Matthew P. Campbell

UniCarb-DB

UNLABELLEDnGlycosylation is one of the most important post-translational modifications of proteins, known to be involved in pathogen recognition, innate immune response and protection of epithelial membranes. However, when compared to the tools and databases available for the processing of high-throughput proteomic data, the glycomic domain is severely lacking. While tools to assist the analysis of mass spectrometry (MS) and HPLC are continuously improving, there are few resources available to support liquid chromatography (LC)-MS/MS techniques for glycan structure profiling. Here, we present a platform for presenting oligosaccharide structures and fragment data characterized by LC-MS/MS strategies. The database is annotated with high-quality datasets and is designed to extend and reinforce those standards and ontologies developed by existing glycomics databases.nnnAVAILABILITYnhttp://www.unicarb-db.org

UniCarbKB: building a knowledge platform for glycoproteomics

The UniCarb KnowledgeBase (UniCarbKB; http://unicarbkb.org) offers public access to a growing, curated database of information on the glycan structures of glycoproteins. UniCarbKB is an international effort that aims to further our understanding of structures, pathways and networks involved in glycosylation and glyco-mediated processes by integrating structural, experimental and functional glycoscience information. This initiative builds upon the success of the glycan structure database GlycoSuiteDB, together with the informatic standards introduced by EUROCarbDB, to provide a high-quality and updated resource to support glycomics and glycoproteomics research. UniCarbKB provides comprehensive information concerning glycan structures, and published glycoprotein information including global and site-specific attachment information. For the first release over 890 references, 3740 glycan structure entries and 400 glycoproteins have been curated. Further, 598 protein glycosylation sites have been annotated with experimentally confirmed glycan structures from the literature. Among these are 35 glycoproteins, 502 structures and 60 publications previously not included in GlycoSuiteDB. This article provides an update on the transformation of GlycoSuiteDB (featured in previous NAR Database issues and hosted by ExPASy since 2009) to UniCarbKB and its integration with UniProtKB and GlycoMod. Here, we introduce a refactored database, supported by substantial new curated data collections and intuitive user-interfaces that improve database searching.

GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination

UNLABELLEDnSequencing oligosaccharides by exoglycosidases, either sequentially or in an array format, is a powerful tool to unambiguously determine the structure of complex N- and O-link glycans. Here, we introduce GlycoDigest, a tool that simulates exoglycosidase digestion, based on controlled rules acquired from expert knowledge and experimental evidence available in GlycoBase. The tool allows the targeted design of glycosidase enzyme mixtures by allowing researchers to model the action of exoglycosidases, thereby validating and improving the efficiency and accuracy of glycan analysis.nnnAVAILABILITY AND IMPLEMENTATIONnhttp://www.glycodigest.org.

GlyTouCan: an accessible glycan structure repository

Rapid and continued growth in the generation of glycomic data has revealed the need for enhanced development of basic infrastructure for presenting and interpreting these datasets in a manner that engages the broader biomedical research community. Early in their growth, the genomic and proteomic fields implemented mechanisms for assigning unique gene and protein identifiers that were essential for organizing data presentation and for enhancing bioinformatic approaches to extracting knowledge. Similar unique identifiers are currently absent from glycomic data. In order to facilitate continued growth and expanded accessibility of glycomic data, the authors strongly encourage the glycomics community to coordinate the submission of their glycan structures to the GlyTouCan Repository and to make use of GlyTouCan identifiers in their communications and publications. The authors also deeply encourage journals to recommend a submission workflow in which submitted publications utilize GlyTouCan identifiers as a standard reference for explicitly describing glycan structures cited in manuscripts.

Students in Space: Student Practices in Non-Traditional Classrooms

The discourse of the non-traditional classroom has found itself fundamentally intertwined with the rationalities of creating learning relevant for the future-orientated twenty-first century. In such an imaginary the idea of the conventional classroom – with its four walls, blackboard, ‘closed’ door, teacher-centred pedagogy and student learning conceptualised through the logics of the industrial era – is being renegotiated. This article focuses on an empirical examination of some of the changes to student classroom practice enabled by the material conditions of non-traditional learning spaces. In particular, it highlights the ways in which non-traditional learning spaces have become complex settings through which students negotiate increased learner autonomy, co-operative learning, acceptable classroom behaviour and fluid relations with teachers and peers. The article presents a discussion of the discourse of ‘twenty-first-century learning’ and focuses on non-traditional classrooms as an example of a localised expression of this discourse, supported by ethnographic data generated from field visits to three primary schools in Sydney, Australia to explore student practices enabled by such spaces.

