GENETICS. The Human Variome Project

An ambitious plan to collect, curate, and make accessible information on genetic variations affecting human health is beginning to be realized.     

Conversion rates of aldicarb and its oxidation products in soils. II. Aldicarb sulphoxide

The loss of aldicarb sulphoxide was studied in incubation experiments with soil from four plough layers and two deeper layers. The loss during the 111 days of the experiment could be described by first-order kinetics. The half-lives at 15°C ranged from 20 days in a clay loam to 46 days in a peaty sand. The loss of sulphoxide in deeper layers was considerably slower than in the corresponding top layers of a soil profile. In soil from a silty layer at 70–90 cm depth the half-life was about 53 days. In soil from a sand layer at 90–110 cm depth a loss of only about 15% was measured after 111 days of incubation. First-order rate constants for sulphoxide conversion in a clay loam at 6, 15 and 25°C were found to be 0.009, 0.033, and 0.05 day^?1 respectively; in a greenhouse soil these rate constants were 0.0052, 0.019 and 0.04 day^?1 respectively. The fractions of aldicarb sulphoxide that were oxidised to sulphone at 15°C in soil from plough layers were computed to range from 0.52 to 0.76.     

Fragmentation and recreational use affect tree regeneration in urban forests

The aim of this study was to test whether fragmentation or recreational use affect tree regeneration in urban forests, and to quantify these effects. We sampled tree saplings at different distances from edges in spruce (Picea abies) dominated forests, and at different distances from paths that represented different levels of wear. Generalized linear mixed models were used to test our hypotheses. We found that fragmentation favours the regeneration of deciduous trees in urban spruce dominated forests: distance from the edge had a pronounced effect on regeneration, at least up to 80 m into the forests. Saplings of Betula pendula, Populus tremula, other deciduous species and Pinus sylvestris benefited from edge conditions. Betula pubescens saplings, however, were most abundant in the interior and small Sorbus aucuparia saplings at 25–30 m from the edge. All species suffered from the direct effects of trampling, while varying responses of species to distance from the paths were observed up to 6 m, and possibly further. As trees essentially define the living conditions for other forest species, we suggest that the spatial extent of edge and trampling effects should be studied for different types of forests. This knowledge should then be used in urban forestry and planning to define the threshold value that will allow for at least some “intact” interior. We suggest a diameter larger than 160 m to support indigenous species in boreal spruce dominated forests.     

Soil Nematode Populations Beneath Faecal Pats from Grazing Cattle Treated with the Ivermectin Sustained-release Bolus or Fed the Nematophagous Fungus Duddingtonia flagrans to Control Nematode Parasites

The size and composition of the nematode assemblage in soil under faecal pats derived from young cattle treated or untreated with either ivermectin sustained-release boluses, or the nematophagous fungus Duddingtonia flagrans, were studied in each of three years. Soil samples taken 4, 6, 8 and 10 weeks after four deposition dates in 1998 showed significant temporal effects in many taxa and treatment effects in a few genera. In 2000, soil samples taken 10 weeks after deposition in July, August and September showed treatment effects in the plant-associated Tylenchus and Cephalenchus, and the bacterial-feeding Cephalobus 1 and Cephalobus 2 taxa. However, overall it was found that the nematode assemblages were similar below all three types of pat, and the assemblages varied with the season of deposition. D. flagrans, the novel biological control agent being tested against the free-living stages of nematode parasites of cattle, had no detectable impact on the size or the structure of the soil nematode communities under the faecal pats.     

Food inputs, water quality and nutrient accumulation in integrated pond systems: A multivariate approach

