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PomBase (https://www.pombase.org), the model organism database (MOD) for fission yeast, was recently awarded Global Core Biodata Resource (GCBR) status by the Global Biodata Coalition (GBC; https://globalbiodata.org/) after a rigorous selection process. In this MOD review, we present PomBase's continuing growth and improvement over the last 2 years. We describe these improvements in the context of the qualitative GCBR indicators related to scientific quality, comprehensivity, accelerating science, user stories, and collaborations with other biodata resources. This review also showcases the depth of existing connections both within the biocuration ecosystem and between PomBase and its user community., Competing Interests: Conflicts of interest: The authors declare no conflicts of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)

The fission yeast Schizosaccharomyces japonicus has recently emerged as a powerful system for studying the evolution of essential cellular processes, drawing on similarities as well as key differences between S. japonicus and the related, well-established model Schizosaccharomyces pombe. We have deployed the open-source, modular code and tools originally developed for PomBase, the S. pombe model organism database (MOD), to create JaponicusDB (www.japonicusdb.org), a new MOD dedicated to S. japonicus. By providing a central resource with ready access to a growing body of experimental data, ontology-based curation, seamless browsing and querying, and the ability to integrate new data with existing knowledge, JaponicusDB supports fission yeast biologists to a far greater extent than any other source of S. japonicus data. JaponicusDB thus enables S. japonicus researchers to realize the full potential of studying a newly emerging model species and illustrates the widely applicable power and utility of harnessing reusable PomBase code to build a comprehensive, community-maintainable repository of species-relevant knowledge., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)

PomBase (www.pombase.org), the model organism database (MOD) for the fission yeast Schizosaccharomyces pombe, supports research within and beyond the S. pombe community by integrating and presenting genetic, molecular, and cell biological knowledge into intuitive displays and comprehensive data collections. With new content, novel query capabilities, and biologist-friendly data summaries and visualization, PomBase also drives innovation in the MOD community., (© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.)

Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task. Their underlying algorithms differ in many aspects, and therefore the comparison of the pipelines provides insights into their best use and interpretation of the outcomes. Both of these bioinformatics tools are based on several specialized algorithms pipelined together, but whereas MG-RAST is a user-friendly webserver that clusters rRNA sequences based on their similarity to create Operational Taxonomic Units (OTU), QIIME2 employs DADA2 in the construction of Amplicon Sequence Variants (ASV) by applying an error model that considers the abundance of each sequence and its similarity to other sequences. Taxonomic compositions obtained from the analyses of amplicon sequences of DNA from swine intestinal gut and faecal microbiota samples using MG-RAST and QIIME2 were compared at domain-, phylum-, family- and genus-levels in terms of richness, relative abundance and diversity. We found significant differences between the microbiota profiles obtained from each pipeline. At domain level, bacteria were relatively more abundant using QIIME2 than MG-RAST; at phylum level, seven taxa were identified exclusively by QIIME2; at family level, samples processed in QIIME2 showed higher evenness and richness (assessed by Shannon and Simpson indices). The genus-level compositions obtained from each pipeline were used in partial least squares-discriminant analyses (PLS-DA) to discriminate between sample collection sites (caecum, colon and faeces). The results showed that different genera were found to be significant for the models, based on the Variable Importance in Projection, e.g. when using sequencing data processed by MG-RAST, the three most important genera were Acetitomaculum, Ruminococcus and Methanosphaera, whereas when data was processed using QIIME2, these were Candidatus Methanomethylophilus, Sphaerochaeta and Anaerorhabdus. Furthermore, the application of differential filtering procedures before the PLS-DA revealed higher accuracy when using non-restricted datasets obtained from MG-RAST, whereas datasets obtained from QIIME2 resulted in more accurate discrimination of sample collection sites after removing genera with low relative abundances (<1%) from the datasets. Our results highlight the differences in taxonomic compositions of samples obtained from the two separate pipelines, while underlining the impact on downstream analyses, such as biomarkers identification., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity 1-4 . Sparse taxon sampling has previously been proposed to confound phylogenetic inference 5 , and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Biological processes are accomplished by the coordinated action of gene products. Gene products often participate in multiple processes, and can therefore be annotated to multiple Gene Ontology (GO) terms. Nevertheless, processes that are functionally, temporally and/or spatially distant may have few gene products in common, and co-annotation to unrelated processes probably reflects errors in literature curation, ontology structure or automated annotation pipelines. We have developed an annotation quality control workflow that uses rules based on mutually exclusive processes to detect annotation errors, based on and validated by case studies including the three we present here: fission yeast protein-coding gene annotations over time; annotations for cohesin complex subunits in human and model species; and annotations using a selected set of GO biological process terms in human and five model species. For each case study, we reviewed available GO annotations, identified pairs of biological processes which are unlikely to be correctly co-annotated to the same gene products (e.g. amino acid metabolism and cytokinesis), and traced erroneous annotations to their sources. To date we have generated 107 quality control rules, and corrected 289 manual annotations in eukaryotes and over 52 700 automatically propagated annotations across all taxa.

