A sequential threshold cure model for genetic analysis of time-to-event data

In analysis of time-to-event data, classical survival models ignore the presence of potential nonsusceptible (cured) individuals, which, if present, will invalidate the inference procedures. Existence of nonsusceptible individuals is particularly relevant under challenge testing with specific pathogens, which is a common procedure in aquaculture breeding schemes. A cure model is a survival model accounting for a fraction of nonsusceptible individuals in the population. This study proposes a mixed cure model for time-to-event data, measured as sequential binary records. In a simulation study survival data were generated through 2 underlying traits: susceptibility and endurance (risk of dying per time-unit), associated with 2 sets of underlying liabilities. Despite considerable phenotypic confounding, the proposed model was largely able to distinguish the 2 traits. Furthermore, if selection is for improved susceptibility rather than endurance, the error of applying a classical survival model was nonnegligible. The difference was most pronounced for scenarios with substantial underlying genetic variation in endurance and when the 2 underlying traits were lowly genetically correlated. In the presence of nonsusceptible individuals, the method provides a novel and more accurate tool for utilization of time-to-event data, and has also been proven successful when applied to zero-inflated longitudinal binary data.     

Studies on degradation and outflow rate of protein supplements in the rumen of sheep and cattle

The rates of disappearance (p) of protein from fish-meal, meat-and-bone meal, soya-bean meal, cottonseed meal, linseed-meal and groundnut-meal were described when nylon bags were incubated in the rumens of sheep and cattle given either barley or dried grass. The exponential equation p = a + b (1 ? e^?ct),where a, b and c are constants, e is the natural logarithm, and p the amount disappearing in time, t, was used. There was no consistent difference between the degradabilities determined with sheep and cattle. Degradation was finally combined with different outflow rate (k) and the effective degradability (P) was described as the equation $\text{P}\text{=}\text{a + (bc)}\text{(c + k)}$.     

Responses of plasma Epo and kidney and liver Epo mRNA to hemorrhage in perinatal pigs

Despite the fact that pig fetuses in late gestation have extensive erythropoiesis, low blood pO₂ and low hemoglobin concentrations, piglets are born without detectable concentrations of plasma erythropoietin (Epo). In the present study, we have examined the hypothesis that long-term hypoxic stimuli are less efficient than short-term stimuli in stimulating Epo production in perinatal pigs. From fetuses collected by hysterectomy 5 days before term, new-born piglets and piglets 2 and 5 weeks old, blood in amounts corresponding to 2% of body weight was withdrawn from the jugular vein. Twenty-four hours later the animals were killed and their kidney and liver Epo mRNA analysed by a competitive RT-PCR assay. Plasma Epo concentration was estimated by a solid-phase, two-site sequential chemiluminescent enzyme immunometric assay. We found that in nearly fully developed fetuses and in new-born piglets, the concentration of Epo mRNA did not increase upon bleeding. This is in contrast to earlier findings in sheep. In 2- and 5-week-old piglets, bleeding was associated with a 12–15-fold increase in kidney Epo mRNA. In the 2- and 5-week-old piglets, bleeding evoked increased translation of Epo mRNA into the protein hormone. Also in new-born piglets, increased plasma levels of Epo accompanied bleeding, whereas significant changes in gene Epo expression were not observed.     

Effect of contamination of pasture with military explosives on grazing behaviour in sheep

Abstract

Ungulates grazing in military training areas may be exposed to non-combusted fragments of various explosives, among which 2-methyl-1,3,5-trinitrobenzene (TNT) and 1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) are two of the most common. This study investigated if sheep react to their pastures being contaminated with TNT or HMX. The experiment was conducted in fenced-in study areas on grass-dominated pasture. The eight sheep studied did not differentiate between clean pasture and contaminated pasture when choosing freely between plots containing TNT, HMX or no contamination. The results indicate that sheep grazing military training areas are unlikely to have behavioural responses reducing time spent grazing sites where TNT or HMX are present as fragments in the field layer.     

