Associations of natural variation in the CD163 and other candidate genes on host response of nursery pigs to porcine reproductive and respiratory syndrome virus infection

Pigs with complete resistance to porcine reproductive and respiratory syndrome (PRRS) virus (PRRSV) have been produced by genetically knocking out the CD163 gene that encodes a receptor of the PRRSV for entry into macrophages. The objectives of this study were to evaluate associations of naturally occurring single nucleotide polymorphisms (SNPs) in the CD163 gene and in three other candidate genes (CD169, RGS16, and TRAF1) with host response to PRRSV-only infection and to PRRS vaccination and PRRSV/porcine circovirus 2b (PCV2b) coinfection. SNPs in the CD163 gene were not included on SNP genotyping panels that were used for previous genome-wide association analyses of these data. An additional objective was to identify the potential genetic interaction of variants at these four candidate genes with a mutation in the GBP5 gene that was previously identified to be associated with host response to PRRSV infection. Finally, the association of SNPs with expression level of the nearby gene was tested. Several SNPs in the CD163, CD169, and RGS16 genes were significantly associated with host response under PRRSV-only and/or PRRSV/PCV2b coinfection. The effects of all SNPs that were significant in the PRRSV-only infection trials depend on genetic background. The effects of some SNPs in the CD163, CD169, and RGS16 genes depend on genotype at the putative causative mutation in the GBP5 gene, which indicates a potential biological interaction of these genes with GBP5. In addition, genome-wide association results for the PRRSV-only infection trials revealed that SNPs located in the CDK5RAP2 or MEGF9 genes, near the TRAF1 gene, had suggestive effects on PRRS viral load, which indicates that these SNPs might contribute to PRRSV neuropathogenesis. In conclusion, natural genetic variants in the CD163, CD169, and RGS16 genes are associated with resistance to PRRSV and/or PCV2b infection and appear to interact with the resistance quantitative trait locus in the GBP5 gene. The identified SNPs can be used to select for increased natural resistance to PRRSV and/or PRRSV-PCV2b coinfection.     

Reference points for predators will progress ecosystem‐based management of fisheries

Ecosystem‐based management of fisheries aims to allow sustainable use of fished stocks while keeping impacts upon ecosystems within safe ecological limits. Both the FAO Code of Conduct for Responsible Fisheries and the Aichi Biodiversity Targets promote these aims. We evaluate implementation of ecosystem‐based management in six case‐study fisheries in which potential indirect impacts upon bird or mammal predators of fished stocks are well publicized and well studied. In particular, we consider the components needed to enable management strategies to respond to information from predator monitoring. Although such information is available in all case‐studies, only one has a reference point defining safe ecological limits for predators and none has a method to adjust fishing activities in response to estimates of the state of the predator population. Reference points for predators have been developed outside the fisheries management context, but adoption by fisheries managers is hindered a lack of clarity about management objectives and uncertainty about how fishing affects predator dynamics. This also hinders the development of adjustment methods because these generally require information on the state of ecosystem variables relative to reference points. Nonetheless, most of the case‐studies include precautionary measures to limit impacts on predators. These measures are not used tactically and therefore risk excessive restrictions on sustainable use. Adoption of predator reference points to inform tactical adjustment of precautionary measures would be an appropriate next step towards ecosystem‐based management.     

Genomics,genetics and breeding of common bean in Africa: A review of tropical legume project

Common bean (Phaseolus vulgaris L.) is an important legume crop worldwide. The International Centre for Tropical Agriculture (CIAT) and its national partners in Africa aim to overcome production constraints of common bean and address the food, nutrition needs and market demands through development of multitrait bean varieties. Breeding is guided by principles of market‐driven approaches to develop client‐demanded varieties. Germplasm accessions from especially two sister species, P. coccineus and P. acutifolius, have been utilized as sources of resistance to major production constraints and interspecific lines deployed. Elucidation of plant mechanisms governing pest and disease resistance, abiotic stress tolerance and grain nutritional quality guides the selection methods used by the breeders. Molecular markers are used to select for resistance to key diseases and insect pests. Efforts have been made to utilize modern genomic tools to increase scale, efficiency, accuracy and speed of breeding. Through gender‐responsive participatory variety selection, market‐demanded varieties have been released in several African countries. These new bean varieties are a key component of sustainable food systems in the tropics.     

Chronic toxicity of unresolved complex mixtures (UCM) of hydrocarbons in marine sediments

