disease - mycobacterium-tuberculosis
Currently, genetic typing of microorganisms is widely used in several major fields of microbiological research. Taxonomy, research aimed at elucidation of evolutionary dynamics or phylogenetic relationships, population genetics of microorganisms, and microbial epidemiology all rely on genetic typing data for discrimination between genotypes. Apart from being an essential component of these fundamental sciences, microbial typing clearly affects several areas of applied microbiogical research. The epidemiological investigation of outbreaks of infectious diseases and the measurement of genetic diversity in relation to relevant biological properties such as pathogenicity, drug resistance, and biodegradation capacities are obvious examples. The diversity among nucleic acid molecules provides the basic information for all fields described above. However, researchers in various disciplines tend to use different vocabularies, a wide variety of different experimental methods to monitor genetic variation, and sometimes widely differing modes of data processing and interpretation. The aim of the present review is to summarize the technological and fundamental concepts used in microbial taxonomy, evolutionary genetics, and epidemiology. Information on the nomenclature used in the different fields of research is provided, descriptions of the diverse genetic typing procedures are presented, and examples of both conceptual and technological research developments for Escherichia coli are included. Recommendations for unification of the different fields through standardization of laboratory techniques are made
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