Dense fine-mapping study identifies new susceptibility loci for primary biliary cirrhosis

We genotyped 2,861 cases of primary biliary cirrhosis (PBC) from the UK PBC Consortium and 8,514 UK population controls across 196,524 variants within 186 known autoimmune risk loci. We identified 3 loci newly associated with PBC (at P <5 × 10(-8)), increasing the number of known susceptibility loci to 25. The most associated variant at 19p12 is a low-frequency nonsynonymous SNP in TYK2, further implicating JAK-STAT and cytokine signaling in disease pathogenesis. An additional five loci contained nonsynonymous variants in high linkage disequilibrium (LD; r(2) > 0.8) with the most associated variant at the locus. We found multiple independent common, low-frequency and rare variant association signals at five loci. Of the 26 independent non-human leukocyte antigen (HLA) signals tagged on the Immunochip, 15 have SNPs in B-lymphoblastoid open chromatin regions in high LD (r(2) > 0.8) with the most associated variant. This study shows how data from dense fine-mapping arrays coupled with functional genomic data can be used to identify candidate causal variants for functional follow-up.

Defining the molecular basis for the first potent and selective orthosteric agonists of the FFA2 free fatty acid receptor

FFA2 is a G protein-coupled receptor that responds to short chain fatty acids (SCFAs) and has generated interest as a therapeutic target for metabolic and inflammatory conditions. However, definition of its functions has been slowed by a dearth of selective ligands that can distinguish it from the closely related FFA3. At present, the only selective ligands described for FFA2 suffer from either poor potency, altered signaling due to allosteric modes of action, or a lack of function at non-human orthologs of the receptor. To address the need for novel selective ligands, we synthesized two compounds potentially having FFA2 activity and examined the molecular basis of their function. These compounds were confirmed to be potent and selective FFA2 agonists that interact with the orthosteric binding site. A combination of ligand structure-activity relationship, pharmacological analysis, homology modeling, species ortholog comparisons and mutagenesis studies were then employed to define the molecular basis of selectivity and function of these ligands. From this, we identified key residues within both extracellular loop 2 (ECL2) and the transmembrane domain (TM) regions of FFA2 critical for ligand function. One of these ligands was active with reasonable potency at rodent orthologs of FFA2 and demonstrated the role of FFA2 in the regulation of lipolysis in murine 3T3-L1 adipocytes. Together, these findings describe the first potent and selective FFA2 orthosteric agonists and demonstrate key aspects of ligand interaction within the orthosteric binding site of FFA2 that will be invaluable in future ligand development at this receptor.

Invention and uninvention in nuclear weapons politics

If there is one uncontroversial point in nuclear weapons politics it is that uninventing nuclear weapons is impossible. This article seeks to make this claim controversial by showing that it is premised on attenuated understandings of invention and the status of objects operative through familiar but problematic conceptual dualisms. The claimed impossibility of uninvention is an assertion that invention is irreversible. Drawing on “new materialism” this article produces a different understanding of invention, reinvention, and uninvention as ontologically similar practices of techno-political invention. On the basis of empirical material on the invention and re-invention of nuclear weapons, and an in-depth ethnography of laboratories inventing a portable radiation detector, both the process of invention and the “objects” themselves (weapons and detectors) are shown to be fragile and not wholly irreversible processes of assembling diverse actors (human and non-human) and provisionally stabilizing their relations. Nuclear weapons cannot be uninvented! Why not?

Laterality as an indicator of emotional stress in ewes and lambs during a separation test

We assessed motor laterality in sheep to explore species-specific brain hemi-field dominance and how this could be affected by genetic or developmental factors. Further, we investigated whether directionality and strength of laterality could be linked to emotional stress in ewes and their lambs during partial separation. Forty-three ewes and their singleton lambs were scored on the (left/right) direction of turn in a y-maze to rejoin a conspecific (laterality test). Further, their behavioural response (i.e. time spent near the fence, vocalisations, and activity level) during forced separation by an open-mesh fence was assessed (separation test). Individual laterality was recorded for 44.2 % ewes (significant right bias) and 81.4 % lambs (equally biased to the left and the right). There was no significant association in side bias between dams and offspring. The Chi-squared test revealed a significant population bias for both groups (p < 0.05). Evolutionary adaptive strategies or stimuli-related visual laterality may provide explanation for this decision-making process. Absolute strength of laterality (irrespective of side) was high (Kolmogorov–Smirnov test, dams: D = 0.2; p < 0.001; lambs: D = 0.36, p < 0.0001). The Wilcoxon test showed that lateralised lambs and dams spent significantly more time near each other during separation than non-lateralised animals (p < 0.05), and that lateralised dams were also more active than non-lateralised ones. Arguably, the lateralised animals showed a greater attraction to their pair because they were more disturbed and thus required greater reassurance. The data show that measures of laterality offer a potential novel non-invasive indicator of separation stress.

