Reaping the rewards of learning within agricultural knowledge systems: An account of a PhD learning system

Despite the existence and application of mandatory agri-environmental policy for many decades, significant environmental sustainability problems remain attributable to the agricultural sector. Participatory types of extension practices are believed to have a potential to enable extension organisations to enhance the supports provided to farmers to help meet the requirements and objectives of these policies. To test this proposition, the PhD researcher used a learning systems approach for exploring the interplay between farmer subjectivities, the European Union’s policy of cross compliance and the extension practices of Teagasc, the Irish Agriculture and Food Development Authority. Three learning sub-systems were employed in the investigation. The first used the principles of Participatory Action Research for revealing stakeholders’ perceptions of Teagasc’s cross compliance extension service. This process resulted in the attainment of rich insights about extension practices, however it also revealed that a significant number of farmers were experiencing socio-cultural difficulties with the application and enforcement of cross compliance. To better understand the implications of these subjectivities, a second sub-system was created to learn about farmers’ experiences of the policy. This process surfaced diverse insights about farmers’ personal experiences of cross compliance. A final sub-system employed systems thinking and practice for appraising the utility of the learning arising from the previous sub-systems for improving interactions between farmers, extension organisations and cross compliance. The combined findings of the thesis indicate that there is considerable potential for extension organisations to use participatory practices for developing rich understandings of farmers’ preferences for mandatory agri-environmental policy and its related extension practices. However, a limitation in realising participant preferences is that extension organisations appear to have little influence over the application and enforcement of mandatory agri-environmental policy. Overcoming this participatory barrier will require sustained collective learning targeted at understanding how stakeholders can work together to develop agri-environmental policies that are socially, financially and environmentally sustainable. This paper explores how this ‘sustained collective learning’ may be realised taking a specific account of the learnings developed within and following the completion of the PhD Learning System. The insights elucidated will be of interest to scholars and extension practitioners involved in similar learning endeavours

Tree pruner: An efficient tool for selecting data from a biased genetic database

<p>Abstract</p> <p>Background</p> <p>Large databases of genetic data are often biased in their representation. Thus, selection of genetic data with desired properties, such as evolutionary representation or shared genotypes, is problematic. Selection on the basis of epidemiological variables may not achieve the desired properties. Available automated approaches to the selection of influenza genetic data make a tradeoff between speed and simplicity on the one hand and control over quality and contents of the dataset on the other hand. A poorly chosen dataset may be detrimental to subsequent analyses.</p> <p>Results</p> <p>We developed a tool, <it>Tree Pruner</it>, for obtaining a dataset with desired evolutionary properties from a large, biased genetic database. Tree Pruner provides the user with an interactive phylogenetic tree as a means of editing the initial dataset from which the tree was inferred. The tree visualization changes dynamically, using colors and shading, reflecting Tree Pruner actions. At the end of a Tree Pruner session, the editing actions are implemented in the dataset.</p> <p>Currently, Tree Pruner is implemented on the Influenza Research Database (IRD). The data management capabilities of the IRD allow the user to store a pruned dataset for additional pruning or for subsequent analysis. Tree Pruner can be easily adapted for use with other organisms.</p> <p>Conclusions</p> <p>Tree Pruner is an efficient, manual tool for selecting a high-quality dataset with desired evolutionary properties from a biased database of genetic sequences. It offers an important alternative to automated approaches to the same goal, by providing the user with a dynamic, visual guide to the ongoing selection process and ultimate control over the contents (and therefore quality) of the dataset.</p

Influenza research database: an integrated bioinformatics resource for influenza research and surveillance.

