Session Four Panel Discussion: Open Research Knowledge, Skills, and Training

Join Louise Saul, Milena Dobreva, Tapas Kumar Mohanty, and Camilla Elphick, along with panel chair Simon Smith to discuss their talks and to think about the impacts of Knowledge, Training, and Skills on the challenges of open research.&nbsp

Delivering OR Training: Creating Development Opportunities for Research Enabling Staff

Librarians and research support staff play an essential role in promoting engagement with Open Research Practices at UK Higher Education Institutions (UK HEIs), through providing training and academic engagement. However, individuals in these roles may not often gain the opportunity to contextualise the content of their teaching within the wider field, or to receive recognition for their work in driving academic standards. We describe the development of a pedagogical wrapper at the University of Bristol by Dr Kirsty Merrett. The aim of the wrapper is to support research enablers, such as librarians, in disseminating their areas of expertise to research support staff at other UK HEIs who are then supported to deliver the content in a form that is tailored to their institution. We evaluate how this has been implemented via the UK Reproducibility Network’s ‘Train-the-Trainer’ programme. We also describe how this has led to career development incentives for librarians that are aligned with the UK Professional Standards Framework. The importance of retaining the specialist knowledge of research enabling individuals, by providing defined career pathways and opportunities, is acknowledged for roles such as technicians however remains undefined for research support staff such as librarians. We hope that by sharing our experiences in this, we will provide a case study to support other research enablers

Cyclooxygenase in GtoPdb v.2025.3

Prostaglandin (PG) G/H synthase, most commonly referred to as cyclooxygenase (COX, (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate,hydrogen-donor : oxygen oxidoreductase) activity, catalyses the formation of PGG2 from arachidonic acid. Hydroperoxidase activity inherent in the enzyme catalyses the formation of PGH2 from PGG2. COX-1 and -2 can be nonselectively inhibited by ibuprofen, ketoprofen, naproxen, indomethacin and paracetamol (acetaminophen). PGH2 may then be metabolised to prostaglandins and thromboxanes by various prostaglandin synthases in an apparently tissue-dependent manner

GDNF Family Receptor (GFR) in GtoPdb v.2025.3

GDNF family receptors (GFR) are extrinsic co-receptors, where ligand binding to the extracellular domain of the glycosylphosphatidylinositol-linked cell-surface GFRs activates a transmembrane tyrosine kinase enzyme, RET. The endogenous ligands are typically dimeric, linked through disulphide bridges: glial cell-derived neurotrophic factor GDNF (211 aa); neurturin (197 aa); artemin (237 aa) and persephin (156 aa), referred to as GDNF family ligands (GFLs). There is evidence for RET-dependent and RET-independent signalling [5]. Growth/Differentiation Factor 15 (GDF15) has been shown to activate GFRAL, a transmembrane protein that similarly forms a complex with RET [8, 10]

Type XI RTKs: TAM (TYRO3-, AXL- and MER-TK) receptor family in GtoPdb v.2025.3

The TAM receptor family, named from the first letter of each of its constituents, respond to growth arrest specific protein 6 and protein S. These ligands are secreted plasma proteins which undergo vitamin K-dependent post-translational modifications generating carboxyglutamate-rich domains which are able to bind to negatively-charged surfaces of apoptotic cells. Members of this RTK family represented a novel structural motif, when originally sequenced

