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.     

Induction of spawning in Pacific white shrimp Litopenaeus vannamei (Boone, 1931) by injection of its molt inhibiting hormone isoform II produced in E. coli

The optimization of reproductive parameters in shrimp farming continues to be a challenge for most producing countries. Although the crustacean neuropeptides have been studied extensively in the last two decades, the functions of most of these neuropeptides remained putative. Among them, molt‐inhibiting hormone isoform II (MIH II) has shown an important role in vitellogenesis. In this study, the cDNA encoding mature MIH II peptide was isolated by RT‐PCR from the L. vannamei eyestalk. The cDNA was cloned into pET28a bacterial expression vector. Recombinant MIH II was obtained in the form of insoluble inclusion bodies and purified to ~88% purity. Two doses of rMIH II and a negative control group were assayed in vivo. The stages of ovarian maturation and spawning were recorded during 72 hr post‐injection. The results showed that ovarian maturation occurred approximately in 9% and 33% of females injected with rMIH II at the doses of 300 and 600 ng/gbw respectively. Neither maturation nor spawning was detected in the negative control group. Females injected with 600 ng/gbw, which showed vitellogenic stages III and IV, spawned. These preliminary results argue that the hormone rMIH II could be a promising candidate to induce spawning in L. vannamei shrimp.     

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.     

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.     

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.