Bluehead wrasses undergo dramatic, socially cued female-to-male sex change. We apply transcriptomic and methylome approaches in this wild coral reef fish to identify the primary trigger and subsequent molecular cascade of gonadal metamorphosis. Our data suggest that the environmental stimulus is exerted via the stress axis and that repression of the aromatase gene (encoding the enzyme converting androgens to estrogens) triggers a cascaded collapse of feminizing gene expression and identifies notable sex-specific gene neofunctionalization. Furthermore, sex change involves distinct epigenetic reprogramming and an intermediate state with altered epigenetic machinery expression akin to the early developmental cells of mammals. These findings reveal at a molecular level how a normally committed developmental process remains plastic and is reversed to completely alter organ structures.

The birds and reptiles, collectively known as the sauropsids, can be subdivided phylogenetically into the archosaurs (birds, crocodiles), the testudines (turtles), the squamates (lizards, snakes) and the rhynchocephalia (tuatara). The structural framework of the epidermal appendages from the sauropsids, which include feathers, claws and scales, has previously been characterised by electron microscopy, infrared spectroscopy and X-ray diffraction analyses, as well as by studies of the amino acid sequences of the constituent β-keratin proteins (also referred to as the corneous β-proteins). An important omission in this work, however, was the lack of sequence and structural data relating to the epidermal appendages of the rhynchocephalia (tuatara), one of the two branches of the lepidosaurs. Considerable effort has gone into sequencing the tuatara genome and while this is not yet complete, there are now sufficient sequence data for conclusions to be drawn on the similarity of the β-keratins from the tuatara to those of other members of the sauropsids. These results, together with a comparison of the X-ray diffraction pattern of tuatara claw with those from seagull feather and goanna claw, confirm that there is a common structural plan in the β-keratins of all of the sauropsids, and not just those that comprise the archosaurs (birds and crocodiles), the testudines (turtles) and the squamates (lizards and snakes)., (Copyright © 2019 Elsevier Inc. All rights reserved.)

Periparturient pain is a welfare concern and could contribute to piglet losses. This has led to studies investigating post-farrowing analgesia. A clear reduction in pain has not been demonstrated, partly due to a lack of pain indicators. This study quantified behaviours as potential pain indicators (PPIn) in sows: i) before, during and after farrowing, and ii) 2min before and after piglet births. Twenty-five sows were observed during and after, and ten pre-farrowing. Behaviour recorded included: 1) back leg forward (back leg pulled forward and/or in); 2) tremble (movement as if shivering); 3) back arch (leg(s) stretch forming an arched back); 4) paw (leg scraped in pawing motion); and 5) tail flick (tail moved rapidly up and down). Behaviours were analysed using generalized linear models and Spearman's rank correlations. All PPIn were rare or absent pre-farrowing, highest during farrowing, and back leg forward, tremble and back arch were greater in the early post-farrowing period. Several significant positive correlations between PPIn during and post-farrowing were found. Back arch, tail flick and paw were higher before than after a piglet birth, and were more frequent earlier in the birth order. Back leg forward and tremble did not differ before and after births, and tremble increased with birth order. These behaviours, which were absent or rare pre-farrowing, present during farrowing and were lower afterwards, and showed consistent individual variation, may be quantitatively associated with pain. Spontaneous behaviours could be used to test the efficacy of analgesics or identify sows that may benefit., (Crown Copyright © 2016. Published by Elsevier Ltd. All rights reserved.)

There is a moral obligation to minimize pain in pigs used for human benefit. In livestock production, pigs experience pain caused by management procedures, e.g., castration and tail docking, injuries from fighting or poor housing conditions, "management diseases" like mastitis or streptococcal meningitis, and at parturition. Pigs used in biomedical research undergo procedures that are regarded as painful in humans, but do not receive similar levels of analgesia, and pet pigs also experience potentially painful conditions. In all contexts, accurate pain assessment is a prerequisite in (a) the estimation of the welfare consequences of noxious interventions and (b) the development of more effective pain mitigation strategies. This narrative review identifies the sources of pain in pigs, discusses the various assessment measures currently available, and proposes directions for future investigation.

The concept that postnatal health and development can be influenced by events that occur in utero originated from epidemiological studies in humans supported by numerous mechanistic (including epigenetic) studies in a variety of model species. Referred to as the 'developmental origins of health and disease' or 'DOHaD' hypothesis, the primary focus of large-animal studies until quite recently had been biomedical. Attention has since turned towards traits of commercial importance in farm animals. Herein we review the evidence that prenatal risk factors, including suboptimal parental nutrition, gestational stress, exposure to environmental chemicals and advanced breeding technologies, can determine traits such as postnatal growth, feed efficiency, milk yield, carcass composition, animal welfare and reproductive potential. We consider the role of epigenetic and cytoplasmic mechanisms of inheritance, and discuss implications for livestock production and future research endeavours. We conclude that although the concept is proven for several traits, issues relating to effect size, and hence commercial importance, remain. Studies have also invariably been conducted under controlled experimental conditions, frequently assessing single risk factors, thereby limiting their translational value for livestock production. We propose concerted international research efforts that consider multiple, concurrent stressors to better represent effects of contemporary animal production systems.

