Modelling credit spreads with time volatility, skewness, and kurtosis

This paper seeks to identify the macroeconomic and financial factors that drive credit spreads on bond indices in the US credit market. To overcome the idiosyncratic nature of credit spread data reflected in time varying volatility, skewness and thick tails, it proposes asymmetric GARCH models with alternative probability density functions. The results show that credit spread changes are mainly explained by the interest rate and interest rate volatility, the slope of the yield curve, stock market returns and volatility, the state of liquidity in the corporate bond market and, a heretofore overlooked variable, the foreign exchange rate. They also confirm that the asymmetric GARCH models and Student-t distributions are systematically superior to the conventional GARCH model and the normal distribution in in-sample and out-of-sample testing

Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica

Genome duplication is widespread in wild and crop plants. However, little is known about genome-wide selection in polyploids due to the complexity of duplicated genomes. In polyploids, the patterns of purifying selection and adaptive substitutions may be affected by masking owing to duplicated genes or homeologs as well as effective population size. Here, we resequence 25 accessions of the allotetraploid Arabidopsis kamchatica, which is derived from the diploid species A. halleri and A. lyrata. We observe a reduction in purifying selection compared with the parental species. Interestingly, proportions of adaptive non-synonymous substitutions are significantly positive in contrast to most plant species. A recurrent pattern observed in both frequency and divergence–diversity neutrality tests is that the genome-wide distributions of both subgenomes are similar, but the correlation between homeologous pairs is low. This may increase the opportunity of different evolutionary trajectories such as in the HMA4 gene involved in heavy metal hyperaccumulation

R-SNARE Homolog MoSec22 Is Required for Conidiogenesis, Cell Wall Integrity, and Pathogenesis of Magnaporthe oryzae

Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins mediate intracellular vesicle fusion, which is an essential cellular process of the eukaryotic cells. To investigate the role of SNARE proteins in the rice blast fungus Magnaporthe oryzae, MoSec22, an ortholog of Saccharomyces cerevisiae SNARE protein Sec22, was identified and the MoSEC22 gene disrupted. MoSec22 restored a S. cerevisiae sec22 mutant in resistance to cell wall perturbing agents, and the ΔMosec22 mutant also exhibited defects in mycelial growth, conidial production, and infection of the host plant. Treatment with oxidative stress inducers indicated a breach in cell wall integrity, and staining and quantification assays suggested abnormal chitin deposition on the lateral walls of hyphae of the ΔMosec22 mutant. Furthermore, hypersensitivity to the oxidative stress correlates with the reduced expression of the extracellular enzymes peroxidases and laccases. Our study thus provides new evidence on the conserved function of Sec22 among fungal organisms and indicates that MoSec22 has a role in maintaining cell wall integrity affecting the growth, morphogenesis, and virulence of M. oryzae

Crocins with high levels of sugar conjugation contribute to the yellow colours of early-spring flowering

