Recommendations for improving the home office project licence abstracts

The Freedom of Information Act 2000 prompted the Government to evaluate how public understanding about the use of animals in scientific research can be improved and how animal experimentation is regulated within the UK. This resulted in the publication of anonymous project licence abstracts. Here, the abstracts published between December 2004 and October 2005 have been evaluated, by using a scoring system which takes into account their content and format, in order to assess whether they provide information that will facilitate the increased implementation of reduction, refinement and replacement strategies. The potential impact of freely-available Home Office project licence abstracts on public attitudes to animal testing and on the quality of animal-based research, is also discussed. Although some abstracts scored well, in general, the abstracts were found to be severely lacking in detail about the welfare of experimental animals. Thus, the abstracts tend to present a distorted picture of animal-based research. Many abstracts lack the details which would reveal how the licensing criteria had been met. It is concluded that, in their current form, the project abstracts are not sufficiently informative. A number of recommendations are made, which address this problem.     

Botulinum toxin testing in animals: the questions remain unanswered

Questions are raised concerning the testing of botulinum toxin in animals, and the British Government's answers to Parliamentary Questions on this issue are reviewed, with an emphasis on the potential for reducing, refining and replacing the animal tests, which can involve substantial severity, and on the responsibility of the Home Office so see that the Three Rs approach is fully applied in this specific case.     

An analysis of the Home Office Statistics of Scientific Procedures on Living Animals, Great Britain 2004

The 2004 Statistics of Scientific Procedures on Living Animals were released by the Home Office in December 2005. They indicate that, for the third year running, there has been a significant increase in the number of laboratory animal procedures undertaken in Great Britain, and that increasing numbers of animals are involved. The overall trends in the use of toxicological and non-toxicological procedures involving animals are described. Particular emphasis is placed on the production and use of genetically modified animals, the production of biological materials, and acute toxicity testing. The use of non-human primates and dogs is also discussed. The implications of these latest statistics are considered with reference to the implementation of the Three Rs and their consequences for animal welfare.     

Scientific procedures on living animals in Great Britain in 2003: the facts, figures and consequences

The statistics for animal procedures performed in 2003 were recently released by the Home Office. They indicate that, for the second year running, there was a significant increase in the number of laboratory animal procedures undertaken in Great Britain. The species and genera used, the numbers of toxicology and non-toxicology procedures, and the overall trends, are described. The implications of these latest statistics are discussed with reference to key areas of interest and to the impact of existing regulations and pending legislative reforms.     

The fourth EC report on the statistics of laboratory animal use: trends, recommendations and future prospects

At the beginning of 2005, the European Commission published its fourth report on the statistics of the number of animals used for experimental and other scientific purposes. A total of 10.7 million animals were used within the Member States of the European Union (EU) in 2002, an increase of almost a million animals since the 1999 report. France, Germany and the UK continue to be the largest users of animals for scientific purposes, and mice, rats, fish and birds remain the most commonly-used animals. For the first time, all 15 Member States used the standardised EU tables, as had been agreed in 1998. This has made it easier to identify areas on which Three Rs initiatives should be focused. Nevertheless, the reporting system still has a number of serious deficiencies. In particular, there are insufficient data on the numbers of animals that are kept or bred for research purposes, the numbers of transgenic animals, and the severity of procedures that are applied.     

Casualty departments and the monitoring of drug dependence.

In a month-long prospective survey of patients attending London casualty departments with drug-related problems, 395 drug-dependent patients were identified. A check against the official Home Office index of notified addicts showed that 226 (57%) were not known to the Home Office. Of 92 patients who used narcotics only 53% were known with certainty to the Home Office, and when the source of notification was checked it became clear that in at least 77% of incidents involving narcotic addicts in casualty departments the addict was not reported. Repeated research in casualty departments could play a valuable role in monitoring drug dependence and might provide information supplementary to that obtained from the specialised drug treatment clinics and other sources of notification.     

An update on DNA barcoding: low species coverage and numerous unidentified sequences

DNA barcoding was proposed in 2003, the Consortium for the Barcode of Life was established in 2004, and the movement has since attracted more than $80 million funding. Here we investigate how many species of multicellular animals have been barcoded. We compare the numbers in a public database (GenBank as of January 2012) with those in the Barcode of Life Database (BOLD) and find that GenBank contains COI (cytochrome c oxidase subunit 1) sequences for ca. 60 000 species while BOLD reports barcodes for ca. 150 000 species. The discrepancy is likely due to a large amount of unpublished data in BOLD. Overall, the species coverage remains sparse, growth rates are low, and the barcode accumulation curve for Metazoa is linear with only 4788 species having been added in 2011. In addition, the vast majority of species in the public database (73%) were barcoded by projects that are unlikely to be related to the DNA barcoding movement. Particularly surprising was the large number of DNA barcodes in GenBank that were not identified to species (Jan 2012: 74%), with insect barcodes often being identified only to order. Of these several hundred thousand have since been suppressed by NCBI because they did not satisfy the iBOL/GenBank early release agreement. Species coverage is considerably better for target taxa of DNA barcoding campaigns (e.g. birds, fishes, Lepidoptera), although it also falls short of published campaign targets. © The Willi Hennig Society 2012     

