Spatial clustering of swine influenza in Ontario on the basis of herd-level disease status with different misclassification errors

This approach maximizes sensitivity of serology-based monitoring systems by considering spatial clustering of herds classified as false positive by herd testing, allowing outbreaks to be detected in an early phase. The primary objective of this study was to determine whether swine herds infected with influenza viruses cluster in space, and if so, where they cluster. The secondary objective was to investigate the combining of a multivariate spatial scan statistic with herd test results to maximize the sensitivity of the surveillance system for swine influenza. We tested for spatial clustering of swine influenza using the Cuzick–Edwards test as a global test. The location of the most likely spatial clusters of cases for each subtype and strain in a sample of 65 sow and 72 finisher herds in 2001 (Ontario, Canada), and 76 sow herds in 2003 (Ontario, Canada) was determined by a spatial scan statistic in a purely spatial Bernoulli model based on single and multiple datasets.

A case herd was defined by true herd-disease status for sow or finisher herds tested for H1N1, and by apparent herd-disease status for sow herds tested for two H3N2 strains (A/Swine/Colorado/1/77 (Sw/Col/77) and A/Swine/Texas/4199-2/98 (Sw/Tex/98)). In sow herds, there was no statistically significant clustering of H1N1 influenza after adjustment for pig-farm density. Similarly, spatial clustering was not found in finisher herds. In contrast, clustering of H3N2 Sw/Col/77 (prevalence ratio = 12.5) and H3N2 Sw/Tex/98 (prevalence ratio = 15) was identified in an area close to a region with documented isolation of avian influenza isolates from pigs.

For the H1N1 subtype tested by ELISA, we used an approach that minimized overall misclassification at the herd level. This could be more applicable for detecting clusters of positive farms when herd prevalence is moderate to high than when herd prevalence is low. For the H3N2 strains we used an approach that maximized herd-level sensitivity by minimizing the herd cut-off. This is useful in situations where prevalence of the pathogen is low. The results of applying a multivariate spatial scan statistic approach, led us to generate the hypothesis that an unknown variant of influenza of avian origin was circulating in swine herds close to an area where avian strains had previously been isolated from swine. Maximizing herd sensitivity and linking it with the spatial information can be of use for monitoring of pathogens that exhibit the potential for rapid antigenic change, which, consequently, might then lead to diminished cross-reactivity of routinely used assays and lower test sensitivity for the newly emerged variants. Veterinary authorities might incorporate this approach into animal disease surveillance programs that either substantiate freedom from disease, or are aimed at detecting early incursion of a pathogen, such as influenza virus, or both.     

Assessment of Genetic Variability in the Coding Sequence of Melatonin Receptor Gene (MTNR1A) in Tropical Arid Sheep Breeds of India

Seasonal behaviour in sheep, which varies in tropical and temperate environmental conditions, is a matter of study, because it can provide a clue to address the problem of seasonality in sheep. Melatonin receptor is the membrane‐bound G‐coupled receptor, sensing the message of photoperiodic cues thorough melatonin. Restriction fragment length polymorphism (RFLP) studies were carried out to assess the variability of gene at G612A and C606T SNPs in MTNR1A gene, which have been studied to be markers for out‐of‐season breeding. Allelic frequency distribution corresponded to higher frequency of GG and CC genotype, in tropical arid sheep breed in comparison with temperate region sheep breed. PCR amplification of MTNR1A gene of 30 animals was performed and single nucleotide polymorphisms (SNPs) identification was carried out using Lasergene software. Seven SNPs/mutations were identified, but most of them were synonymous, except the one G706A, leading to substitution of valine by isoleucine. Polyphen‐2 analysis of G706A mutation revealed that it is a benign mutation. Two important SNPs C426T and G555A, which were identified in temperate sheep breeds, could not be traced in Magra and Marwari breeds of sheep. Thus, the Magra and Marwari breeds of tropical, arid region demonstrated the presence of both polymorphic SNPs markers G612A and C606T, associated with out‐of‐season breeding. GG and CC genotypes were having a higher prevalence in the studied population.     

