Personalities in female domesticated pigs: behavioural and physiological indications

The inconclusive evidence so far on the existence of distinct personality types in domesticated pigs, led us to perform the present experiment. A total of 128 gilts from 31 sows were systematically studied from birth to slaughter in two identical trials. Intra-test consistency in individual behavioural andror physiological reactions was studied in three different tests. We were not able to show consistencies in reactions of gilts over time to a backtest (at 2–4 days and 4 weeks of age) and to a novel environment test (at 10 and 24 weeks of age). Individual aggression, however, as measured in a group-feeding competition test in stable groups (at 10 and 24 weeks of age), proved to be highly consistent. Explanations for these discrepancies in intra-test consistencies are critically discussed. Inter-test consistencies were determined by relating the individual reactions of gilts to the backtest to various characteristics and responses to tests at a later age. The highest correlations were found when resistance in the first backtest was involved. No evidence was found for the existence of specific isolated categories of animals with respect to this resistance. For further analysis, extreme responding gilts in the first backtest (roughly the top and bottom 25% of the distribution) were classified as low resistant (LR; <3 escape attempts; n=31) or high resistant (HR; >4 escape attempts; n=45). By comparisons of mean responses of LR and HR gilts within groups, we have established a relationship between the backtest and several other variables. Behaviourally, the HR gilts showed more aggression in the group-feeding competition tests. Also, in the competition for the most productive teats at the anterior, a predominant position of HR piglets at this site was observed during the suckling period. The latter piglets also gained more weight during this period than LR ones. Compared to HR pigs, in the first novel environment test LR pigs hesitated longer to leave their home pens and to contact a human, but no difference in their locomotory behaviour was observed. Contrasts between LR and HR pigs in the second novel environment test were reduced or absent. Physiologically, when compared to HR gilts, LR ones had a higher reactivity of the hypothalamic–pituitary–adrenocortical (HPA) system. This was shown by higher cortisol responses to the first novel environment test, to routine weighing at 25 weeks of age, and to administration of a high dose of ACTH. It is discussed that these findings for LR and HR gilts, may provide support for the existence of behavioural and physiological responses in pigs, resembling those of proactive and reactive rodents.

Teaching and Assessing Engineering Design Thinking with Virtual Internships and Epistemic Network Analysis

An engineering workforce of sufficient size and quality is essential for addressing significant global challenges such as climate change, world hunger, and energy demand. Future generations of engineers will need to identify challenging issues and design innovative solutions. To prepare young people to solve big and increasingly global problems, researchers and educators need to understand how we can best educate young people to use engineering design thinking. In this paper, we explore virtual internships, online simulations of 21st-century engineering design practice, as one method for teaching engineering design thinking. To assess the engineering design thinking, we use epistemic network analysis (ENA), a tool for measuring complex thinking as it develops over time based on discourse analysis. The combination of virtual internships and ENA provides opportunities for students to engage in authentic engineering design, potentially receive concurrent feedback on their engineering design thinking, and develop the identity, values, and ways of thinking of professional engineers

A de novo assembly of the common frog (Rana temporaria) transcriptome and comparison of transcription following exposure to Ranavirus and Batrachochytrium dendrobatidis

This is the final version. Available on open access from Public Library of Science via the DOI in this recordata Availability: All raw data is available through EMBL-EBI Array Express, accession number E-MTAB-3632Amphibians are experiencing global declines and extinctions, with infectious diseases representing a major factor. In this study we examined the transcriptional response of metamorphic hosts (common frog, Rana temporaria) to the two most important amphibian pathogens: Batrachochytrium dendrobatidis (Bd) and Ranavirus. We found strong up-regulation of a gene involved in the adaptive immune response (AP4S1) at four days post-exposure to both pathogens. We detected a significant transcriptional response to Bd, covering the immune response (innate and adaptive immunity, complement activation, and general inflammatory responses), but relatively little transcriptional response to Ranavirus. This may reflect the higher mortality rates found in wild common frogs infected with Ranavirusas opposed to Bd. These data provide a valuable genomic resource for the amphibians, contribute insight into gene expression changes after pathogen exposure, and suggest potential candidate genes for future host-pathogen research.European UnionRoyal SocietyZoological Society of LondonEuropean Research Counci

Norovirus whole genome sequencing by SureSelect target enrichment: a robust and sensitive method

Norovirus full genome sequencing is challenging due to sequence heterogeneity between genomes. Previous methods have relied on PCR amplification, which is problematic due to primer design, and RNASeq which non-specifically sequences all RNA in a stool specimen, including host and bacterial RNA.Target enrichment uses a panel of custom-designed 120-mer RNA baits which are complementary to all publicly available norovirus sequences, with multiple baits targeting each position of the genome, thus overcoming the challenge of primer design. Norovirus genomes are enriched from stool RNA extracts to minimise sequencing non-target RNA.SureSelect target enrichment and Illumina sequencing was used to sequence full genomes from 507 norovirus positive stool samples with RT-qPCR Ct values 10-43. Sequencing on an Illumina MiSeq in batches of 48 generated on average 81% on-target-reads per sample and 100% genome coverage with >12,000-fold read depth. Samples included genotypes GI.1, GI.2, GI.3, GI.6, GI.7, GII.1, GII.2, GII.3, GII.4, GII.5, GII.6, GII.7, GII.13, GII.14 and GII.17. Once outliers are accounted for, we generate over 80% genome coverage for all positive samples, regardless of Ct value.164 samples were tested in parallel with conventional PCR genotyping of the capsid shell domain. 164/164 samples were successfully sequenced, compared to 158/164 that were amplified by PCR. Four of the samples that failed capsid PCR had low titres, suggesting target enrichment is more sensitive than gel-based PCR. Two samples failed PCR due to primer mismatches; target enrichment uses multiple baits targeting each position, thus accommodating sequence heterogeneity between norovirus genomes

