Broad range 16S rRNA gene PCR compared to bacterial culture to confirm presumed synovial infection in horses

The objectives of the present study were to evaluate the accuracy of broad range 16S rRNA gene PCR compared to bacterial culture for the detection of synovial infection in horses. The study included 57 synovial fluid samples from horses with presumed synovial infection and a control group consisting of 31 synovial fluid samples originating from clinically normal horses and horses with aseptic synovial inflammation. All samples were analysed by 16S PCR with reverse line blot (RLB) hybridisation. Synovial fluid samples were cultured using conventional agar plate methods (APM) and/or blood culture medium (BCM). The results of the study showed a superior detection rate (89.5%) for 16S PCR with RLB. Bacterial culture had lower sensitivity, but highly acceptable detection rates (77.6%) were observed using BCM. APM had very low sensitivity (37.8%) and infection was never detected by plate isolation without positive incubation in BCM. The highest sensitivity (91.8%) for the detection of synovial infection was achieved when the results of incubation in BCM and 16S PCR were combined. For all the tests, the specificity was higher than 90%.     

Evolution of farm management, nitrogen efficiency and economic performance on Dutch dairy farms reducing external inputs

The implementation of the statutory Mineral Accounting System (MINAS) in the Netherlands in the period 1998–2003 required large reductions in nutrient inputs of dairy farms. Patterns in farm management adjustments throughout 6 years and their effectiveness in terms of nitrogen use efficiency (NUE) and economic performance were evaluated for 45 commercial farms participating in a regional nutrient management project.

Six groups of farms were identified that differed in initial NUE and the change therein. Three groups of farms that were able to rapidly reduce fertilizer N input and establish a consistent farm management strategy were most successful in improving NUE. These farms had a higher gross margin per 100 kg milk than farms without a consistent strategy. The three effective strategies were primarily characterized by (i) continuous, gradual adjustment of the integrated farm management combined with a slight reduction in milk production per ha (re-balancing) versus increasing productivity per animal, thereby reducing maintenance N requirements, while (ii) maintaining or (iii) increasing the production intensity per ha. It was concluded that different approaches to improve NUE can be successful, also in economic terms, although a direct relationship between NUE and gross margin was not observed. The probably implicit choice for adoption of a strategy may be governed by farm endowment and the farmer's skills and objectives.     

Estimating the impacts of water pricing on smallholder irrigators in North West Province, South Africa

Worldwide growing water scarcity has increased the call for economic instruments to stimulate rational water use in agriculture. Furthermore, cost-recovery is now widely accepted as a cornerstone of sustainable water management. In many developing countries, where agricultural water use is often still subsidised, water pricing policies are developed for allocating water efficiently and achieving sustainability of water systems. However, the impacts of water pricing policies on irrigation water use and on farm production systems is mostly unknown. We introduce an innovative two-stage methodology that allows estimating these effects at farm level. Applying the method to small-scale irrigators in South Africa, we show that water demand is quite responsive even to small changes in water price. In addition, the introduction of a water price significantly decreases farm profit. This appears to be a problem primarily for the poorer farmers.     

Moisture movement and thickness swelling in oriented strandboard. Part 2: Analysis using a nuclear magnetic resonance imaging body scanner

The previous paper in this series demonstrates the use of a nuclear magnetic resonance (NMR) micro-imaging system to observe the movement of liquid water through small specimens (11 × 16 mm² cross-section) of oriented strandboard (OSB) and solid wood. In the present paper, a NMR body scanner is utilized to obtain images of moisture penetration into ASTM D 1037–99 standard sized (152 × 152 mm²) thickness swelling specimens at different intervals during water soaking. As with the micro-imaging study, silicone was applied to the surfaces and edges of some of the specimens in order to observe the directional characteristics of moisture movement through OSB. Specimens with commercially applied edge sealant were also included in the study in order to observe the effectiveness of the sealant of reducing moisture penetration and thickness swelling. The presence of voids and areas of low density were shown to contribute significantly to moisture penetration into the specimens.     

An enrichment microsphere immunoassay for the detection of <Emphasis Type="Italic">Pectobacterium atrosepticum</Emphasis> and <Emphasis Type="Italic">Dickeya dianthicola</Emphasis> in potato tuber extracts

An enrichment microsphere immunoassay (MIA) was developed, based on the Luminex xMAP® technology, for the simultaneous (duplex) detection of Pectobacterium atrosepticum (former name Erwinia carotovora subsp. atroseptica) (Pca) and Dickeya dianthicola (former name Erwinia chrysanthemi) (Dcd) in potato plant extracts. Target bacteria in the extracts were enriched for 48 h in a semi-selective broth containing polypectate under low oxygen conditions. Samples were subsequently incubated with antibody-coated colour-coded microspheres (beads) and with secondary antibodies conjugated with Alexa Fluor® 532, a reporter dye. Samples were analyzed with the Luminex analyzer, in which one laser identified each microsphere and another laser the reporter dye conjugated to the secondary antibodies. The assay required minimal sample preparation, could be completed in 1 h, was performed in 96 wells microtitreplates and required no wash steps. The limit of detection for the duplex enrichment MIA was 100–1000 cfu ml^?1, which was a hundred times lower than of an enrichment-ELISA. Without enrichment, the sensitivity of MIA and ELISA was largely similar and ranged between 10⁶ and 10⁷ cells ml^?1. No difference in sensitivity was found between a MIA in a single or duplex format. In a comparative test with non-infected potato plant extracts and extracts from plants infected with Pca or Dcd, results of the enrichment MIA correlated well with those of the enrichment ELISA and enrichment PCR. These results indicate that MIA can be reliably used for multiplex detection of soft rot Enterbacteriaceae in crude potato plant extracts. The technology is an attractive and cost-effective alternative to other detection methods, including ELISA.     