Estimating the mass of asteroid 253 mathilde from tracking data during the NEAR flyby

The terminal navigation of the Near Earth Asteroid Rendezvous (NEAR) spacecraft during its close flyby of asteroid 253 Mathilde involved coordinated efforts to determine the heliocentric orbits of the spacecraft and Mathilde and then to determine the relative trajectory of the spacecraft with respect to Mathilde. The gravitational perturbation of Mathilde on the passing spacecraft was apparent in the spacecraft tracking data. As a result of the accurate targeting achieved, these data could be used to determine Mathilde's mass as 1.033 (+/- 0.044) x 10(20) grams. Coupled with a volume estimate provided by the NEAR imaging team, this mass suggests a low bulk density for Mathilde of 1.3 grams per cubic centimeter.     

In situ evidence for an ancient aqueous environment at Meridiani Planum, Mars

Sedimentary rocks at Eagle crater in Meridiani Planum are composed of fine-grained siliciclastic materials derived from weathering of basaltic rocks, sulfate minerals (including magnesium sulfate and jarosite) that constitute several tens of percent of the rock by weight, and hematite. Cross-stratification observed in rock outcrops indicates eolian and aqueous transport. Diagenetic features include hematite-rich concretions and crystal-mold vugs. We interpret the rocks to be a mixture of chemical and siliciclastic sediments with a complex diagenetic history. The environmental conditions that they record include episodic inundation by shallow surface water, evaporation, and desiccation. The geologic record at Meridiani Planum suggests that conditions were suitable for biological activity for a period of time in martian history.     

Rigidin E,a New Pyrrolopyrimidine Alkaloid from a Papua New Guinea Tunicate Eudistoma Species

A new pyrrolopyrimidine alkaloid, rigidin E (1) and the known metabolites rigidin (2) and 1-methylherbipoline (3) have been isolated from a Papua New Guinea tunicate Eudistoma sp. A combination of spectroscopic data were used to determine the structures of these metabolites.     

Determination of Solute Organic Concentration in Contaminated Soils Using a Chemical-equilibrium Soil Column System

Groundwater risk assessment of contaminated soils implies determination of the solute concentration leaching out of the soil. Determination based on estimation techniques or simple experimental batch approach has proven inadequate. Two chemical equilibrium soil column leaching tests for determination of solute concentration in a contaminated soil were developed; (1) a chemical Equilibrium and Recirculation column test for Volatile organic chemicals (ER-V) and (2) a chemical Equilibrium and Recirculation column test for Hydrophobic organic chemicals (ER-H). The two test systems were evaluated using two soils with different content of organic carbon (f_oc of 1.5 and 6.5%, respectively). A quadruple blind test of the ER-V system using glass beads in stead of soil showed an acceptable recovery (65–85%) of all of the 11 VOCs tested. Only for the most volatile compound (heptane, K_H～80) an unacceptable recovery was found (9%). The contact time needed for obtaining chemical equilibrium was tested in the ER-H system by performing five test with different duration (1, 2, 4, 7 and 19 days) using the low organic carbon soil. Seven days of contact time appeared sufficient for achieving a solute equilibrium concentration. The repeatability of both test systems (evaluated by performing five identical tests) was considered acceptable (8–16% and 7–28% for the ER-V and ER-H system, respectively). Comparing determined solute concentration in both systems for volatile and hydrophobic chemicals with estimated concentrations using an K_ow–K_oc relation and determined total soil concentrations, large differences between measured and estimated solute concentrations were observed, especially for the hydrophobic chemicals (PAHs). This clearly illustrates the need for a reliable method to measure solute phase concentration of PAHs in contaminated soils. Overall a reliable and reproducable system for determining solute concentration of a wide range of organic compounds in contaminated soils has been developed.     

Effect of altered carbohydrate traits in hulless barley (Hordeum vulgare L.) on nutrient profiles and availability and nitrogen to energy synchronization

