Evaluation of radiometric faecal culture and direct PCR on pooled faeces for detection of Mycobacterium avium subsp. paratuberculosis in cattle

Dilution rates for pooled faecal culture (PFC) and direct IS900 polymerase chain reaction (D-PCR) tests were evaluated on faecal samples from infected cows mixed with uninfected faeces in dilutions from 1 in 5 to 1 in 50. PFC was performed by radiometric culture, with confirmation by IS900 PCR and restriction endonuclease analysis (PCR/REA) on growth, and by mycobactin dependency testing on solid medium. Using 37 culture positive faecal samples from 12 subclinical cows, 83.8% and 94.6% of samples were confirmed positive in the PFC assay at dilutions of 1 in 50 and 1 in 30, respectively. Lower dilutions (1 in 5 to 1 in 20) provided only marginally better sensitivity, and confirmation of PFC growth by PCR/REA was significantly more sensitive than mycobactin dependency. D-PCR had significantly lower sensitivity than PFC confirmed by PCR/REA, with pools of 1 in 50, 30, 10 and 5 yielding positive results in 64.9%, 70.3%, 78.4% and 83.8% of samples, respectively. Cattle considered to be shedding 1.5 x 10(6) viable M. avium subsp. paratuberculosis (Map)/g faeces (on the basis of estimated losses in processing and growth rates in radiometric broth) were positive at dilutions up to 1 in 50 in the PFC and D-PCR. Those shedding 5 x 10(5) viable Map/g were positive in the PFC at dilutions up to 1 in 40, but required a 1 in 10 dilution or less for D-PCR. The results suggest that for cattle shedding relatively high concentrations of Map in faeces (>2 x 10(5) viable Map/g), maximal dilutions of 1 in 30 for PFC and 1 in 10 for D-PCR would be applicable.     

Incidence and effects of West Nile virus infection in vaccinated and unvaccinated horses in California

A prospective cohort study was used to estimate the incidence of West Nile virus (WNV) infection in a group of unvaccinated horses (n = 37) in California and compare the effects of natural WNV infection in these unvaccinated horses to a group of co-mingled vaccinated horses (n = 155). Horses initially were vaccinated with either inactivated whole virus (n = 87) or canarypox recombinant (n = 68) WNV vaccines during 2003 or 2004, prior to emergence of WNV in the region. Unvaccinated horses were serologically tested for antibodies to WNV by microsphere immunoassay incorporating recombinant WNV E protein (rE MIA) in December 2003, December 2004, and every two months thereafter until November 2005. Clinical neurologic disease attributable to WNV infection (West Nile disease (WND)) developed in 2 (5.4%) of 37 unvaccinated horses and in 0 of 155 vaccinated horses. One affected horse died. Twenty one (67.7%) of 31 unvaccinated horses that were seronegative to WNV in December, 2004 seroconverted to WNV before the end of the study in November, 2005. Findings from the study indicate that currently-available commercial vaccines are effective in preventing WND and their use is financially justified because clinical disease only occurred in unvaccinated horses and the mean cost of each clinical case of WND was approximately 45 times the cost of a 2-dose WNV vaccination program.     

Intra- and interobserver assessments of intestinal wall thickness and segmentations from transverse sections of feline abdominal ultrasound images

Measurements of intestinal wall thicknesses from ultrasound imaging (US) are routinely used to support diagnoses of intestinal disorders in cats, however published studies describing observer agreement are currently lacking. The aim of this retrospective, observer agreement study was to quantify inter- and intraobserver repeatability and agreement in the measurement of intestinal wall layer thicknesses and the segmentation of transverse sections of small intestines in US images of 20 cats. Intestinal wall layer thickness measurements of the mucosa, submucosa, muscularis, serosa layer, and total thickness of these layers were performed on five cats with small cell epitheliotropic lymphoma, five with inflammatory bowel disease, and 10 with other conditions. Thickness measurements and the segmentation encompassing the serosa layer were obtained from five observers four times non-sequentially. The average standard deviation in thickness measurements (95% confidence interval) in the mucosa, submucosa, muscularis, serosa, and total thickness were 0.35 (0.07–0.95), 0.24 (0.07-0.52), 0.22 (0.06-0.49), 0.20 (0.05-0.49), and 0.57 (0.11-1.60) mm, respectively. The average intraclass correlation coefficients, which estimates the degree of consistency in thickness measurements and segmentation areas for each observer, ranged from 0.355 to 0.870 and 0.850 to 0.993, respectively. The interclass correlation coefficient, which estimates the degree of consistency when measuring a thickness or segmentation area over all observers ranged from 0.115 to 0.753, and 0.811 to 0.902, respectively. The overall average Dice Coefficient, which estimates the extent of overlap of the segmentations for all observers was 0.957 (0.933 to 0.972). Our results suggest segmentations of small intestines have a higher interobserver agreement than measurements of intestinal wall thicknesses.     

