A new web-based genomics resource for bioinformatics analysis of Rhipicephalus (Boophilus) microplus: CattleTickBase

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Prompting transdisciplinary research: Promising futures for using the performance metaphor in research

Transdisciplinary research is increasingly recognised as important for investigating and addressing 'wicked' problems such as climate change, food insecurity and poverty, but is far from commonplace. There are structural impediments to transdisciplinarity such as university structures, publication requirements and funding preferences that perpetuate disciplinary differences and researchers often lack transdisciplinary experience and expertise. In this paper we present a heuristic that aims to encourage researchers to think about their current research as performance and then imagine different performances, with the view to encouraging reflection and creativity about the transdisciplinary potential and dilemmas. The heuristic is inspired by the metaphor of performance that Erving Goffman uses to understand everyday, face-to-face interactions. The heuristic includes scaffolding for imagining research as performance through a transdisciplinary lens, a suggested process for using the tool, and examples based on the every day research projects. The paper describes the application of the heuristic in a graduate masterclass, reflecting on whether it does indeed 'prompt' transdisciplinary research. Limitations and lessons learned for further refinement of the heuristic are also included. The authors conclude that the heuristic has a range of uses including for self-reflection, and as a practical learning tool that can also be used at the start of integrative research projects

‘Younger People Have Like More of an Imagination, No Offence’: Participant Perspectives on Public Engagement

© 2012, Copyright Taylor & Francis Group, LLC. A wide range of work has reported on the outcomes of public engagement activities and the views expressed by public participants towards specific areas of science and technology. Such work has rarely gone on to explore with public participants their attitudes to the engagement experienced itself, often focusing instead on more practical or quantifiable aspects. This article draws on public participants’ reactions to 11 ‘engagement’ events, occurring across the UK in 2007–2008. Reporting on 33 semi-structured interviews, we focus on their views of participation and engagement in terms of motivations, expectations and expertise. The results suggest that participants have considerable expectations in terms of information and interaction, operate with critical but respectful notions of other ‘publics’ and expertise, and may develop habitual tendencies regarding engagement

The interaction of human and Epstein–Barr virus miRNAs with Multiple Sclerosis risk loci

Although the causes of Multiple Sclerosis (MS) still remain largely unknown, multiple lines of evidence suggest that Epstein–Barr virus (EBV) infection may contribute to the development of MS. Here, we aimed to identify the potential contribution of EBV-encoded and host cellular miRNAs to MS pathogenesis. We identified differentially expressed host miRNAs in EBV infected B cells (LCLs) and putative host/EBV miRNA interactions with MS risk loci. We estimated the genotype effect of MS risk loci on the identified putative miRNA:mRNA interactions in silico. We found that the protective allele of MS risk SNP rs4808760 reduces the expression of hsa-mir-3188-3p. In addition, our analysis suggests that hsa-let-7b-5p may interact with ZC3HAV1 differently in LCLs compared to B cells. In vitro assays indicated that the protective allele of MS risk SNP rs10271373 increases ZC3HAV1 expression in LCLs, but not in B cells. The higher expression for the protective allele in LCLs is consistent with increased IFN response via ZC3HAV1 and so decreased immune evasion by EBV. Taken together, this provides evidence that EBV infection dysregulates the B cell miRNA machinery, including MS risk miRNAs, which may contribute to MS pathogenesis via interaction with MS risk genes either directly or indirectly

Novel Approaches to Detect Serum Biomarkers for Clinical Response to Interferon-β Treatment in Multiple Sclerosis

Interferon beta (IFNβ) is the most common immunomodulatory treatment for relapsing-remitting multiple sclerosis (RRMS). However, some patients fail to respond to treatment. In this study, we identified putative clinical response markers in the serum and plasma of people with multiple sclerosis (MS) treated with IFNβ. In a discovery-driven approach, we use 2D-difference gel electrophoresis (DIGE) to identify putative clinical response markers and apply power calculations to identify the sample size required to further validate those markers. In the process we have optimized a DIGE protocol for plasma to obtain cost effective and high resolution gels for effective spot comparison. APOA1, A2M, and FIBB were identified as putative clinical response markers. Power calculations showed that the current DIGE experiment requires a minimum of 10 samples from each group to be confident of 1.5 fold difference at the p<0.05 significance level. In a complementary targeted approach, Cytometric Beadarray (CBA) analysis showed no significant difference in the serum concentration of IL-6, IL-8, MIG, Eotaxin, IP-10, MCP-1, and MIP-1α, between clinical responders and non-responders, despite the association of these proteins with IFNβ treatment in MS

