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Fernandez-Ugalde O.,Public University of Navarra | Virto I.,Public University of Navarra | Barre P.,CNRS ENS Geology Laboratory | Gartzia-Bengoetxea N.,NEIKER Teknalia | And 3 more authors.

Lithogenic and/or secondary carbonates are present in many semi-arid Mediterranean soils. Their role in aggregation dynamics is not completely known, and can determine the sensitivity of these soils to land-use changes and soil management. The objective of this work was to test the hierarchical model of aggregation, and to determine the relationship between aggregates formation and organic matter decomposition in calcareous soils of semi-arid Mediterranean regions, by comparing macroaggregation in the upper horizon of a calcareous soil (Typic Calcixerept) with a non-calcareous soil (Typic Haploxerept) and a decarbonated terra rosa (Calcic Haploxerept) following fresh straw addition under controlled laboratory conditions during 105. days. We hypothesized that aggregation would work according to the hierarchical model in the non-calcareous soil (NONCALC) and in the decarbonated terra rosa (DECALC), but not in the calcareous soil (CALC). The three soils had similar organic C concentrations and C/N ratio, but differed in their carbonates and clay minerals content: NONCALC had a similar proportion of clay-size silicates than CALC (~. 10%), and the DECALC had a similar proportion of total clay-sized particles than CALC (including carbonates, ~. 20%). An increase in the amount of macroaggregates (> 250 μm) and microaggregates (50-250μm) held within macroaggregates associated to an increase in the fungal activity when maize straw was added, a decline of macroaggregates with time associated to organic matter decomposition, a higher concentration of organic C and maize-derived C in microaggregates within macroaggregates than in free microaggregates, and a transfer of maize-derived C from macroaggregates to free microaggregates with time confirmed that aggregation worked according to the hierarchical model in NONCALC and DECALC. In CALC, however, the hierarchical model worked only partially. Macroaggregates formation was also stimulated by organic residues addition according to the model, but stable macroaggregates showed longer turnover rates and no relationship between straw decomposition and their decline was observed. From this, we postulate that carbonates can help stabilizing macroaggregates formed from fresh organic matter decomposition through abiotic processes, such as dissolution and re-precipitation. These results help to understand field data obtained in semi-arid calcareous agricultural soils, where it has been observed that aggregation is not always directly correlated to organic matter concentration, but that increases in soil organic matter can promote aggregation. They also indicate the need for considering the composition of the mineral fraction when modelling soil structure in semi-arid Mediterranean soils. © 2011 Elsevier B.V. Source

Martin I.,CSIC - Biological Research Center | Ruiz M.F.,CSIC - Biological Research Center | Sanchez L.,NEIKER Teknalia
BMC Developmental Biology

Background: The gene transformer-2, which is involved in sex determination, has been studied in Drosophila, Musca, Ceratitis, Anastrepha and Lucilia. All these members of Diptera belong to the suborder Brachycera. In this work, it is reported the isolation and characterisation of genes transformer-2 of the dipterans Sciara ocellaris and Bradysia coprophila (formerly Sciara coprophila), which belong to the much less extensively analysed Sciaridae Family of the Suborder Nematocera, which is paraphyletic with respect to Suborder Brachycera. Results: The transformer-2 genes of the studied Sciara species were found to be transcribed in both sexes during development and adult life, in both the soma and germ lines. They produced a single primary transcript, which follows the same alternative splicing in both sexes, giving rise to different mRNAs isoforms. In S. ocellaris the most abundant mRNA isoform encoded a full-length protein of 251 amino acids, while that of B. coprophila encoded a protein of 246 amino acids. Both showed the features of the SR protein family. The less significant mRNA isoforms of both species encoded truncated, presumably non-functional Transformer-2 proteins. The comparison of the functional Sciara Transformer-2 proteins among themselves and those of other insects revealed the greatest degree of conservation in the RRM domain and linker region. In contrast, the RS1 and RS2 domains showed extensive variation with respect to their number of amino acids and their arginine-serine (RS) dipeptide content. The expression of S. ocellaris Transformer-2 protein in Drosophila XX pseudomales lacking the endogenous transformer-2 function caused their partial feminisation. Conclusions: The transformer-2 genes of both Sciaridae species encode a single protein in both sexes that shares the characteristics of the Transformer-2 proteins of other insects. These proteins showed conserved sex-determination function in Drosophila; i.e., they were able to form a complex with the endogenous Drosophila Transformer protein that controls the female-specific splicing of the Drosophila doublesex pre-mRNA. However, it appears that the complex formed between the Drosophila Transformer protein and the Sciara Transformer-2 protein is less effective at inducing the female-specific splicing of the endogenous Drosophila doublesex pre-mRNA than the DrosophilaTransformer-Transformer2 complex. This suggests the existence of species-specific co-evolution of the Transformer and Transformer-2 proteins. © 2011 Martín et al; licensee BioMed Central Ltd. Source

Ruiz-Larranaga O.,University of the Basque Country | Garrido J.M.,NEIKER Teknalia | Iriondo M.,University of the Basque Country | Manzano C.,University of the Basque Country | And 6 more authors.
Animal Genetics

