Molecular epidemiology of two fowl cholera outbreaks on a free-range chicken layer farm.

Two outbreaks of fowl cholera on a multiage free-range egg farm were investigated. The outbreaks occurred in 1994 and 2002. A total of 22 strains of Pasteurella multocida were available for study, 11 from the 1994 outbreak and 11 from the 2002 outbreak. Lesions typical of acute fowl cholera were seen in the 1994 outbreak, whereas both acute and chronic fowl cholera occurred in the 2002 outbreak. The isolates were examined in an extended phenotypic typing methodology, by a P. multocida-specific polymerase chain reaction (PCR), by the Heddleston somatic serotyping scheme, and by restriction endonuclease analysis (REA) typing using the enzyme HpaII. All 22 strains had the same phenotypic properties, all were confirmed as P. multocida by PCR, all were Heddleston serovar 4, and all had the same REA pattern. The results indicate that these 2 outbreaks were caused by the same clone of P. multocida--despite the 8-year time period between the outbreaks.     

Evaluation of concurrent perineal hernia in adult male dogs presenting with nontraumatic,acquired inguinal hernias

A possible association between the development of nontraumatic, acquired inguinal hernias (NAIH) and perineal hernias (PH) has been postulated in adult dogs. The objective of this study was to evaluate the frequency of concurrent diagnosis of PH in dogs presented with NAIH and determine potential risk factors for concurrent PH and NAIH. Medical records of adult male dogs presented for NAIH to 4 hospitals between 2007 and 2017 were retrospectively reviewed. Twenty-one dogs with NAIH were included, 8 of which had concurrent PH. There were no significant differences between dogs with and without PH; however, among dogs with both conditions, intact dogs (8.1 ± 1.4 years) were younger than neutered dogs (11.7 ± 1.0 years; P = 0.007). Thirty-eight percent of male dogs presenting for NAIH had concurrent PH, indicating that these conditions commonly occur together. Dogs presenting for NAIH should be carefully evaluated for concurrent PH before surgical intervention.     

Validation of the periodicity of growth zone formation in the otoliths of four fish species from the Upper Zambezi ecoregion,southern Africa

In the Upper Zambezi and Okavango ecoregions, Brycinus lateralis, Hepsetus cuvieri, Schilbe intermedius and Serranochromis macrocephalus are important in subsistence fisheries, while S. intermedius and S. macrocephalus are often caught in commercial catches. Despite their importance, there is little information on their age and growth and age validation. Growth zone deposition rate in otoliths of B. lateralis, H. cuvieri, S. intermedius and S. macrocephalus was validated as annual using edge analysis in this study. Annual deposition of growth zones was corroborated by a fluorochrome marking experiment. Both methods demonstrated that one growth zone was deposited annually. Edge analysis demonstrated that the highest proportion of opaque zones was detected between August and December, most likely as a result of slow growth during lower temperature water during the preceding winter. With growth zone deposition validated as annual, future research should focus on determining the growth, maturity and mortality rates of these species, parameters which are important for their management.     

Key Factors Affecting Reproductive Success of Thoroughbred Mares and Stallions on a Commercial Stud Farm

To evaluate factors contributing to fertility of thoroughbred mares, data from 3743 oestrous periods of 2385 mares were collected on a large thoroughbred farm in Ireland. Fourteen stallions (mean age 8.3 years; range 4–15 years) had bred 2385 mares (mean age 9.4 years; range 3–24 years). Maiden mares accounted for 12%, mares with a foal at foot for 64%, and barren, slipped or rested mares for 24% of the total. The mean pregnancy rate per cycle was 67.8% (68.6% in year 1 and 66.9% in year 2). Backward stepwise multivariable logistic regression analysis was utilized to develop two models to evaluate mare factors, including mare age, reproductive status, month of foaling, dystocia, month of cover, foal heat, cycle number, treatments, walk‐in status and stallion factors including stallion identity, stallion age, shuttle status, time elapsed between covers and high stallion usage on the per cycle pregnancy rate and pregnancy loss. Old age (p < 0.001) and cover within 20 days post‐partum (p < 0.003) were associated with lowered pregnancy rates. High mare age (p < 0.05) and barren, slipped or rested reproductive status (p = 0.05) increased the likelihood of pregnancy loss. Uterine inflammation or infection, if appropriately treated, did not affect fertility. Only high usage of stallions (used more than 21 times in previous week) was associated with lowered (p = 0.009) pregnancy rates. However, shuttle stallions were more likely to have increased (p = 0.035) pregnancy survival, perhaps reflecting a bias in stallion selection. In conclusion, mare age exerted the greatest influence on fertility; nonetheless, thoroughbreds can be effectively managed to achieve high reproductive performance in a commercial setting.     

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.

