Expert knowledge for translating land cover/use maps to General Habitat Categories (GHC)

Monitoring biodiversity at the level of habitats and landscape is becoming widespread in Europe and elsewhere as countries establish international and national habitat conservation policies and monitoring systems. Earth Observation (EO) data offers a potential solution to long-term biodiversity monitoring through direct mapping of habitats or by integrating Land Cover/Use (LC/LU) maps with contextual spatial information and in situ data. Therefore, it appears necessary to develop an automatic/semi-automatic translation framework of LC/LU classes to habitat classes, but also challenging due to discrepancies in domain definitions. In the context of the FP7 BIO_SOS (www.biosos.eu) project, the authors demonstrated the feasibility of the Food and Agricultural Organization Land Cover Classification System (LCCS) taxonomy to habitat class translation. They also developed a framework to automatically translate LCCS classes into the recently proposed General Habitat Categories classification system, able to provide an exhaustive typology of habitat types, ranging from natural ecosystems to urban areas around the globe. However discrepancies in terminology, plant height criteria and basic principles between the two mapping domains inducing a number of one-to-many and many-to-many relations were identified, revealing the need of additional ecological expert knowledge to resolve the ambiguities. This paper illustrates how class phenology, class topological arrangement in the landscape, class spectral signature from multi-temporal Very High spatial Resolution (VHR) satellite imagery and plant height measurements can be used to resolve such ambiguities. Concerning plant height, this paper also compares the mapping results obtained by using accurate values extracted from LIght Detection And Ranging (LIDAR) data and by exploiting EO data texture features (i.e. entropy) as a proxy of plant height information, when LIDAR data are not available. An application for two Natura 2000 coastal sites in Southern Italy is discussed.     

夏季的池塘

池塘中形形色色的生物在夏季达到了生命活动的高峰。植物在炎热的天气和强烈的阳光下生长快速，并且会开出美艳的花朵，吸引那些以植物为生存环境的动物。您看那蜻蜓，它的变形过程是多么美妙迷人，从生存在水中的幼虫-变为贴附在植物上的蛹-最后成为了一个会飞的昆虫，它在离开水之后依然是您池塘忠实的客人（和捕蝇能手）。     

Molecular genetic mapping of peach

Summary A project to develop a linkage map of the peach (Prunus persica) genome is underway using an F2 population segregating for several morphological characters and pest resistance e.g., nectarine (g), weeping shape (pl) and aphid resistance (Rml). The RAPID technique was used to analyse 270 plants. Linkage analysis of the F2 population was performed using the MAPMAKER software. Eight linkage groups were established and RAPID markers flanking thepl gene were found.     

Comparison of different pollen viability assays to evaluate pollen fertility of potato dihaploids

Summary The main obstacle in breeding potato (Solanum tuberosum L.) dihaploids is the severe limitation of male fertility. To determine pollen viability assays that correlate well to fertility in crosses, results of five different pollen viability assays were compared by correlation analysis with fruit and seed set characters in test crosses, and to pollen tube growth in situ (PL-test). The methods used were: staining the pollen cells with carmino acetic acid (CAA-test); in vitro pollen germination (PG-test); and detection of pollen staining rates after incubation with fluoresceine diacetate (FDA-test), 2-3-5-triphenyle tetrazolium chloride (TTC-test), and 5-bromo-4-chloro-3-indolyle--galactoside (X-Gal-test).The results of test crosses and pollen tube growth in situ correlated with the results of all other assays with the following ranking, from highest to lowest: enzyme activity assays (X-Gal-test, FDA-test, TTC-test), in vitro pollen germination (PG-test), and pollen staining by CAA. The newly developed X-Gal-test for monitoring -galactosidase activity showed the least variation of all assays investigated. Thus, this highly reproducible simple procedure is recommended for male fertility screening.Abbreviations B/F Berries obtained per 100 flowers - CAA Carmino acetic acid - FDA Fluoresceine diacetate - PG Pollen germination rate in vitro - PL Pollen tube growth in situ - S/B Seeds per berry - S/F Seeds per pollinated flower - TTC 2-3-5-triphenyle tetrazolium chloride - X-Gal 5-bromo-4-chloro-3-indolyle--galactoside     

Recent advances in molecular marker techniques: Insight into QTL mapping,GWAS and genomic selection in plants

Recent advances in sequencing technology have brought several novel platforms for marker development and subsequent genotyping. The high-throughput and cost effective marker techniques have changed the entire scenario of marker applications. The huge genotypic data obtained with next generation sequencing (NGS) also demands analytical tools, statistical advances, and comprehensive understanding to cope with breeding applications. In the present review, we discussed different available marker techniques, their strengths, and limitations. Emphasis was given on software tools, analytical pipelines, workbenches, and online resources available for marker development. Comparison of SNP genotyping involving complexity reduction techniques like GBS, RRL, RAD, and array-based platforms were presented in a view to describe suitability for specific purposes. We found that genotyping by whole genome re-sequencing has great potential, and could be a routine application in the near future with continuously decreasing cost of sequencing. Microsatellites, still a valuable option for breeders, have also advanced with NGS. Here a catalogue of tools for microsatellite evaluation in short sequence reads was provided. The most common applications of molecular marker like QTL mapping, genome-wide association mapping (GWAS), and genomic selection were highlighted. The present review will be helpful for the effective utilization of available resources and for the planning of crop improvement programs employing molecular marker techniques.     

Traces of human migrations in Helicobacter pylori populations

Helicobacter pylori, a chronic gastric pathogen of human beings, can be divided into seven populations and subpopulations with distinct geographical distributions. These modern populations derive their gene pools from ancestral populations that arose in Africa, Central Asia, and East Asia. Subsequent spread can be attributed to human migratory fluxes such as the prehistoric colonization of Polynesia and the Americas, the neolithic introduction of farming to Europe, the Bantu expansion within Africa, and the slave trade.     