A participatory on-farm study was conducted to explore the effects of food input patterns on water quality and sediment nutrient accumulation in ponds, and to identify different types of integrated pond systems. Ten integrated agriculture-aquaculture (IAA) farms, in which ponds associate with fruit orchards, livestock and rice fields were monitored in the Mekong delta of Vietnam. Pond mass balances for nitrogen (N), organic carbon (OC) and phosphorus (P) were determined, and pond water quality and sediment nutrient accumulation were monitored. Data were analyzed using multivariate canonical correlation analysis, cluster analysis and discriminant analysis. The main variability in pond water quality and sediment nutrients was related with food inputs and water exchange rates. Water exchange rate, agro-ecological factors, pond physical properties and human waste input were major variables used to classify ponds. Classification was into: (1) low water exchange rate ponds in the fruit-dominated area, (2) low water exchange rate ponds in the rice-dominated area receiving homemade feed, and (3) high water exchange rate ponds in the rice-dominated areas receiving wastes. Pond water exchange rate was human-controlled and a function of food input patterns, which were determined by livelihood strategies of IAA-households. In the rice-dominated area with deep ponds, higher livestock and human wastes were found together with high water exchange rates. In these ponds, large organic matter loads reduced dissolved oxygen and increased total phosphorus concentrations in the water and increased nutrient (N, OC and P) accumulation in the sediments. In the rice-dominated area with wide ponds, higher homemade feed amounts were added to the ponds with low water exchange rate. This resulted in high phytoplankton biomass and high primary productivity. The contrary occurred in the fruit-dominated area, where fish were grown in shallow and narrow ponds, receiving more plant residue which resulted in lower phytoplankton biomass and lower sediment nutrient accumulation.     

Induction of mutants of Fusarium oxysporum f. sp. lycopersici with altered virulence

Mutants ofFusarium oxysporum f. sp.lycopersici were obtained by UV irradiation. The mutants of race 1 and race 2 caused disease symptoms on plants with resistance genes against the corresponding wild type strains. Mutants of race 1 of the pathogen were stable, whereas mutants of race 2 lost the ability to cause disease symptoms in plants carrying the 1–2 resistance gene, after prolonged maintenenance on potato dextrose agar. Mutants of race 1 resembled race 2 in pathogenicity and they were vegetatively compatible with race 2, but no longer with race 1. These results suggest that the isolated strains with an altered virulence pattern have mutations in loci involved in avirulence.     

A severe outbreak of contagious ecthyma (orf) in a free-ranging musk ox (Ovibos moschatus) population in Norway

During July-October 2004, 19 (18 calves, 1 yearling) free-ranging musk oxen (Ovibos moschatus) at Dovre, Norway, were observed with contagious echtyma-like lesions, and 16 of them were euthanized. Six musk oxen were subjected to necropsy, histopathological and microbiological examinations. All euthanized animals had lesions consistent with contagious ecthyma presenting as wart-like, scabby lesions on the muzzle, lips, oral mucosa and limbs to a variable extent. The histopathological examination showed pustular dermatitis characterized by epidermal proliferation, reticular degeneration, degenerating keratinocytes with intracytoplasmic eosinophilic inclusion bodies, vesicopustules, microabscesses and multifocal ulcerations in the epidermis which was covered by a serocellular crust. Pathology and bacteriology showed evidence of secondary infections in the skin and draining lymph nodes. Electron microscopy (negative staining) of lesions from four animals detected parapoxvirus with the typical arrangement of the outer protein filaments. Parapoxvirus DNA was detected in tissue samples from two examined animals by polymerase chain reaction (PCR) with primers from the B2L-gene. A DNA sequence of 326 nucleotides from the amplicon was compared with similar DNA sequences from parapoxvirus isolated from sheep, reindeer, musk ox and cattle. The outbreak was caused by a virus similar to other circulating orf virus variants in Norway. Antibodies against parapoxvirus were detected with a virus neutralization test in 3 of 35 musk oxen (8.6%) sampled at Dovre between 2004 and 2006. This is the first report of a severe outbreak of contagious ecthyma in free-ranging musk oxen.     

