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Transposable elements (TEs), such as endogenous retroviruses (ERVs), are common in the genomes of vertebrates. ERVs result from retroviral infections of germ-line cells, and once integrated into host DNA they become part of the host's heritable genetic material. ERVs have been ascribed positive effects on host physiology such as the generation of novel, adaptive genetic variation and resistance to infection, as well as negative effects as agents of tumorigenesis and disease. The avian leukosis virus subgroup E family (ALVE) of endogenous viruses of chickens has been used as a model system for studying the effects of ERVs on host physiology, and approximately 30 distinct ALVE proviruses have been described in the Gallus gallus genome. In this report we describe the development of a software tool, which we call Vermillion, and the use of this tool in combination with targeted next-generation sequencing (NGS) to increase the number of known proviruses belonging to the ALVE family of ERVs in the chicken genome by 4-fold, including expanding the number of known ALVE elements on chromosome 1 (Gga1) from the current 9 to a total of 40. Although we focused on the discovery of ALVE elements in chickens, with appropriate selection of target sequences Vermillion can be used to develop profiles of other families of ERVs and TEs in chickens as well as in species other than the chicken. [ABSTRACT FROM AUTHOR]

Accurate and complete reporting of study methods, results and interpretation are essential components for any scientific process, allowing end-users to evaluate the internal and external validity of a study. When animals are used in research, excellence in reporting is expected as a matter of continued ethical acceptability of animal use in the sciences. Our primary objective was to assess completeness of reporting for a series of studies relevant to mitigation of pain in neonatal piglets undergoing routine management procedures. Our second objective was to illustrate how authors can report the items in the Reporting guidElines For randomized controLled trials for livEstoCk and food safety (REFLECT) statement using examples from the animal welfare science literature. A total of 52 studies from 40 articles were evaluated using a modified REFLECT statement. No single study reported all REFLECT checklist items. Seven studies reported specific objectives with testable hypotheses. Six studies identified primary or secondary outcomes. Randomization and blinding were considered to be partially reported in 21 and 18 studies, respectively. No studies reported the rationale for sample sizes. Several studies failed to report key design features such as units for measurement, means, standard deviations, standard errors for continuous outcomes or comparative characteristics for categorical outcomes expressed as either rates or proportions. In the discipline of animal welfare science, authors, reviewers and editors are encouraged to use available reporting guidelines to ensure that scientific methods and results are adequately described and free of misrepresentations and inaccuracies. Complete and accurate reporting increases the ability to apply the results of studies to the decision-making process and prevent wastage of financial and animal resources. [ABSTRACT FROM AUTHOR]

A survey of UK based pig farmers and veterinarians was conducted, in order to investigate attitudes to pain and the use of pain relief in pigs. Survey respondents were asked to indicate which anti-inflammatory drugs they used or prescribed for pigs, how often these were administered, and the level of pain they associated with particular conditions. The survey found that veterinarians used a range of anti-inflammatory products to treat pigs with lameness. While both farmers and veterinarians gave similar pain scores overall, farmers rated gastrointestinal disease as more painful and conversely veterinarians scored lameness higher. Female and younger respondents gave higher pain scores than males and older respondents. Overall, farmers and veterinarians had a positive attitude towards pain relief in pigs with the majority agreeing that animals recovered more promptly w hen pain relief was administered. Most farmers agreed that the recognition and management of pain is an important part of pig husbandry, and many expressed an interest in finding out more about identifying pain in this species as well as the treatment options available. The study highlighted potential barriers to the increased application of pain relief in pigs in that almost one-third of veterinarians and two-thirds of farmers did not agree that they discussed pain management with each other, while other respondents indicated that they found it difficult to recognise pain in pigs, and did not know how to treat it appropriately. [ABSTRACT FROM AUTHOR]

A key indicator of resource use within farming is technical efficiency, which measures the amount of physical output attainable from a given set of inputs. The social aspects, in particular the treatment of animals, have generally been ignored within these measurement schemas. In addition, animal welfare will affect the production technology under which farms operate, and some allowance for this is needed within the measurement approach. This is the first paper to apply animal welfare as a discriminating technology within a technical efficiency framework. Using results from an animal welfare monitoring study coupled with resource usage data, it presents an adjusted measure of technical efficiency applied to a sample of British dairy farms and compares differences in lameness management strategies for herds. We employ both a categorical and nondiscretionary variant of the data envelopment analysis approach to measure technical efficiencies and adjust for various degrees of lameness prevalence among these farms. This paper finds that farms with low rates of lameness (below 10% of the cattle herd) tend to have significantly higher technical efficiencies than those with lameness rates of above 10% of the herd. Farms that have levels of lameness of between 10 to 20% of the herd and higher levels of lameness (above 20% of the herd) did not differ significantly. Furthermore, low lameness farms are inefficient in terms of labor and stocking density, but this is outweighed by the gain in milk yield obtained on these farms. Consequently, we argue for a whole-farm, rather than a partial indicator, approach to assessing efficiency when noneconomic factors such as lameness are accounted for. From a policy perspective, we support programs that encourage active lameness management. [ABSTRACT FROM AUTHOR]