Macrophage coordination of the interferon lambda immune response

Lambda interferons (IFN-λs) are a major component of the innate immune defense to viruses, bacteria, and fungi. In human liver, IFN-λ not only drives antiviral responses, but also promotes inflammation and fibrosis in viral and non-viral diseases. Here we demonstrate that macrophages are primary responders to IFN-λ, uniquely positioned to bridge the gap between IFN-λ producing cells and lymphocyte populations that are not intrinsically responsive to IFN-λ. While CD14+ monocytes do not express the IFN-λ receptor, IFNLR1, sensitivity is quickly gained upon differentiation to macrophages in vitro. IFN-λ stimulates macrophage cytotoxicity and phagocytosis as well as the secretion of pro-inflammatory cytokines and interferon stimulated genes that mediate immune cell chemotaxis and effector functions. In particular, IFN-λ induced CCR5 and CXCR3 chemokines, stimulating T and NK cell migration, as well as subsequent NK cell cytotoxicity. Using immunofluorescence and cell sorting techniques, we confirmed that human liver macrophages expressing CD14 and CD68 are highly responsive to IFN-λ ex vivo. Together, these data highlight a novel role for macrophages in shaping IFN-λ dependent immune responses both directly through pro-inflammatory activity and indirectly by recruiting and activating IFN-λ unresponsive lymphocytes

Ribosomal protein S6 mRNA is a biomarker upregulated in multiple sclerosis, downregulated by interferon treatment, and affected by season

Background

Ocular surface immune transcriptome and tear cytokines in corneal infection patients

BackgroundMicrobial keratitis is one of the leading causes of blindness globally. An overactive immune response during an infection can exacerbate damage, causing corneal opacities and vision loss. This study aimed to identify the differentially expressed genes between corneal infection patients and healthy volunteers within the cornea and conjunctiva and elucidate the contributing pathways to these conditions’ pathogenesis. Moreover, it compared the corneal and conjunctival transcriptomes in corneal-infected patients to cytokine levels in tears.MethodsCorneal and conjunctival swabs were collected from seven corneal infection patients and three healthy controls under topical anesthesia. RNA from seven corneal infection patients and three healthy volunteers were analyzed by RNA sequencing (RNA-Seq). Tear proteins were extracted from Schirmer strips via acetone precipitation from 38 cases of corneal infection and 14 healthy controls. The cytokines and chemokines IL-1β, IL-6, CXCL8 (IL-8), CX3CL1, IL-10, IL-12 (p70), IL-17A, and IL-23 were measured using an antibody bead assay.ResultsA total of 512 genes were found to be differentially expressed in infected corneas compared to healthy corneas, with 508 being upregulated and four downregulated (fold-change (FC) &lt;−2 or &gt; 2 and adjusted p &lt;0.01). For the conjunctiva, 477 were upregulated, and 3 were downregulated (FC &lt;−3 or ≥ 3 and adjusted p &lt;0.01). There was a significant overlap in cornea and conjunctiva gene expression in patients with corneal infections. The genes were predominantly associated with immune response, regulation of angiogenesis, and apoptotic signaling pathways. The most highly upregulated gene was CXCL8 (which codes for IL-8 protein). In patients with corneal infections, the concentration of IL-8 protein in tears was relatively higher in patients compared to healthy controls but did not show statistical significance.ConclusionsDuring corneal infection, many genes were upregulated, with most of them being associated with immune response, regulation of angiogenesis, and apoptotic signaling. The findings may facilitate the development of treatments for corneal infections that can dampen specific aspects of the immune response to reduce scarring and preserve sight

Virtual learning object for the simulated evaluation of acute pain in nursing students

