Mating type ratios and pathogenicity in Diplodia shoot blight fungi populations: Comparative analysis

Diplodia sapinea and Diplodia scrobiculata are opportunistic pathogens of Pinus species. Several studies about taxonomy, impact and epidemiology of these fungi have been conducted in previous years, which have provided useful information and have raised new issues. These diseases produce a considerable impact on plantations resulting in significant economic losses. The main aims of this study are to increase the knowledge of the potential of genetic exchange and the relative aggressiveness of these organisms that can persist in healthy tissues of asymptomatic trees. A collection of 250 isolates among which are 149 strains collected from Pinus radiata plantations in Basque Country (Spain) and 101 strains from different countries was included in this work. Mating type ratios were analysed and compared using the structure of the MAT locus (MAT1‐1‐1 and MAT1‐2‐1). Inoculations of Pinus radiata seedlings were performed in a biosafety greenhouse (P2) to confirm pathogenicity of isolates and compare their aggressiveness. The frequency of occurrence of both idiomorphs of D. sapinea in Basque Country isolates was close to 1:1, however, for collection of isolates of this fungus from around the world, the ratio was 1:2. Furthermore, the spatial distribution of the two mating types in the Basque Country was random. Despite no detection of a sexual state, these results could suggest sexual reproduction behaviour. The pathogenicity of all strains in the collection was confirmed. Although aggressiveness (in terms of lesion lengths resulting from inoculation) varied greatly, no statistically significant effects of MAT type or pathogen species were detected.     

How is agroforestry perceived in Europe? An assessment of positive and negative aspects by stakeholders

Whilst the benefits of agroforestry are widely recognised in tropical latitudes few studies have assessed how agroforestry is perceived in temperate latitudes. This study evaluates how stakeholders and key actors including farmers, landowners, agricultural advisors, researchers and environmentalists perceive the implementation and expansion of agroforestry in Europe. Meetings were held with 30 stakeholder groups covering different agroforestry systems in 2014 in eleven EU countries (Denmark, France, Germany, Greece, Hungary, Italy, Netherlands, Portugal, Spain, Sweden and the United Kingdom). In total 344 valid responses were received to a questionnaire where stakeholders were asked to rank the positive and negative aspects of implementing agroforestry in their region. Improved biodiversity and wildlife habitats, animal health and welfare, and landscape aesthetics were seen as the main positive aspects of agroforestry. By contrast, increased labour, complexity of work, management costs and administrative burden were seen as the most important negative aspects. Overall, improving the environmental value of agriculture was seen as the main benefit of agroforestry, whilst management and socio-economic issues were seen as the greatest barriers. The great variability in the opportunities and barriers of the systems suggests enhanced adoption of agroforestry across Europe will be most likely to occur with specific initiatives for each type of system.     

Characterization of HMW-GS and evaluation of their diversity in morphologically elite synthetic hexaploid wheats

High molecular weight glutenin subunit composition and variation in 95 Elite-1 synthetic hexaploid (SH) wheats (Triticum turgidum/Aegilops tauschii; 2n = 6× = 42; AABBDD) were determined by sodium dodecyl sulphate polyacrylamide gel electrophoresis method (SDS-PAGE). Twenty two different alleles at Glu-1 loci in SHs were observed. Forty four different patterns of HMW-GS in synthetics were found. This higher HMW glutenin composition was due to higher proportion of D-genome encoded subunits in these SHs. 8% urea/SDS-PAGE better discriminated subunit 2* than 12% gels. However 12% urea/SDS-PAGE allowed differentiated mobility of Glu-D^t1 subunits. Genetic variability at Glu-D^t1 locus was greater than Glu-A1 and Glu-B1 loci. The relative high frequency of superior alleles, Glu-B1b and Glu-D^t1d indicated the superior bread making quality attributes embedded in these synthetic hexaploid wheats. Of the 95 Elite-1 SHs 27.1% possessed superior alleles at Glu-A1 and 51% had superior alleles at Glu-B1 locus. At Glu-D^t1 frequency of inferior allele 1Dx2 + 1Dy12 was very low (5.26%) and nine different rare alleles along with the higher frequency (22.1%) of D-genome encoded subunit, 1Dx5 + 1Dy10, were observed. These superior alleles shall form the priority selective sieve for their usage in wheat improvement efforts.     

Functional targeting of DNA damage to a nuclear pore-associated SUMO-dependent ubiquitin ligase

Recent findings suggest important roles for nuclear organization in gene expression. In contrast, little is known about how nuclear organization contributes to genome stability. Epistasis analysis (E-MAP) using DNA repair factors in yeast indicated a functional relationship between a nuclear pore subcomplex and Slx5/Slx8, a small ubiquitin-like modifier (SUMO)-dependent ubiquitin ligase, which we show physically interact. Real-time imaging and chromatin immunoprecipitation confirmed stable recruitment of damaged DNA to nuclear pores. Relocation required the Nup84 complex and Mec1/Tel1 kinases. Spontaneous gene conversion can be enhanced in a Slx8- and Nup84-dependent manner by tethering donor sites at the nuclear periphery. This suggests that strand breaks are shunted to nuclear pores for a repair pathway controlled by a conserved SUMO-dependent E3 ligase.     

Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes

The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order.     

Stability of hydrolytic enzyme activity and microbial phosphorus during storage of tropical rain forest soils

Storage can markedly influence microbial and biochemical properties in soils, yet recommendations for sample storage are based on studies of temperate soils that regularly experience extended cold periods. We assessed the influence of storage conditions on microbial phosphorus and the activity of four hydrolytic enzymes (phosphomonoesterase, phosphodiesterase, β-glucosidase, and N-acetyl-β-d-glucosaminidase) in three lowland tropical forest soils from the Republic of Panama that experience a constant warm temperature. The soils spanned a strong rainfall gradient and contained contrasting physical and chemical properties (pH 3.6-5.9; total carbon 26-50 g C kg⁻¹; clay 33-62%; total phosphorus 0.30-0.60 g P kg⁻¹). Storage treatments were: (i) room temperature (22 °C in the dark), (ii) refrigerated (4 °C in the dark), (iii) air-dried (10 d, 22 °C), and (iv) frozen (−35 °C). There were significant changes in enzyme activities and microbial phosphorus during refrigerated and room temperature storage, although changes were relatively small during the first two weeks. An initial marked decline in enzyme activities for one soil analyzed within 2 h of sampling was attributed to a flush of activity caused by sampling and soil preparation (sieving, etc.). For longer-term storage (>2 weeks), ambient laboratory temperature appeared preferable to freezing and cold storage, because one month of storage caused a marked decline in enzyme activities and microbial phosphorus in one soil. Freezing preserved the activities of some enzymes in some soils at rates comparable to cold or room temperature storage, but caused a marked decline in microbial phosphorus in two soils. Air-drying caused a marked decline in microbial phosphorus and the activity of all enzymes. We therefore conclude that enzyme assays and microbial phosphorus should be determined in tropical forest soils after no more than two weeks storage in the dark at ambient laboratory temperature.     

Regional scale effects of human density and forest disturbance on large-bodied vertebrates throughout the Yucatán Peninsula, Mexico

The occupancy probability of 35 large-bodied bird and mammal species was examined in relation to patch- and landscape-scale habitat and disturbance variables in 147 forest patches distributed throughout the Mexican Yucatán Peninsula. Occupancy was assessed on the basis of interviews with local informants. The most important predictors of vertebrate species richness, composition, and patch occupancy were human population density and the extent and quality of forest cover. Most forest species responded positively to forest extent, while felids in particular were sensitive to human population density. However, the effects of human density on patch occupancy operated at extremely local scales. Effects were stronger at a smaller grain size, offering optimistic prospects for conservation strategies that incorporate human population effects. Three arboreal frugivores (Ateles geoffroyi, Alouatta pigra, and Ramphastos sulfuratus) were strongly associated with total basal area of trees bearing fleshy fruits. The degree of hunting pressure was not related to human population density, and affected the occupancy probability of three game species, two of which (Mazama spp., Crax rubra) are among the most preferred prey across the Yucatán Peninsula. Levels of patch occupancy across this region varied considerably among species, and were best explained by body size and degree of forest habitat specificity, large-bodied species and habitat specialists being the most vulnerable. This study provides a quantitative assessment of the conservation potential of large vertebrates in Mesoamerica and identifies disturbance-sensitive species. This can inform regional-scale conservation planning at a time when low deforestation in parts of the Yucatán Peninsula still provides a narrow window of conservation opportunity given the rapid human population growth.     

Global mapping of the yeast genetic interaction network

A genetic interaction network containing approximately 1000 genes and approximately 4000 interactions was mapped by crossing mutations in 132 different query genes into a set of approximately 4700 viable gene yeast deletion mutants and scoring the double mutant progeny for fitness defects. Network connectivity was predictive of function because interactions often occurred among functionally related genes, and similar patterns of interactions tended to identify components of the same pathway. The genetic network exhibited dense local neighborhoods; therefore, the position of a gene on a partially mapped network is predictive of other genetic interactions. Because digenic interactions are common in yeast, similar networks may underlie the complex genetics associated with inherited phenotypes in other organisms.     

Evaluation of peripheral blood lymphocyte subsets in family-owned dogs naturally infected by Ehrlichia canis

Previous research suggested that clinical manifestations, histopathological lesions, and even infection maintenance in the course of canine monocytic ehrlichiosis (CME) are directly related to the immune response developed by the host. In the present study, blood lymphocyte subsets were analyzed by multiparametric flow cytometry in 37 dogs with naturally occurring CME and 47 healthy dogs used as controls. T, T helper (Th), T cytotoxic (Tc), B, non-T, non-B lymphocytes and those that express MHC class II were characterized in every dog. Animals with CME showed higher relative values of T and Tc cells and a higher absolute number of Tc cells in peripheral blood. The percentage of Th cells and the absolute and relative values of B cells were higher in healthy animals than in CME-affected dogs. The significance of these changes on the pathogenesis of natural Ehrlichia canis infection in dogs needs further evaluation.