Synthesis of semantic modelling and risk analysis methodology applied to animal welfare

Decision-making on animal welfare issues requires a synthesis of information. For the assessment of farm animal welfare based on scientific information collected in a database, a methodology called 'semantic modelling' has been developed. To date, however, this methodology has not been generally applied. Recently, a qualitative Risk Assessment approach has been published by the European Food Safety Authority (EFSA) for the first time, concerning the welfare of intensively reared calves. This paper reports on a critical analysis of this Risk Assessment (RA) approach from a semantic-modelling (SM) perspective, emphasizing the importance of several seemingly self-evident principles, including the definition of concepts, application of explicit methodological procedures and specification of how underlying values and scientific information lead to the RA output. In addition, the need to include positive aspects of welfare and overall welfare assessments are emphasized. The analysis shows that the RA approach for animal welfare could benefit from SM methodology to support transparent and science-based decision-making.     

Role assessment,reserve strategy,and acquisition of information in asymmetric animal conflicts

It was formerly argued that alternative evolutionarily stable strategies (ESSs) are possible for animal contests characterized by some asymmetry that can be perceived with perfect accuracy. Where roles A and B refer to the asymmetry between opponents, ESSs are: ‘fight when A, retreat when B’, and vice versa. Either can be an ESS, but only if the ‘reserve strategy’ (=what an animal does when it fights) is sufficiently damaging. We examine the ‘war of attrition’ (winner = opponent that persists longer). In a population at either ESS, reserve strategy is never normally shown; it is therefore subject to drift unless the selective action of rare individuals which break the convention is considered. These could arise either by mutation or by mistakes in role assessment. When mutations and mistakes simply specify that occasionally an animal fights when it ‘should’ retreat, selection adjusts reserve strategy to a level where only one ESS (the ‘commonsense’ ESS) is possible, if the asymmetry is relevant to payoff. Thus for asymmetries in fighting ability or resource value, the individual with the lower score will retreat. However, we are particularly concerned with cases where both payoff-relevant aspects (fighting ability and resource value) are asymmetric. If opponents sustain contest costs at rates K_A and K_B, and their resource values are V_A and V_B, an ‘optimal assessor’ strategy defined by the interaction between the two asymmetries, is a unique ESS. It obeys the rule ‘fight on estimating role A, where V_A/K_A>V_B/K_B; retreat in B’. If mistakes can occur in both roles, but are very rate, the ESS is not fundamentally altered though there will be infinitesimal tendencies for persisting in role B. Selection to improve assessment abilities intensifies as abilities improve, but is weak if roles A and B are rather similar. Over a range of similarity between roles, an ‘owner wins’ convention may be adopted if ownership correlates positively with role A and an individual cannot tell when it would otherwise pay him to break the convention. We also examine a contest in which information about roles can be acquired only during a contest itself, and at a cost. Much depends on the rate at which information is acquired relative to the rate at which costs are expended, and on whether contests normally escalate in intensity, remain at the same level, or de-escalate. Selection favours short contests when costs are high relative to resource value, where the outcome of a round contains much information about fighting ability, and where the actual disparity in fighting ability is large.     

Stem cells, regenerative medicine, and animal models of disease

The field of stem cell biology and regenerative medicine is rapidly moving toward translation to clinical practice, and in doing so has become even more dependent on animal donors and hosts for generating cellular reagents and assaying their potential therapeutic efficacy in models of human disease. Advances in cell culture technologies have revealed a remarkable plasticity of stem cells from embryonic and adult tissues, and transplantation models are now needed to test the ability of these cells to protect at-risk cells and replace cells lost to injury or disease. With such a mandate, issues related to acceptable sources and controversial (e.g., chimeric) models have challenged the field to provide justification of their potential efficacy before the passage of new restrictions that may curb anticipated breakthroughs. Progress from the use of both in vitro and in vivo regenerative medicine models already offers hope both for the facilitation of stem cell phenotyping in recursive gene expression profile models and for the use of stem cells as powerful new therapeutic reagents for cancer, stroke, Parkinson's, and other challenging human diseases that result in movement disorders. This article describes research in support of the following three objectives: (1) To discover the best stem or progenitor cell in vitro protocols for isolating, expanding, and priming these cells to facilitate their massive propagation into just the right type of neuronal precursor cell for protection or replacement protocols for brain injury or disease, including those that affect movement such as Parkinson's disease and stroke; (2) To discover biogenic factors--compounds that affect stem/progenitor cells (e.g., from high-throughput screening and other bioassay approaches)--that will encourage reactive cell genesis, survival, selected differentiation, and restoration of connectivity in central nervous system movement and other disorders; and (3) To establish the best animal models of human disease and injury, using both small and large animals, for testing new regenerative medicine therapeutics.     