To limit tail biting incidence, most pig producers in Europe tail dock their piglets. This is despite EU Council Directive 2008/120/EC banning routine tail docking and allowing it only as a last resort. The paper aims to understand what it takes to fulfil the intentions of the Directive by examining economic results of four management and housing scenarios, and by discussing their consequences for animal welfare in the light of legal and ethical considerations. The four scenarios compared are: 'Standard Docked', a conventional housing scenario with tail docking meeting the recommendations for Danish production (0.7 m2/pig); 'Standard Undocked', which is the same as 'Standard Docked' but with no tail docking, 'Efficient Undocked' and 'Enhanced Undocked', which have increased solid floor area (0.9 and 1.0 m2/pig, respectively) provision of loose manipulable materials (100 and 200 g/straw per pig per day) and no tail docking. A decision tree model based on data from Danish and Finnish pig production suggests that Standard Docked provides the highest economic gross margin with the least tail biting. Given our assumptions, Enhanced Undocked is the least economic, although Efficient Undocked is better economically and both result in a lower incidence of tail biting than Standard Undocked but higher than Standard Docked. For a pig, being bitten is worse for welfare (repeated pain, risk of infections) than being docked, but to compare welfare consequences at a farm level means considering the number of affected pigs. Because of the high levels of biting in Standard Undocked, it has on average inferior welfare to Standard Docked, whereas the comparison of Standard Docked and Enhanced (or Efficient) Undocked is more difficult. In Enhanced (or Efficient) Undocked, more pigs than in Standard Docked suffer from being tail bitten, whereas all the pigs avoid the acute pain of docking endured by the pigs in Standard Docked. We illustrate and discuss this ethical balance using numbers derived from the above-mentioned data. We discuss our results in the light of the EU Directive and its adoption and enforcement by Member States. Widespread use of tail docking seems to be accepted, mainly because the alternative steps that producers are required to take before resorting to it are not specified in detail. By tail docking, producers are acting in their own best interests. We suggest that for the practice of tail docking to be terminated in a way that benefits animal welfare, changes in the way pigs are housed and managed may first be required.

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., (© The Author 2015. Published by Oxford University Press on behalf of Poultry Science Association.)

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 when 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., (Copyright © 2014 Elsevier Ltd. All rights reserved.)

The research communities studying microbial model organisms, such as Escherichia coli or Saccharomyces cerevisiae, are well served by model organism databases that have extensive functional annotation. However, this is not true of many industrial microbes that are used widely in biotechnology. In this Opinion piece, we use Pichia (Komagataella) pastoris to illustrate the limitations of the available annotation. We consider the resources that can be implemented in the short term both to improve Gene Ontology (GO) annotation coverage based on annotation transfer, and to establish curation pipelines for the literature corpus of this organism., (Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Motivation: Detailed curation of published molecular data is essential for any model organism database. Community curation enables researchers to contribute data from their papers directly to databases, supplementing the activity of professional curators and improving coverage of a growing body of literature. We have developed Canto, a web-based tool that provides an intuitive curation interface for both curators and researchers, to support community curation in the fission yeast database, PomBase. Canto supports curation using OBO ontologies, and can be easily configured for use with any species., Availability: Canto code and documentation are available under an Open Source license from http://curation.pombase.org/. Canto is a component of the Generic Model Organism Database (GMOD) project (http://www.gmod.org/)., (© The Author 2014. Published by Oxford University Press.)

Numerous studies have shown that prenatal stress (PNS) can have profound effects on postnatal well-being. Here, the domestic pig (Sus scrofa) was used to investigate PNS effects owing to the direct relevance for farm animal welfare and the developing status of the pig as a large animal model in translational research. Pregnant primiparous sows were exposed, in mid-gestation, to either a social stressor (mixing with unfamiliar conspecifics) or were kept in stable social groups. The ratio of levels of mRNAs for corticotropin releasing hormone (CRH) receptors 1 and 2 in the amygdala, measured for the first time in the pig, was substantially increased in 10-week-old female, but not male, PNS progeny indicating a neurobiological propensity for anxiety-related behaviour. Mature female offspring were observed at parturition in either a behaviourally restrictive crate or open pen. Such PNS sows showed abnormal maternal behaviour in either environment, following the birth of their first piglet. They spent more time lying ventrally, more time standing and showed a higher frequency of posture changes. They were also more reactive towards their piglets, and spent longer visually attending to their piglets compared to controls. Associated with this abnormal maternal care, piglet mortality was increased in the open pen environment, where protection for piglets is reduced. Overall, these data indicate that PNS females have their brain development shifted towards a pro-anxiety phenotype and that PNS can be causally related to subsequent impaired maternal behaviour in adult female offspring., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Pigs are mixed into new social groups at various stages of production, and this study investigated the response of gilts to mixing with older unfamiliar sows. Four groups of 6 gilts and 1 group of 5 gilts were housed in stable groups until the most recently bred female reached d 39 of gestation. Then, stable groups were split such that 15 gilts remained in their home pens (CON) and 14 gilts were mixed (MIX) with 3 multiparous sows for 1 wk (M1), returned to the home pen for 1 wk, and then mixed with 3 different sows for 1 wk (M2). Continuous behavioral observations of gilt location in the pen, posture, aggressive, and other social interactions were made from the start of M1 and M2 for 5 h. Five-minute scans of location, posture, and behavior as well as salivary cortisol measurements were taken before, during, and after each mix week, whereas skin lesions were counted before and after each mix. During the mixed period, MIX gilts spent more (P ≤ 0.009) time in the individual feeding stalls, ventral lying, sitting, involved in aggression, and idle and less (P < 0.001) time in the straw-bedded area, lateral lying, and performing exploratory behavior (chewing, nosing, and rooting) than CON gilts. Additionally, MIX gilts had greater (P < 0.001) salivary cortisol concentrations and accumulated more (P < 0.001) skin lesions during mixing sessions compared to CON gilts. Mixed gilts in M2 spent more (P ≤ 0.013) time in the feeding stalls and ventral lying and less (P ≤ 0.029) time standing and in the dunging passageway compared to M1. Compared to M1, gilts had lower (P < 0.001) salivary cortisol concentrations and fewer (P ≤ 0.027) lesions in front and middle regions of the body during M2. During M2, salivary cortisol concentration was positively correlated with time spent in the dunging passageway (Spearman's rank correlation [rs] = 0.650, P = 0.022) and negatively correlated with time spent in the feeding stalls (rs = -0.762, P = 0.004). Results indicated that gilts adapted their behavior during M2 by using the feeding stalls more, and they became less active, especially when interacting with the sows. Despite this adaptation in M2, lesions and salivary cortisol in M IX gilts were much greater than in CON gilts, highlighting the severity of mixing gilts with multiparous sows.