Effects of common carp Cyprinus carpio (L.) and feed addition in rohu Labeo rohita (Hamilton) ponds on nutrient partitioning among fish, plankton and benthos

The effects of introducing common carp (CC) and of adding artificial feed to fertilized rohu ponds on water quality and nutrient accumulation efficiency were studied. All ponds were stocked with 15 000 rohu ha^?1. Treatments included ponds with rohu alone, rohu plus 5000 common carp ha^?1 and rohu plus 10 000 CC ha^?1. A comparison was also made between supplementally fed and non‐fed ponds. The overall highest nitrogen (N) and phosphorus (P) concentrations were observed in ponds with 5000 CC ha^?1, followed by ponds with 10 000 and 0 CC ha^?1. The largest fractions of N and P inputs accumulating in fish, phytoplankton and zooplankton were observed in ponds with 5000 CC ha^?1, followed by ponds with 10 000 CC ha^?1 and subsequently ponds without CC. Relatively more nutrients accumulated in benthic organisms in ponds without than in ponds with CC. A smaller fraction of the nutrient input was retained in fish, plankton and benthic organisms in ponds without CC compared with ponds with CC. Compared with 5000 CC ha^?1, stocking 10 000 CC ha^?1 can be considered as overstocking, because this leads to lower fish production and relatively less nutrients retained in plankton and benthic organisms.     

The distribution of nematodes and soil microbial communities across soil aggregate fractions and farm management systems

We hypothesized that nematode and microbial communities vary between soil aggregate fractions due to variations in physical and/or resource constraints associated with each fraction and that this, in turn, contributes to management impacts on whole soil food webs. Nematode and microbial communities were examined within three soil fractions: large macroaggregates (LM; >1000 μm), small macroaggregates (SM; 250-1000 μm) and inter-aggregate soil and space (IS; <250 μm) isolated from soils of four agricultural management systems: conventional tomato (CON), organic tomato (ORG), a minimum till grain-legume intercrop with continuous cover (CC) and an unmanaged riparian corridor (RC). Aggregate fractions appeared to influence nematode assemblages more than did management system. In general the IS and LM fractions contained higher densities of all nematode trophic groups than did SM. Management × fraction interactions for bacterivores and fungivores, however; suggested a non uniform trend across management systems. The IS fraction exhibited stronger trophic links, per the nematode structure index (SI), while the LM and SM fractions had more active fungal decomposition channels as indicated by the channel index (CI). Higher adult to juvenile ratios in the LM and IS than the SM fraction, and a positive correlation between nematode density in the IS fraction and the proportion of macroaggregates in the soil, indicated an association between soil structure and nematode distribution. Microbial communities varied across both aggregate fractions and management systems. Phospholipid fatty acid (PLFA) analysis suggested that the LM fraction contained greater microbial biomass, gram positive bacteria, and eukaryotes than the IS fraction, while SM contained intermediate PLFA associated with these groups. Total PLFA was greater under RC and ORG than under CC or CON. Total PLFA was positively correlated with % C in soil fractions while nematode abundance exhibited no such relationship. Our findings suggest that microbial communities are more limited by resource availability than by habitable pore space or predation, while nematode communities, although clearly resource-dependent, are better associated with habitable pore space for the soil fractions studied here.     

Comparison of the glucosinolate-myrosinase systems among daikon (Raphanus sativus, Japanese white radish) varieties

Myrosinase is a cytosolic plant enzyme present in daikon ( Raphanus sativus, Japanese white radish) roots that hydrolyzes 4-methylthio-3-butenyl glucosinolate (MTBGLS) into the natural pungent agent 4-methylthio-3-butenyl isothiocyanate (MTBITC), which possesses antimicrobial, antimutagenic, and anticarcinogenic properties. The concentration of MTBGLS, myrosinase activity, and production of MTBITC in seven daikon varieties (one conventional and six heirlooms) were determined to rank the activity of the glucosinolate-myrosinase system and identify critical factors influencing the production of MTBITC. The six heirloom varieties produced 2.0-11.5 times higher levels of MTBITC as compared to the conventional variety, Aokubi, which is consumed by the present Japanese population. The myrosinase was located exclusively in the outer epidermal layer in Aokubi, and MTBGLS was widely distributed throughout the root tissue. Although the skin is a potentially rich source of myrosinase in Aokubi, the skin is usually peeled off in the current practice of preparing daikon for cooking. New practices are therefore proposed for the preparation of daikon tubers that eliminate the peeling of the skin to avoid removing the enzyme needed to convert MTBGLS to the health-beneficial MTBITC. It is also concluded that the consumption of heirloom daikon varieties in addition to changes in food preparation will optimize the health benefits of daikon.