Does subjective rating reflect behavioural coding? Personality in 2 month-old dog puppies: An open-field test and adjective-based questionnaire

A number of studies have recently investigated personality traits in non-human species, with the dog gaining popularity as a subject species for research in this area. Recent research has shown the consistency of personality traits across both context and time for adult dogs, both when using questionnaire based methods of investigation and behavioural analyses of the dogs' behaviour. However, only a few studies have assessed the correspondence between these two methods, with results varying considerably across studies. Furthermore, most studies have focused on adult dogs, despite the fact that an understanding of personality traits in young puppies may be important for research focusing on the genetic basis of personality traits. In the current study, we sought to evaluate the correspondence between a questionnaire based method and the in depth analyses of the behaviour of 2-month old puppies in an open-field test in which a number of both social and non-social stimuli were presented to the subjects. We further evaluated consistency of traits over time by re-testing a subset of puppies. The correspondence between methods was high and test-retest consistency (for the main trait) was also good using both evaluation methods. Results showed clear factors referring to the two main personality traits 'extroversion,' (i.e. the enthusiastic, exuberant approach to the stimuli) and 'neuroticism,' (i.e. the more cautious and fearful approach to the stimuli), potentially similar to the shyness-boldness dimension found in previous studies. Furthermore, both methods identified an 'amicability' dimension, expressing the positive interactions the pups directed at the humans stranger, and a 'reservedness' dimension which identified pups who largely chose not to interact with the stimuli, and were defined as quiet and not nosey in the questionnaire.

A tool for the evaluation of slaughter horse welfare during unloading

This study aimed to develop a scientific and practical tool to be used to assess horse welfare after commercial transport over long journeys. A set of physical, behavioural and environmental measures was selected, covering welfare aspects of both transport and unloading procedures. The protocol was field-tested on 51 intra-EU commercial transports arriving at different sites in Italy. Univariate analysis was implemented to look for associations between the input variables (environmental hazards potentially affecting the animal well-being during long transports) and the outcome variables (direct evaluation of the animal condition). No severe welfare impairments were recorded (ie dead on arrival, severe injuries, non-ambulatory animals), while milder ones were more frequent at unloading (eg slipping; 36.7%, reluctance to move; 9.6%). Correlations emerged between ramp slope and falling; type of ramp floor and slipping; fast gait and the presence of gaps between the ramp and the floor. The horses' behaviour was also related to the type of handling procedure used. The measures were repeatable and practical to apply and score during real-time unloading. This work provides a sound basis for a new and practical welfare assessment tool for horses travelling over long journeys. Careful and constant application of this protocol would provide stakeholders with the opportunity to track and monitor changes in the industry over time, as well as to identify high risk areas in transport routines.

Rhetorical Topographies of Post-Earthquake L'Aquila: Locality, Activism, and Citizenship Engagement

Thesis (Ph.D.)--University of Washington, 2014

IMP: Imperial Metagenomics Pipeline for high-throughput sequence data

We have developed an in-house pipeline for the processing and analyses of sequence data generated during Illumina technology-based metagenomic studies of the human gut microbiota. Each component of the pipeline has been selected following comparative analysis of available tools; however, the modular nature of software facilitates replacement of any individual component with an alternative should a better tool become available in due course. The pipeline consists of quality analysis and trimming followed by taxonomic filtering of sequence data allowing reads associated with samples to be binned according to whether they represent human, prokaryotic (bacterial/archaeal), viral, parasite, fungal or plant DNA. Viral, parasite, fungal and plant DNA can be assigned to species level on a presence/absence basis, allowing – for example – identification of dietary intake of plant-based foodstuffs and their derivatives. Prokaryotic DNA is subject to taxonomic and functional analyses, with assignment to taxonomic hierarchies (kingdom, class, order, family, genus, species, strain/subspecies) and abundance determination. After de novo assembly of sequence reads, genes within samples are predicted and used to build a non-redundant catalogue of genes. From this catalogue, per-sample gene abundance can be determined after normalization of data based on gene length. Functional annotation of genes is achieved through mapping of gene clusters against KEGG proteins, and InterProScan. The pipeline is undergoing validation using the human faecal metagenomic data of Qin et al. (2014, Nature 513, 59–64). Outputs from the pipeline allow development of tools for the integration of metagenomic and metabolomic data, moving metagenomic studies beyond determination of gene richness and representation towards microbial-metabolite mapping. There is scope to improve the outputs from viral, parasite, fungal and plant DNA analyses, depending on the depth of sequencing associated with samples. The pipeline can easily be adapted for the analyses of environmental and non-human animal samples, and for use with data generated via non-Illumina sequencing platforms.

