Effect of Puumala hantavirus infection on human umbilical vein endothelial cell hemostatic function: platelet interactions, increased tissue factor expression and fibrinolysis regulator release

201

Microsatellite markers spanning the apple ( Malus x domestica Borkh.) genome

A new set of 148 apple microsatellite markers has been developed and mapped on the apple reference linkage map Fiesta x Discovery. One-hundred and seventeen markers were developed from genomic libraries enriched with the repeats GA, GT, AAG, AAC and ATC; 31 were developed from EST sequences. Markers derived from sequences containing dinucleotide repeats were generally more polymorphic than sequences containing trinucleotide repeats. Additional eight SSRs from published apple, pear, and Sorbus torminalis SSRs, whose position on the apple genome was unknown, have also been mapped. The transferability of SSRs across Maloideae species resulted in being efficient with 41% of the markers successfully transferred. For all 156 SSRs, the primer sequences, repeat type, map position, and quality of the amplification products are reported. Also presented are allele sizes, ranges, and number of SSRs found in a set of nine cultivars. All this information and those of the previous CH-SSR series can be searched at the apple SSR database ( http://www.hidras.unimi.it ) to which updates and comments can be added. A large number of apple ESTs containing SSR repeats are available and should be used for the development of new apple SSRs. The apple SSR database is also meant to become an international platform for coordinating this effort. The increased coverage of the apple genome with SSRs allowed the selection of a set of 86 reliable, highly polymorphic, and overall the apple genome well-scattered SSRs. These SSRs cover about 85% of the genome with an average distance of one marker per 15c

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development

Collaborative project to identify direct and distant pedigree relationships in apple

Pedigree information is fundamentally important in breeding programs, enabling breeders to know the source of valuable attributes and underlying alleles and to enlarge genetic diversity in a directed way. Many apple cultivars are related to each other through both recent and distant common ancestors. As apple trees are clonally propagated, long-lived, and widely adapted, many of the ancestors of modern cultivars are still present in global germplasm collections. Use of apple SNP arrays enables identification of direct and distant pedigree relationships with precision. An example is the elucidation of the \u27Honeycrisp\u27 pedigree using the 8K SNP array, which enabled further findings regarding the inheritance of important alleles for traits including scab resistance and soft scald susceptibility. To facilitate more discoveries across apple germplasm, a large-scale collaborative apple pedigree reconstruction project has been initiated. This project utilizes output from the Illumina Infinium 20K and Affymetrix Axiom 480K apple SNP arrays, a high quality genetic linkage map for the 20K array SNPs, and a data curation pipeline developed through the FruitBreedomics and RosBREED projects. Techniques using shared haplotype length statistics will be used alongside historical information to deduce distant pedigree relationships. The project involves various experts, germplasm collections, and academic institutions around the world and is open for further extension. It will provide findings useful for breeding programs, germplasm collections, geneticists, and historians

An urban perinatal health programme of strategies to improve perinatal health

Promotion of a healthy pregnancy is a top priority of the health care policy in many European countries. Perinatal mortality is an important indicator of the success of this policy. Recently, it was shown that the Netherlands has relatively high perinatal death rates when compared to other European countries. This is in particular true for large cities where perinatal mortality rates are 20-50% higher than elsewhere. Consequently in the Netherlands, there is heated debate on how to tackle these problems. Without the introduction of measures throughout the entire perinatal health care chain, pregnancy outcomes are difficult to improve. With the support of health care professionals, the City of Rotterdam and the Erasmus University Medical Centre have taken the initiative to develop an urban perinatal health programme called 'Ready for a Baby'. The main objective of this municipal 10-year programme is to improve perinatal health and to reduce perinatal mortality in all districts to at least the current national average of 10 per 1000. Key elements are the understanding of the mechanisms of the large health differences between women living in deprived and nondeprived urban areas. Risk guided care, orientation towards shared-care and improvement of collaborations between health care professionals shapes the interventions that are being developed. Major attention is given to the development of methods to improve risk-selection before and during pregnancy and methods to reach low-educated and immigrant groups

Microbial Translocation Is Associated with Extensive Immune Activation in Dengue Virus Infected Patients with Severe Disease

