Multiplex real-time PCR for the detection and differentiation of equid herpesvirus 1 (EHV-1) and equid herpesvirus 4 (EHV-4)

A multiplex real-time PCR was designed to detect and differentiate equid herpesvirus 1 (EHV-1) and equid herpesvirus 4 (EHV-4). The PCR targets the glycoprotein B gene of EHV-1 and EHV-4. Primers and probes were specific to each equine herpesvirus type and can be used in monoplex or multiplex PCRs, allowing the differentiation of these two closely related members of the Alphaherpesvirinae. The two probes were minor-groove binding probes (MGB) labelled with 6-carboxy-fluorescein (FAM) and VIC for detection of EHV-1 and EHV-4, respectively. Ten EHV-1 isolates, six EHV-1 positive clinical samples, one EHV-1 reference strain (EHV-1.438/77), three EHV-4 positive clinical samples, two EHV-4 isolates and one EHV-4 reference strain (EHV-4 405/76) were included in this study. EHV-1 isolates, clinical samples and the reference strain reacted in the EHV-1 real-time PCR but not in the EHV-4 real-time PCR and similarly EHV-4 clinical samples, isolates and the reference strain were positive in the EHV-4 real-time PCR but not in the EHV-1 real-time PCR. Other herpesviruses, such as EHV-2, EHV-3 and EHV-5 were all negative when tested using the multiplex real-time PCR. When bacterial pathogens and opportunistic pathogens were tested in the multiplex real-time PCR they did not react with either system. The multiplex PCR was shown to be sensitive and specific and is a useful tool for detection and differentiation of EHV-1 and EHV-4 in a single reaction. A comprehensive equine herpesvirus disease investigation procedure used in our laboratory is also outlined. This procedure describes the combination of alphaherpesvirus multiplex real-time PCR along with existing gel-based PCRs described by other authors.     

Endoscopic assessment and treatment of lesions of the deep digital flexor tendon in the navicular bursae of 20 lame horses

REASONS FOR PERFORMING STUDY: Clinical lesions of the deep digital flexor tendon and navicular bone are being reported with increasing frequency. However, the role of direct visualisation by navicular bursoscopy in the diagnosis and management of such injuries has not been explored. HYPOTHESIS: Navicular bursoscopy: 1) corroborates information obtained from other, noninvasive imaging modalities; 2) allows direct visualisation of lesions unidentified by other diagnostic modalities; 3) provides further information on morphology of lesions; and 4) permits minimally invasive surgical access to lesions. METHODS: The case records of all horses that underwent diagnostic navicular bursoscopy for the investigation of lameness admitted to 2 referral clinics (the Royal Veterinary College and Reynolds House Referrals) were evaluated retrospectively. Follow-up information was obtained by telephone questionnaire. RESULTS: Twenty-three bursae were examined endoscopically in 20 horses. Tears of the deep digital flexor tendon were seen in all horses (22 bursae). In 8 bursae, cartilage lesions were also present and in one bursa this was the only abnormal finding. Computed tomography and low field magnetic resonance imaging predicted tendon lesions in most cases, but failed to identify cartilage damage. Greater than 6 month follow-up information was available for 15 animals of which 11 were sound and 9 had returned to preoperative levels of performance. CONCLUSION: Lameness localised to the foot may result from tears of the deep digital flexor tendon and/or navicular fibrocartilage loss. Navicular bursoscopy allows comprehensive evaluation of these changes and also permits appropriate lesion management. POTENTIAL RELEVANCE: The diagnostic information obtained from and therapeutic options offered by bursoscopy justify its use in horses with clinical findings localising lameness to the navicular bursa.     

Perceptions of veterinarians and clients to expressions of clinical uncertainty

OBJECTIVES: The aim of this study was to explore the attitudes of veterinarians and clients towards expressions of clinical uncertainty. METHODS: Questionnaires that assessed the respondent's attitudes towards expressions of clinical uncertainty were completed by clients at six small animal practices. In addition, questionnaires that evaluated what veterinarians thought their client's attitudes would be towards expressions of clinical uncertainty were completed by veterinarians. The responses from clients and veterinarians were statistically compared. RESULTS: Veterinarians significantly underestimated the desire of clients to be told about uncertainties in treatment and significantly overestimated how the expression of uncertainty would generally reduce client confidence. Veterinarians significantly overestimated the loss of client confidence resulting from saying "I am not sure about this" and from asking a nurse for advice. Both clients and veterinarians considered that verbal expressions of uncertainty would lead to a greater reduction in client confidence than behavioural expressions of uncertainty. CLINICAL SIGNIFICANCE: This study suggests that most clients want to be told about their veterinarian's clinical uncertainties, and how this uncertainty is expressed can markedly influence client confidence.     