Ligand-gated ion channels in GtoPdb v.2025.3

Ligand-gated ion channels (LGICs) are integral membrane proteins that contain a pore which allows the regulated flow of selected ions across the plasma membrane. Ion flux is passive and driven by the electrochemical gradient for the permeant ions. These channels are open, or gated, by the binding of a neurotransmitter to an orthosteric site(s) that triggers a conformational change that results in the conducting state. Modulation of gating can occur by the binding of endogenous, or exogenous, modulators to allosteric sites. LGICs mediate fast synaptic transmission, on a millisecond time scale, in the nervous system and at the somatic neuromuscular junction. Such transmission involves the release of a neurotransmitter from a pre-synaptic neurone and the subsequent activation of post-synaptically located receptors that mediate a rapid, phasic, electrical signal (the excitatory, or inhibitory, post-synaptic potential). However, in addition to their traditional role in phasic neurotransmission, it is now established that some LGICs mediate a tonic form of neuronal regulation that results from the activation of extra-synaptic receptors by ambient levels of neurotransmitter. The expression of some LGICs by non-excitable cells is suggestive of additional functions.By convention, the LGICs comprise the excitatory, cation-selective, nicotinic acetylcholine [959, 210], 5-HT3 [68, 1441], ionotropic glutamate [856, 1375] and P2X receptors [659, 1330] and the inhibitory, anion-selective, GABAA [1066, 83] and glycine receptors [878, 1539]. The nicotinic acetylcholine, 5-HT3, GABAA and glycine receptors (and an additional zinc-activated channel) are pentameric structures and are frequently referred to as the Cys-loop receptors due to the presence of a defining loop of residues formed by a disulphide bond in the extracellular domain of their constituent subunits [966, 1357]. However, the prokaryotic ancestors of these receptors contain no such loop and the term pentameric ligand-gated ion channel (pLGIC) is gaining acceptance in the literature [573]. The ionotropic glutamate and P2X receptors are tetrameric and trimeric structures, respectively. Multiple genes encode the subunits of LGICs and the majority of these receptors are heteromultimers. Such combinational diversity results, within each class of LGIC, in a wide range of receptors with differing pharmacological and biophysical properties and varying patterns of expression within the nervous system and other tissues. The LGICs thus present attractive targets for new therapeutic agents with improved discrimination between receptor isoforms and a reduced propensity for off-target effects. The development of novel, faster screening techniques for compounds acting on LGICs [359] will greatly aid in the development of such agents

Ceramide turnover in GtoPdb v.2025.3

Ceramides are a family of sphingophospholipids synthesized in the endoplasmic reticulum, which mediate cell stress responses, including apoptosis, autophagy and senescence, Serine palmitoyltransferase generates 3-ketosphinganine, which is reduced to dihydrosphingosine. N-Acylation allows the formation of dihydroceramides, which are subsequently reduced to form ceramides. Once synthesized, ceramides are trafficked from the ER to the Golgi bound to the ceramide transfer protein, CERT (COL4A3BP, Q9Y5P4). Ceramide can be metabolized via multiple routes, ensuring tight regulation of its cellular levels. Addition of phosphocholine generates sphingomyelin while carbohydrate is added to form glucosyl- or galactosylceramides. Ceramidase re-forms sphingosine or sphinganine from ceramide or dihydroceramide. Phosphorylation of ceramide generates ceramide phosphate. The determination of accurate kinetic parameters for many of the enzymes in the sphingolipid metabolic pathway is complicated by the lipophilic nature of the substrates

3.6.5.2 Small monomeric GTPases in GtoPdb v.2025.3

Small G-proteins, are a family of hydrolase enzymes that can bind and hydrolyze guanosine triphosphate (GTP). They are a type of G-protein found in the cytosol that are homologous to the alpha subunit of heterotrimeric G-proteins, but unlike the alpha subunit of G proteins, a small GTPase can function independently as a hydrolase enzyme to bind to and hydrolyze a guanosine triphosphate (GTP) to form guanosine diphosphate (GDP). The best-known members are the Ras GTPases and hence they are sometimes called Ras subfamily GTPases

SLC3 and SLC7 families of heteromeric amino acid transporters (HATs) in GtoPdb v.2025.3

The SLC3 and SLC7 families combine to generate functional transporters, where the subunit composition is a disulphide-linked combination of a heavy chain (SLC3 family) with a light chain (SLC7 family) [1]

Lithic industries and stylistic entities during the Early Neolithic (LBK) in the Rhine-Meuse-Seine basins

The study of the decorated ceramics of the Rubané or Linearbandkeramik (LBK) has long structured the construction of the chronological sequence of the Early Neolithic of northwestern Europe. Recent contributions make it possible to individualize regional stylistic groups. Examination of the different regional corpuses shows that, following the break-up of a common stylistic stage known as the Flomborn entity, the decorative elements of each region evolved differently giving rise to individualised entities that sometimes seem very homogeneous in terms of the style of decorations used (e.g., the Rhine-Meuse ensemble of the Middle Rubané). This contribution aims to compare the results obtained from the ceramic corpus with those of the lithic industry. It shows that out of a common base, regional differences emerged that are also quite significant, whether from the point of view of the procurement of raw materials, reduction process or tool typology. For example, the geographical networks of raw material circulation reveal preferential axes between certain regions (such as the northern and southern parts of the Ardennes Massif) or, on the contrary, border effects that must be compared and contrasted with the entities previously defined on the basis of decorated ceramics. The theoretical significance of these initial observations and the contribution that the techno-economic analysis of lithic industries can drive to the understanding of the relations between communities in the Early Neolithic of the Rhine-Meuse-Seine basins will be examined through network analysis