250 research outputs found

    Are we missing a mesopelagic-demersal coupling?

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    Despite demersal trawling monitoring programs are not aimed at quantifying mesopelagic organisms, they are recurrently captured as by catch between 30 and 800 m depth. These species are mostly diel vertical migrants, with differentiated behavior from benthic and demersal ones. Nevertheless, they are sometimes captured in large quantities (both abundance and biomass) although absent on other occasions. The co-occurrence observed with demersal populations may probably be due to the daytime and location of samplings, i.e. depth and type of bottom (habitat). In order to understand the mesopelagic-demersal coupling, we discuss spatio-temporal patterns observed along the Spanish Mediterranean coast during the 1994-2012 MEDITS survey.FEM

    Molecular characterization of the diet of the planktonic community in Málaga Bay (NW Alboran Sea)

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    The seasonal changes in structure and functioning of the pelagic trophic web in Málaga Bay (NW Alboran Sea) are related to the annual hydrological cycle. However, time series analyses have shown that the relationship between interannual hydrological variability and the plankton community composition is weak. This might be due to different human-induced pressures (nutrient pollution, coastal fisheries) acting on different compartments of the trophic web. The net effect of all these factors would depend on how the ecosystem channels changes in the composition and abundance of each trophic level. Interactions of phytoplankton-ciliates-zooplankton might have a central role in the regulation of the trophic web in Málaga Bay, although the trophic relations of the dominant groups remain still undefined. In order to identify the dominant trophic relationships we aimed to characterise the diet of key ichthyo- and mesozooplankton species in the field. Given that gut content preys (phyto- and microplankton) are fragile and not easy to identify visually, we developed species-specific molecular markers to detect their presence/absence within the predators gut

    A new wildland fire danger index for a Mediterranean region and some validation aspects

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    Wildland fires are the main cause of tree mortality in Mediterranean Europe and a major threat to Spanish forests. This paper focuses on the design and validation of a new wildland fire index especially adapted to a Mediterranean Spanish region. The index considers ignition and spread danger components. Indicators of natural and human ignition agents, historical occurrence, fuel conditions and fire spread make up the hierarchical structure of the index. Multi-criteria methods were used to incorporate experts¿ opinion in the process of weighting the indicators and to carry out the aggregation of components into the final index, which is used to map the probability of daily fire occurrence on a 0.5-km grid. Generalised estimating equation models, which account for possible correlated responses, were used to validate the index, accommodating its values onto a larger scale because historical records of daily fire occurrence, which constitute the dependent variable, are referred to cells on a 10-km grid. Validation results showed good index performance, good fit of the logistic model and acceptable discrimination power. Therefore, the index will improve the ability of fire prevention services in daily allocation of resources.The authors acknowledge the support received from the Ministry of Science and Innovation through the research project Modelling and Optimisation Techniques for a Sustainable Development, Ref. EC02008-05895-C02-01/ECON.Vicente López, FJD.; Crespo Abril, F. (2012). A new wildland fire danger index for a Mediterranean region and some validation aspects. 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International Journal of Wildland Fire, 18(6), 640. doi:10.1071/wf07136Maingi, J. K., & Henry, M. C. (2007). Factors influencing wildfire occurrence and distribution in eastern Kentucky, USA. International Journal of Wildland Fire, 16(1), 23. doi:10.1071/wf06007Martell, D. L., Otukol, S., & Stocks, B. J. (1987). A logistic model for predicting daily people-caused forest fire occurrence in Ontario. Canadian Journal of Forest Research, 17(5), 394-401. doi:10.1139/x87-068Martínez, J., Vega-Garcia, C., & Chuvieco, E. (2009). Human-caused wildfire risk rating for prevention planning in Spain. Journal of Environmental Management, 90(2), 1241-1252. doi:10.1016/j.jenvman.2008.07.005Moffett, A., Garson, J., & Sarkar, S. (2005). MultCSync: a software package for incorporating multiple criteria in conservation planning. Environmental Modelling & Software, 20(10), 1315-1322. doi:10.1016/j.envsoft.2004.10.001Nieto, H., Aguado, I., Chuvieco, E., & Sandholt, I. (2010). 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Wildland fire probabilities estimated from weather model-deduced monthly mean fire danger indices. International Journal of Wildland Fire, 17(3), 305. doi:10.1071/wf06162Romero-Calcerrada, R., Novillo, C. J., Millington, J. D. A., & Gomez-Jimenez, I. (2008). GIS analysis of spatial patterns of human-caused wildfire ignition risk in the SW of Madrid (Central Spain). Landscape Ecology, 23(3), 341-354. doi:10.1007/s10980-008-9190-2Saaty, T. L. (1987). RANK GENERATION, PRESERVATION, AND REVERSAL IN THE ANALYTIC HIERARCHY DECISION PROCESS. Decision Sciences, 18(2), 157-177. doi:10.1111/j.1540-5915.1987.tb01514.xSahin, Y. G., & Ince, T. (2009). Early Forest Fire Detection Using Radio-Acoustic Sounding System. Sensors, 9(3), 1485-1498. doi:10.3390/s90301485López, A. S., San-Miguel-Ayanz, J., & Burgan, R. E. (2002). Integration of satellite sensor data, fuel type maps and meteorological observations for evaluation of forest fire risk at the pan-European scale. 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    Genome Sequence and Comparative Genome Analysis of Lactobacillus casei: Insights into Their Niche-Associated Evolution