Involvement of mammalian Mus81 in genome integrity and tumor suppression

Mus81-Eme1 endonuclease has been implicated in the rescue of stalled replication forks and the resolution of meiotic recombination intermediates in yeast. We used gene targeting to study the physiological requirements of Mus81 in mammals. Mus81-/- mice are viable and fertile, which indicates that mammalian Mus81 is not essential for recombination processes associated with meiosis. Mus81-deficient mice and cells were hypersensitive to the DNA cross-linking agent mitomycin C but not to gamma-irradiation. Remarkably, both homozygous Mus81-/- and heterozygous Mus81+/- mice exhibited a similar susceptibility to spontaneous chromosomal damage and a profound and equivalent predisposition to lymphomas and other cancers. These studies demonstrate a critical role for the proper biallelic expression of the mammalian Mus81 in the maintenance of genomic integrity and tumor suppression.     

Conditional dynamics of interacting quantum dots

Conditional quantum dynamics, where the quantum state of one system controls the outcome of measurements on another quantum system, is at the heart of quantum information processing. We demonstrate conditional dynamics for two coupled quantum dots, whereby the probability that one quantum dot makes a transition to an optically excited state is controlled by the presence or absence of an optical excitation in the neighboring dot. Interaction between the dots is mediated by the tunnel coupling between optically excited states and can be optically gated by applying a laser field of the right frequency. Our results represent substantial progress toward realization of an optically effected controlled-phase gate between two solid-state qubits.     

The ecoresponsive genome of Daphnia pulex

We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.     

Regional Sediment Deficits in the Dutch Lowlands: Implications for Long-Term Land-Use Options (8 pp)

Background, Aim and Scope   Coastal and river plains are the surfaces of depositional systems, to which sediment input is a parameter of key-importance. Their habitation and economic development usually requires protection with dikes, quays, etc., which are effective in retaining floods but have the side effect of retarding sedimentation in their hinterlands. The flood-protected Dutch lowlands (so-called dike-ring areas) have been sediment-starved for up to about a millennium. In addition to this, peat decomposition and soil compaction, brought about by land drainage, have caused significant land subsidence. Sediment deficiency, defined as the combined effect of sediment-starvation and drainage-induced volume losses, has already been substantial in this area, and it is expected to become urgent in view of the forecasted effects of climate change (sea-level rise, intensified precipitation and run-off). We therefore explore this deficiency, compare it with natural (Holocene) and current human sediment inputs, and discuss it in terms of long-term land-use options. Materials and Methods: We use available 3D geological models to define natural sediment inputs to our study area. Recent progress in large-scale modelling of peat oxidation and compaction enables us to address volume loss associated with these processes. Human sediment inputs are based on published minerals statistics. All results are given as first-order approximations. Results: The current sediment deficit in the diked lowlands of the Netherlands is estimated at 136 ± 67 million m3/a. About 85% of this volume is the hypothetical amount of sediment required to keep up with sea-level rise, and 15% is the effect of land drainage (peat decomposition and compaction). The average Holocene sediment input to our study area (based on a total of 145 km3) is ~14 million m3/a, and the maximum (millennium-averaged) input ~26 million m3/a. Historical sediment deficiency has resulted in an unused sediment accommodation space of about 13.3 km3. Net human input of sediment material currently amounts to ~23 million m3/a. Discussion: As sedimentary processes in the Dutch lowlands have been retarded, the depositional system's natural resilience to sea-level rise is low, and all that is left to cope is human countermeasure. Preserving some sort of status quo with water management solutions may reach its limits in the foreseeable future. The most viable long-term solutions therefore seem a combination of allowing for more water in open country (anything from flood-buffer zones to open water) and raising lands that are to be built up (enabling their lasting protection). As to the latter, doubling or tripling the use of filling sand in a planned and sustained effort may resolve up to one half of the Dutch sediment deficiency problems in about a century. Conclusions: Conclusions, Recommendations and Perspectives. We conclude that sediment deficiency – past, present and future – challenges the sustainable habitation of the Dutch lowlands. In order to explore possible solutions, we recommend the development of long-term scenarios for the changing lowland physiography, that include the effects of Global Change, compensation measures, costs and benefits, and the implications for long-term land-use options. Recommendations and Perspectives: -