The effect of irrigation and nitrogen fertilizer on rapeseed (Brassica napus) production in South-Eastern Australia

Summary A field trial was conducted to determine the response of rapeseed (Brassica napus cv. Marnoo) to two irrigation treatments and six nitrogen fertilizer treatments. Response to nitrogen was greater with than without irrigation. Oil content was increased with irrigation but decreased under increasing nitrogen application, and was inversely related to seed nitrogen concentration. Oil yields averaged 1,168 kg ha^–1 under irrigated treatments compared with 835 kg ha^–1 under rainfed treatments. Maximum oil yield (approx. 1,557 kg ha^–1) was obtained from the irrigated treatment fertilized with 100 kg N ha^–1 applied at sowing.     

Assessing the options for upland livestock systems under CAP reform: Developing and applying a livestock systems model within whole-farm systems analysis

This paper presents a scenario-based analysis of the impacts of Common Agricultural Policy (CAP) reform for upland agriculture using a Welsh case-study. Specifically the paper examines the impacts of the introduction of the single-farm payment (SFP), the modulation of direct payments under Pillar I of the CAP and the increase in agri-environment payments under Pillar II. Three enterprises are examined, upland sheep rearing with lamb finishing, spring- and autumn-calving suckler-cattle with calf rearing. These enterprises are modelled under conditions in 2002/3, 2004/5 and for the reformed CAP in 2005/6. To support this analysis a livestock system model (LSM) was implemented. The model assesses alternative management regimen using a flexible state-transition approach. This simplifies the realisation and parameterisation of potentially complex management regimen. The model tracks fodder requirements to achieve targets based on defined diets. The LSM underpins whole-farm analyses of stocking-rates, labour and other resource requirements and net-farm income. From the case study the paper concludes that the impacts of the introduction of the CAP reform on the financial performance of the systems are small but negative (a net reduction of around 5% in support). The larger reduction in direct payments (15–18%) is partially offset by agri-environment measures. The paper concludes that while SFP encourages a more market-oriented outlook, the adaptive capacity within systems as they stand is very limited. There are a range of possible adaptation strategies, but for the uplands the extensification of cattle systems by reducing stock numbers and cutting back on labour seems most probable.     

The effect of irrigation and nitrogen fertilizer on rapeseed (Brassica napes) production in South-Eastern Australia

Summary A field trial was conducted to determine the response of rapeseed (Brassica napus cv. Marnoo) to two irrigation treatments and six nitrogen fertilizer treatments. Dry matter accumulation, leaf area development and seed yield were measured. The dry matter and seed yield response to applied nitrogen was greater under irrigated compared to rainfed conditions. Maximum seed yield (approx. 3.8 t ha^–1) was obtained from the irrigated treatment receiving 100 kg N ha^–1 applied at sowing. This high rate of N application at sowing led to more rapid leaf area development and higher maximum LAI compared to treatments supplied with split application of the same amount of N at sowing and rosette stages. Greater partitioning of dry matter into the leaf component and higher specific leaf areas under the higher N regime were largely responsible for this increase. Higher maximum LAI's were associated with greater numbers of pods per plant, which combined with longer leaf area duration led to higher final seed yields.     

