LDSO: a program to simulate pedigrees and molecular information under various evolutionary forces

Simulations are a major tool to evaluate new statistical methods and optimize experimental designs in the genomic era. However, this can only be achieved when the simulations are close enough to reality, as well as diverse enough to be realistic. For mapping studies, it is thus critical to re-create as much as possible the forces generating linkage (mutation, random drift, changes in population sizes, selection and pedigree structure) and the mechanisms producing trait genetic architecture (additivity, dominance, epistasis). We present here a computer program (ldso) simulating these phenomena. Optional outputs provide statistics on the linkage disequilibrium (LD) structure and the identity by descent between chromosomal segments, facilitating further data analyses. Furthermore, ldso enables the simulation of genomic data in known pedigrees, which sticks as precisely as possible to recent population history and structures of the long-range LD, allowing optimization of fine-mapping strategies.     

Calcium homeostasis and its relationship to superoxide production in blood and milk neutrophils of lactating goats

Polymorphonuclear neutrophils (PMN), which comprise over 70% of the somatic cells in goat milk, are a major cellular component of innate immunity in the goat mammary gland. However, the function of milk PMNs is modified after diapedesis compared to PMNs in blood. As many aspects of PMN activity depend directly on intracellular Ca²⁺ concentration ((Ca²⁺)_i), the present study aimed to determine the changes in Ca²⁺ homeostasis of milk PMNs from lactating goats compared to autologous blood PMNs, and to examine the significance of these variations to the immuno-competency of milk PMNs. The intracellular Ca²⁺ store of freshly prepared milk cells was estimated from the elevation of (Ca²⁺)_i after ionomycin treatment, which was found to be significantly less than blood PMNs. Replenishment of the intracellular Ca²⁺ store in milk cells after intracellular Ca²⁺ depletion by Bapta-AM followed by spiking with 2.5 mM Ca²⁺ for 20 min was also compared to that of blood PMNs, showing that after depletion/spiking the intracellular Ca²⁺ store in milk cells was much less than blood PMNs. The production of superoxide anion (O₂^?) in vitro in response to (Ca²⁺)_i-dependent or (Ca²⁺)_i-independent modulators was used to evaluate the relevance of altered Ca²⁺ homeostasis on the immuno-competency of milk cells compared to blood PMNs. The results indicated that milk cells produced similarly low levels of O₂^? as blood PMNs when treated with ionomycin. However, the amount of O₂^? produced by milk cells in response to phorbol 12-myristate 13-acetate (PMA) stimulation, although greater than ionomycin treatment, was significantly less than that of blood PMNs. The capacity for O₂^? production by both cell types in response to PMA reverted to the resting state with use of the protein kinase C (PKC) inhibitor, staurosporine. In conclusion, the current study demonstrated an irreversible shortage of intracellular Ca²⁺ in the milk PMNs of lactating goats compared to blood PMNs. It also showed that preliminary O₂^–production, primed by ionomycin treatment, remained unchanged in milk PMNs, despite the shortage in intracellular Ca²⁺, but decreased O₂^? production capacity, mediated via the PKC pathway, in milk PMN. It is suggested that the defects in Ca²⁺ homeostasis in milk PMNs of lactating goats is partially attributable for the post-diapedesis functionality modifications.     

Analysis of Amblyomma surveillance data in the Caribbean: Lessons for future control programmes

Amblyomma variegatum, the Tropical Bont Tick (TBT), is the principal vector of heartwater and is associated with dermatophilosis, major causes of losses in animal production and mortality in Caribbean livestock. From 1995 to 2007, the Caribbean Amblyomma Programme (CAP) supported treatment and surveillance activities in 11 islands of the Eastern Caribbean with an initial objective of eradicating TBT. In addition to control activities, surveillance data were collected between 1997 and 2006 in a unique regional database. We report the analysis of the surveillance data from four islands (Nevis, St Kitts, St Lucia, and Barbados) where control and surveillance followed the initial protocol and where enough data were collected. We describe the evolution of TBT infestation levels and the efforts carried out throughout the surveillance period. Logistic regression identified factors associated with herds found infested with TBT. Overall, treatment programmes were associated with a decrease in proportion of TBT-infested farms. High surveillance efforts were carried out throughout the 1997–2007 period for all island of interest, but inadequate level of surveillance was observed in several quarters especially for St Kitts. Third quarter of the year, as indication of adult TBT seasonality on livestock, was significantly associated with the risk of detecting TBT in Nevis and St Kitts livestock farms. Also, presence of cattle in Nevis farms was shown associated with an increasing probability of farms being declared TBT-infested. Outcomes of these analyses provide basis for recommendations to improve future national and regional control and surveillance activities. This analysis demonstrates the usefulness of long term and adequate surveillance data for control programmes and identification of factors associated with risk of having infested herds.     