The prenatal period is of critical importance in defining how individuals respond to their environment throughout life. Stress experienced by pregnant females has been shown to have detrimental effects on offspring biology in humans and a variety of other species. It also is becoming increasingly apparent that prenatal events can have important consequences for the behavior, health, and productivity of offspring in farmed species. Pregnant cattle may experience many potentially important stressors, for instance, relating to their social environment, housing system and physical environment, interactions with humans and husbandry procedures, and their state of health. We examined the available literature to provide a review of the implications of prenatal stress for offspring welfare in cattle. The long-term effects of dystocia on cattle offspring also are reviewed. To ensure a transparent and repeatable selection process, a systematic review approach was adopted. The research literature clearly demonstrates that prenatal stress and difficult births in beef and dairy cattle both have implications for offspring welfare and performance. Common husbandry practices, such as transport, were shown to influence offspring biology and the importance of environmental variables, including thermal stress and drought, also were highlighted. Maternal disease during pregnancy was shown to negatively impact offspring welfare. Moreover, dystocia-affected calves suffer increased mortality and morbidity, decreased transfer of passive immunity, and important physiological and behavioral changes. This review also identified considerable gaps in our knowledge and understanding of the effects of prenatal stress in cattle.

Scientific assessment of affective states in animals is challenging but vital for animal welfare studies. One possible approach is Qualitative Behavioural Assessment (QBA), a 'whole animal' methodology which integrates information from multiple behavioural signals and styles of behavioural expression (body language) directly in terms of an animal's emotional expression. If QBA provides a valid measure of animals' emotional state it should distinguish between groups where emotional states have been manipulated. To test this hypothesis, QBA was applied to video-recordings of pigs, following treatment with either saline or the neuroleptic drug Azaperone, in either an open field or elevated plus-maze test. QBA analysis of these recordings was provided by 12 observers, blind to treatment, using a Free Choice Profiling (FCP) methodology. Generalised Procrustes Analysis was used to calculate a consensus profile, consisting of the main dimensions of expression. Dimension one was positively associated with terms such as 'Confident' and 'Curious' and negatively with 'Unsure' and 'Nervous'. Dimension two ranged from 'Agitated'/'Angry' to 'Calm'/'Relaxed'. In both tests, Azaperone pre-treatment was associated with a more positive emotionality (higher scores on dimension one reflecting a more confident/curious behavioural demeanour) than control pigs. No effect of drug treatment on dimension two was found. Relationships between qualitative descriptions of behaviour and quantitative behavioural measures, taken from the same recordings, were found. Overall, this work supports the use of QBA for the assessment of emotionality in animals.

This study assessed the effect of pre-natal social stress and post-natal pain on the reproductive development of young (approximately day 40) pigs. Male pigs carried by sows that were stressed by mixing with unfamiliar older sows for two 1-week periods during mid-pregnancy had lower plasma testosterone (0.54 vs 0.86 ng/ml, S.E.D.=0.11; P=0.014) and oestradiol (E(2); 22.9 vs 38.7 pg/ml, S.E.D.=7.80; P=0.021) concentrations compared with males carried by unstressed control sows. Although there was no effect of pre-natal stress on female E(2) concentrations, female pigs carried by stressed sows had fewer primordial ovarian follicles (log -4.32/μm(2) vs -4.00/μm(2), s.e.d.=0.136; P=0.027). Tail amputation on day 3 after birth reduced E(2) concentrations in female (4.78 vs 6.84 pg/ml, s.e.d.=0.86; P=0.03) and in male (25.6 vs 34.9 pg/ml, S.E.D.=3.56; P=0.021) pigs and reduced both testis weight (0.09% of body weight vs 0.10% of body weight, S.E.D.=0.003; P=0.01) and the percentage of proliferating Leydig cells (1.97 vs 2.12, S.E.D.=0.114; P=0.036) compared with sham-amputated littermate controls. There was a significant (P=0.036) interaction between the effects of pre-natal stress and post-natal pain on testicular expression of the steroidogenic enzyme 17α-hydroxylase, such that amputation increased expression in pigs born to control sows, but reduced expression in animals born to stressed sows. This study shows that stressful procedures associated with routine animal husbandry can disrupt the developing reproductive axis.