Crocus sativus is the source of saffron spice, the processed stigma which accumulates glucosylated apocarotenoids known as crocins. Crocins are found in the stigmas of other Crocuses, determining the colourations observed from pale yellow to dark red. By contrast, tepals in Crocus species display a wider diversity of colours which range from purple, blue, yellow to white. In this study, we investigated whether the contribution of crocins to colour extends from stigmas to the tepals of yellow Crocus species. Tepals from seven species were analysed by UPLC-PDA and ESI-Q-TOF-MS/MS revealing for the first time the presence of highly glucosylated crocins in this tissue. beta-carotene was found to be the precursor of these crocins and some of them were found to contain rhamnose, never before reported. When crocin profiles from tepals were compared with those from stigmas, clear differences were found, including the presence of new apocarotenoids in stigmas. Furthermore, each species showed a characteristic profile which was not correlated with the phylogenetic relationship among species. While gene expression analysis in tepals of genes involved in carotenoid metabolism showed that phytoene synthase was a key enzyme in apocarotenoid biosynthesis in tepals. Expression of a crocetin glucosyltransferase, previously identified in saffron, was detected in all the samples. The presence of crocins in tepals is compatible with the role of chromophores to attract pollinators. The identification of tepals as new sources of crocins is of special interest given their wide range of applications in medicine, cosmetics and colouring industries.The laboratory is supported by the Spanish Ministerio de Ciencia e Innovacion (BIO2009-07803) and participates in the IBERCAROT network (112RT0445). Dr. Ahrazem was funded by FPCYTA through the INCRECYT Programme. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Rubio-Moraga, A.; Ahrazem, O.; Rambla Nebot, JL.; Granell Richart, A.; Gómez Gómez, L. (2013). Crocins with high levels of sugar conjugation contribute to the yellow colours of early-spring flowering. PLoS ONE. 8(9):71946-71946. https://doi.org/10.1371/journal.pone.0071946S719467194689Auldridge, M. E., McCarty, D. R., & Klee, H. J. (2006). Plant carotenoid cleavage oxygenases and their apocarotenoid products. Current Opinion in Plant Biology, 9(3), 315-321. doi:10.1016/j.pbi.2006.03.005AKIYAMA, K. (2007). Chemical Identification and Functional Analysis of Apocarotenoids Involved in the Development of Arbuscular Mycorrhizal Symbiosis. Bioscience, Biotechnology, and Biochemistry, 71(6), 1405-1414. doi:10.1271/bbb.70023Lendzemo, V. W., Kuyper, T. W., Matusova, R., Bouwmeester, H. J., & Ast, A. V. (2007). 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Planta, 219(6), 955-966. doi:10.1007/s00425-004-1299-1Harpke, D., Meng, S., Rutten, T., Kerndorff, H., & Blattner, F. R. (2013). Phylogeny of Crocus (Iridaceae) based on one chloroplast and two nuclear loci: Ancient hybridization and chromosome number evolution. Molecular Phylogenetics and Evolution, 66(3), 617-627. doi:10.1016/j.ympev.2012.10.007Mathew B (1982) The crocus - A revision of the Genus crocus; Batsford B, editor. London.Nørbæk, R., Nielsen, K., & Kondo, T. (2002). Anthocyanins from flowers of Cichorium intybus. Phytochemistry, 60(4), 357-359. doi:10.1016/s0031-9422(02)00055-9Zhu, C., Bai, C., Sanahuja, G., Yuan, D., Farré, G., Naqvi, S., … Christou, P. (2010). The regulation of carotenoid pigmentation in flowers. Archives of Biochemistry and Biophysics, 504(1), 132-141. doi:10.1016/j.abb.2010.07.028OHMIYA, A. (2011). Diversity of Carotenoid Composition in Flower Petals. 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Study of «Redhaven» peach and its white-fleshed mutant suggests a key role of CCD4 carotenoid dioxygenase in carotenoid and norisoprenoid volatile metabolism. BMC Plant Biology, 11(1), 24. doi:10.1186/1471-2229-11-24Campbell, R., Ducreux, L. J. M., Morris, W. L., Morris, J. A., Suttle, J. C., Ramsay, G., … Taylor, M. A. (2010). The Metabolic and Developmental Roles of Carotenoid Cleavage Dioxygenase4 from Potato. Plant Physiology, 154(2), 656-664. doi:10.1104/pp.110.158733Ahrazem, O., Rubio-Moraga, A., Lopez, R. C., & Gomez-Gomez, L. (2009). The expression of a chromoplast-specific lycopene beta cyclase gene is involved in the high production of saffron’s apocarotenoid precursors. Journal of Experimental Botany, 61(1), 105-119. doi:10.1093/jxb/erp283Ahrazem, O., Rubio-Moraga, A., Trapero, A., & Gomez-Gomez, L. (2011). Developmental and stress regulation of gene expression for a 9-cis-epoxycarotenoid dioxygenase, CstNCED, isolated from Crocus sativus stigmas. Journal of Experimental Botany, 63(2), 681-694. doi:10.1093/jxb/err293Moraga, Á., Mozos, A., Ahrazem, O., & Gómez-Gómez, L. (2009). Cloning and characterization of a glucosyltransferase from Crocus sativus stigmas involved in flavonoid glucosylation. BMC Plant Biology, 9(1), 109. doi:10.1186/1471-2229-9-109Tarantilis, P. A., Tsoupras, G., & Polissiou, M. (1995). Determination of saffron (Crocus sativus L.) components in crude plant extract using high-performance liquid chromatography-UV-visible photodiode-array detection-mass spectrometry. Journal of Chromatography A, 699(1-2), 107-118. doi:10.1016/0021-9673(95)00044-nWalter, M. H., Fester, T., & Strack, D. (2000). Arbuscular mycorrhizal fungi induce the non-mevalonate methylerythritol phosphate pathway of isoprenoid biosynthesis correlated with accumulation of the «yellow pigment» and other apocarotenoids. The Plant Journal, 21(6), 571-578. doi:10.1046/j.1365-313x.2000.00708.xGómez-Miranda, B., Rupérez, P., & Leal, J. A. (1981). 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Identification of a yellow pigment formed in maize roots upon mycorrhizal colonization. Phytochemistry, 38(1), 53-55. doi:10.1016/0031-9422(94)00538-5Rychener, M., Bigler, P., & Pfander, H. (1984). Isolierung und Strukturaufkl�rung von Neapolitanose (O-?-D-Glucopyranosyl-(1?2)-O-[?-D-glucopyranosyl-(1?6)]-(D-glucose), einem neuen Trisaccharid aus den Stempeln von Gartenkrokussen (Crocus neapolitanus var.). Helvetica Chimica Acta, 67(2), 386-391. doi:10.1002/hlca.19840670205Lu, S., Van Eck, J., Zhou, X., Lopez, A. B., O’Halloran, D. M., Cosman, K. M., … Li, L. (2006). The Cauliflower Or Gene Encodes a DnaJ Cysteine-Rich Domain-Containing Protein That Mediates High Levels of β-Carotene Accumulation. The Plant Cell, 18(12), 3594-3605. doi:10.1105/tpc.106.046417Rubio, A., Rambla, J. L., Santaella, M., Gómez, M. D., Orzaez, D., Granell, A., & Gómez-Gómez, L. (2008). Cytosolic and Plastoglobule-targeted Carotenoid Dioxygenases fromCrocus sativusAre Both Involved in β-Ionone Release. 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Modeling protein network evolution under genome duplication and domain shuffling