Integração de um sistema de gestão de informação clínica hospitalar numa unidade de cuidados continuados

O crescimento da população idosa impõe o desenvolvimento de serviços de qualidade orientados para as necessidades comuns desta faixa etária. A área dos cuidados continuados corresponde a um segmento em crescimento com um forte potencial de desenvolvimento no que concerne ao domínio dos sistemas de informação (SI). O presente trabalho pressupõe o acompanhamento do processo de integração de um SI de uma Unidade Hospitalar (UH) numa Unidade de Cuidados Continuados (UCC) para idosos. A análise envolveu o recurso à Teoria Actor-network (ANT), enquanto posicionamento teórico de relevo para o desenvolvimento de SI. Esta teoria coloca, equitativamente, em destaque os factores humano e não humano como concorrentes para o sucesso no desenvolvimento de um SI. O processo em destaque neste trabalho envolveu a análise compreensiva dos SI das unidades de saúde envolvidas; monitorização e descrição do processo de integração do SI de inspiração hospitalar na UCC; avaliação do resultado final; estabelecimento de requisitos fundamentais para o desenho de um SI adaptado a uma organização prestadora de cuidados continuados a idosos. Estas etapas foram desenvolvidas tendo por base a concretização de 3 ciclos, integradores dos conceitos da ANT com o processo de Engenharia de Requisitos: Ciclo 1 - análise do sistema sócio-técnico; Ciclo 2 – desenho do novo sistema sócio-técnico; Ciclo 3 – transformação da rede sócio-técnica. A metodologia inerente ao processo envolveu a análise documental, realização de notas de campo, entrevista e questionário. Os requisitos são apresentados através da conceptualização de um SI denominado Gestão de Cuidados Residenciais (GCR). Conclui-se, que para que um SI resulte com eficácia, eficiência e efetividade para uma organização, deverá revelar-se adaptado ao propósito e missão da organização em causa, sob pena de induzir fragilidade ao ciclo operacional e ao modelo de gestão de informação.

Bioprocess design of canine adenovirus vectors for gene therapy applications

The potential of human adenovirus vectors as vehicles for gene transfer with clinical applications in vaccination, cancer treatment and in many monogenic and acquired diseases has been demonstrated in several studies and clinical trials. However, the clinical use of these vectors can be limited by pre-existing humoral and cellular anti-capsid immunity. One way to circumvent this bottleneck while keeping the advantages of using adenovirus vectors is using non-human viruses such as Canine Adenovirus type 2 (CAV-2). Moreover, CAV-2 vectors present attractive features to develop potential treatment of neurodegenerative and ocular disorders. While the interest in CAV-2 vectors increases, scalable and robust production processes are required to meet the need for preclinical and possibly clinical uses.(...)

Construction of bovine adenovirus type 3 E1 and E3, substitution plasmids and the sequencing analysis of DNA pol and pTP /

The relative ease to concentrate and purify adenoviruses, their well characterized mid-sized genome, and the ability to delete non-essential regions from their genome to accommodate foreign gene, made adenoviruses a suitable candidate for the construction of vectors. The use of adenoviral vectors in gene therapy, vaccination, and as a general vector system for expressing foreign genes have been documented for some time. In this study, the objective was to rescue a BAV3 E1 or E3 recombinant vector carrying the kanamycin resistant gene, a dominant selectable marker with useful applications in studying vectored gene expression in mammalian cells. To accomplish the objective of this study, more information about BAV3 DNA sequences was required in order to make the manipulation of the virus genome accessible. Therefore, sequencing of the BAV3 genome from 1 1 .7% to 30.8% was carried out. Analysis of the determined sequences revealed the primary structure of important viral gene products coded by E2 including BAV3 DNA pol and precursor to terminal protein. Comparative analysis of these proteins with their counterparts from human and non human adenoviruses revealed important insights as to the evolutionary lineage of BAV3. In order to insert the kanamycin resistance gene in either E1 or E3, it was necessary to delete BAV3 sequences to accommodate the foreign gene so as not to exceed the limit of the packaging capacity of the virus. To construct a recombinant BAV3 in which a foreign gene was inserted in the deleted E1 region, an E1 shuttle vector was constructed. This involved the deletion from the viral sequences a region between 1.3% to 9% and inserting the kanamycin resistance gene to replace the deletion. The E1 shuttle vector contained the left (0%- 53.9%) segment of the genome and was expected to generate BAV3 recombinants that can be grown and propagated in cells that can complement the missing E1 functions. To construct a similar shuttle vector for E3 deletion, DNA sequences extending from 78.9% to 82.5% (1281 bp) were deleted from within the E3 region that had been cloned into a plasmid vector. The deleted region corresponds to those that have been shown to be non-essential for viral replication in cell culture. The resulting plasmid was used to construct another recombinant plasmid with BAV3 DNA sequences extending from 37.1% to 100% and with a deletion of E3 sequences that were replaced by kanamycin resistance gene. This shuttle plasmid was used in cotransfections with digested viral DNA in an attempt to rescue a recombinant BAV3 carrying the kanamycin resistance gene to replace the deleted E3. In spite of repeated attempts of transfection, El or E3 recombinant BAV3 were not isolated. It seems that other approaches should be applied to make a final conclusion on BAV3 infectivity.