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    Lactobacillus casei is remarkably adaptable to diverse habitats and widely used in the food industry. To reveal the genomic features that contribute to its broad ecological adaptability and examine the evolution of the species, the genome sequence of L. casei ATCC 334 is analyzed and compared with other sequenced lactobacilli. This analysis reveals that ATCC 334 contains a high number of coding sequences involved in carbohydrate utilization and transcriptional regulation, reflecting its requirement for dealing with diverse environmental conditions. A comparison of the genome sequences of ATCC 334 to L. casei BL23 reveals 12 and 19 genomic islands, respectively. For a broader assessment of the genetic variability within L. casei, gene content of 21 L. casei strains isolated from various habitats (cheeses, n = 7; plant materials, n = 8; and human sources, n = 6) was examined by comparative genome hybridization with an ATCC 334-based microarray. This analysis resulted in identification of 25 hypervariable regions. One of these regions contains an overrepresentation of genes involved in carbohydrate utilization and transcriptional regulation and was thus proposed as a lifestyle adaptation island. Differences in L. casei genome inventory reveal both gene gain and gene decay. Gene gain, via acquisition of genomic islands, likely confers a fitness benefit in specific habitats. Gene decay, that is, loss of unnecessary ancestral traits, is observed in the cheese isolates and likely results in enhanced fitness in the dairy niche. This study gives the first picture of the stable versus variable regions in L. casei and provides valuable insights into evolution, lifestyle adaptation, and metabolic diversity of L. casei

    The stress of starvation: glucocorticoid restraint of beta cell development

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    Developmental insults during gestation, such as under-nutrition, are known to restrict the number of beta cells that form in the fetal pancreas and are maintained in adulthood, leading to increased risk of type 2 diabetes. There are now substantial data indicating that glucocorticoids mediate this effect of under-nutrition on beta cell mass and that even at physiological levels they restrain fetal beta cell development in utero. There are emerging clues that this occurs downstream of endocrine commitment by neurogenin 3 but prior to terminal beta cell differentiation. Deciphering the precise mechanism will be important as it might unveil new pathways by which to manipulate beta cell mass that could be exploited as novel therapies for patients with diabetes

    Downregulation of urokinase plasminogen activator receptor expression inhibits Erk signalling with concomitant suppression of invasiveness due to loss of uPAR–β1 integrin complex in colon cancer cells

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    Cancer invasion is regulated by cell surface proteinases and adhesion molecules. Interaction between specific cell surface molecules such as urokinase plasminogen activator receptor (uPAR) and integrins is crucial for tumour invasion and metastasis. In this study, we examined whether uPAR and beta1 integrin form a functional complex to mediate signalling required for tumour invasion. We assessed the expression of uPAR/beta1 integrin complex, Erk signalling pathway, adhesion, uPA and matrix metalloproteinase (MMP) expression, migration/invasion and matrix degradation in a colon cancer cell line in which uPAR expression was modified. Antisense inhibition of the cell surface expression of uPAR by 50% in human colon carcinoma HCT116 cells (A/S) suppressed Erk-MAP kinase activity by two-fold. Urokinase plasminogen activator receptor antisense treatment of HCT116 cells was associated with a 1.3-fold inhibition of adhesion, approximately four-fold suppression of HMW-uPA secretion and inhibition of pro-MMP-9 secretion. At a functional level, uPAR antisense resulted in a four-fold decline in migration/invasion and abatement of plasmin-mediated matrix degradation. In empty vector-transfected cells (mock), uPA strongly elevated basal Erk activation. In contrast, in A/S cells, uPA induction of Erk activation was not observed. Urokinase plasminogen activator receptor associated with beta1 integrin in mock-transfected cells. Disruption of uPAR-beta1 integrin complex in mock-transfected cells with a specific peptide (P25) inhibited uPA-mediated Erk-MAP kinase pathway and inhibited migration/invasion and plasmin-dependent matrix degradation through suppression of pro-MMP-9/MMP-2 expression. This novel paradigm of uPAR-integrin signalling may afford opportunities for alternative therapeutic strategies for the treatment of cancer

    Chromatin Organization in Sperm May Be the Major Functional Consequence of Base Composition Variation in the Human Genome

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    Chromatin in sperm is different from that in other cells, with most of the genome packaged by protamines not nucleosomes. Nucleosomes are, however, retained at some genomic sites, where they have the potential to transmit paternal epigenetic information. It is not understood how this retention is specified. Here we show that base composition is the major determinant of nucleosome retention in human sperm, predicting retention very well in both genic and non-genic regions of the genome. The retention of nucleosomes at GC-rich sequences with high intrinsic nucleosome affinity accounts for the previously reported retention at transcription start sites and at genes that regulate development. It also means that nucleosomes are retained at the start sites of most housekeeping genes. We also report a striking link between the retention of nucleosomes in sperm and the establishment of DNA methylation-free regions in the early embryo. Taken together, this suggests that paternal nucleosome transmission may facilitate robust gene regulation in the early embryo. We propose that chromatin organization in the male germline, rather than in somatic cells, is the major functional consequence of fine-scale base composition variation in the human genome. The selective pressure driving base composition evolution in mammals could, therefore, be the need to transmit paternal epigenetic information to the zygote
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