BackgroundThe recent emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about other important virus characteristics.DesignThe Influenza Research Database (IRD, http://www.fludb.org) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization and comparative genomics analysis, together with personal log in-protected 'workbench' spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature.ResultsTo demonstrate the utility of the data and analysis tools available in IRD, two scientific use cases are presented. A comparison of hemagglutinin sequence conservation and epitope coverage information revealed highly conserved protein regions that can be recognized by the human adaptive immune system as possible targets for inducing cross-protective immunity. Phylogenetic and geospatial analysis of sequences from wild bird surveillance samples revealed a possible evolutionary connection between influenza virus from Delaware Bay shorebirds and Alberta ducks.ConclusionsThe IRD provides a wealth of integrated data and information about influenza virus to support research of the genetic determinants dictating virus pathogenicity, host range restriction and transmission, and to facilitate development of vaccines, diagnostics, and therapeutics

[Study Protocol] Palliative long-term abdominal drains versus repeated drainage in individuals with untreatable ascites due to advanced cirrhosis: study protocol for a feasibility randomised controlled trial

Background: UK deaths due to chronic liver diseases such as cirrhosis have quadrupled over the last 40 years, making this condition now the third most common cause of premature death. Most patients with advanced cirrhosis (end–stage liver disease, [ESLD]) develop ascites. This is often managed with diuretics, but if refractory then the fluid is drained from the peritoneal cavity every 10-14 days by large volume paracentesis (LVP), a procedure requiring hospital admissions. As the life expectancy of patients with ESLD and refractory ascites (if ineligible for liver transplantation) is on average ≤ 6 months, frequent hospital visits are inappropriate from a palliative perspective. One alternative is long-term abdominal drains (LTAD), used successfully in patients whose ascites is due to malignancy. Although inserted in hospital, these drains allow ascites management outside of a hospital setting. LTAD have not been formally evaluated in patients with refractory ascites due to ESLD. Methods: Due to uncertainty about appropriate outcome measures and whether patients with ESLD would wish or be able to participate in a study, a feasibility randomised controlled trial (RCT) was designed. Patients were consulted on trial design. We plan to recruit 48 patients with refractory ascites and randomise them (1:1) to either a) LTAD or b) current standard of care (LVP) for 12 weeks. Outcomes of interest include acceptability of LTAD to patients, carers and healthcare professionals as well as recruitment and retention rates. Palliative care Outcome Scale (IPOS), the Short Form Liver Disease Quality of Life (SF-LDQOL), the EuroQol (EQ-5D) and carer (Zarit Burden Interview [ZBI-12]) reported outcomes will also be assessed. Preliminary data on cost effectiveness will be collected and patients and healthcare professionals will be interviewed about their experience of the trial with a view to identifying barriers to recruitment. Discussion: LTAD could potentially improve end-of-life care in patients with refractory ascites due to ESLD by improving symptom control, reducing hospital visits and enabling some self-management. Our trial is designed to see if such patients can be recruited, as well as informing the design of a subsequent definitive trial. Trial registration: ISRCTN30697116, date assigned: 07/10/201

BioHealthBase: informatics support in the elucidation of influenza virus host–pathogen interactions and virulence

The BioHealthBase Bioinformatics Resource Center (BRC) (http://www.biohealthbase.org) is a public bioinformatics database and analysis resource for the study of specific biodefense and public health pathogens—Influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin. The BioHealthBase serves as an extensive integrated repository of data imported from public databases, data derived from various computational algorithms and information curated from the scientific literature. The goal of the BioHealthBase is to facilitate the development of therapeutics, diagnostics and vaccines by integrating all available data in the context of host–pathogen interactions, thus allowing researchers to understand the root causes of virulence and pathogenicity. Genome and protein annotations can be viewed either as formatted text or graphically through a genome browser. 3D visualization capabilities allow researchers to view proteins with key structural and functional features highlighted. Influenza virus host–pathogen interactions at the molecular/cellular and systemic levels are represented. Host immune response to influenza infection is conveyed through the display of experimentally determined antibody and T-cell epitopes curated from the scientific literature or as derived from computational predictions. At the molecular/cellular level, the BioHealthBase BRC has developed biological pathway representations relevant to influenza virus host–pathogen interaction in collaboration with the Reactome database (http://www.reactome.org)

Specialist multidisciplinary input maximises rare disease diagnoses from whole genome sequencing