Glomalin in aggregate size classes from three different farming systems

Glomalin was measured in soil from farming systems managed for 8 years by chisel tillage (CT), more intensive tillage for organic (ORG) production, and no tillage (NT) on Acrisols (FAO Soil Units) in the Mid-Atlantic region of the U.S. Whole soil and aggregate size classes of >2.00, 0.50–2.00 and 0.21–0.50 mm (macroaggregates), 0.05–0.21 mm (microaggregates), and <0.05 mm (fine material) were examined. Glomalin-related soil protein (GRSP) was extracted from 1-g samples (four plots per treatment) with 100 mM sodium pyrophosphate, pH 9.0, at 121 °C in three extraction cycles. Extracts were pooled and quantified by using the Bradford protein assay. Concentrations of GRSP and total carbon (C) in aggregates were linearly related across aggregate size classes for all treatments (GRSP = 0.101C + 0.56, r² = 0.95). No tillage had significantly greater whole soil GRSP than did CT or ORG (P = 0.01). Mean values for GRSP in aggregates of NT were higher than for CT or ORG aggregates by 0.53 and 0.66 mg g⁻¹ aggregates, respectively. There were no differences among treatments in GRSP concentrations in fine material. In NT the concentration of GRSP increased as aggregate size increased in contrast to the disturbed treatments, CT or ORG, where there were no differences in GRSP concentration across aggregate size fractions. Larger proportions of GRSP were distributed in macroaggregates of NT compared to CT and ORG in contrast to larger proportions in microaggregates of CT and ORG than in NT. Although soil disturbance in ORG farming is greater than for CT farming, both treatments had similar GRSP concentrations and distributions.     

Growth of lucerne (Medicago sativa,L.) in response to frequency of irrigation and gypsum application on a heavy clay soil

Summary Effects of weekly (W) and fortnightly (F) irrigation schedules on established stands of lucerne (Medicago sativa L.) grown on gypsum treated (G) and untreated (C) heavy clay soil were investigated. Two irrigations were applied under the fortnightly regime and four under the weekly schedule during a single cutting cycle. Growth and light interception were measured during both the vegetative and mature phases of growth.Leaf expansion, light interception and dry matter production were greater under treatments W _G and W _C, with yield increasing from 3.4 t ha^–1 under the fortnightly schedule to 5.0 t ha-1 with weekly irrigation. Gypsum treatment was effective under the more frequent irrigation schedule. Specific leaf area and the proportion of stem were both increased by treatments W _G and W _C. The responses to irrigation were therefore characteristic of those elicited by a more favourable plant moisture status. Growth was analysed in terms of light interception, the efficiency of utilisation of intercepted light, the proportion of the daily dry matter gain retained by the leaves and leaf expansion. The analysis demonstrated that impaired leaf expansion contributed to a decline of approximately 15% in yield, and that impaired efficiencies of utilisation of intercepted light contributed to losses of approximately 30% under the less frequent irrigation schedule.A comparison of growth rates and efficiencies of energy conversion with published data showed that satisfactory rates of growth and levels of productivity were achieved on the heavy soils of the local region using gypsum treatment and the more frequent irrigation schedule.     

The future of tropical species in secondary forests: A quantitative review

Deforestation and degradation of tropical old-growth forests has the potential to cause catastrophic species extinctions. In this review, we assess whether regenerating secondary forests (SF) can support species typically found in old-growth forest (OG) and so prevent extinctions. We review 65 studies that compare faunal diversity in SF and corresponding OG, and compare the similarity of species composition both within and between these two forest types using the Sorensen, Morisita-Horn and Sorensen-Chao indices. Comparisons between traditional similarity indices and Sorensen-Chao, which minimizes sampling biases, indicated that limited sampling effort consistently reduced apparent similarity between SF and OG and that similarity between SF and OG is actually higher than previously appreciated. Similarity, which ranges from 0 to 1, varied from 0.49 to 0.92 between replicate OG sites and was correlated with similarity between SF and OG. This correlation might be an artefact of variation among studies in sampling effort, especially for vertebrates where small samples reduce apparent similarity across all comparisons, as well as a real effect of variation among studies in landscape heterogeneity and the presence of species with patchy distributions. Therefore, similarity between SF and OG cannot be interpreted without an understanding of background variation in OG. Similarity between different SF sites provided no evidence that disturbance specialists dominate SF. Similarity to OG increased rapidly with SF age; when SF was contiguous with OG; when SF was growing in small clearings; and after low intensity land uses including clearing only, shifting agriculture and tree plantations. This describes the most frequently observed tropical SF; isolated from roads and on hilly terrain unsuitable for mechanized agriculture. Thus, our analyses indicate that tropical SF can play an important role in biodiversity conservation particularly when OG forests are nearby. An important caveat remains, however. Abundance, geographic range and levels of habitat specialization are often related. Widespread, abundant, habitat generalists might dominate similarity analyses even when relatively rare OG specialists are present. Additional species-level analyses of habitat specialization will be needed before the conservation value of tropical SF is fully understood.     

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.