     

Metsulfuron methyl sorption-desorption in field-moist soils

Pesticide sorption coefficients (K(d)) are generally obtained using batch slurry methods. As a consequence, the results may not adequately reflect sorption processes in field-moist or unsaturated soil. The objective of this study was to determine sorption of metsulfuron methyl, a weak acid, in field-moist soils. Experiments were performed using low density (i.e., 0.3 g mL(-)(1)) supercritical fluid carbon dioxide (SF-CO(2)) to convert anionic metsulfuron methyl to the molecular species and remove it from the soil water phase only, thus allowing calculation of sorption coefficients (K(d)) at low water contents. K(d) values for sorption of the metsulfuron methyl molecular species on sandy loam, silt loam, and clay loam soil at 11% water content were 120, 180, and 320 mL g(-)(1), respectively. Using neutral species K(d) values, the pK(a) of metsulfuron methyl, and the pH of the soil, we could successfully predict the K(d) values obtained using the batch slurry technique, which typically has a predominance of anionic species in solution during the sorption characterization. This application of supercritical fluid extraction to determine sorption coefficients, combined with sulfonylureas' pK(a) values and the soil pH, will provide an easy method to predict sorption in soil at different pH levels.     

Factors influencing the abundance of three common nearshore fishes in south‐west Lake Michigan

Variation in the distribution and abundance of nearshore fishes is critical to understand food web processes and fishery management issues in Lake Michigan. This study characterised patterns in abundance of three common nearshore species, yellow perch Perca flavescens (Mitchell), round goby Neogobius melanostomus (Pallas) and alewife Alosa pseudoharengus (Wilson), in relation to spatio‐temporal, abiotic and biotic factors using gillnet sampling conducted across 5 years at multiple locations representing different substrates. Significant variations were observed in alewife and round goby catches between locations. A negative relationship between round goby and age‐0 yellow perch catch was observed, indicating potential competition between the two species. This study demonstrates that variability in nearshore fish communities can be driven by factors including substrate and interspecific interactions. Given the prominent role these species play in Lake Michigan's food web and thus their importance to fishery production, a thorough understanding of these factors is warranted.     

Exploring Patterns of Exotic Earthworm Distribution in a Temperate Hardwood Forest in South-Central New York, USA

Exotic earthworms invading forests in Canada and northeastern United States that were naturally devoid of large detritivores cause major changes in ecosystem function. To assess their long-term impacts, studies are needed to elucidate the factors that control the patterns of earthworm invasion at the landscape level. We analyzed the distribution patterns of exotic earthworms in a northern hardwood forest in south-central New York (USA), as explained by landscape variables thought to be important in determining earthworm distribution. Forest type, slope angle, elevation, and the distance to agricultural clearings and wet refugia were significant predictors of earthworm presence, whereas local wetness index and the distance to streams and roads were not. Forest type and distance to agricultural clearings were the two most significant predictors. Our data suggest that areas close to agricultural clearings, dominated by mixed hardwoods, and located towards valley bottoms or on gentle slopes are very likely to support communities of exotic earthworms. Steeper slopes, areas dominated by American beech or eastern hemlock, and locations in the core of extensive forest landscapes have lower probabilities of invasion by exotic earthworms. When applied to a nearby area, our statistical model correctly predicted earthworm presence for 67% of 377 sampling points. Most of the mistakes were incorrect predictions of earthworm absence, suggesting that our statistical model slightly underestimated earthworm presence, possibly because of the pervasive influence of active agricultural fields adjacent to the test site.     

Swine trichinosis in mid-atlantic slaughterhouses: Possible relationship to hog marketing systems

Digests of diaphragms from 33 482 hogs slaughtered in the mid-atlantic states were examined for the presence of Trichinella spiralis larvae. The samples were obtained from 7 slaughterhouses, ranging in slaughter capacity from less than 50 per day to more than 4000 per day. The sources of the hogs varied from “backyard” operations, raising hogs for home use, to commercial farms. The means by which hogs were brought to the slaughterhouse also differed; the larger slaughterhouses often purchased directly from the producer while the smaller slaughterhouses (1000 hogs per day or less) usually purchased through dealers or brokers. Infected hogs were detected more frequently than was expected from previously-published prevalence studies; overall, 0.58% of samples examined contained T. spiralis larvae. All of the infected hogs were marketed through the smaller slaughterhouses (less than 1000 per day) and nearly all were marketed through brokers. The mean number of larvae per gram of diaphragm, determined by slaugterhouses type, ranged from 0.5 to 74.6; most infections were light although 5 had counts of 1000–2480.Most of the positive samples were obtained from one slaughterhouse, the data from which exhibited marked differences in the frequency of infection by day of the week; 128 positive samples of the total of 190 found were obtained on Fridays, although only 10% of all samples were obtained on that day. Analysis of the geographic origin of shipments containing infected hogs revealed that most originated in New Jersey and Pennsylvania, although the hogs shipped from the latter state might originated in New England or Maryland. Attempts to trace back infected hogs for further epidemiological investigation were largely futile, owing to the absence of an identification system.