Diagnostic whole genome sequencing (WGS) is increasingly used in rare diseases. However, standard, semi-automated WGS analysis may overlook diagnoses in complex disorders. Here, we show that specialist multidisciplinary analysis of WGS, following an initial 'no primary findings' (NPF) report, improves diagnostic rates and alters management. We undertook WGS in 102 adults with diagnostically challenging primary mitochondrial disease phenotypes. NPF cases were reviewed by a genomic medicine team, thus enabling bespoke informatic approaches, co-ordinated phenotypic validation, and functional work. We enhanced the diagnostic rate from 16.7% to 31.4%, with management implications for all new diagnoses, and detected strong candidate disease-causing variants in a further 3.9% of patients. This approach presents a standardised model of care that supports mainstream clinicians and enhances diagnostic equity for complex disorders, thereby facilitating access to the potential benefits of genomic healthcare. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project: http://www.genomicsengland.co.uk

Community research report

University College Cork introduced its first Community-based Participatory Research (CBPR) module in 2016. The module was funded and supported by Horizon2020 funding, specifically the EnRRICH project (Enhancing Responsible Research and Innovation through Curricula in Higher Education). The module is a 5-credit module for PhD students from all disciplines in the early stages of their PhD at University College Cork. Following two fruitful partnerships in the areas of social justice / equality, community family support services and older persons, there was a keen interested to explore partnerships in markedly different areas such as environmental sustainability. A dialogue ensued with CEF where the opportunity and feasibility to collaborate on the CBPR module was explored

Functional Analysis of Conserved Motifs in Influenza Virus PB1 Protein

The influenza virus RNA polymerase complex is a heterotrimer composed of the PB1, PB2, and PA subunits. PB1, the catalytic core and structural backbone of the polymerase, possesses four highly conserved amino acid motifs that are present among all viral RNA-dependent RNA polymerases. A previous study demonstrated the importance of several of these conserved amino acids in PB1 for influenza polymerase activity through mutational analysis. However, a small number of viruses isolated in nature possesses non-consensus amino acids in one of the four motifs, most of which have not been tested for their replicative ability. Here, we assessed the transcription/replication activities of 25 selected PB1 mutations found in natural isolates by using minireplicon assays in human and avian cells. Most of the mutations tested significantly reduced polymerase activity. One exception was mutation K480R, observed in several pandemic (H1N1) 2009 viruses, which slightly increased polymerase activity relative to wild-type. However, in the background of the pandemic A/California/04/2009 (H1N1) virus, this mutation did not affect virus titers in cell culture. Our results further demonstrate the functional importance of the four conserved PB1 motifs in influenza virus transcription/replication. The finding of natural isolates with non-consensus PB1 motifs that are nonfunctional in minireplicon assays suggests compensatory mutations and/or mixed infections which may have ‘rescued’ the inactive PB1 protein

De novo variants in ATXN7L3 lead to developmental delay, hypotonia and distinctive facial features

Deubiquitination is critical for the proper functioning of numerous biological pathways such as DNA repair, cell cycle progression, transcription, signal transduction, and autophagy. Accordingly, pathogenic variants in deubiquitinating enzymes (DUBs) have been implicated in neurodevelopmental disorders (ND) and congenital abnormalities. ATXN7L3 is a component of the DUB module of the SAGA complex, and two other related DUB modules, and serves as an obligate adaptor protein of 3 ubiquitin-specific proteases (USP22, USP27X or USP51). Through exome sequencing and GeneMatching, we identified nine individuals with heterozygous variants in ATXN7L3. The core phenotype included global motor and language developmental delay, hypotonia, and distinctive facial characteristics including hypertelorism, epicanthal folds, blepharoptosis, a small nose and mouth, and low-set posteriorly rotated ears. In order to assess pathogenicity, we investigated the effects of a recurrent nonsense variant [c.340C&gt;T; p.(Arg114Ter)] in fibroblasts of an affected individual. ATXN7L3 protein levels were reduced, and deubiquitylation was impaired, as indicated by an increase in histone H2Bub1 levels. This is consistent with the previous observation of increased H2Bub1 levels in Atxn7l3-null mouse embryos, which have developmental delay and embryonic lethality. In conclusion, we present clinical information and biochemical characterization supporting ATXN7L3 variants in the pathogenesis of a rare syndromic ND