Über die Zusammensetzung des Weizeneiweißes bei verschieden hohen N-Gaben

Zusammenfassung Es ist bei den Winterweizen-Sorten Hubertus und Austro Bankut festgestellt worden, daß die N-Düngung nur sehr kleine Unterschiede in der Aminosäurezusammensetzung des Weizeneiweißes hervorruft. Es ist jedoch auffallend, daß die meisten dieser kleinen Differenzen bei beiden Weizensorten beobachtet wurden: Steigt durch die N-Düngung der Eiweißgehalt der Körner, so erhöhen sich die Anteile von Prolin und Glutaminsäure im Weizeneiweiß und die Anteile von Lysin und Arginin nehmen etwas ab. Die anderen im Einzelfalle beobachteten Änderungen der Anteile von Histidin, Threonin und Valin kann man nicht als gesichert ansehen, sie bedürfen weiterer Untersuchungen.Wie eine Berechnung des EAA-Index nachOser zeigte, spielen die als Folge der N-Düngung beobachteten kleinen Differenzen der Aminosäurezusammensetzung des Weizeneiweißes bei der Beurteilung der Biologischen Wertigkeit des Weizenproteins keine Rolle.     

Quantitative genetic aspects of coat color in horses

The aim of this study was to estimate genetic parameters for coat color in horses. Besides defining coat color classes (gray, chestnut, bay, and black), the phenotypes were also measured quantitatively according to standardized international procedures (Commission Internationale de l'Eclairage L*, a*, b*), where L* describes lightness, a* describes color saturation from red to green, and b* describes color saturation from yellow to blue. The total color saturation was derived from a* and b* and referred to as Chroma. A total of 294 horses from the breeds Lipizzan, Nonius, Arabian Pure Bred, Shagya Arabian, and Gidran were measured at neck, shoulder, and belly. Heritabilities (within and between breeds or color classes) and repeatabilities were estimated using REML from univariate animal models defined separately for gray and nongray horses. For gray horses, the estimated within-breed heritabilities for L* ranged from 0.45 to 0.49 and for a*, b*, and Chroma from 0.09 to 0.52, indicating moderate polygenic effect. For nongray horses, between-color class heritabilities were high (0.70 to 0.85) and within-color class heritabilities were negligible (except for L* measured on neck and belly, 0.21 and 0.34, respectively). Additionally, the importance of L* was described by the relation with the total melanin content of horse coat hair; for gray and nongray horses, a strong negative linear relationship was detected (P < 0.01). The spectrometric measures and the results of this study demonstrate a possible approach to the estimation of the polygenic component involved in coat color inheritance.     

GFAJ-1 is an arsenate-resistant, phosphate-dependent organism

The bacterial isolate GFAJ-1 has been proposed to substitute arsenic for phosphorus to sustain growth. We have shown that GFAJ-1 is able to grow at low phosphate concentrations (1.7 μM), even in the presence of high concentrations of arsenate (40 mM), but lacks the ability to grow in phosphorus-depleted (<0.3 μM), arsenate-containing medium. High-resolution mass spectrometry analyses revealed that phosphorylated central metabolites and phosphorylated nucleic acids predominated. A few arsenylated compounds, including C6 sugar arsenates, were detected in extracts of GFAJ-1, when GFAJ-1 was incubated with arsenate, but further experiments showed they formed abiotically. Inductively coupled plasma mass spectrometry confirmed the presence of phosphorus in nucleic acid extracts, while arsenic could not be detected and was below 1 per mil relative to phosphorus. Taken together, we conclude that GFAJ-1 is an arsenate-resistant, but still a phosphate-dependent, bacterium.     

Analysis of the immunoproteome of Mycoplasma mycoides subsp. mycoides small colony type reveals immunogenic homologues to other known virulence traits in related Mycoplasma species

Contagious bovine pleuropneumonia (CBPP) caused by Mycoplasma mycoides subsp. mycoides small colony type (MmmSC) has been eradicated in the developed world, but it is still present in many countries of sub-Saharan Africa. After initially successful control measures in the 1960s it has been spreading due to a lack of money, fragmentation of veterinary services, uncontrolled cattle movement, insufficient vaccine efficacy and sensitivity of current diagnostic tests.In this study we used two-dimensional polyacrylamide gel electrophoresis followed by immunoblot with sera from MmmSC-infected animals and MALDI-ToF mass spectrometry to identify novel immunogenic proteins as candidate molecules for improved diagnostics and vaccines. We identified 24 immunogens recognized by pooled sera from experimentally infected cattle. Furthermore, a serum from an animal with acute clinical disease as well as severe pathomorphological lesions recognized 13 additional immunogens indicating variation in the antibody responses to CBPP amongst cattle. Most immunogens showed compelling similarity to protein/gene sequences in the two ruminant pathogens M. capricolum subsp. capricolum and M. mycoides subsp. mycoides large colony type both belonging to the mycoides cluster. Three of these proteins, namely glycerol-3-phosphate oxidase, adenylosuccinate synthase, and glyceraldehyde-3-phosphate dehydrogenase, had no compelling homologue in the other distantly related bovine pathogen M. agalactiae. In addition, translation elongation factor Tu, heat shock protein 70, pyruvate dehydrogenase, and FKBP-type peptidyl-prolyl isomerase, which have been found to mediate adhesion to host tissue in other mycoplasmas were shown to be expressed and recognized by sera. These proteins have potential for the development of improved diagnostic tests and possibly vaccines.