Computing fuzzy associations for the analysis of biological literature

The increase of information in biology makes it difficult for researchers in any field to keep current with the literature. The MEDLINE database of scientific abstracts can be quickly scanned using electronic mechanisms. Potentially interesting abstracts can be selected by matching words joined by Boolean operators. However this means of selecting documents is not optimal. Nonspecific queries have to be effected, resulting in large numbers of irrelevant abstracts that have to be manually scanned To facilitate this analysis, we have developed a system that compiles a summary of subjects and related documents on the results of a MEDLINE query. For this, we have applied a fuzzy binary relation formalism that deduces relations between words present in a set of abstracts preprocessed with a standard grammatical tagger. Those relations are used to derive ensembles of related words and their associated subsets of abstracts. The algorithm can be used publicly at http:// www.bork.embl-heidelberg.de/xplormed/.     

The use of non-human primates in regulatory toxicology: comments submitted by FRAME to the Home Office

The Home Office have circulated a document that summarises the discussions of a Primate Stakeholders Forum. The Forum took place in January 2004, and was convened to address the issues raised and the recommendations made in the Animal Procedures Committee 2002 report on the use of primates under the Animals (Scientific Procedures) Act 1986. The report emphasises the need for more resources focused on alternatives to toxicological testing in primates, including harmonising worldwide regulatory requirements, investigating the relevance of primate models, and improving the retrospective analysis of procedures involving primates. The document called for reasoned comments about the report to be submitted to the Home Office. In response, FRAME submitted a comprehensive paper, which evaluated each of the Animal Procedures Committees recommendations, along with the Home Office Forums comments. FRAME believes that, in coming to a decision as to whether primates should be used for regulatory testing, there must be full consideration of all the information available, including whether the ethological needs of any given species can be met prior to, during and following experimental use. Where these needs cannot be met, there must be a concerted effort to develop alternative models for research and testing. However, this should not detract from the ultimate goal of phasing out primate research altogether.     

Text-analysis reveals taxonomic and geographic disparities in animal pollination literature

Ecological systematic reviews and meta-analyses have significantly increased our understanding of global biodiversity decline. However, for some ecological groups, incomplete and biased datasets have hindered our ability to construct robust, predictive models. One such group consists of the animal pollinators. Approximately 88% of wild plant species are thought to be pollinated by animals, with an estimated annual value of $230–410 billion dollars. Here we apply text-analysis to quantify the taxonomic and geographical distribution of the animal pollinator literature, both temporally and spatially. We show that the publication of pollinator literature increased rapidly in the 1980s and 1990s. Taxonomically, we show that the distribution of pollinator literature is concentrated in the honey bees (Apis) and bumble bees (Bombus), and geographically in North America and Europe. At least 25% of pollination-related abstracts mention a species of honey bee and at least 20% a species of bumble bee, and approximately 46% of abstracts are focussed on either North America (32%) or Europe (14%). Although these results indicate strong taxonomic and geographic biases in the pollinator literature, a large number of studies outside North America and Europe do exist. We then discuss how text-analysis could be used to shorten the literature search for ecological systematic reviews and meta-analyses, and to address more applied questions related to pollinator biodiversity, such as the identification of likely interacting plant–pollinator pairs and the number of pollinating species.     

Comments on UK options for transposition of European Directive 2010/63/EU

The British Government's proposals for the transposition of European Directive 2010/63/EU are discussed under five main headings: direct transposition without major effects on the UK legislation, introduction of stricter requirements in the Directive, retention of stricter controls in the Animals [Scientific Procedures] Act 1986, questions requiring further consideration, and matters of concern. The Home Office had published a consultation on the options in 2011, which resulted in 98 responses from organisations and 13,458 responses from individuals. Our main concerns relate to the use of non-human primates, the annual publication of the UK statistics on laboratory animal use, and the provision of greater transparency on how animals are used, and why. Finally, we conclude that the new Directive and its transposition into the national laws of the Member states provide a renewed opportunity for genuine commitment to the Three Rs, leading to progressive and significant Reduction, Refinement and Replacement.     