Marsupials from space: fluctuating asymmetry, geographical information systems and animal conservation

We report the development of a new quantitative method of assessing the effects of anthropogenic impacts on living beings; this method allows us to assess actual impacts and to travel backwards in time to assess impacts. In this method, we have crossed data on fluctuating asymmetry (FA, a measure of environmental or genetic stress), using Didelphis albiventris as a model, with geographical information systems data relating to environmental composition. Our results show that more impacted environments resulted in statistically higher levels of FA. Our method appears to be a useful and flexible conservation tool for assessing anthropogenic impacts.     

Vegetarianism, coronary disease risk factors and coronary heart disease

Recent studies of vegetarians confirm a lower risk of fatal heart disease amongst such subjects. Lipid levels are lower in vegetarians, even when the diet of comparable meat-eaters is low in fat. This may partly explain the lower mortality, but it is not clear whether the absence of meat or some other aspect of the vegetarian diet is causal in this relationship.     

An analysis of the regulation of DNA synthesis by cdk2, Cip1, and licensing factor

The activation of DNA replication appears to involve at least four steps. These include origin recognition, origin unwinding, primer synthesis, and a switching step to a continuous elongation mode. Moreover, in higher eukaryotes a number of studies have shown that much of the DNA replication which occurs is restricted to specific sites within the nuclei. It has been proposed that these replication foci are composed of a large number of origin sites which are clustered together into an aggregate. The molecular basis for this aggregation is currently not well understood. Regulation of the activation of DNA replication is a complicated process. The G1-S kinase cdk2 is a positive regulator of replication. The p21 protein is a negative regulator of replication both by inhibiting cdk2 kinase and the replication protein PCNA. Moreover, it has been proposed that origin usage is restricted to a single firing per cell cycle by a "licensing factor." Using a cell-free replication system derived from Xenopus eggs we have investigated at what step in the replication process these regulators participate. We present evidence that the clustered organization of DNA into foci is not a transient arrangement, but rather, it persists following DNA replication. We also find that foci form on both sperm chromatin and bacteriophage lambda DNA incubated in extracts depleted of cdk2 kinase. Therefore, our data support the conclusion that organization of chromatin into foci is an early event in the replication pathway preceding activation of cdk2 kinase. With respect to the role of cdk2 during activation of DNA replication we find that in cdk2-depleted extracts primer synthesis does not occur and RP-A remains tightly associated with foci. This strongly suggests that cdk2 kinase is required for activating the origin unwinding step of the replication process. Consistent with this interpretation we find that addition of rate limiting quantities of the cdk2 inhibitor p21 protein to an extract delays primer synthesis. Interestingly, in the presence of p21 primer synthesis does occur after a delay and then replication arrests. This is consistent with the published demonstration that p21 can inhibit PCNA, a protein required for replication beyond the priming step. Therefore, our results provide additional support to the proposal that the post-priming switching step is a key regulatory step in replication. With respect to the role of licensing factor during DNA replication it has recently been shown that treatment of mitotic extracts with kinase inhibitor DMAP inactivates "licensing factor."(ABSTRACT TRUNCATED AT 400 WORDS)     

Spatial heterogeneity, social structure and disease dynamics of animal populations

Social groupings, population dynamics and population movements of animals all give rise to spatio-temporal variations in population levels. These variations may be of crucial importance when considering the spread of infectious diseases since infection levels do not increase unless there is a sufficient pool of susceptible individuals. This paper explores the impact of social groupings on the potential for an endemic disease to develop in a spatially explicit model system. Analysis of the model demonstrates that the explicit inclusion of space allows asymmetry between groups to arise when this was not possible in the equivalent spatially homogeneous system. Moreover, differences in movement behaviours for susceptible and infected individuals gives rise to different spatial profiles for the populations. These profiles were not observed in previous work on an epidemic system. The results are discussed in an ecological context with reference to furious and dumb strains of infectious diseases.     