Early marine survival and movements of escaped Atlantic salmon Salmo salar L. juveniles from a land‐based smolt farm during autumn

The aim of this study was to examine early marine survival and movements of simulated escaped Atlantic salmon Salmo salar L. pre‐smolt and smolt from a commercial smolt farm during autumn. One‐third of the pre‐smolt most likely died in the immediate vicinity of the release location, whereas the corresponding mortality for smolts was lower (8.5%) during the 5‐week study period. The surviving pre‐smolt left the farm area after 2–3 days, predominantly along the shore. In contrast, most of the surviving smolts left the farm area during the first day and 54% seemed to move away from the shore and adopt a more pelagic movement pattern than pre‐smolt. The number of surviving fish recorded in the fjord decreased throughout the study period, possibly due to a combination of fish migrating out of the fjord or undetected mortality. Compared with existing knowledge on migration of released farmed smolts during spring, our results indicate less directional and slower movement rates during autumn. Only two of the tagged fish were detected upstream in the rivers following release. A rapid dispersion of escapees indicates that the potential for recapturing escapees is limited unless recapture efforts are initiated immediately after escape. Hence, there is a need for development of technology that detects and prevents escapees to enter the sea.     

The Norwegian minke whale DNA register: a data base monitoring commercial harvest and trade of whale products

The application of genetics for the management of natural resources is expanding, and within this field, DNA registers will play an increasing role. The Norwegian minke whale DNA register, established in 1996, was designed primarily as a control system to detect any attempts at illegal trade of products derived from other stocks of minke whale, or other whale species, under cover of the legal Norwegian harvest originating from the Northeast Atlantic. The register contains genetic data for 7644 of 7751 whales landed in the period 1997–2010. Profiles are established from sequencing part of the mtDNA control region, analysis of 10 STRs and a sex‐determining marker. Probabilities of genotypes matching between two randomly selected whales are 6.0^?04 and 3.0^?08 for five and eight of the STR loci, respectively. This permits verification of traded whale products via match to the register. The register has also been used in a number of ad hoc scientific studies resulting through the accumulation of genetic, demographic and biological data. Here, we review the register’s logistics, specifications and evaluate the potential to apply similar registers to control the exploitation of other marine species.     

Short-term effects of whole-tree harvesting on understory plant species diversity and cover in two Norway spruce sites in southern Norway

Effects of clear-cut harvesting on ground vegetation plant species diversity and their cover are investigated at two Norway spruce sites in southern Norway, differing in climate and topography. Experimental plots at these two sites were either harvested conventionally (stem-only harvesting) or whole trees including crowns, twigs and branches were removed (whole-tree harvesting), leaving residue piles on the ground for some months. We compare the number of plant species in different groups and their cover sums before and after harvesting, and between the different treatments, using non-parametric statistical tests. An overall loss of ground vegetation biodiversity is induced by harvesting and there is a shift in cover of dominant species, with negative effects for bryophytes and dwarf shrubs and an increase of graminoid cover. Differences between the two harvesting methods at both sites were mainly due to the residue piles assembled during whole-tree harvesting and the physical damage made during the harvesting of residues in these piles. The presence of the residue piles had a clear negative impact on both species numbers and cover. Pile residue harvesting on unfrozen and snow-free soil caused more damage to the forest floor in the steep terrain at the western site compared to the eastern site.     

Association between average daily gain,faecal dry matter content and concentration of Lawsonia intracellularis in faeces

Background

The objective of this study was to investigate the association between average daily gain and the number of Lawsonia intracellularis bacteria in faeces of growing pigs with different levels of diarrhoea.

Methods

A longitudinal field study (n = 150 pigs) was performed in a Danish herd from day 29 to 47 post weaning. Every third day all pigs were weighed, subjected to a clinical examination and faecal samples were obtained. Faecal samples were subjected to dry matter determination and absolute quantification by PCR for L. intracellularis and porcine circovirus type 2 (PCV2). Association between average daily gain, faecal dry matter content, numbers of L. intracellularis bacteria and PCV2 genome copies in faeces was investigated in a multilevel mixed-effects linear model.

Results

Increasing numbers of L. intracellularis log₁₀ bacteria/g faeces were significantly associated with decreasing average daily gain (P < 0.001). The association was decreasing with increasing faecal dry matter content (P < 0.01). The number of PCV2 log₁₀ copies/g faeces was not significantly associated with average daily gain of the pigs (P > 0.5).

Conclusion

The results suggest a potential application of a PCR quantifying L. intracellularis in growing pigs. Faecal dry matter content must be taken into consideration in interpretation of such test results.