Descriptive spatial epidemiology of subclinical Salmonella infection in finisher pig herds: application of a novel method of spatially adaptive smoothing

We describe the spatial epidemiological features of the 6.8 million meat-juice serological tests that were conducted between 1995 and 2004 as part of the Danish swine Salmonella control programme. We investigated pig and farm density using edge-corrected kernel estimations. Pigs were aggregated at the county level to assess county-level risk, and then we investigated farm-level risk by giving farms a case or non-case label using a cut-off of 40% of pigs positive. Conditional probability surfaces, correcting for the underlying population at risk, were produced for each year of the study period using a novel kernel estimator with a spatially adaptive smoothing bandwidth. This approach improves on previous methods by allowing focussed estimation of risk in areas of high population density while maintaining stable estimates in regions where the data are sparse. Two spatial trends in the conditional probability of a farm being a case were evident: (1) over the whole country, with the highest risk in the west compared to the east; and (2) on the Jutland peninsula with the highest risk in the north and south. At the farm-level a consistent area of risk was the south-west of Jutland. Case farms tended to aggregate indicating spatial dependency in the data. We found no association between pig or farm density and Salmonella risk. We generated hypotheses for this spatial pattern of risk and we conclude that this spatial pattern should be considered in the development of surveillance strategies and as a basis for further, more detailed analyses of the data.     

Full pedigree quantitative trait locus analysis in commercial pigs using variance components

In commercial livestock populations, QTL detection methods often use existing half-sib family structures and ignore additional relationships within and between families. We reanalyzed the data from a large QTL confirmation experiment with 10 pig lines and 10 chromosome regions using identity-by-descent (IBD) scores and variance component analyses. The IBD scores were obtained using a Monte Carlo Markov Chain method, as implemented in the LOKI software, and were used to model a putative QTL in a mixed animal model. The analyses revealed 61 QTL at a nominal 5% level (out of 650 tests). Twenty-seven QTL mapped to areas where QTL have been reported, and eight of these exceeded the threshold to claim confirmed linkage (P < 0.01). Forty-two of the putative QTL were detected previously using half-sib analyses, whereas 46 QTL previously identified by half-sib analyses could not be confirmed using the variance component approach. Some of the differences could be traced back to the underlying assumptions between the two methods. Using a deterministic approach to estimate IBD scores on a subset of the data gave very similar results to LOKI. We have demonstrated the feasibility of applying variance component QTL analysis to a large amount of data, equivalent to a genome scan. In many situations, the deterministic IBD approach offers a fast alternative to LOKI.     

Inhibition of DNA polymerase β activity in isolated bovine liver nuclei by captan and related compounds

The effects on DNA synthesis of the fungicide captan and several structurally related compounds were investigated in isolated bovine liver nuclei. Captan, folpet, captafol, and trichloromethanesulfenyl chloride inhibited DNA synthesis to the same degree with ID₅₀ values of approximately 50 μM in a 40-min assay. The inhibition is concentration dependent and the degree of inhibition increases with time. Studies with structural analogs of captan indicated that inhibition of DNA synthesis by captan is mediated through the trichloromethylthio moiety of the captan molecule. In addition, the data indicate thiophosgene is probably not the toxic species involved in the inhibition of DNA synthesis. The isolated nuclei used in this study were shown to exhibit only a single DNA polymerase activity which was determined to be of the β or low-molecular-weight type. In addition to its inhibition in intact nuclei, captan inhibited the activity of the β polymerase in nuclear extracts as well as in partially purified enzyme preparations. These results indicate that captan inhibits DNA synthesis in our preparation of isolated nuclei by acting directly on the DNA polymerase-catalyzed reaction rather than by causing a nonspecific or indirect effect in the nuclear system such as alterations in the nuclear membrane or aggregation of the nuclei. The site of captan's inhibitory action is the DNA polymerase molecule. The interaction of captan with the polymerase results in irreversible inhibition of the enzyme. Interaction of captan with the template, if it occurs, does not appear to be involved in mediating the inhibition.     

The hymenopterous parasites of Nitidulidae

The known information on hymenopterous parasites of Nitidulidae was consolidated in this article. Species of parasites, nitidulid hosts and, where possible, plant host of the nitidulids are provided along with citations to sources of information. Thirty-three species of hymenopterous parasites are recorded in nine different families. Since nomenclature of several of the parasites has changed, it was updated with the assistance of specialists.     

Whole farm implications on the application of variable rate technology to every cropped field

In the last 10 years precision agriculture has evolved and it is now possible to manage cropping inputs at the sub field scale. However, the expected return generated by these management practices varies with the amount and predictability of the spatial variation in crop yield across the field and may vary from field to field across the farm. We analysed the spatial variation of crop yield from 20 fields totalling 2832 ha from a 5200 ha farm in Western Australia at the field and the sub field scale to determine the economic value of introducing variable rate management (VRT) strategies to fields across the entire farm. In this case study, 6 out of 20 fields generated an additional economic payoff of AU$15/ha when managed with VRT over uniform management. Sensitivity analysis found that the starting levels of soil fertility were an important driver of the payoff for managing a field with VRT. If starting soil fertility was low and uniform across the field, then no fields generated an economic return of more than AU$7.00/ha when managed with VRT. Other factors, including commodity price, fertiliser price, amount of variation in crop yield within the field moderately increased the value of adopting VRT across fields within farm the value of VRT increased if fertiliser budgets were constrained, particularly if the yield distribution of the field was negatively skewed. While VRT does add value to many fields across the farm, the gains are small and the technology must be implemented cheaply for it to be viable.     