Use of information on disease diagnoses from databases for animal health economic,welfare and food safety purposes: strengths and limitations of recordings

Many animal health, welfare and food safety databases include data on clinical and test-based disease diagnoses. However, the circumstances and constraints for establishing the diagnoses vary considerably among databases. Therefore results based on different databases are difficult to compare and compilation of data in order to perform meta-analysis is almost impossible. Nevertheless, diagnostic information collected either routinely or in research projects is valuable in cross comparisons between databases, but there is a need for improved transparency and documentation of the data and the performance characteristics of tests used to establish diagnoses. The objective of this paper is to outline the circumstances and constraints for recording of disease diagnoses in different types of databases, and to discuss these in the context of disease diagnoses when using them for additional purposes, including research. Finally some limitations and recommendations for use of data and for recording of diagnostic information in the future are given. It is concluded that many research questions have such a specific objective that investigators need to collect their own data. However, there are also examples, where a minimal amount of extra information or continued validation could make sufficient improvement of secondary data to be used for other purposes. Regardless, researchers should always carefully evaluate the opportunities and constraints when they decide to use secondary data. If the data in the existing databases are not sufficiently valid, researchers may have to collect their own data, but improved recording of diagnostic data may improve the usefulness of secondary diagnostic data in the future.     

Celiac disease: risk assessment, diagnosis, and monitoring

Celiac disease is an autoimmune disorder occurring in genetically susceptible individuals, triggered by gluten and related prolamins. Well identified haplotypes in the human leukocyte antigen (HLA) class II region (either DQ2 [DQA*0501-DQB*0201] or DQ8 [DQA*0301-DQB1*0302]) confer a large part of the genetic susceptibility to celiac disease.Celiac disease originates as a result of a combined action involving both adaptive and innate immunity. The adaptive immune response to gluten has been well described, with the identification of specific peptide sequences demonstrating HLA-DQ2 or -DQ8 restrictive binding motifs across various gluten proteins. As for innate immunity, through specific natural killer receptors expressed on their surface, intra-epithelial lymphocytes recognize nonclassical major histocompatibility complex (MHC)-I molecules such as MICA, which are induced on the surface of enterocytes by stress and inflammation, and this interaction leads to their activation to become lymphokine-activated killing cells. Four possible presentations of celiac disease are recognized: (i) typical, characterized mostly by gastrointestinal signs and symptoms; (ii) atypical or extraintestinal, where gastrointestinal signs/symptoms are minimal or absent and a number of other manifestations are present; (iii) silent, where the small intestinal mucosa is damaged and celiac disease autoimmunity can be detected by serology, but there are no symptoms; and, finally, (iv) latent, where individuals possess genetic compatibility with celiac disease and may also show positive autoimmune serology, that have a normal mucosa morphology and may or may not be symptomatic.The diagnosis of celiac disease still rests on the demonstration of changes in the histology of the small intestinal mucosa. The classic celiac lesion occurs in the proximal small intestine with histologic changes of villous atrophy, crypt hyperplasia, and increased intraepithelial lymphocytosis. Currently, serological screening tests are utilized primarily to identify those individuals in need of a diagnostic endoscopic biopsy. The serum levels of immunoglobulin (Ig)A anti-tissue transglutaminase (or TG2) are the first choice in screening for celiac disease, displaying the highest levels of sensitivity (up to 98%) and specificity (around 96%). Anti-endomysium antibodies-IgA (EMA), on the other hand, have close to 100% specificity and a sensitivity of greater than 90%. The interplay between gliadin peptides and TG2 is responsible for the generation of novel antigenic epitopes, the TG2-generated deamidated gliadin peptides. Such peptides represent much more celiac disease-specific epitopes than native peptides, and deamidated gliadin antibodies (DGP) have shown promising results as serological markers for celiac disease. Serology has also been employed in monitoring the response to a gluten-free diet.Despite the gluten-free diet being so effective, there is a growing demand for alternative treatment options. In the future, new forms of treatment may include the use of gluten-degrading enzymes to be ingested with meals, the development of alternative, gluten-free grains by genetic modification, the use of substrates regulating intestinal permeability to prevent gluten entry across the epithelium, and, finally, the availability of different forms of immunotherapy.     

Genetic polymorphisms, lipoproteins and coronary artery disease risk

Association studies between gene variants (polymorphisms) and measured intermediate phenotypes, such as lipid/lipoprotein levels, or disease endpoints such as coronary artery disease, are commonplace in the literature. But have we learnt anything from the shortcomings in study design and analytical strategies that have resulted in much controversy in this field over the last few years? This review highlights some of these problems. Using the lipoprotein lipase gene as an example, we evaluate new approaches to identifying polymorphisms that will stand up to linkage disequilibrium/association studies with complex disorders in this post Human Genome Project age, and emphasize the importance of gene-environment interaction in assessing the impact of gene variants.     