Issues of teacher professional learning within ‘non-traditional’ classroom environments:

In response to the demands of the ‘21st century learner’, classroom environments are increasingly moving away from traditional models of a single-teacher isolated in their classroom. There is an advent of ‘non-traditional’ environments that challenge long-held practices in teaching. To support these changes there is a pressing need to create opportunities for professional learning. This article reports on a study undertaken within three primary schools that had recently adopted ‘non-traditional’ classroom environments. The study aimed to identify how these new spaces were shaping teaching practices and the challenges that they presented for professional learning. This article presents findings from this study with recommendations for how systems and schools can better manage the opportunities presented by these ‘non-traditional’ environments.

Developing Critical Moral Agency Through Workplace Engagement

This chapter undertakes an exploration of the intersection of work integrated learning and the development of professional ethics, arguing for a focus on the development of an awareness of critical moral agency within the emerging professional. The chapter considers the construct of agency in the workplace alongside issues of power and subjugation created through the positioning of the emerging professional. Developing from this consideration it is argued that work integrated learning, combined with an effective and integrated professional ethics curriculum can empower the emerging professional to transform practice through accessing opportunities of agency.

Developing a postgraduate work-based curriculum using an Intervention Mapping Approach

ABSTRACT Advanced practitioner skill development has become an important focus in health service delivery as increasingly complex consumer needs, practice environments and national professional registration requirements impact on professional work practices. Increasingly, work-based or workplace learning experiences are being seen as an effective means for maintaining skill currency across working lives. Currently there is limited literature on pedagogical practices to support the educational and training requirements associated with development across a persons working life. This paper reports on an example of how an intervention mapping framework was used to guide the development, implementation and evaluation of a work-based praxis course for students in an interprofessional, online postgraduate mental health programme. The intervention mapping framework provided a stepped process to guide decision-making and allowed the incorporation of theory and evidence into the course design. This approach provided a stepped process to guide decision-making and allowed the incorporation of theory and evidence into the course design. While the use of the intervention mapping framework is often used within health promotion arenas, particularly for the effective design of health promotion educational programmes, it is argued that this framework can be utilised effectively when developing curriculum for use within higher education programmes.

GlycoStore: a database of retention properties for glycan analysis

SummarynGlycoStore is a curated chromatographic, electrophoretic and mass-spectrometry composition database of N-, O-, glycosphingolipid (GSL) glycans and free oligosaccharides associated with a range of glycoproteins, glycolipids and biotherapeutics. The database is built on publicly available experimental datasets from GlycoBase developed in the Oxford Glycobiology Institute and then the National Institute for Bioprocessing Research and Training (NIBRT). It has now been extended to include recently published and in-house data collections from the Bioprocessing Technology Institute (BTI) A*STAR, Macquarie University and Ludger Ltd. GlycoStore provides access to approximately 850 unique glycan structure entries supported by over 8500 retention positions determined by: (i) hydrophilic interaction chromatography (HILIC) ultra-high performance liquid chromatography (U/HPLC) and reversed phase (RP)-U/HPLC with fluorescent detection; (ii) porous graphitized carbon (PGC) chromatography in combination with ESI-MS/MS detection; and (iii) capillary electrophoresis with laser induced fluorescence detection (CE-LIF). GlycoStore enhances many features previously available in GlycoBase while addressing the limitations of the data collections and model of this popular resource. GlycoStore aims to support detailed glycan analysis by providing a resource that underpins current workflows. It will be regularly updated by expert annotation of published data and data obtained from the project partners.nnnAvailability and implementationnhttp://www.glycostore.org.nnnSupplementary informationnSupplementary data are available at Bioinformatics online.

Professional Identities and Ethics: The Role of Work-Integrated Learning in Developing Agentic Professionals

Abstract nMuch rhetoric around the construct of a work-ready graduate has focused on the technical abilities of students to fulfill the expectations of the future workplace. Efforts have been made to extend from the technical skills (e.g., skills in calculation for engineers) to include soft or behavioral skills (e.g., communication). However, within previous models of understanding of the work-ready graduate there has been little done to explore them as critical moral agents within the workplace. That is, whilst the focus has been on being work-ready, it is argued here that in current and future workplaces it is more important for university graduates to be profession-ready. Our understanding of the profession-ready graduate is characterized by the ability to demonstrate capacities in critical thinking and reflection, and to have an ability to navigate the ethical challenges and shape the organizational culture of the future workplace. n nThis chapter aims to explore a movement of thinking away from simply aspiring to develop work-ready graduates, expanding this understanding to argue for the development of profession-ready graduates. The chapter begins with an exploration of the debates around the characteristics of being work-ready, and through a consideration of two professional elements: professional identity and critical moral agency, argues for a reframing of work-readiness towards professional-readiness. The chapter then considers the role of work-integrated learning (WIL) in being able to support the development of the profession-ready graduate.