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., (Copyright © 2011 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

The consequences of tail-docking (at 2-4 days) and prenatal stress (maternal social stress during the 2nd third of pregnancy) on baseline nociceptive thresholds and responses to acute inflammatory challenge were investigated in juvenile pigs in two studies. Nociceptive thresholds were assessed on the tail root and on the hind foot using noxious mechanical and cold stimulation before and after acute inflammatory challenge by intradermal injection of 30 μg capsaicin (study 1) or 3% carrageenan (study 2) into the tail root. Four groups of 8 (study 1, n=14-16 pigs/treatment) or 5 (study 2, n=6 pigs/treatment/sex) week-old pigs were exposed to the main factors: maternal stress and treatment (docked vs. intact tails). In study 1, tail docking did not significantly alter thresholds to noxious mechanical stimulation, whilst prenatally stressed pigs had significantly higher baseline thresholds to noxious mechanical stimulation on the tail root and on the hind foot than unstressed pigs, whether tail-docked or intact. Capsaicin injection induced localised mechanical allodynia around the tail root in all treatment groups, but had no effect on noxious plantar mechanical responses; however prenatally stressed offspring exhibited significantly attenuated response thresholds to capsaicin compared to controls. In study 2 tail docking did not alter thresholds to either mechanical or noxious cold stimulation. Baseline response durations to noxious cold stimulation of the tail root were significantly shorter in both sexes of prenatally stressed pigs, whilst male but not female prenatally stressed pigs exhibited significantly higher baseline thresholds to mechanical stimulation than controls, although results in female pigs tended towards significance. Carrageenan injection into the tail root induced localised mechanical and cold allodynia in all treatment groups, effects that were attenuated in prenatally stressed pigs. Collectively, these findings indicate that prenatal stress can induce long-term alterations in nociceptive responses, manifest as a reduced sensitivity to noxious mechanical and cold stimulation and evoked inflammatory allodynia. Neonatal tail-docking does not lead to long-term alterations in nociception in pigs., (Copyright © 2011 Elsevier Inc. All rights reserved.)

The ability to assess emotionality is important within animal welfare research. Yet, for farm animals, few tests of emotionality have been well validated. Here we investigated the construct validity of behavioural measures of pig emotionality in an open-field test by manipulating the experiences of pigs in three ways. In Experiment One (pharmacological manipulation), pigs pre-treated with Azaperone, a drug used to reduce stress in commercial pigs, were more active, spent more time exploring and vocalised less than control pigs. In Experiment Two (social manipulation), pigs that experienced the open-field arena with a familiar companion were also more exploratory, spent less time behaviourally idle, and were less vocal than controls although to a lesser degree than in Experiment One. In Experiment Three (novelty manipulation), pigs experiencing the open field for a second time were less active, explored less and vocalised less than they had done in the first exposure to the arena. A principal component analysis was conducted on data from all three trials. The first two components could be interpreted as relating to the form (cautious to exploratory) and magnitude (low to high arousal) of the emotional response to open-field testing. Based on these dimensions, in Experiment One, Azaperone pigs appeared to be less fearful than saline-treated controls. However, in Experiment Two, exposure to the arena with a conspecific did not affect the first two dimensions but did affect a third behavioural dimension, relating to oro-nasal exploration of the arena floor. In Experiment Three, repeat exposure altered the form but not the magnitude of emotional response: pigs were less exploratory in the second test. In conclusion, behavioural measures taken from pigs in an open-field test are sensitive to manipulations of their prior experience in a manner that suggests they reflect underlying emotionality. Behavioural measures taken during open-field exposure can be useful for making assessments of both pig emotionality and of their welfare., (Copyright © 2011 Elsevier Inc. All rights reserved.)

The behavior of groups of housed, lactating dairy cattle was observed over 2 winter housing periods on 20 organic farms and 20 conventional farms in the United Kingdom. Three methods were used: (1) 6 video-clips of 10 min duration were captured of cows feeding at sections of the feed-bunk face during the peak feeding period (0 to 90 min) and continuously observed for aggressive interactions among cows; (2) the proportion of cows at the feed-bunk face was scanned every 15 min for 4.5h to include the peak feeding period (0 to 255 min); and (3) all nonfeeding behaviors were scanned every 15 min for 2.5h after the peak feeding period (120 to 255 min). The latter scans were analyzed post hoc for measures of cow comfort (freestall farms only). Management and health data were collected on each farm. On farms with open-fronted feed-bunk faces, a greater number of aggressive interactions occurred at the feed-bunk face at peak feeding time on organic farms than on conventional farms (organic = 36.3 ± 4.4; conventional = 29.1 ± 3.0). Higher proportions of cows were at the feed-bunk face at peak feeding on organic farms than on conventional farms (organic=0.58 ± 0.04; conventional=0.48 ± 0.03). Housing type (freestall versus straw pen) explained most differences in postfeeding behavior (proportion of ruminating cow in alleyways: freestalls=0.16±0.06 vs. straw-pen=0.08 ± 0.03), with few differences between organic and conventional herds. On freestall farms, the proportions of cows on organic farms lying down postfeeding was smaller than in conventional herds (organic=0.38 ± 0.09 vs. conventional=0.43 ± 0.07). Differences in behavior around peak feeding time could be associated with the reduction in food "quality" on organic farms compared with the energy requirement of the cows, with cows on organic farms being highly motivated to feed. A correlation was observed between farms that had high amounts of lying and farms that had high lameness prevalence (R(2)=55.3), suggesting a complex relationship between comfort and pain. Overall, the behavior of dairy cows on organic farms was not different from that of conventionally reared cows, and the results suggest that most behavioral welfare problems relating to housing could be alleviated by management practices., (Copyright © 2011 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.)

