Development and validation of species-specific primers that provide a molecular diagnostic for virus-vector longidorid nematodes and related species in German viticulture

The nematode species Longidorus attenuatus, L. elongatus, L. macrosoma and Paralongidorus maximusare economically important pests to the viticulture industry due to their ability to vector two nepoviruses (Raspberry Ringspot Virus and Tomato Black Ring Virus) to grapevines. In Germany, these species occur in vineyard soil with other non-vector but morphologically similar longidorid species, L. helveticus, L.profundorum and L. sturhani. Species-specific primers were designed from ribosomal DNA for all seven species to facilitate taxonomic identification for non-specialists. Primers were assessed for their reliability by screening, where possible, a number of populations of each species. Furthermore, their selectivity and sensitivity were determined when challenged with closely related longidorid species and general nematode communities typical of vineyard soil. A multiplex approach using a common forward primer combined with species-specific reverse primers enabled three target nematode species to be detected in the same PCR reaction. All primers were highly specific, detecting all nematode developmental forms from disparate populations and were sufficiently sensitive to detect a single target nematode within a whole nematode community typical of a vineyard soil comprising of a range of non-target species. Given their specificity, sensitivity and reliability, these diagnostic primers should be of great benefit to both phytosanitary/quarantine services related to the viticulture industry and also as a decision management tool for growers.     

A Bayesian meta-analysis of the effects of administering an intra-vaginal (CIDR) device in combination with other hormones on the reproductive performance of cycling, anoestrous and inseminated cows

AIMS: To evaluate the effectiveness of treatment programmes that included controlled internal drug-releasing (CIDR) devices containing progesterone (P4) in improving synchrony of oestrus, and conception and pregnancy rates in cycling, anoestrous and inseminated dairy cows, using meta-analysis. To describe the difference in response between cycling and anoestrous cows to CIDR-based synchrony programmes. METHODS: Scientific papers written in the English language between 1989 and 2002 that investigated the effects of treatment programmes including CIDR devices on reproductive performance in dairy heifers or lactating dairy cows were identified using a computerised literature search. The criteria for inclusion incorporated evidence that treatment allocation was completely randomised; the population studied was lactating dairy cows; and that data were available on submission, conception and pregnancy rates and their associated measures of variability. Reproductive outcomes from 25 synchrony trials (total n=11,058 cows) were analysed. Summary measures of the effect of treatment on reproductive outcome were assessed using fixed- and random-effects Bayesian meta-analysis models. RESULTS: Treatment programmes including a CIDR device increased the risk of submission in cycling cows (predicted Bayesian RR=2.86, 95% credible interval=1.46-5.67). Compared with controls, synchrony programmes including CIDR devices in cycling dairy cows had no effect on the risk of conception to first service post-treatment (predicted Bayesian RR=1.00, 95% credible interval=0.80-1.24). Compared with controls, synchrony programmes including CIDR devices had no effect on the risk of pregnancy throughout the mating period (predicted Bayesian RR=1.02, 95% credible interval=0.89-1.17). In anoestrous cows, CIDR treatment had no effect on the risk of conception to first service post-treatment and no effect on the risk of pregnancy throughout the mating period, compared with anoestrous, untreated controls (predicted Bayesian RR=0.91 and 0.97, respectively; 95% credible interval=0.68-1.26 and 0.59-1.60, respectively). CONCLUSION: The results of this meta-analysis showed that synchrony programmes using CIDR devices combined with other hormones reliably enhanced submission rates in lactating dairy cows. The relatively small number of trials with data suitable for analysis and the heterogeneity of results at the individual trial level limited our ability to confirm either a beneficial or deleterious effect of treatment on conception or pregnancy rates. Further randomised, controlled trials to evaluate the effectiveness of this form of reproductive therapy in commercial dairy farms are needed.     

Fishing, trophic cascades, and the process of grazing on coral reefs

Since the mass mortality of the urchin Diadema antillarum in 1983, parrotfishes have become the dominant grazer on Caribbean reefs. The grazing capacity of these fishes could be impaired if marine reserves achieve their long-term goal of restoring large consumers, several of which prey on parrotfishes. Here we compare the negative impacts of enhanced predation with the positive impacts of reduced fishing mortality on parrotfishes inside reserves. Because large-bodied parrotfishes escape the risk of predation from a large piscivore (the Nassau grouper), the predation effect reduced grazing by only 4 to 8%. This impact was overwhelmed by the increase in density of large parrotfishes, resulting in a net doubling of grazing. Increased grazing caused a fourfold reduction in the cover of macroalgae, which, because they are the principal competitors of corals, highlights the potential importance of reserves for coral reef resilience.     

Molecular characterization of Haemophilus parasuis ferric hydroxamate uptake (fhu) genes and constitutive expression of the FhuA receptor

Bacteria have evolved a set of highly specialized proteins to capture iron in iron-depleted environments. The acquisition and uptake of iron present in the extracellular milieu of eukaryotic organisms is indispensable for the growth and survival of microbial pathogens in the course of infection. Haemophilus parasuis is the causative agent of Gl?sser disease, which is responsible for considerable financial losses in pig-rearing worldwide. To gain insight into the mechanisms involved in siderophore-mediated iron uptake in H. parasuis, genes in the H. parasuis ferric hydroxamate uptake (Fhu) region were amplified in the work being reported here. As has been described in A. pleuropneumoniae, an Fhu genomic region was also present in H. parasuis, being composed of four potential consecutive open reading frames (ORF) designated as fhuC, fhuD, fhuB, and fhuA, respectively. By immunoblotting, using a cross-reactive polyclonal antibody raised against Actinobacillus pleuropneumoniae FhuA protein, it was demonstrated that this protein was constitutively expressed in H. parasuis and its level of expression was not modified under conditions of restricted iron availability. This is the first report describing the presence of the fhu genes in H. parasuis. Our results indicate that FhuA protein expression is not affected under iron-restricted conditions, however, it is one of the targets of the humoral immune response.     

Lineages of acidophilic archaea revealed by community genomic analysis

Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)-based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16S ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of <0.006 cubic micrometer.