Expression of metallothionein-I, -II, and -III in Alzheimer disease and animal models of neuroinflammation

In recent years it has become increasingly clear that the metallothionein (MT) family of proteins is important in neurobiology. MT-I and MT-II are normally dramatically up-regulated by neuroinflammation. Results for MT-III are less clear. MTs could also be relevant in human neuropathology. In Alzheimer disease (AD), a major neurodegenerative disease, clear signs of inflammation and oxidative stress were detected associated with amyloid plaques. Furthermore, the number of cells expressing apoptotic markers was also significantly increased in these plaques. As expected, MT-I and MT-II immunostaining was dramatically increased in cells surrounding the plaques, consistent with astrocytosis and microgliosis, as well as the increased oxidative stress elicited by the amyloid deposits. MT-III, in contrast, remained essentially unaltered, which agrees with some but not all studies, of AD. In situ hybridization results in a transgenic mouse model of AD amyloid deposits, the Tg2576 mouse, which expresses human Abeta precursor protein harboring the Swedish K670N/M671L mutations, are in accordance with results in human brains. Overall, these and other studies strongly suggest specific roles for MT-I, MT-II, and MT-III in brain physiology.     

Pharmacological systemic analysis of gardenia fructus against non-alcoholic fatty liver disease and validation of animal models

[Purpose]We aimed to investigate the systemic pharmacological analysis of gardenia fructus (GF) and the proof of concepts. We examined the antioxidant and anti-inflammatory effects in high-fat (HF) diet mice.[Methods]The active compounds of GF and the target genes were identified using the Traditional Chinese Medicine Database and Analysis Platform (oral bioavailability ≥ 30%, Caco-2 permeability ≥ -0.4, and drug-likeness ≥ 0.18). The rats were divided into four groups: untreated group, HF group, HF and metformin (17 mg/kg) treated group, and HF and treated with GF (28 mg/kg) for 8 weeks group. Hepatic lesion changes and markers were analyzed using hematoxylin and eosin staining and immunohistochemistry assay.[Results]In the systemic analysis, we identified 14 active compounds including A, B, and C. From these 14 compounds, 242 biological target genes were identified. The top 10 Gene Ontology were analyzed using GO-biological process analysis: removal of superoxide radicals, regulation of endothelial cell apoptotic process, and cellular response to lipopolysaccharide. GF extracts in high-fat diet-induced non-alcoholic fatty liver disease (NAFLD) mice models significantly regulated hepatic lesion markers, such as mTOR, 8-Hydroxy-2''-deoxyguanosine as well as oxidative stress activities, TGF-β, and phosphorylation of ERK1/2.[Conclusion]These results suggest that GF, as an exercise supplement, can alleviate NAFLD disease or fatty liver inflammation. Further studies are required to verify the synergistic effect of GF treatment combined with exercise, which is known to alleviate NAFLD and fatty liver inflammation.     

Sequence and analysis of the nodABC region of Rhizobium fredii USDA257, a nitrogen-fixing symbiont of soybean and other legumes.

We cloned and analyzed nodABC from Rhizobium fredii USDA257. These genes are thought to have common functions in initiation of nitrogen-fixing nodules by all rhizobia. In USDA257, they were located in a 9.2-kb EcoRI fragment that was not closely linked to either of two copies of the regulatory gene, nodD. nodABC was present in a 3,094-base pair (bp) sequenced region, which also included a consensus nod-box promoter. The three open reading frames contained 654, 642, and 1,239 bp, respectively, and encoded deduced proteins of 21.9, 23.4, and 44.7 kD. The sequence of the nodABC region of USDA257 was generally homologous with corresponding regions from other rhizobia, but it diverged significantly in the 5' non-translated region and in the 3'terminus of nodC. nodC was not translationally coupled to nodSU, as in another soybean symbiont, Bradyrhizobium japonicum, and the deduced NodC protein was the shortest of any such proteins yet described. Site-directed mutagenesis of the 9.2-kb EcoRI fragment confirmed that nodA, nodB, and nodC are essential for nodulation of soybean, but failed to identify other linked nod genes. Daidzein, a major isoflavone from soybean roots, was the most potent of nine tested flavonoids in activating a plasmid-borne nodC::lacZ fusion. The 9.2-kb fragment complemented nodA-, nodB-, and nodC- mutants of R. meliloti to the Nod+ phenotype on Medicago sativa, M. truncatula, and Trigonella foenum-graecum. Nodule numbers, percentage of nodulated plants, and shoot dry weights, however, were considerably less than in plants inoculated with mutants complemented with nodABC from R. meliloti.     