Four hulless barley cultivars (zero-amylose waxy, CDC Fibar; 5%-amylose waxy, CDC Rattan; normal-amylose, CDC McGwire and high-amylose, HB08302) were developed at the Crop Development Centre, University of Saskatchewan, with differences in carbohydrates traits on the basis of amylose (1–20% DM) and β-glucan (5–10% DM) content. The objectives of this research were to determine: 1) the effect of the alteration of these carbohydrate traits in hulless barley on nutrient availability in ruminants, and 2) carbohydrate structure conformation on hourly effective rumen degradation ratio, in comparison with hulled barley-CDC Copeland. Among the hulless barley lines, HB08302 was greater (P < 0.05) in rumen bypass crude protein (BCP: 52.1% CP), effective degradability (ED) of neutral detergent fibre (EDNDF: 74 g/kg DM) than these in CDC Fibar, whereas CDC Fibar showed greater (P < 0.05) effective degradable crude protein (EDCP: 90 g/kg DM) than the other hulless barley lines. Compared with hulless barley, the hulled CDC Copeland showed relatively greater (P < 0.05) BNDF (62.5% NDF or 98 g/kg DM), starch degradation rate (K_d: 17.4%/h) and EDST (75.9% ST) but reduced (P < 0.05) rumen undegradable protein (RUP: 49 g/kg DM). With the respect to hourly effective degradation (ED) ratios, hulless barley cultivars exhibited relatively optimal hourly ED ratios, ranging from 23 to 34 g N/kg CHO, higher than the hulled barley. Among hulless barley cultivars, CDC Fibar and Rattan had the highest (P < 0.05) ratios (34 g N/kg CHO), while the ratio for CDC McGwire (23 g N/kg CHO) was the lowest (P > 0.05). In conclusion, hulless barley lines with altered carbohydrate traits have the potential to increase rumen nutrient availability to ruminants. The altered carbohydrate conformation of hulless barley affected hourly ED ratios, thus affecting rumen nitrogen to energy synchronization.     

Predicted truly absorbed protein supply to dairy cattle from hulless barley (Hordeum vulgare L.) with altered carbohydrate traits with multi-year samples

Hulless barley breeding lines varying in amylose (1–20% DM) and β-glucan content (5–10% DM) have been developed at the Crop Development Centre, Canada. The objectives of this large-scale study were to 1) determine and confirm the effect of these new hulless barley lines (zero-amylose waxy, CDC Fibar; 5%-amylose waxy, CDC Rattan; normal-amylose, CDC McGwire and high-amylose, HB08302) with altered carbohydrate traits on 1) metabolic characteristics of protein; 2) intestinal digestion of various nutrients and 3) modeling nutrient supply from these barley varieties by using NRC Dairy 2001 model and DVE/OEB system. CDC Copeland was included as a hulled barley control. Among the hulless barley lines, CDC Fibar contained the highest and CDC McGwire contained the lowest total digestible protein (TDP: 147 vs. 116 g/kg DM). HB08302 was greater (P < 0.05) in intestinal digestible protein (IDP: 40.6% RUP) but relatively lower (P < 0.05) in total digestible protein (TDP: 120 g/kg DM). Compared with hulless barley, hulled barley showed relatively lower (P < 0.05) intestinal digestible protein (38 vs. 53 g/kg DM) and total digestible protein (102 vs. 129 g/kg DM). In modeling nutrient supply from the DVE/OEB system, the results showed hulled barley was lower (P < 0.01) in true protein supplied to the small intestine (TPSI: 127 vs. 142 g/kg DM), lower in truly absorbed rumen bypassed feed protein in small intestine (ABCP^DVE: 43 vs. 58 g/kg DM), lower in truly absorbed protein in the small intestine (DVE: 95 vs. 111 g/kg DM), and lower in degraded protein balance (OEB^DVE: −39 vs. −23 g/kg DM) than the hulless barley lines but greater (P < 0.01) in undigested inorganic matter (9 g/kg DM). From NRC Dairy 2001 model, CDC Fibar was greater (P < 0.05) in degraded protein balance (OEB^NRC: −30 g/kg DM) and metabolizable protein (MP: 118 g/kg DM) than the other hulless barley lines, while hulled barley was relatively lower (P < 0.01) in total metabolizable protein (MP: 83 vs. 105 g/kg DM). Our correlation results suggested that TDP was negatively correlated to amylose (r = −0.85, P < 0.001) but positively correlated to β-glucan level (r = 0.74, P < 0.001) in hulless barley cultivars. The DVE and OEB^DVE as well as MP were negatively correlated (P < 0.05) to amylose level but positively correlated to β-glucan level (P < 0.05). In conclusion, altered carbohydrate traits in the hulless barley varieties have the potential to increase intestinal nutrient availability to ruminants and significantly improved the truly absorbed protein supply to dairy cattle compared to hulled barley. Hulless barley with lower amylose and higher β-glucan level could provide greater (P < 0.05) truly digested protein in the small intestine, better synchronized available energy and N and increase metabolizable protein supply to ruminants.