Background:Severe dengue virus (DENV) disease is associated with extensive immune activation, characterized by a cytokine storm. Previously, elevated lipopolysaccharide (LPS) levels in dengue were found to correlate with clinical disease severity. In the present cross-sectional study we identified markers of microbial translocation and immune activation, which are associated with severe manifestations of DENV infection.Methods:Serum samples from DENV-infected patients were collected during the outbreak in 2010 in the State of São Paulo, Brazil. Levels of LPS, lipopolysaccharide binding protein (LBP), soluble CD14 (sCD14) and IgM and IgG endotoxin core antibodies were determined by ELISA. Thirty cytokines were quantified using a multiplex luminex system. Patients were classified according to the 2009 WHO classification and the occurrence of plasma leakage/shock and hemorrhage. Moreover, a (non-supervised) cluster analysis based on the expression of the quantified cytokines was applied to identify groups of patients with similar cytokine profiles. Markers of microbial translocation were linked to groups with similar clinical disease severity and clusters with similar cytokine profiles.Results:Cluster analysis indicated that LPS levels were significantly increased in patients with a profound pro-inflammatory cytokine profile. LBP and sCD14 showed significantly increased levels in patients with severe disease in the clinical classification and in patients with severe inflammation in the cluster analysis. With both the clinical classification and the cluster analysis, levels of IL-6, IL-8, sIL-2R, MCP-1, RANTES, HGF, G-CSF and EGF were associated with severe disease.Conclusions:The present study provides evidence that both microbial translocation and extensive immune activation occur during severe DENV infection and may play an important role in the pathogenesis

Development and test of 21 multiplex PCRs composed of SSRs spanning most of the apple genome

A series of 21 multiplex (MP) polymerase chain reactions containing simple sequence repeat (SSR) markers spanning most of the apple genome has been developed. Eighty-eight SSR markers, well distributed over all 17 linkage groups (LGs), have been selected. Eighty-four of them were included in 21 different MPs while four could not be included in any MPs. The 21 MPs were then used to genotype approximately 2,000 DNA samples from the European High-quality Disease-Resistant Apples for a Sustainable agriculture project. Two SSRs (CH01d03 and NZAL08) were discarded at an early stage as they did not produce stable amplifications in the MPs, while the scoring of the multilocus (ML) SSR Hi07d11 and CN44794 was too complex for large-scale genotyping. The testing of the remaining 80 SSRs over a large number of different genotypes allowed: (1) a better estimation of their level of polymorphism; as well as of (2) the size range of the alleles amplified; (3) the identification of additional unmapped loci of some ML SSRs; (4) the development of methods to assign alleles to the different loci of ML SSRs and (5) conditions at which an SSR previously described as ML would amplify alleles of a single locus to be determined. These data resulted in the selection of 75 SSRs out of the 80 that are well suited and recommended for large genotyping project

Alguns dados sobre a Fauna entomológica da ilha das Flores - Açores

IV Expedição Científica do Departamento de Biologia - Flores 1989Com este trabalho, realizado em Julho de 1989 nas Flores - a ilha mais ocidental do Arquipélago dos Açores -, acrescentaram-se onze espécies de Lepidópteros à lista referenciada para aquela ilha, pertencendo uma à família Lycaenidae (Lampides boeticus L.), oito a familia Noctuidae (Agrotis ipsilon HFN., Brotolomia meticulosa L., Chrysodeixis chalcites ESPER., Heliothis armigera HBN., Noctua atlantica WARREN, Noctua pronuba L., Peridroma saucia HBN., Sesamia nonagrioides LEF.), uma à família Nymphalidae (Vanessa atalanta L.) e uma a família Pyralidae (Glyphodes unionalis HBN.). Entre os demais insectos, foram identificadas cerca de duas dezenas e meia de espécies, distribuídas pelas Ordens Dermaptera, Orthoptera, Dictyoptera, Heteroptera, Homoptera, Coleoptera, Neuroptera, Diptera, Hymenoptera e Collembola. Salienta-se ainda a importância, do ponto de vista agronómico, das pragas Mythimna unipuncta (HAWORTH) e Xestia c-nigrun L. naquela ilha.RÉSUMÉ: Avec ce travail, réalisé en Juillet 1989 a Flores - l'île plus occidental de l'archipel des Açores, onze espèces de Lépidoptères ont été ajoutées à la liste des espèces connus pour cette île, dont une appartient a la famille Lycaenidae (Lampides boelicus L.), huit à la famille Noctuidae (Agrotis ipsilon HFN., Brotolomia meticulosa L. Chrysodeicis chalcites ESPER., Heliothis armigera HBN., Noctua atlantica WARREN, Noctua pronuba L., Peridroma saucia HBN., Sesamia nonagrioides LEF.), une à la famille Nymphalidae (Vanessa atalanta L.) et une à la famille Pyralidae (Glyphodes unionalis HBN.). Parmi les autres insects ont été identifiés environ deux dizaines et demie d'espèces, lesquelles sont réparties par les Ordres Dermaptera, Orthoptera, Dictyoptera, Heteroptera, Homoptera, Coleoptera, Neuroptera, Diptera, Hymenoptera et Collembola. On remarque I'importance, du point de vue agronomique, des ravageurs Mythimna unipuncra (HAWORTH) et Xestia c-nigrum L. dans cette île