Interpretation of solute profile dynamics in irrigated soils

Summary Knowledge of the flux of water flowing through macropores in soils is required to devise management strategies for efficient fertiliser use and to prevent fast movement of solutes and pollutants to groundwaters. Water and solute balances in soil profiles were used to develop a simple model for assessing the magnitude of macropore flow. Fluxes of water bypassing the soil matrix were calculated at 35 sites to be between 0 and 415 mm y^–1, with the flux being < 200 mm y^–1 at most sites. The maximum flux was three times the flux flowing through the soil matrix but only one third of that infiltrating the soil. The flux of macropore flow was not simply related to soil types or soil properties, although the highest fluxes did occur in cracking soils. A qualitative method of using soil chloride profiles to indicate the occurrence (but not magnitude) of bypass flux was also demonstrated. Both these quantitative and qualitative assessments of bypass flow should assist in interpreting root-zone hydrology in soils.     

The River Wadu role play — ten years experience

This paper describes a role playing planning exercise that has been used for training agriculturists, engineers and agricultural economists for more than ten years. It sets out the objectives and key features of the exercise and the experience that has been gained in its use. The exercise has been found to successfully test and integrate subject matter expertise acquired from formal teaching. It also highlights the multiple and often conflicting objectives of irrigation planning, and the need for full evaluation of alternatives and sound technical judgements under conditions of inadequate data and time pressure. The exercise is also successful in developing professional personal skills such as group working, interviewing and presentation, and is recommended as an effective training aid.     

A postscript: Macroeconomics and structural adjustment — the minimum for water sector specialists

The need for a grasp of macroeconomic concepts and methods for microeconomists and technical specialists is stressed. At this juncture policy failure is commonplace. Experience in using the World Bank Structural Adjustment in Lowinca as a training exercise is discussed.     

Irrigation and food security in the 21st century

Global food projections indicate that food prices in the next threedecades will likely be stable or decline, but progress inreducing malnutrition in developing countries will be slow. Smallshortfalls in crop productivity growth would lead to rising foodprices and worsening malnutrition. Increased food production fromirrigation is essential, and will require expansion of irrigatedarea and water supplies, and improved efficiency of use of existingwater supplies. Neither of these growth factors will prove easy, andboth will require complex institutional and policy reforms. Failureto meet food production needs through efficient expansion andintensification of irrigated agriculture would increase pressure onland resources and hasten the process of environmental degradation.Irrigation and water development strategies have been hampered bya lack of understanding of the links between water scarcity, foodproduction, food security, and environmental sustainability.Research to improve this understanding would have high payoffs.     

Evaporation from fetch-limited water bodies

An analytic model to calculate evaporation from fetch-limited water bodies is described. By modifying the surface boundary condition to an analytic solution to the advection-diffusion equation for specific humidity in the air flow over a water body, we are able to solve for the entire specific humidity field q (x, z) from a single measurement of humidity, surface temperature, and wind speed. Comparisons of model predictions with measurements from Rushy Billabong, a small turbid lake, over a 146 day period show that on average the model underestimates evaporation rates by 12%. We believe that the evaporation shortfall is due to the downwind advection of heat within the billabong when the billabong is highly stratified in temperature. When the thermal stratification is weak, the advection of heat within the water column is less important and the model is an accurate predictor of evaporation.