A mechanical stimulator and force measurement system was developed to quantify withdrawal thresholds to noxious mechanical stimulation of the foot in young pigs. The device and associated PC software have design and control features not previously used in other mechanical stimulators. The device, capable of delivering stimulus rates between 2 and 17 mm/s, maximum force 27 N, was validated in a cross-over study on 8 juvenile pigs (6-8 weeks of age) to check the repeatability and reliability of force threshold measurement and assess its ability to measure changes in force threshold following an inflammatory challenge. Threshold force measurements were obtained over several time periods before and after the pigs received a 0.25 ml subcutaneous injection of 3% carrageenan in 0.01 M phosphate buffered saline (PBS) or PBS in the hind foot. Consistent withdrawal thresholds were measured in injected (ipsilateral) and contralateral feet, 24 h and 30 min prior to injection (mean 8.4; 95% CI 7.1-9.7 N). Carrageenan injection, but not PBS injection, induced a significant decrease in withdrawal thresholds 90 min after injection (4.6+/-0.9 N) which remained reduced for 6h after injection. The testing system provided reliable and reproducible measurements of foot withdrawal thresholds to noxious mechanical force in young pigs (weight range 32-39 kg), and was capable of detecting and monitoring changes in threshold sensitivity following the induction of acute local inflammation in the foot. The system is suitable for studying nociceptive mechanisms in pigs.

Pre-natal stress (PNS) or undernutrition can have numerous effects on an individual's biology throughout their lifetime. Some of these effects may be adaptive by allowing individuals to tailor their phenotype to environmental conditions. Here we investigated, in the domestic pig Sus scrofa, whether one possible consequence of a predicted adverse environment could be altered pain perception. The behavioural response of piglets to the surgical amputation ('docking') of their tail or a sham procedure was measured for 1 min in piglets born to mothers who either experienced mid-gestation social stress or were left undisturbed throughout pregnancy. A behavioural pain score was found to predict the docked status of piglets with high discriminant accuracy. Piglets exposed to PNS had a significantly higher pain score than controls, and for each litter of tail-docked piglets, the average pain score was correlated with mid-gestation maternal cortisol levels. The data presented here provide evidence that the experience of stress in utero can result in a heightened acute response to injury in early life. Speculatively, this may represent an adaptive alteration occurring as a consequence of a pre-natal 'early warning' of environmental adversity.

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.

This study aimed to compare the prevalence of lameness on organic and non-organic dairy farms in the United Kingdom (UK) and to assess which cow and farm factors influenced lameness levels. Forty organic and 40 non-organic dairy farms across the UK were repeatedly visited over a 2.5 year period. On each visit all milking cows were locomotion scored, and information about farm housing, management and husbandry practices was recorded on-farm. Over the whole study, the mean herd lameness prevalence was 16.2%, 16.3% and 19.3% in the autumn, winter and spring observation periods, respectively. Lameness prevalence was lower (P=0.012) on organic farms compared to non-organic farms. Numerous specific factors were found to significantly influence the prevalence of lameness. This study provided evidence that organic management reduced herd lameness. It supported previous research which suggested that lameness is a serious problem on many farms in the UK and further emphasised the multi-factorial aetiology of lameness problems.

There have been increases in the number of organic dairy farms in the UK in recent years. However, there is little information on the impact of organic regulations on cow welfare. As part of a larger study, we aimed to investigate differences between organic and non-organic farms in management practices and winter housing quality. Forty organic and 40 non-organic farms throughout the UK were visited. Organic and non-organic farms were paired for housing type, and as far as possible for herd size, genetic merit and location. A detailed questionnaire covering key aspects of dairy management was carried out with each farmer. On a subset of twenty pairs, an assessment of the quality of the winter housing for both lactating and dry cows was undertaken, covering the parlour, bedding, loafing and feeding areas. Management practices and building conditions varied greatly within farm types and there was considerable overlap between organic and non-organic farms. Milk yield, level and composition of concentrate feed, management of heifers and calving, and use of 'alternative treatments' to prevent and treat mastitis differed between organic and non-organic farms. In all other respects there were no differences between farm types. Building dimensions per cow did not differ, even though organic recommendations advise greater space per cow than recommended for non-organic farms. The similarity between organic and non-organic farms in most respects indicates that cow housing and health, based on both the described management regimes and the farmers' perceptions of disease incidence, on organic dairy farms is neither compromised by the regulations, nor considerably better than on non-organic farms.