Activity of brainstem cholinergic neurons during 22 kHz ultrasonic vocalization in rats /

Adult rats emit 22 kHz ultrasonic alann calls in aversive situations. This type of call IS a component of defensive behaviour and it functions predominantly to warn conspecifics about predators. Production of these calls is dependent on the central cholinergic system. The laterodorsal tegmental nucleus (LDT) and pedunculopontine tegmental nucleus (PPT) contain largely cholinergic neurons, which create a continuous column in the brainstem. The LDT projects to structures in the forebrain, and it has been implicated in the initiation of 22 kHz alarm calls. It was hypothesized that release of acetylcholine from the ascending LDT terminals in mesencephalic and diencephalic areas initiates 22 kHz alarm vocalization. Therefore, the tegmental cholinergic neurons should be more active during emission of alarm calls. The aim of this study was to demonstrate increased activity of LDT cholinergic neurons during emission of 22 kHz calls induced by air puff stimuli. Immunohistochemical staining of the enzyme choline acetyltransferase identified cell bodies of cholinergic neurons, and c-Fos immunolabeling identified active cells. Double labeled cells were regarded as active cholinergic cells. There were significantly more (panimals than in control (non-vocalizing air puffed and naIve non-airpuffed) animals. Although the numbers were low, there were also significantly more (panimals than in the non-vocalizing controls. Such a difference between vocalizing and control animals was not found in the neighbouring PPT nucleus. Results suggest that there are cholinergic and non-cholinergic cells, which are selectively active in the LDT during emission of 22 kHz alarm calls.

Niagara alternative food projects : networks, discourses and nature /

This thesis undertakes an exploration of the nature of alternative food projects in Niagara. A review of various theoretical approaches to the study of food and agriculture, suggests that actor-network theory offers the most useful lens through which to understand these projects. In particular, actor-network theory facilitates non-dualistic theorisations of power and scale and a commitment to the inclusion of non-humans in the 'social' sciences. The research is based on 19 in-depth interviews with actors involved in various urban and rural projects including community supported agriculture, community gardens, chefs using local seasonal food, a winery that grows organically, the good food box, a value-added small business, and organic producers. The analysis consists of four themes. The first analytical section pays special attention to the prominence of agri-tourism in Niagara, and examines the ways in which the projects in the sample interact with agri-tourist networks. In the second section the discussion focuses on the discourses and practices of resistance among Niagara alternative food actors. The participants' interviews suggest there are more discourses of resistance toward agri-tourist than toward dominant food networks. The third section questions commodity chain theorisations of alternative food projects. In particular, this section shows how the inclusion of non-human actors in an analysis confounds conceptualisations of 'short' and 'local' chains. The final analytical section assesses relations of power in Niagara alternative food projects. Three important conclusions arise from this research. First, Niagara alternative food projects cannot be conceptualised as operating at the 'local' scale. Broadening the scope of analysis to include non-human actors, it becomes apparent that these projects actually draw on a variety of extra-local actors. They are at once local and global. Second, the projects in this sample are simultaneously part of alternative, dominant and agri-tourist networks. While Niagara alternative food projects do perform many of the roles characteristic of alternative food systems, they are also involved in practices of development, business, and class distinction. Thus, alternative food networks should not be understood as separate from and in direct opposition to dominant food networks. Despite the second conclusion, this research determines that Niagara alternative food projects have made significant strides in the reworking of power. The projects represented in this thesis do engage in resistant practices and are associated with increased levels ofjustice.