<p>Abstract</p> <p>Background</p> <p>Successive whole genome duplications have recently been firmly established in all major eukaryote kingdoms. Such <it>exponential </it>evolutionary processes must have largely contributed to shape the topology of protein-protein interaction (PPI) networks by outweighing, in particular, all <it>time-linear </it>network growths modeled so far.</p> <p>Results</p> <p>We propose and solve a mathematical model of PPI network evolution under successive genome duplications. This demonstrates, from first principles, that evolutionary conservation and scale-free topology are intrinsically linked properties of PPI networks and emerge from <it>i) </it>prevailing <it>exponential </it>network dynamics under duplication and <it>ii) asymmetric divergence </it>of gene duplicates. While required, we argue that this asymmetric divergence arises, in fact, spontaneously at the level of protein-binding sites. This supports a refined model of PPI network evolution in terms of protein domains under exponential and asymmetric duplication/divergence dynamics, with multidomain proteins underlying the combinatorial formation of protein complexes. Genome duplication then provides a powerful source of PPI network innovation by promoting local rearrangements of multidomain proteins on a genome wide scale. Yet, we show that the overall conservation and topology of PPI networks are robust to extensive domain shuffling of multidomain proteins as well as to finer details of protein interaction and evolution. Finally, large scale features of <it>direct </it>and <it>indirect </it>PPI networks of <it>S. cerevisiae </it>are well reproduced numerically with only two adjusted parameters of clear biological significance (<it>i.e</it>. network effective growth rate and average number of protein-binding domains per protein).</p> <p>Conclusion</p> <p>This study demonstrates the statistical consequences of genome duplication and domain shuffling on the conservation and topology of PPI networks over a broad evolutionary scale across eukaryote kingdoms. In particular, scale-free topologies of PPI networks, which are found to be robust to extensive shuffling of protein domains, appear to be a simple consequence of the conservation of protein-binding domains under asymmetric duplication/divergence dynamics in the course of evolution.</p