Wildfire Effects on Understory Vegetation,Natural Regeneration,and Forest Floor Fuels in a Sierran Mixed Conifer Stand

Wildfire effects on understory shrubs and herbs, regeneration of the seedling and sapling size classes, and downed and dead fuels were assessed in a mixed conifer stand located in the Lake Tahoe Basin in which California white fir (Abies concolor var. lowiana [Gord.] Lemm.) was most abundant but with Jeffrey pine (Pinus jeffreyi Grev. & Balf.) also prevalent. In burned and unburned stand portions, prefire measurements served as a basis of comparison for the postfire measurements pertinent to each study component. Fire severely suppressed the understory vegetation, which was dominated by shrubs such as bush chinquapin (Chrysolepis sempervirens [Kellogg] Hjelmqvist) and antelope bitterbrush (Purshia tridentata [Pursh] DC.), while a tepid postfire recovery of most of the preexisting species in the burned stand portion was augmented by new ones, including shrubs such as snowbrush (Ceanothus velutinus Douglas ex Hook.) and whitethorn (Ceanothus cordulatus Kellogg) ceanothus and herbs such as Holboell's rockcress (Arabis holboellii Hornem.). Tree seedling abundance was also substantially reduced in the burned portion, but the postfire population was dominated by Jeffrey pine whereas white fir had been most prevalent originally. Sapling regeneration was eliminated from the burned stand portion regardless of species. Downed and dead fuel loading was severely diminished by the fire, especially regarding fine fuels, permitting subsequent sheet erosion to imperil new seedling regeneration. These results contribute to an understanding of the direction and pace of postwildfire succession on sites occupied by Sierra Nevada mixed conifer and similar forest cover types, which is critical in decisions concerning the need for, and extent of, postfire site rehabilitation measures.     

Distribution and induction of cytochrome P450 1A1 in the rainbow trout brain

Cytochrome P450 (CYP) 1A1 participates in the activation as well as detoxification of environmental pollutants such as aromatic hydrocarbons. This CYP form is also efficiently induced by aromatic hydrocarbons. The presence of CYP 1A1 in the brain might thus be of physiological and toxicological importance. In the present investigation on rainbow trout, the distribution of 7-ethoxyresorufin-O-deethylase (EROD) activity, a cytochrome CYP 1A1 catalyzed reaction, was measured in whole tissue homogenates from brain parts. In control fish, a relatively high activity was found in the rainbow trout olfactory bulb compared to the other brain parts. Although an EROD induction (3 to 7-fold) by β-naphthoflavone (BNF) was recorded in all brain parts from the rainbow trout, the highest induced activity was measured in the olfactory bulbs. To ascertain the distribution of EROD activity in cells, whole brain tissue was subfractionated by differential centrifugation. The fractionation scheme separated mitochondria (P2 fraction) and microsomes (P3 fraction) as determined by marker enzymes and electron microscopy. In control rainbow trout, a low EROD activity could be measured in the P2 fraction. BNF induced the EROD activity in both P2 and P3 fractions. Western blotting showed the induction by BNF of a protein band in the P2 and P3 fractions with a molecular mass around 58,000 when highly specific anti-cod CYP 1A1 antibodies were used. ELISA measurements confirmed the induction of CYP 1A1 protein in the rainbow trout brain subcellular fractions.     

Microarray analysis of differential utilization of plant-based diets by rainbow trout

Microarray analysis was conducted using liver samples from two families of rainbow trout that differed in their growth responses when compared between individuals fed a fishmeal or plant protein-based diet. Differential expression relating to dietary utilization between the two families found significant changes in expression of 33 expressed sequence tags (ESTs). Eight of the differentially expressed ESTs had identified mammalian homologs that had been previously researched with identified cellular interactions and functions. Utilizing pathway analysis software to analyze sequences annotated with known mammalian genes, we were able to map gene pathways and process interactions. From this information, we were able to infer that the metabolic changes associated with utilization of plant protein versus fishmeal were associated with differential regulation of genes related to cell oxidative stress, proliferation, growth and survival. Furthermore, we inferred from the changes we observed in immune response gene expression that ingestion of this plant-based diet upregulated the expression of genes involved in immunoregulatory processes.     

Effects of a plant parasitic nematode (Heterodera trifolii) on clover roots and soil microbial communities

We studied the effects of the root endoparasitic nematode Heterodera trifolii on rhizodeposition and the root architecture of white clover (Trifolium repens). Rhizosphere solutions were collected from the root systems of plants growing with and without H. trifolii (200 juveniles per inoculated plant) in sand-based microlysimeters. The organic carbon (C) content of these solutions was analyzed, and they were applied to plant-free soils to investigate microbial responses. Although plant biomass was unaffected by nematodes, the architecture of the root systems was significantly altered, with a decrease in overall root length and an increase in the density of lateral branches from the primary root. The presence of nematodes reduced the concentration of organic compounds in the rhizosphere solutions but only on the final sampling date (75 days). Analysis of microbial signature phospholipid fatty acids revealed no change in the structure of the microbial communities in soils to which rhizosphere solutions were applied. However, these microorganisms did respond with changes in substrate utilization patterns (community-level physiological profiles). Microbes in soils that received rhizosphere solutions from the nematode-infected clover showed lower utilization of most substrates but higher utilization of oligosugars. These responses appear to be related to changes in roots and rhizodeposition associated with nematode infection of clover roots. The results of this study suggest that root herbivory can negatively impact carbon-limited soil microbial communities via changes in root architecture that moderate rhizodeposition.