The presence of hock injury was assessed in the milking herds of 80 dairy farms (40 organic, 40 nonorganic) across the United Kingdom. A wide range of information on farm management and husbandry was gathered via interview to assess the factors contributing to hock damage for all 80 farms, and a comprehensive building appraisal was conducted for 40 farms visited during the winter housing period. The prevalence of hock lesions was lower on organic compared with nonorganic farms (37.2 vs. 49.1%). Prevalence of hock damage was greater in the spring than fall (59.9 vs. 21.6%) and cows housed in free-stalls had a greater prevalence of hock lesions than those housed on straw (46.0 vs. 25.0%). Prevalence of hock damage increased with lactation number. In the analysis of fall/spring data, the age first mated, herd biosecurity, duration of summer grazing, and cow milk yield were significant factors relating to herd hock damage. Larger herds had a greater proportion of cows with hock swellings. Farms with a shorter calving interval had more cows with hock swellings. Factors relating to housing conditions that were positively associated with the prevalence of hock damage were low feed face space per cow, inferior passageway cleanliness, low total standing area per cow, and the type of bedding added to the free-stall. To assess whether free-stall versus straw-pen or organic versus nonorganic farms had different sets of risk factors, the data were reanalyzed for these types separately. For the straw-pen farms a high culling rate was associated with more hock damage. Within nonorganic farms, the length of summer grazing was significant, with longer periods meaning less hock injury. The prevalence of hock injuries on many UK farms, both organic and nonorganic, exceeded levels that are deemed acceptable for cow comfort. Efforts are needed to improve housing standards to reduce the prevalence of hock injury and consequently improve cow welfare. [ABSTRACT FROM AUTHOR]

Early life experiences can be important in determining offspring phenotypes and may influence interaction with the environment and hence health, welfare, and productivity. The prenatal environment of poultry can be divided into the pre-lay environment and the egg storage/incubation environment, both of which can affect offspring outcomes. The ability to separate maternal and egg/incubation effects makes birds well suited to this type of research. There are many factors, including feeding and nutrition, environmental conditions, husbandry practices, housing system, social environment, infectious environment, and maternal health status, that can influence both the health and performance and behavior and cognition of the offspring. There are some aspects of the environments that can be changed to produce beneficial effects in the offspring, like addition of certain additives to feed or short changes in incubation temperatures, while other aspects should be avoided to reduce negative effects, such as unpredictable feeding and lighting regimens. Measures of offspring characteristics may prove to be a useful method of assessing parent stock welfare if known stressors result in predictable offspring outcomes. This has the advantage of assessing the parent environment without interfering with the animals and possibly affecting their responses and could lead to improved welfare for the animals. [ABSTRACT FROM AUTHOR]

The numbers of organic dairy farms are increasing in the United Kingdom and in other parts of the world. On organic farms, the use of veterinary medicines is restricted. Because of this, there is concern that cow health is poorer on these farms. As udder health is primarily maintained by the use of antimicrobials, the effect of organic status on mastitis and somatic cell counts (SCC) is important to investigate. The aim of this study was therefore to determine whether the organic status and other management factors affect SCC. A group of 80 dairy farms was used in the study: 40 organic farms and 40 nonorganic farms. The farms were recruited in pairs, and each organic:nonorganic pair was matched for herd size, housing type, genetic merit for milk production and geographical location. Somatic cell count data were extracted from national databases for a standard year (2004), and analyzed using stepwise logistic regression models. The organic status of the farm did not appear in the final model, indicating no major influence of organic status on SCC. There were, however, several effects of management on SCC. Somatic cell counts were lower on farms where the udders were not cleaned or cleaned only when dirty. Somatic cell counts were also lower on farms that kept cows in larger management groups and where the majority, but not all cases of mastitis are treated with antimicrobials. It can be concluded that the control measures used on the organic farms in this study are at least as effective as those used on nonorganic farms in controlling SCC. Other management factors are influential and attention to these factors will allow farmers to reduce SCC. [ABSTRACT FROM AUTHOR]