Cephalopod biology and care,a COST FA1301 (Cephs<Emphasis Type="Italic">In</Emphasis>Action) training school: anaesthesia and scientific procedures

Cephalopods are the sole invertebrates included in the list of regulated species following the Directive 2010/63/EU. According to the Directive, achieving competence through adequate training is a requisite for people having a role in the different functions (article 23) as such carrying out procedures on animals, designing procedures and projects, taking care of animals, killing animals. Cephalopod Biology and Care Training Program is specifically designed to comply with the requirements of the “working document on the development of a common education and training framework to fulfil the requirements under the Directive 2010/63/EU”. The training event occurred at the ICM-CSIC in Barcelona (Spain) where people coming from Europe, America and Asia were instructed on how to cope with regulations for the use of cephalopod molluscs for scientific purposes. The training encompasses discussion on the guidelines for the use and care of animals and their welfare with particular reference to procedures that may be of interest for neuroscience. Intensive discussion has been carried out during the training sessions with focus on behavioural studies and paradigms, welfare assessment, levels of severity of scientific procedures, animal care, handling, transport, individual identification and marking, substance administration, anaesthesia, analgesia and humane killing.     

Evolutionary change of the numbers of homeobox genes in bilateral animals

It has been known that the conservation or diversity of homeobox genes is responsible for the similarity and variability of some of the morphological or physiological characters among different organisms. To gain some insights into the evolutionary pattern of homeobox genes in bilateral animals, we studied the change of the numbers of these genes during the evolution of bilateral animals. We analyzed 2,031 homeodomain sequences compiled from 11 species of bilateral animals ranging from Caenorhabditis elegans to humans. Our phylogenetic analysis using a modified reconciled-tree method suggested that there were at least about 88 homeobox genes in the common ancestor of bilateral animals. About 50-60 genes of them have left at least one descendant gene in each of the 11 species studied, suggesting that about 30-40 genes were lost in a lineage-specific manner. Although similar numbers of ancestral genes have survived in each species, vertebrate lineages gained many more genes by duplication than invertebrate lineages, resulting in more than 200 homeobox genes in vertebrates and about 100 in invertebrates. After these gene duplications, a substantial number of old duplicate genes have also been lost in each lineage. Because many old duplicate genes were lost, it is likely that lost genes had already been differentiated from other groups of genes at the time of gene loss. We conclude that both gain and loss of homeobox genes were important for the evolutionary change of phenotypic characters in bilateral animals.     

Replacing animal use in physiology and pharmacology teaching in selected universities in Eastern Europe--charting a way forward

The aims of this study were to explore the use of animals in teaching and the implementation of innovative technology-based teaching practices across a small sample of universities in Eastern Europe. The research methods used were a questionnaire circulated four weeks before a workshop took place (in October 2009, in Belgrade, Serbia), as well as focused, face-to-face group discussions, led by one of the authors during the workshop. Twenty-two faculty (physiologists and pharmacologists), from 13 Eastern European countries, attended the meeting. Fourteen of the eighteen schools represented at the workshop were making use of animals, in some instances in quite large numbers, for their teaching. For example, a single department at a Romanian university used over 250 animals per annum, and at least 1130 animals were used, per annum, across all of the institutions. The species used in largest numbers were the rat (34%), frog/toad (29%), mouse (22%), rabbit (10%), guinea-pig (4%) and dog (1%). None of the universities sampled had implemented institution-wide virtual learning environments (VLEs), although there were isolated instances of local use of VLEs. There was relatively little current use of technology-based teaching and learning resources, but there was considerable enthusiasm to modernise teaching and to introduce innovative learning and teaching methods. The major perceived barrier to the introduction of replacement alternatives was the lack of versions in local languages. There was a consensus view that developing local language exemplars and evaluating their usefulness was likely to have the greatest impact on animal use, at least in the short-term.     

The effect of daily disturbance on the breeding performance of mice

The United Kingdom Home Office Code of Practice for the housing and care of breeding animals requires that, 'the general well-being of all animals must be checked at least once daily'. However, excessive daily disturbance of rodent breeding colonies could be counter-productive to animal welfare if it increases pre-weaning mortality. An experiment involving 100 breeding cages of BALB/c mice compared daily inspection of the mouse cages, but without disturbing the mice within the nest, with daily inspection in which every individual was studied even if this involved removing the cage lid and disturbing the nest. No statistically significant differences were found between the two groups in breeding performance or pre-weaning mortality, though the disturbed group produced marginally fewer offspring and had slightly higher mortality. Average weaning weight did not differ between the groups, but sexual dimorphism at weaning was significantly increased in the disturbed group. It is concluded that there are unlikely to be any welfare benefits in an inspection regimen that involves disturbance of breeding mice, provided the cage is inspected daily.     