Approaches in biotechnological applications of natural polymers

Natural polymers, such as gums and mucilage, are biocompatible, cheap, easily available and non-toxic materials of native origin. These polymers are increasingly preferred over synthetic materials for industrial applications due to their intrinsic properties, as well as they are considered alternative sources of raw materials since they present characteristics of sustainability, biodegradability and biosafety. As definition, gums and mucilages are polysaccharides or complex carbohydrates consisting of one or more monosaccharides or their derivatives linked in bewildering variety of linkages and structures. Natural gums are considered polysaccharides naturally occurring in varieties of plant seeds and exudates, tree or shrub exudates, seaweed extracts, fungi, bacteria, and animal sources. Water-soluble gums, also known as hydrocolloids, are considered exudates and are pathological products; therefore, they do not form a part of cell wall. On the other hand, mucilages are part of cell and physiological products. It is important to highlight that gums represent the largest amounts of polymer materials derived from plants. Gums have enormously large and broad applications in both food and non-food industries, being commonly used as thickening, binding, emulsifying, suspending, stabilizing agents and matrices for drug release in pharmaceutical and cosmetic industries. In the food industry, their gelling properties and the ability to mold edible films and coatings are extensively studied. The use of gums depends on the intrinsic properties that they provide, often at costs below those of synthetic polymers. For upgrading the value of gums, they are being processed into various forms, including the most recent nanomaterials, for various biotechnological applications. Thus, the main natural polymers including galactomannans, cellulose, chitin, agar, carrageenan, alginate, cashew gum, pectin and starch, in addition to the current researches about them are reviewed in this article.. }To the Conselho Nacional de Desenvolvimento Cientfíico e Tecnológico (CNPq) for fellowships (LCBBC and MGCC) and the Coordenação de Aperfeiçoamento de Pessoal de Nvíel Superior (CAPES) (PBSA). This study was supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit, the Project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124-FEDER-027462) and COMPETE 2020 (POCI-01-0145-FEDER-006684) (JAT)

Assembling a consensus on actinic cheilitis: A Delphi study

Aims To discuss the terminology to define and classify actinic cheilitis (AC) and to build a consensus on the diagnostic and therapeutic approaches to AC. Methods Two-round Delphi study using a questionnaire including 34 closed sentences (9 on terminology and taxonomy, 5 on potential for malignant transformation, 12 on diagnostic aspects, 8 on treatment) and 8 open questions. Experts' agreement was rated using a Likert scale (1-7). Results A consensus was reached on 24 out 34 statements (73.5%) and on 5 out of 8 (62.5%) close-ended questions. The response rate was identical in both rounds (attrition of 0%). AC is the term with the highest agreement (median of 7 (strongly agree; IQR: 6-7)) and the lowest dispersion (VC = 21.33). 'Potentially malignant disorder' was the preferred classification group for AC (median of 7) and 85.6% of participants showing some level of agreement (CV < 50). Experts (66.75%) consider AC a clinical term (median: 7; IQR: 4-7) and believe definitive diagnosis can be made clinically (median: 6; IQR: 5-7), particularly by inspection and palpation (median: 5; IQR: 4-6). Histopathological confirmation is mandatory for the management of AC (median: 5; IQR: 2.5-7), even for homogeneous lesions (median: 5; IQR: 3.5-6). Consensus was reached on all treatment statements (VC < 50). Conclusions AC is a potentially malignant disorder with a significant lack of agreement on diagnostic criteria, procedures, biopsy indications and the importance of techniques to assist in biopsy. A consensus was reached on nomenclature and management of this disorder