An integrated approach for increasing breeding efficiency in apple and peach in Europe

Despite the availability of whole genome sequences of apple and peach, there has been a considerable gap between genomics and breeding. To bridge the gap, the European Union funded the FruitBreedomics project (March 2011 to August 2015) involving 28 research institutes and private companies. Three complementary approaches were pursued: (i) tool and software development, (ii) deciphering genetic control of main horticultural traits taking into account allelic diversity and (iii) developing plant materials, tools and methodologies for breeders. Decisive breakthroughs were made including the making available of ready-to-go DNA diagnostic tests for Marker Assisted Breeding, development of new, dense SNP arrays in apple and peach, new phenotypic methods for some complex traits, software for gene/QTL discovery on breeding germplasm via Pedigree Based Analysis (PBA). This resulted in the discovery of highly predictive molecular markers for traits of horticultural interest via PBA and via Genome Wide Association Studies (GWAS) on several European genebank collections. FruitBreedomics also developed pre-breeding plant materials in which multiple sources of resistance were pyramided and software that can support breeders in their selection activities. Through FruitBreedomics, significant progresses were made in the field of apple and peach breeding, genetics, genomics and bioinformatics of which advantage will be made by breeders, germplasm curators and scientists. A major part of the data collected during the project has been stored in the FruitBreedomics database and has been made available to the public. This review covers the scientific discoveries made in this major endeavour, and perspective in the apple and peach breeding and genomics in Europe and beyond

QTL dynamics for fruit firmness and softening around an ethylene-dependent polygalacturonase gene in apple (Malus×domestica Borkh.)

Apple fruit are well known for their storage life, although a wide range of flesh softening occurs among cultivars. Loss of firmness is genetically coordinated by the action of several cell wall enzymes, including polygalacturonase (PG) which depolymerizes cell wall pectin. By the analysis of ‘Fuji’ (Fj) and ‘Mondial Gala’ (MG), two apple cultivars characterized by a distinctive ripening behaviour, the involvement of Md-PG1 in the fruit softening process was confirmed to be ethylene dependent by its transcript being down-regulated by 1-methylcyclopropene treatment in MG and in the low ethylene-producing cultivar Fj. Comparing the PG sequence of MG and Fj, a single nucleotide polymorphism (SNP) was discovered. Segregation of the Md-PG1SNP marker within a full-sib population, obtained by crossing Fj and MG, positioned Md-PG1 in the linkage group 10 of MG, co-located with a quantitative trait locus (QTL) identified for fruit firmness in post-harvest ripening. Fruit firmness and softening analysed in different stages, from harvest to post-storage, determined a shift of the QTL from the top of this linkage group to the bottom, where Md-ACO1, a gene involved in ethylene biosynthesis in apple, is mapped. This PG–ethylene-related gene has beeen positioned in the apple genome on chromosome 10, which contains several QTLs controlling fruit firmness and softening, and the interplay among the allelotypes of the linked loci should be considered in the design of a marker-assisted selection breeding scheme for apple texture