Follow-up of Cases of Opiate Addiction from the Time of Notification to the Home Office

Follow-up of 108 opiate addicts for a period of six to seven years showed that 35 were still being prescribed opiates, 25 were off drugs, 19 were dead, and for 29 it was not certain whether they were on or off drugs. Most patients who came off drugs did so in the first two years after notification to the Home Office. Clearly treatment is more likely to be successful if given early in the life history of the addict, when it is appropriate to give treatment based on withdrawal of drugs rather than substitution.     

基于涉案兽类12S rRNA基因的NCBI数据库序列可靠性分析

本研究以常用于动物种属鉴定的12S rRNA基因位点为研究对象,利用所测得的17种常见涉案兽类12S rRNA基因部分片段序列及NCBI数据库中下载的该物种DNA序列及其近缘物种DNA序列,构建系统进化树。根据进化树的聚类情况,判断NCBI数据库中的相关基因序列或物种名称的正确性,并对其中错误序列的登陆号进行标记,以防对后续涉案动物的准确鉴定造成影响。分别从17种常见涉案兽类(共26份样本)中提取线粒体DNA,并利用通用引物扩增线粒体DNA上的12S rRNA基因部分片段并进行测序分析。通过NCBI数据库的Blast比对功能,筛选出与本研究物种同源性由高到低的物种,并从NCBI基因数据库中下载此类近缘物种的12S rRNA基因序列共351条,利用MEGA7.0软件构建该物种及其近缘物种系统进化树。通过比对发现NCBI中登录号为KP202279等3个序列所对应物种拉丁名错误。登录号为AY184436等11个序列所对应物种拉丁名可能存在疑问。GenBank中某些物种拉丁名有同种异名现象。因此,NCBI数据库数据可靠性有待进一步验证,只能作为涉案物种鉴定的参考数据之一,可借助构建系统进化树等方法来确认其结果的准确性。     

Mangrove Restoration: Do We Know Enough?

Mangrove restoration projects have been attempted, with mixed results, throughout the world. In this paper, I first examine goals of existing mangrove restoration projects and determine whether these goals are clear and adequate, and whether or not they account for the full range of biological diversity and ecological processes of mangrove ecosystems. Many restored mangrove forests resemble forest plantations rather than truly integrated ecosystems, but mangrove plantations can be a first step toward mangrove rehabilitation. Mangrove restoration projects that involve associated aquaculture or mariculture operations tend to be more likely to approximate the biological diversity and ecological processes of undisturbed mangrove ecosystems than are projects that focus only on the trees. These integrated restoration projects also provide a higher economic return than do silvicultural projects alone. Second, I briefly assess whether existing ecological data are sufficient to undergird successful restoration of mangal and define criteria for determining whether or not a mangrove ecosystem has been restored successfully. These criteria include characteristics of vegetation (forest) structure, levels of primary production, composition of associated animal communities, and hydrology. Finally, I suggest ways to improve mangrove restoration projects and identify key research needs required to support these efforts. Ecological theories derived from other wetland and upland systems rarely have been applied to either “basic” or “applied” mangrove forest studies, to the detriment of restoration projects, whereas lessons from restoration of the relatively species‐poor mangrove ecosystems could be beneficially applied to restoration projects in other contexts. An international database of mangrove restoration projects would reduce the likelihood that unsuccessful restoration projects would be repeated elsewhere. Clear criteria for evaluating success, greater accessibility of information by managers in the developing world, intensified international cooperation, and application of relevant ecological theories will improve the success rate of mangrove restoration projects.     

The trade of medicinal animals in Brazil: current status and perspectives

In cities, the trade of medicinal products derived from animals, especially as raw materials, is concentrated in local and traditional markets. The lack of studies on commercialised medicinal faunas restricts an evaluation of the impact of this activity on the exploited species. Within this context, this work reviewed the literature on the trade of medicinal animals in local markets, focusing on urban zootherapy in Brazil and the social factors involved in these practices. Our results reveal that at least 131 species are sold for medicinal purposes in markets and open fairs in Brazil, but results obtained from statistical estimators suggest that this trade actually encompasses a greater richness of species. The medicinal animals sold in Brazil are used to treat 126 illnesses and/or symptoms. Despite the trade of wild animals, including species that are present on the list of endangered species, being forbidden in Brazil, it has been demonstrated that this activity remains common in some Brazilian cities, occurring illicitly and without due monitoring by competent environmental agencies. The results illustrate the need for further research, which should encompass a larger number of cities, especially in regions where information on this subject is currently lacking.