Publications (20) View all
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Article: Evidence of complement genes in the sea-star Asterias rubens. Comparisons with the sea urchin.
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ABSTRACT: The axial organ of the sea star Asterias rubens is a primitive immune organ. The B-like cells, when stimulated by various antigens, produce antibody substances correlating with Ig kappa genes, .On the other hand,component complement genes were found. For each component, one or several contigs were analyzed. It is said that Asterias forbesi, another sea-star, in earlier results, showed complement-like activity. A brief comparison with the complement system in sea urchin was performed, especially about the C3 component.Immunology letters 02/2013; · 2.91 Impact Factor -
Book: DeepSuperSage analysis of the Vicia faba transcriptome in response to Ascochyta fabae infection
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ABSTRACT: Understanding the host response to Ascochyta fabae in faba bean ( Vicia faba L.), is crucial to elucidate the biology of host resistance. In an attempt to unravel the faba bean – A. fabae interaction, we performed genome-wide transcriptome profiling by deepSuperSAGE that quantified the early transcriptional changes elicited by the fungus in the resistant 29H faba bean genotype. The total number of 26 bp tags obtained was 1,313,009, of which 51,484 were unique sequences (UniTags) and 161 of them corresponded to fungal sequences. Sequences with a full match of the 26 bp revealed 2,222 tags with a significant P-value that were expressed differentialy between inoculated and control leaves. After gene ontology (GO) annotation, 2,143 of these matched to databases sequences (approximately 1/3 into each GO domain). At a 2.7-fold change threshold, 1,197 sequences were significantly differentially expressed in infected as compared to control leaves. Of these, nearly half were up- and the other downregulated. The most enriched GO terms corresponded to tags related with photosynthesis metabolism or structural components. Ten of them can be associated with plant defense, due to their association with responses to the jasmonic acid pathway, pectin esterase activity or gene silencing. Validation of the SuperSAGE data by qPCR of ten differentially expressed UniTags confirmed a rapid increase or decrease in mRNA 8 to 12 hours after inoculation in most of the up-regulated tags and, less consistently, in the downregulated ones. This study represents the most comprehensive analysis of the Ascochyta-response transcriptome of faba bean available to date. The applicability of these tags will increase as more faba bean genomic and cDNA sequences become available.01/2013; -
Article: DeepSuperSage analysis of the Vicia faba transcriptome in response to Ascochyta fabae infection
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ABSTRACT: Understanding the host response to Ascochyta fabae in faba bean ( Vicia faba L.), is crucial to elucidate the biology of host resistance. In an attempt to unravel the faba bean – A. fabae interaction, we performed genome-wide transcriptome profiling by deepSuperSAGE that quantified the early transcriptional changes elicited by the fungus in the resistant 29H faba bean genotype. The total number of 26 bp tags obtained was 1,313,009, of which 51,484 were unique sequences (UniTags) and 161 of them corresponded to fungal sequences. Sequences with a full match of the 26 bp revealed 2,222 tags with a significant P-value that were expressed differentialy between inoculated and control leaves. After gene ontology (GO) annotation, 2,143 of these matched to databases sequences (approximately 1/3 into each GO domain). At a 2.7-fold change threshold, 1,197 sequences were significantly differentially expressed in infected as compared to control leaves. Of these, nearly half were up- and the other downregulated. The most enriched GO terms corresponded to tags related with photosynthesis metabolism or structural components. Ten of them can be associated with plant defense, due to their association with responses to the jasmonic acid pathway, pectin esterase activity or gene silencing. Validation of the SuperSAGE data by qPCR of ten differentially expressed UniTags confirmed a rapid increase or decrease in mRNA 8 to 12 hours after inoculation in most of the up-regulated tags and, less consistently, in the downregulated ones. This study represents the most comprehensive analysis of the Ascochyta-response transcriptome of faba bean available to date. The applicability of these tags will increase as more faba bean genomic and cDNA sequences become available.2013. 01/2013; 52(1). -
Article: SuperTAG Methylation-Specific Digital Karyotyping (SMSDK) Reveals Uremia Induced Epigenetic Dysregulation of Atherosclerosis-Related Genes.
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ABSTRACT: BACKGROUND: -Accelerated atherosclerosis is a hallmark of chronic kidney disease (CKD). While the role of epigenetic dysregulation in atherosclerosis is increasingly appreciated, only few studies focused on epigenetics in CKD-associated cardiovascular disease, virtually all of which assessed epigenetic dysregulation globally. We hypothesized that gene-specific epigenetic dysregulation in CKD exists, affecting genes pertinent to inflammation and atherosclerosis. METHODS AND RESULTS: -Ten clinically stable patients undergoing hemodialysis therapy and ten healthy, age and sex matched controls were recruited. Genome-wide analysis of DNA methylation was performed by SuperTAG methylation-specific digital karyotyping (SMSDK), in order to identify genes differentially methylated in CKD. Analysis of 27,043,436 tags revealed 4,288 genomic loci with differential DNA methylation (P < 10(-10)) between hemodialysis patients and control subjects. Annotation of UniTags to promoter databases allowed us to identify 52 candidate genes associated with cardiovascular disease and 97 candidate genes associated with immune / infection diseases. These candidate genes could be classified to distinct proatherogenic processes including lipid metabolism and transport (e.g. HMGCR, SREBF1, LRP5, EPHX2, FDPS), cell proliferation and cell-cycle regulation (e.g. MIK67, TP53, ALOX12), angiogenesis (e.g. ANGPT2, ADAMTS10, FLT4) and inflammation (e.g. TNFSF10, LY96, IFNGR1, HSPA1A, IL12RB1). CONCLUSIONS: -We provide a comprehensive analysis of genome wide epigenetic alterations in CKD, identifying candidate genes associated with proatherogenic and inflammatory processes. These results may spur further research in the field of epigenetics in kidney disease, and point to new therapeutic strategies in CKD-associated atherosclerotic disease.Circulation Cardiovascular Genetics 10/2012; · 6.11 Impact Factor -
Article: Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis.
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ABSTRACT: Understanding the extent of local adaptation in natural populations and the mechanisms that allow individuals to adapt to their native environment is a major avenue in molecular ecology research. Evidence for the frequent occurrence of diverging ecotypes in species that inhabit multiple ecological habitats is accumulating, but experimental approaches to understanding the biological pathways as well as the underlying genetic mechanisms are still rare. Parasites are invoked as one of the major selective forces driving evolution and are themselves dependent on the ecological conditions in a given habitat. Immunological adaptation to local parasite communities is therefore expected to be a key component of local adaptation in natural populations. Here, we use next-generation sequencing technology to compare the transcriptome-wide response of experimentally infected three-spined sticklebacks from a lake and a river population, which are known to evolve under selection by distinct parasite communities. By comparing overall gene expression levels as well as the activation of functional pathways in response to parasite exposure, we identified potential differences between the two stickleback populations at several levels. Our results suggest locally adapted patterns of gene regulation in response to parasite exposure, which may reflect different local optima in the trade-off between the benefits and the disadvantages of mounting an immune response because of quantitative differences of the local parasite communities.Molecular Ecology 09/2012; · 5.52 Impact Factor