Aging,caffeine, and information processing: an event-related potential analysis

Structural and energetic processes in information processing were studied in young and elderly subjects. A visually focussed selective search task was used, in which subjects had to select relevant information, followed by controlled memory search processes to locate a target item. Caffeine was used to manipulate the energetic state of the subjects. During task performance event-related potentials (ERPs) and reaction time (RT) were recorded.Subjects were 15 young and 15 elderly healthy, non-smoking, moderate caffeine consumers (250–600 mg/day). Before the experimental sessions they abstained from caffeine for ≥12 h. In the experiment subjects received 250 mg caffeine or placebo dissolved in decaffeinated coffee.RT data seem to indicate that aging effects are at least partly due to a shift in the speed-accuracy trade-off. ERP results provide evidence for decreased levels of energy resources in the elderly. The identification of relevant information and stimulus evaluation processes were delayed in the elderly, suggesting an additional effect of aging on structural processes. Caffeine improved performance and increased the amplitude of the N1, N2b, and P3b, in both young and old subjects. These results suggest that caffeine makes more energy resources available for task performance. The effects of aging on P3b latency were counteracted by caffeine. Other caffeine effects did not differ significantly between young and elderly subjects.     

Postprandial lipoprotein metabolism, genes and risk of cardiovascular disease

PURPOSE OF REVIEW: Several lines of evidence suggest that postprandial lipemia increases the risk of atherogenesis, and in each of the systems involved in postprandial metabolism the roles of many genes have been explored in order to establish the possible implications of their variability in coronary heart disease risk. RECENT FINDINGS: This report focuses on recent results pertaining to postprandial lipoprotein metabolism and genes, their variability and their relationship with intermediate phenotypes and coronary heart disease. The postprandial lipid response was modified by polymorphisms within the genes for apolipoprotein AI, apolipoprotein E, apolipoprotein B, apolipoprotein CI, apolipoprotein CIII, apolipoprotein AIV, apolipoprotein AV, lipoprotein lipase, hepatic lipase, fatty acid-binding protein-2, the fatty acid transport proteins, microsomal triglyceride transfer protein and scavenger receptor class B type I. We also discuss recent advances in the effects of gene regulation using knockdown animal models on postprandial lipoprotein metabolism. SUMMARY: The review discusses several of these factors as well as the potential impact of gene polymorphism on the variability of postprandial lipoprotein metabolism as intermediate phenotypes for coronary heart disease. The variability in postprandial lipid response is highly complex. Future studies will need to be large if they are to assess the effects of multiple polymorphisms.     

Apolipoprotein C-III, metabolic syndrome, and risk of coronary artery disease

Apolipoprotein C-III (apoC-III) is a marker of triglyceride (TG)-rich lipoproteins, which are often increased in metabolic syndrome (MS). The T-455C polymorphism in the insulin-responsive element of the APOC3 gene influences TG and apoC-III levels. To evaluate the contribution of apoC-III levels and T-455C polymorphisms in the coronary artery disease (CAD) risk of MS patients, we studied 873 patients, 549 with CAD and 251 with normal coronary arteries. Patients were classified also as having or not having MS (MS, n = 270; MS-free, n = 603). Lipids, insulin, apolipoprotein levels, and APOC3 T-455C genotypes were evaluated. ApoC-III levels were significantly increased in MS patients, and the probability of having MS was correlated with increasing quartiles of apoC-III levels. MS patients with CAD had significantly higher apoC-III levels than did CAD-free MS patients. The carriership for the -455C variant multiplied the probability of CAD in MS in an allele-specific way and was associated with increased apoC-III and TG levels. Obesity was less frequent in MS carriers of the -455C allele than in MS noncarriers (21.6% vs. 34.8%, P < 0.05). In conclusion, apoC-III-rich lipoprotein metabolism and the APOC3 polymorphism have relevant impacts on the CAD risk of MS patents.     

Window panes of eternity. Health, disease, and inherited risk

Personal health reflects harmony between individual and experience; it is optimal homeostasis. Disease is an outcome of incongruity leading to dishomeostasis. Relative to earlier times, disease in modern society has higher "heritability" (in the broad meaning of the term). Inherited risks are facts compatible with anticipation and prevention of disease. This viewpoint has major implications for medical practice, deployment of health services, themes of research, and education of health care personnel and citizens.