Background, Aim and Scope  Unresolved complex mixtures (UCM) of hydrocarbons, containing many thousands of compounds which cannot be resolved by conventional gas chromatography (GC), are common contaminants of sediments but little is known of their potential to affect sediment-dwelling organisms. Evidence exists for reduced health status in mussels, arising from aqueous exposure to aromatic UCM components acting through a narcotic mode of action. However, UCM contaminants in sediments may not be sufficiently bioavailable to elicit toxic effects. The aim of our study was therefore to measure the sublethal effects of chronic exposure to model UCM-dominated oils at environmentally realistic concentrations and compare this to effects produced by a UCM containing weathered crude oil. A further aim was to determine which, if any, fractions of the oils were responsible for any observed toxicity. Materials and Methods  Whole oils were spiked into estuarine sediment to give nominal concentrations of 500 μg g⁻¹ dry weight. Juveniles of the estuarine amphipod Corophium volutator were exposed to the contaminated sediment for 35 days and their survival, growth rate and reproductive success quantified. Using an effect-directed fractionation approach, the oils were fractionated into aliphatic and two aromatic fractions by open column chromatography and their toxicity assessed by further chronic exposures using juvenile C. volutator. Results  The growth rates of amphipods were reduced following exposure to the oils although this was only statistically significant for the weathered oil; reproductive success was reduced by all oil exposures. Sediment spiked with UCM fractions also caused reduced growth and reproduction but no particular fraction was found to be responsible for the observed toxicity. Survivorship was not affected by any oil or fraction. Discussion  The study showed that chronic exposure to sediments contaminated by UCM-dominated oils could have population level effects on amphipods. The observed effects could not be explained by hydrocarbons resolved by conventional GC and effects were similar for both UCM-dominated and weathered oils. All of the fractions appeared to contribute to the observed effects; this is in contrast to previous research which had shown that an aliphatic UCM did not cause adverse effects in mussels. Conclusions  To our knowledge, this is the first study to demonstrate population-level effects arising from exposure to sediments contaminated by realistic environmental concentrations of UCM hydrocarbons. The results are consistent with many compounds, at very low individual concentrations, contributing towards the overall observed toxicity. Recommendations  Risk assessments of contaminated sediments should take into account the contribution towards the potential for toxic effects from UCM hydrocarbons. Studies into sediment contamination should report both aliphatic and aromatic UCM concentrations to aid risk assessments. ESS-Submission Editor: Henner Hollert (hollert@uni-heidelberg.de) This paper has been developed from a presentation at SETAC Europe 16^th Annual Meeting 2006 held at the The Hague, The Netherlands.     

Heterosis in fingerlings from a diallel cross between two wild strains of silver perch (Bidyanus bidyanus)

Cross-breeding was investigated as a strategy to improve performance of the Australian native freshwater fish, silver perch ( Bidyanus bidyanus Mitchell) through the exploitation of heterosis during the fingerling phase of production. Growth, and mid and best parent heterosis of two wild strains, Cataract Dam (C_♂× C_♀) and Murray River (M_♂× M_♀) and their reciprocal crosses (C_♂× M_♀ and M_♂× C_♀) were evaluated in cages and ponds through summer, and in tanks in a re-circulating aquaculture system during winter. The M × C cross grew significantly faster than the reciprocal cross and pure strains in cages and tanks, had the lowest coefficients of variation of weight and length and was 20.9% and 16.0% heavier than mid-parent and best-parent average, respectively, when grown in ponds. Differences in growth between the reciprocal crosses were also evident, with C × M expressing significantly less heterosis in cages and tanks. Faster growth of M × C was attributed to greater appetite; however, at sizes approaching 250 g this feeding vigour diminished. The results of this study suggest that use of the M × C cross has the potential to reduce the length of the culture period and lower costs of silver perch production.     

Greater sage-grouse as an umbrella species for sagebrush-associated vertebrates

Widespread degradation of the sagebrush ecosystem in the western United States, including the invasion of cheatgrass, has prompted resource managers to consider a variety of approaches to restore and conserve habitats for sagebrush-associated species. One such approach involves the use of greater sage-grouse, a species of prominent conservation interest, as an umbrella species. This shortcut approach assumes that managing habitats to conserve sage-grouse will simultaneously benefit other species of conservation concern. The efficacy of using sage-grouse as an umbrella species for conservation management, however, has not been fully evaluated. We tested that concept by comparing: (1) commonality in land-cover associations, and (2) spatial overlap in habitats between sage-grouse and 39 other sagebrush-associated vertebrate species of conservation concern in the Great Basin ecoregion. Overlap in species’ land-cover associations with those of sage-grouse, based on the ? (phi) correlation coefficient, was substantially greater for sagebrush obligates than non-obligates . Spatial overlap between habitats of target species and those associated with sage-grouse was low (mean ? = 0.23), but somewhat greater for habitats at high risk of displacement by cheatgrass (mean ? = 0.33). Based on our criteria, management of sage-grouse habitats likely would offer relatively high conservation coverage for sagebrush obligates such as pygmy rabbit (mean ? = 0.84), but far less for other species we addressed, such as lark sparrow (mean ? = 0.09), largely due to lack of commonality in land-cover affinity and geographic ranges of these species and sage-grouse.     

Urban leakage of liquefied petroleum gas and its impact on Mexico city air quality

Alkane hydrocarbons (propane, isobutane, and n-butane) from liquefied petroleum gas (LPG) are present in major quantities throughout Mexico City air because of leakage of the unburned gas from numerous urban sources. These hydrocarbons, together with olefinic minor LPG components, furnish substantial amounts of hydroxyl radical reactivity, a major precursor to formation of the ozone component of urban smog. The combined processes of unburned leakage and incomplete combustion of LPG play a significant role in causing the excessive ozone characteristic of Mexico City. Reductions in ozone levels should be possible through changes in LPG composition and lowered rates of leakage.