Preadaptation of pandemic GII.4 noroviruses in unsampled virus reservoirs years before emergence

The control of re-occurring pandemic pathogens requires understanding the origins of new pandemic variants and the factors that drive their global spread. This is especially important for GII.4 norovirus, where vaccines under development offer promise to prevent hundreds of millions of annual gastroenteritis cases. Previous studies have hypothesized that new GII.4 pandemic viruses arise when previously circulating pandemic or pre-pandemic variants undergo substitutions in antigenic regions that enable evasion of host population immunity, as described by conventional models of antigenic drift. In contrast, we show here that the acquisition of new genetic and antigenic characteristics cannot be the proximal driver of new pandemics. Pandemic GII.4 viruses diversify and spread over wide geographical areas over several years prior to simultaneous pandemic emergence of multiple lineages, indicating that the necessary sequence changes must have occurred before diversification, years prior to pandemic emergence. We confirm this result through serological assays of reconstructed ancestral virus capsids, demonstrating that by 2003, the ancestral 2012 pandemic strain had already acquired the antigenic characteristics that allowed it to evade prevailing population immunity against the previous 2009 pandemic variant. These results provide strong evidence that viral genetic changes are necessary but not sufficient for GII.4 pandemic spread. Instead, we suggest that it is changes in host population immunity that enable pandemic spread of an antigenically preadapted GII.4 variant. These results indicate that predicting future GII.4 pandemic variants will require surveillance of currently unsampled reservoir populations. Furthermore, a broadly acting GII.4 vaccine will be critical to prevent future pandemics

A comprehensive characterization of chronic norovirus infection in immunodeficient hosts.

Letter to the edito

Considering the influence of coronary motion on artery-specific biomechanics using fluid-structure interaction simulation

The endothelium in the coronary arteries is subject to wall shear stress and vessel wall strain, which influences the biology of the arterial wall. This study presents vessel-specific fluid-structure interaction (FSI) models of three coronary arteries, using directly measured experimental geometries and boundary conditions. FSI models are used to provide a more physiologically complete representation of vessel biomechanics, and have been extended to include coronary bending to investigate its effect on shear and strain. FSI both without- and with-bending resulted in significant changes in all computed shear stress metrics compared to CFD (p = 0.0001). Inclusion of bending within the FSI model produced highly significant changes in Time Averaged Wall Shear Stress (TAWSS) + 9.8% LAD, + 8.8% LCx, - 2.0% RCA; Oscillatory Shear Index (OSI) + 208% LAD, 0% LCx, + 2600% RCA; and transverse wall Shear Stress (tSS) + 180% LAD, + 150% LCx and + 200% RCA (all p < 0.0001). Vessel wall strain was homogenous in all directions without-bending but became highly anisotropic under bending. Changes in median cyclic strain magnitude were seen for all three vessels in every direction. Changes shown in the magnitude and distribution of shear stress and wall strain suggest that bending should be considered on a vessel-specific basis in analyses of coronary artery biomechanics

Dissemination of Mycobacterium abscessus via global transmission networks.

Mycobacterium abscessus, a multidrug-resistant nontuberculous mycobacterium, has emerged as a major pathogen affecting people with cystic fibrosis (CF). Although originally thought to be acquired independently from the environment, most individuals are infected with one of several dominant circulating clones (DCCs), indicating the presence of global transmission networks of M. abscessus. How and when these clones emerged and spread globally is unclear. Here, we use evolutionary analyses of isolates from individuals both with and without CF to reconstruct the population history, spatiotemporal spread and recent transmission networks of the DCCs. We demonstrate synchronous expansion of six unrelated DCCs in the 1960s, a period associated with major changes in CF care and survival. Each of these clones has spread globally as a result of rare intercontinental transmission events. We show that the DCCs, but not environmentally acquired isolates, exhibit a specific smoking-associated mutational signature and that current transmission networks include individuals both with and without CF. We therefore propose that the DCCs initially emerged in non-CF populations but were then amplified and spread through the CF community. While individuals with CF are probably the most permissive host, non-CF individuals continue to play a key role in transmission networks and may facilitate long-distance transmission.Funding for this work was provided by The Wellcome Trust (investigator award no. 107032/Z/15/Z to R.A.F.), Fondation Botnar (Programme grant no. 6063) and the UK CF Trust (Innovation Hub award no. 001; Strategic Research Centre award no. 010). M.S., N.A.H. and R.M.D. acknowledge the Cystic Fibrosis Foundation for funding

Deep sequencing reveals persistence of cell-associated mumps vaccine virus in chronic encephalitis.

Routine childhood vaccination against measles, mumps and rubella has virtually abolished virus-related morbidity and mortality. Notwithstanding this, we describe here devastating neurological complications associated with the detection of live-attenuated mumps virus Jeryl Lynn (MuV(JL5)) in the brain of a child who had undergone successful allogeneic transplantation for severe combined immunodeficiency (SCID). This is the first confirmed report of MuV(JL5) associated with chronic encephalitis and highlights the need to exclude immunodeficient individuals from immunisation with live-attenuated vaccines. The diagnosis was only possible by deep sequencing of the brain biopsy. Sequence comparison of the vaccine batch to the MuV(JL5) isolated from brain identified biased hypermutation, particularly in the matrix gene, similar to those found in measles from cases of SSPE. The findings provide unique insights into the pathogenesis of paramyxovirus brain infections