This study aimed to evaluate the results of the application of a virtual learning object for the simulated evaluation of acute pain in the learning of undergraduate nursing students and to verify the opinions of the students regarding the quality of the technology. This was a quasi-experimental, non-randomized, before and after study performed with 14 students in the seventh phase of the undergraduate nursing course of the Federal University of Santa Catarina. The pre (8.84) and post-test (9.31) means revealed significant differences in learning after the intervention (p=0.03). In the qualitative evaluation the flexibility of access, access independent of time/place, freedom to decide the best learning route and the similarity with reality were highlighted. It constitutes a promising educational tool, an interactive experience, similar to reality, dynamic and constructive learning. The application of the technology has brought positive results for learning about pain evaluation, contributing to fill the gap in the teaching of the thematic.El objetivo del estudio fue evaluar los resultados de la aplicación de un objeto virtual de aprendizaje para evaluación simulada de dolor agudo en el aprendizaje de estudiantes de graduación en enfermería y verificar su opinión sobre la calidad de la tecnología. Se trata de un estudio casi experimental, no aleatorio, del tipo antes y después, realizado con 14 estudiantes de la séptima fase de la graduación en enfermería de la Universidad Federal de Santa Catarina. Los promedios de la prueba, antes (8,84) y después (9,31), revelaron diferencia significativa en el aprendizaje después de la intervención (p=0.03). En la evaluación cualitativa se destacaron la flexibilidad de acceso, el acceso independiente de tiempo/lugar, libertad para decidir el mejor curso de aprendizaje y la semejanza con la realidad. Constituye una promisora herramienta educacional, una experiencia interactiva, semejante a la realidad, dinámica y constructiva de aprendizaje. La aplicación de la tecnología presentó resultados positivos para el aprendizaje de la evaluación del dolor, contribuyendo para llenar un vacío en la enseñanza de la temática.O objetivo do estudo foi avaliar os resultados da aplicação de um objeto virtual de aprendizagem para avaliação simulada da dor aguda na aprendizagem de estudantes de graduação em enfermagem e verificar sua opinião sobre a qualidade da tecnologia. Trata-se de estudo quase experimental, não randomizado, do tipo antes e depois, realizado com 14 estudantes da sétima fase da graduação em enfermagem da Universidade Federal de Santa Catarina. As médias de pré (8,84) e pós-teste (9,31) revelaram diferença significativa na aprendizagem, após intervenção (p=0,03). Na avaliação qualitativa, destacaram-se a flexibilidade de acesso, o acesso independente de tempo/lugar, liberdade para decidir o melhor percurso de aprendizagem e a semelhança com a realidade. Constitui promissora ferramenta educacional, uma experiência interativa, semelhante à realidade, dinâmica e construtiva de aprendizagem. A aplicação da tecnologia trouxe resultados positivos para a aprendizagem da avaliação da dor, contribuindo para o preenchimento da lacuna no ensino da temática

The Complete Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira pilosicoli and Comparison with Other Brachyspira Genomes

Background: The anaerobic spirochete Brachyspira pilosicoli colonizes the large intestine of various species of birds and mammals, including humans. It causes ''intestinal spirochetosis'', a condition characterized by mild colitis, diarrhea and reduced growth. This study aimed to sequence and analyse the bacterial genome to investigate the genetic basis of its specialized ecology and virulence. Methodology/Principal Findings: The genome of B. pilosicoli 95/1000 was sequenced, assembled and compared with that of the pathogenic Brachyspira hyodysenteriae and a near-complete sequence of Brachyspira murdochii. The B. pilosicoli genome was circular, composed of 2,586,443 bp with a 27.9 mol% G+C content, and encoded 2,338 genes. The three Brachyspira species shared 1,087 genes and showed evidence of extensive genome rearrangements. Despite minor differences in predicted protein functional groups, the species had many similar features including core metabolic pathways. Genes distinguishing B. pilosicoli from B. hyodysenteriae included those for a previously undescribed bacteriophage that may be useful for genetic manipulation, for a glycine reductase complex allowing use of glycine whilst protecting from oxidative stress, and for aconitase and related enzymes in the incomplete TCA cycle, allowing glutamate synthesis and function of the cycle during oxidative stress. B. pilosicoli had substantially fewer methyl-accepting chemotaxis genes than B. hyodysenteriae and hence these species are likely to have different chemotactic responses that may help to explain their different host range and colonization sites. B. pilosicoli lacked the gene for a new putative hemolysin identified in B. hyodysenteriae WA1. Both B. pilosicoli and B. murdochii lacked the rfbBADC gene cluster found on the B. hyodysenteriae plasmid, and hence were predicted to have different lipooligosaccharide structures. Overall, B. pilosicoli 95/1000 had a variety of genes potentially contributing to virulence. Conclusions/Significance: The availability of the complete genome sequence of B. pilosicoli 95/1000 will facilitate functional genomics studies aimed at elucidating host-pathogen interactions and virulence