Progesterone production in mares and echographic evaluation of the corpora lutea formed after follicular aspiration

Ultrasound‐guided follicular aspiration was performed in 26 Criollo crossbred mares, followed by the evaluation of ultrasonographic images of the Corpus luteum (CL) that was formed after puncture of follicles of different diameters (Group 25–29 mm; Group 30–35 mm and Group >35 mm). Serum progesterone (P₄) concentrations were measured to determine CL function. The size of the CL was measured and the CL was classified based on the following echoscore: 1– anechoic tissue; 2– poorly defined luteal structure with low echogenicity; 3– echogenicity analogous to a luteal structure. The proportion of aspirated follicles that formed a functional CL (based on P₄ concentration) 8 days after aspiration was 57.1% (4/7; CL size 25–29 mm), 75.0% (6/8; CL size 30–35 mm) and 72.7% (8/11; CL size >35 mm), respectively (p > 0.05). The echographic scores of aspirated follicles (indicating the presence or absence of a CL) were consistent with serum P₄ concentrations (p < 0.0001). Of 26 aspirations, 18 resulted in luteal function confirmed by increased progesterone concentrations ([P₄] > 1.0 ng/ml); 17 of these mares (94.4%) had an echoscore (2–3) compatible with luteinization (p = 0.0372). Eight days after aspiration, serum [P₄] > 2.0 ng/ml was associated with high (p = 0.0056) CL echoscore (3) in 15 of 17 mares (88.2%). The echoscore used in this study was valuable as a screening test to detect the presence of a functional CL after aspiration. An echoscore of 3 served as a practical and efficient method to confirm luteinization.     

Pharmacokinetics of ruminally dosed sodium [36Cl]chlorate in beef cattle

The recently recognized potential of sodium chlorate as a possible preharvest food safety tool for pathogen reduction in meat animals has spurred interest in the pharmacokinetics of intraruminally dosed chlorate. Six Loala cattle were assigned (one heifer and one steer per treatment) to one of three intraruminal doses of radiolabeled sodium [36Cl]chlorate (21, 42, or 63 mg/kg body weight) administered in four equal aliquots over a 24-h period. Blood and serum were collected (29 samples in 48 h). Total radioactive residues were measured and the radioactive moieties were speciated. Chlorate appeared rapidly in blood and serum after dosing. For animals administered a dose of 42 or 63 mg/kg, the half-life of absorption was estimated at 0.6-0.9 h. Serum chlorate concentrations progressively increased with aliquot administration until peaking at 6-21 parts per million at 26 h. Between aliquot administrations, serum chlorate levels typically peaked in 3.5 h or less. The half-life of chlorate elimination ranged between 6.9 and 11 h, depending on the dose. Ultimately, absorption of chlorate removes it from its desired site of action, the lower gastrointestinal tract, thereby reducing its efficacy. Further research is needed to develop a chlorate formulation that will allow passage to the lower gastrointestinal tract.     

Distribution and risk factors of bovine cysticercosis in Belgian dairy and mixed herds

Bovine cysticercosis is an important food safety issue that is of economic concern. In Belgium, in the last years an increase in the number of cases, mostly light infections, was observed. The role of contact with contaminated surface water has been hypothesized as the main route of transmission. Based on abattoir records from 2001 till 2003 the distribution and risk factors of bovine cysticercosis among dairy and mixed farms were studied in four provinces, using Geographic Information Systems (GIS) and questionnaires. The risk factors were analysed using a case-control study design. The case group consisted of herds from which homebred cattle with cysticercosis had been detected at the abattoir; the control group was composed of herds where no cases had been detected. Case herds were distributed over the study area. A logistic regression analysis revealed that the location (province), the number of slaughtered cattle, the flooding of pastures, free access of cattle to surface water and the proximity of wastewater effluent were significant explanatory variables for bovine cysticercosis to be recorded in a herd.