Social neuroendocrinology of competition

The relationship between testosterone concentrations and aggressive behaviour in studies of people has produced very inconsistent findings. However, one consistent fmding that has emerged is that competitive and aggressive interactions potentiate testosterone release in both human and non-human species. It has been argued that socially-induced alterations in testosterone concentrations may function to influence ongoing and/or future social behaviour. Nonetheless, few studies have empirically tested this hypothesis. The current series of experiments was designed to address the extent to which competitioninduced fluctuations in testosterone concentrations were associated with ongoing and/or subsequent social behaviour. In Study 1, men (n = 38) provided saliva samples prior to, and at the conclusion of, the Point Subtraction Aggression Paradigm (PSAP). Although baseline testosterone concentrations were not related to aggressive behaviour, there was a positive correlation between change in testosterone and aggressive behaviour such that men who were most aggressive on the PSAP demonstrated the largest increase in testosterone concentrations. Furthermore, a rise in testosterone during the PSAP predicted willingness to choose a subsequent competitive task. In Study 2, men and women provided saliva samples prior to and after competing against a same-sex opponent on the Number Tracing Task (NTT). The outcome of the competition was rigged such that half of the individuals won most of the races, while the other half lost most of the races, thus experimentally creating a winner and loser in the laboratory. Following the competitive interaction, men and women played the PSAP with their same-sex partner. Results indicated that men selected the aggressive response (but not reward or protection responses), more frequently than women. For men assigned to the loss condition, an increase in testosterone concentrations in response to the NTT predicted subsequent aggressive behaviour. For men assigned to the win condition, an increase in testosterone concentrations in response to the NTT predicted subsequent aggressive behaviour, but only among those men who scored high on trait dominance. Change in testosterone and trait dominance did not predict aggressive behaviour in women. In Study 3, men provided saliva samples prior to, during, and at the end of the PSAP. They were randomly assigned to one of four experimental conditions that differed in the extent to which they were provoked and whether they received reward for behaving aggressively (i.e., stealing points). Results indicated that baseline testosterone concentrations did not correlate with aggression in any of the experimental conditions. Consistent with Study 1, there was a positive correlation between change in testosterone and aggressive behaviour among men who were provoked, but did not receive reward for aggression (i.e., reactive condition). Men who were provoked but did not receive reward for aggression enjoyed the task the most and were more likely to choose the competitive versus non-competitive task relative to men assigned to the other experimental conditions. Also, individual differences in aggressive behaviour among these men were positively correlated with the extent to which they enjoyed the task. Together, these studies indicate that testosterone dynamics within the context of competition influence subsequent competitive and aggressive behaviours in humans and that testosterone may be a marker of the intrinsically rewarding nature of costly aggressive behaviour.

La sécurité des xénogreffons : une normativité à bâtir

La xénotransplantation, soit la transplantation de cellules, de tissus ou d'organes d'origine animale chez l'homme, est envisagée comme solution à la pénurie d'organes. Toutefois, cette technologie pourrait être à l'origine de nouvelles maladies. D'où la nécessité d'avoir des mesures visant tant la santé des animaux fournisseurs que la qualité et la sécurité des xénogreffons pour minimiser les risques de transmission de maladies de l'animal à l'homme, appelées xénozoonoses. L'objet de ce mémoire est de vérifier si les normes existantes au Canada et au Québec sont appropriées pour assurer la sécurité des receveurs et de la population. Nous avons d'abord examiné les normes susceptibles de s'appliquer à la surveillance et au contrôle de la santé des animaux fournisseurs. Ne visant que les maladies connues, elles ne répondent pas aux spécificités de la xénotransplantation. Quant aux xénogreffons, leur qualification pose problème: drogues ou instruments. Cette incertitude pourrait affecter l'uniformité des décisions relatives à leur qualité et à leur sécurité. Nous avons aussi étudié la Proposition d'une Norme canadienne pour la xénotransplantation. Cette dernière pourrait certes pallier la situation d'inadéquation de l'encadrement normatif existant au Canada. Une comparaison de cette norme canadienne avec les recommandations de l'OMS et les mesures en place aux ÉtatsUnis nous permet de suggérer comment la bonifier. Il ressort de notre étude que l'encadrement normatif canadien visant la sécurité des xénogreffons demeure à bâtir. Un élément essentiel à considérer dans son élaboration est la nécessité d'instaurer des systèmes de contrôle adéquats et compatibles à l'échelle planétaire.