Nucleotide-Binding Oligomerization Domain 2 (NOD2) has been reported to be a candidate gene for Mycobacterium avium subsp. paratuberculosis (MAP) infection in a Bos taurus × Bos indicus mixed breed based on a genetic association with the c.2197T>C single nucleotide polymorphism (SNP). Nevertheless, this SNP has also been reported to be monomorphic in the B. taurus species. In the present work, 18 SNPs spanning the bovine NOD2 gene have been analysed in a genetic association study of two independent populations of Holstein-Friesian cattle. We found that the C allele of SNP c.1908C>T, located in the 3-UTR region of the gene, is significantly more frequent in infected animals than in healthy ones, which supports the idea that the bovine NOD2 gene plays a role in susceptibility to MAP infection. However, in silico analyses of the NOD2 nucleotide sequence did not yield definitive data about a possible direct effect of SNP c.1908C>T on susceptibility to infection and led us to consider its linkage disequilibrium with the causative variant. A more exhaustive genetic association study including all putative, functional SNPs from this gene and subsequent functional analyses needs to be conducted to achieve a more complete understanding of how different variants of NOD2 may affect susceptibility to MAP infection in cattle. © 2010 Stichting International Foundation for Animal Genetics. Source

Ruiz-Larranaga O.,University of the Basque Country | Garrido J.M.,NEIKER Teknalia | Manzano C.,University of the Basque Country | Iriondo M.,University of the Basque Country | And 7 more authors.
Journal of Dairy Science

Johne's disease is a chronic enteritis caused by Mycobacterium avium ssp. paratuberculosis (MAP) that causes substantial financial losses for the cattle industry. Susceptibility to MAP infection is reported to be determined in part by genetic factors, so marker-assisted selection could help to obtain bovine populations that are increasingly resistant to MAP infection. Solute carrier family 11 member 1 (SLC11A1) was adjudged to be a potential candidate gene because of its role in innate immunity, its involvement in susceptibility to numerous intracellular infections, and its previous association with bovine MAP infection. The objectives of this study were to carry out an exhaustive process of discovery and compilation of polymorphisms in SLC11A1 gene, and to perform a population-based genetic association study to test its implication in susceptibility to MAP infection in cattle. In all, 57 single nucleotide polymorphisms (SNP) were detected, 25 of which are newly described in Bos taurus. Twenty-four SNP and two 3′-untranslated region polymorphisms, previously analyzed, were selected for a subsequent association study in 558 European Holstein-Friesian animals. The SNP c.1067C > G and c.1157-91A > T and a haplotype formed by these 2 SNP yielded significant association with susceptibility to MAP infection. The c.1067C > G is a nonsynonymous SNP that causes an amino acid change in codon 356 from proline to alanine (P356A) that could alter SLC11A1 protein function. This association study supports the involvement of SLC11A1 gene in susceptibility to MAP infection in cattle. Our results suggest that SNP c.1067C > G may be a potential causal variant, although functional studies are needed to assure this point. © 2010 American Dairy Science Association. Source

Ruiz-Larranaga O.,University of the Basque Country | Garrido J.M.,NEIKER Teknalia | Iriondo M.,University of the Basque Country | Manzano C.,University of the Basque Country | And 8 more authors.
Journal of Dairy Science

The intracellular pathogen resistance 1 (Ipr1) gene has been reported to play a role in mediating innate immunity in a mouse model of Mycobacterium tuberculosis infection, and polymorphisms of its human ortholog, SP110 nuclear body protein, have been suggested to be associated with tuberculosis. Thus, the bovine SP110 gene was considered to be a promising candidate for a genetic association study of bovine paratuberculosis, or Johne's disease, a chronic granulomatous enteritis caused by Mycobacterium avium ssp. paratuberculosis (MAP). Initially, single nucleotide polymorphisms (SNP) within the bovine SP110 gene were identified, and subsequently a population-based genetic association study was carried out. Seventeen new SNP along the SP110 gene were identified in Holstein-Friesian cattle, and 6 more were compiled from public databases. A total of 14 SNP were included in the association study of 2 independent populations. The SNP c.587A>G was found to be significantly associated with MAP infection, with the major allele A appearing to confer greater disease susceptibility in one of the analyzed populations. In addition, 2 haplotypes containing this SNP were also found to be associated with infection in the same population. The SNP c.587A>G is a nonsynonymous mutation that causes an amino acid change in codon 196 from asparagine to serine. In silico analyses point to SNP c.587A>G as a putative causal variant for susceptibility to MAP infection. The elucidation of the precise mechanism by which this SNP can exert its effect in the protein and, as a result, in the risk of infection, requires future functional analyses. Likewise, the absence of genetic association in one of the analyzed populations renders it necessary to carry out this study in other independent populations, with the aim of substantiating the repeatability of the present results. Nevertheless, the present results deepen our understanding of the genetic basis of susceptibility and resistance mechanisms related to MAP infection in cattle and, in turn, constitute a step forward toward the implementation of marker-assisted selection in breeding programs aimed at controlling paratuberculosis. © 2010 American Dairy Science Association. Source

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