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 non-organic, 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.

Many of the stressor treatments used in animal models of depression have parallels in the normal experiences of domestic pigs. The experiment described here aimed to assess whether a chronic-intermittent stress regime caused behavioural or physiological changes, indicative of depression, in domestic pigs. Ten juvenile male pigs were exposed to a social and environmental stress regime. Over the stressor period, weight gain was significantly lower in test pigs than in control pigs. Stress treatment had a significant effect on salivary cortisol levels, with test pigs having a higher salivary cortisol concentration than control pigs after the stress treatment but not before. Test pigs showed less ventral lying than control pigs in the post-stress observation. A detrended fluctuation analysis (DFA) of postural behavioural organisation showed that test pigs had a more structured pattern of activity than controls in the post-stress observation and a tendency towards a more structured pattern in the pre-stress observation. There were no major behavioural differences between the two groups during three repeated open field tests. The results suggest that the stressor treatment did create a mild chronic stress, as indicated by the hypercortisolaemia and lower weight gain in the test pigs. However, no unambiguous behavioural indicators of depression were seen. The behavioural analysis did show that fractal techniques, such as DFA, could be applied to pig behaviour and that they can reveal extra novel information about the structure of an individual's behavioural organisation and how it changes in response to complex environmental stressors.

The Artemis Comparison Tool (ACT) allows an interactive visualisation of comparisons between complete genome sequences and associated annotations. The comparison data can be generated with several different programs; BLASTN, TBLASTX or Mummer comparisons between genomic DNA sequences, or orthologue tables generated by reciprocal FASTA comparison between protein sets. It is possible to identify regions of similarity, insertions and rearrangements at any level from the whole genome to base-pair differences. ACT uses Artemis components to display the sequences and so inherits powerful searching and analysis tools. ACT is part of the Artemis distribution and is similarly open source, written in Java and can run on any Java enabled platform, including UNIX, Macintosh and Windows.

Chickens were video recorded while making jumps or flights toward a landing perch, to test hypotheses about visual fixation behaviour. In the first experiment, varying the height above the landing perch of the food container providing the incentive to jump had no effect on head orientation, indicating that the birds were not fixating this object. In the second experiment, hens jumped over six combinations of perch height and distance, and a linear relationship was found at take-off between head orientation and the angular distance of the perch from the horizontal at the eye. This relationship is consistent with fixation of the perch by a linear combination of head and eye rotations, with the head component contributing 73% of the total response. The image of the perch is fixated 20 masculine below that of the bill tip, outside any region of the chicken retina specialised for high acuity vision. Fixation of the perch before jumping must therefore have some function other than inspection with high acuity, such as providing a constraint that enables precise visual control of trajectory and landing manoeuvres.

Corynebacterium diphtheriae is a Gram-positive, non-spore forming, non-motile, pleomorphic rod belonging to the genus Corynebacterium and the actinomycete group of organisms. The organism produces a potent bacteriophage-encoded protein exotoxin, diphtheria toxin (DT), which causes the symptoms of diphtheria. This potentially fatal infectious disease is controlled in many developed countries by an effective immunisation programme. However, the disease has made a dramatic return in recent years, in particular within the Eastern European region. The largest, and still on-going, outbreak since the advent of mass immunisation started within Russia and the newly independent states of the former Soviet Union in the 1990s. We have sequenced the genome of a UK clinical isolate (biotype gravis strain NCTC13129), representative of the clone responsible for this outbreak. The genome consists of a single circular chromosome of 2 488 635 bp, with no plasmids. It provides evidence that recent acquisition of pathogenicity factors goes beyond the toxin itself, and includes iron-uptake systems, adhesins and fimbrial proteins. This is in contrast to Corynebacterium's nearest sequenced pathogenic relative, Mycobacterium tuberculosis, where there is little evidence of recent horizontal DNA acquisition. The genome itself shows an unusually extreme large-scale compositional bias, being noticeably higher in G+C near the origin than at the terminus.

Since the sequencing of the first two chromosomes of the malaria parasite, Plasmodium falciparum, there has been a concerted effort to sequence and assemble the entire genome of this organism. Here we report the sequence of chromosomes 1, 3-9 and 13 of P. falciparum clone 3D7--these chromosomes account for approximately 55% of the total genome. We describe the methods used to map, sequence and annotate these chromosomes. By comparing our assemblies with the optical map, we indicate the completeness of the resulting sequence. During annotation, we assign Gene Ontology terms to the predicted gene products, and observe clustering of some malaria-specific terms to specific chromosomes. We identify a highly conserved sequence element found in the intergenic region of internal var genes that is not associated with their telomeric counterparts.

Leprosy, a chronic human neurological disease, results from infection with the obligate intracellular pathogen Mycobacterium leprae, a close relative of the tubercle bacillus. Mycobacterium leprae has the longest doubling time of all known bacteria and has thwarted every effort at culture in the laboratory. Comparing the 3.27-megabase (Mb) genome sequence of an armadillo-derived Indian isolate of the leprosy bacillus with that of Mycobacterium tuberculosis (4.41 Mb) provides clear explanations for these properties and reveals an extreme case of reductive evolution. Less than half of the genome contains functional genes but pseudogenes, with intact counterparts in M. tuberculosis, abound. Genome downsizing and the current mosaic arrangement appear to have resulted from extensive recombination events between dispersed repetitive sequences. Gene deletion and decay have eliminated many important metabolic activities including siderophore production, part of the oxidative and most of the microaerophilic and anaerobic respiratory chains, and numerous catabolic systems and their regulatory circuits.

Discrepancies in gene and orphan number indicated by previous analyses suggest that S. cerevisiae would benefit from a consistent re-annotation. In this analysis three new genes are identified and 46 alterations to gene coordinates are described. 370 ORFs are defined as totally spurious ORFs which should be disregarded. At least a further 193 genes could be described as very hypothetical, based on a number of criteria. It was found that disparate genes with sequence overlaps over ten amino acids (especially at the N-terminus) are rare in both S. cerevisiae and Sz. pombe. A new S. cerevisiae gene number estimate with an upper limit of 5804 is proposed, but after the removal of very hypothetical genes and pseudogenes this is reduced to 5570. Although this is likely to be closer to the true upper limit, it is still predicted to be an overestimate of gene number. A complete list of revised gene coordinates is available from the Sanger Centre (S. cerevisiae reannotation: ftp://ftp/pub/yeast/SCreannotation).

One hundred and fourteen kilobase pairs (kb) of contiguous genomic sequence have been determined immediately distal to the his5 genetic marker located about 0.9 Mb from the centromere on the long arm of Schizosaccharomyces pombe chromosome 2. The sequence is contained in overlapping cosmid clones c16H5, c12D12, c24C6 and c19G7, of which 20 kb are identical to previously reported sequence from clone c21H7. The remaining 93 781 bp of sequence contains 10 known genes (cdc14, cdm1, cps1, gpa1, msh2, pck2, rip1, rps30-2, sad1 and ubl1), 32 open reading frames (ORFs) capable of coding for proteins of at least 100 amino acid residues in length, one 5S rRNA gene, one tRNA(Pro) gene, one lone Tf1-type long terminal repeat (LTR) and one lone Tf2-type LTR. There is a density of one protein-coding gene per 2.2 kb and 22 of the 42 ORFs (52%) incorporate one or more introns. Twenty-one of the novel ORFs show sequence similarities which suggest functions of their products, including a cyclin C, a MADS box transcription factor, mad2-like protein, telomere binding protein, topoisomerase II-associated protein, ATP-dependent DEAH box RNA helicase, G10 protein, ubiquitin-activating e1-like enzyme, nucleoporin, prolyl-tRNA synthetase, peptidylprolyl isomerase, delta-1-pyrroline-5-carboxylate dehydrogenase, protein transport protein, coatomer epsilon, TCP-1 chaperonin, beta-subunit of 6-phosphofructokinase, aminodeoxychorismate lyase, a phosphate transport protein and a thioredoxin.

Neisseria meningitidis causes bacterial meningitis and is therefore responsible for considerable morbidity and mortality in both the developed and the developing world. Meningococci are opportunistic pathogens that colonize the nasopharynges and oropharynges of asymptomatic carriers. For reasons that are still mostly unknown, they occasionally gain access to the blood, and subsequently to the cerebrospinal fluid, to cause septicaemia and meningitis. N. meningitidis strains are divided into a number of serogroups on the basis of the immunochemistry of their capsular polysaccharides; serogroup A strains are responsible for major epidemics and pandemics of meningococcal disease, and therefore most of the morbidity and mortality associated with this disease. Here we have determined the complete genome sequence of a serogroup A strain of Neisseria meningitidis, Z2491. The sequence is 2,184,406 base pairs in length, with an overall G+C content of 51.8%, and contains 2,121 predicted coding sequences. The most notable feature of the genome is the presence of many hundreds of repetitive elements, ranging from short repeats, positioned either singly or in large multiple arrays, to insertion sequences and gene duplications of one kilobase or more. Many of these repeats appear to be involved in genome fluidity and antigenic variation in this important human pathogen.

Campylobacter jejuni, from the delta-epsilon group of proteobacteria, is a microaerophilic, Gram-negative, flagellate, spiral bacterium-properties it shares with the related gastric pathogen Helicobacter pylori. It is the leading cause of bacterial food-borne diarrhoeal disease throughout the world. In addition, infection with C. jejuni is the most frequent antecedent to a form of neuromuscular paralysis known as Guillain-Barré syndrome. Here we report the genome sequence of C. jejuni NCTC11168. C. jejuni has a circular chromosome of 1,641,481 base pairs (30.6% G+C) which is predicted to encode 1,654 proteins and 54 stable RNA species. The genome is unusual in that there are virtually no insertion sequences or phage-associated sequences and very few repeat sequences. One of the most striking findings in the genome was the presence of hypervariable sequences. These short homopolymeric runs of nucleotides were commonly found in genes encoding the biosynthesis or modification of surface structures, or in closely linked genes of unknown function. The apparently high rate of variation of these homopolymeric tracts may be important in the survival strategy of C. jejuni.