Using the Gene Ontology to Annotate Key Players in Parkinson's Disease

The Gene Ontology (GO) is widely recognised as the gold standard bioinformatics resource for summarizing functional knowledge of gene products in a consistent and computable, information-rich language. GO describes cellular and organismal processes across all species, yet until now there has been a considerable gene annotation deficit within the neurological and immunological domains, both of which are relevant to Parkinson's disease. Here we introduce the Parkinson's disease GO Annotation Project, funded by Parkinson's UK and supported by the GO Consortium, which is addressing this deficit by providing GO annotation to Parkinson's-relevant human gene products, principally through expert literature curation. We discuss the steps taken to prioritise proteins, publications and cellular processes for annotation, examples of how GO annotations capture Parkinson's-relevant information, and the advantages that a topic-focused annotation approach offers to users. Building on the existing GO resource, this project collates a vast amount of Parkinson's-relevant literature into a set of high-quality annotations to be utilized by the research community

A simple, low-cost conductive composite material for 3D printing of electronic sensors

3D printing technology can produce complex objects directly from computer aided digital designs. The technology has traditionally been used by large companies to produce fit and form concept prototypes (‘rapid prototyping’) before production. In recent years however there has been a move to adopt the technology as full-scale manufacturing solution. The advent of low-cost, desktop 3D printers such as the RepRap and Fab@Home has meant a wider user base are now able to have access to desktop manufacturing platforms enabling them to produce highly customised products for personal use and sale. This uptake in usage has been coupled with a demand for printing technology and materials able to print functional elements such as electronic sensors. Here we present formulation of a simple conductive thermoplastic composite we term ‘carbomorph’ and demonstrate how it can be used in an unmodified low-cost 3D printer to print electronic sensors able to sense mechanical flexing and capacitance changes. We show how this capability can be used to produce custom sensing devices and user interface devices along with printed objects with embedded sensing capability. This advance in low-cost 3D printing with offer a new paradigm in the 3D printing field with printed sensors and electronics embedded inside 3D printed objects in a single build process without requiring complex or expensive materials incorporating additives such as carbon nanotubes

The possible existence of Hs in nature from a geochemical point of view

A hypothesis of the existence of a long-lived isotope 271Hs in natural molybdenites and osmirides is considered from a geochemical point of view. It is shown that the presence of Hs in these minerals can be explained only by making an additional ad hoc assumption on the existence of an isobaric pair of 271Bh-271Hs. This assumption could be tested by mass-spectrometric measurements of U, Pb, Kr, Xe, and Zr isotopic shifts.Comment: 5 pages, no figures. Physics of Particles and Nuclei Letters, 2006, Vol. 3, No. 3, pp. 165-168 in pres

Templating hydrogels

Templating processes for creating polymerized hydrogels are reviewed. The use of contact photonic crystals and of non-contact colloidal crystalline arrays as templates are described and applications to chemical sensing and device fabrication are illustrated. Emulsion templating is illustrated in the formation of microporous membranes, and templating on reverse emulsions and double emulsions is described. Templating in solutions of macromolecules and micelles is discussed and then various applications of hydrogel templating on surfactant liquid crystalline mesophases are illustrated, including a nanoscale analogue of colloidal crystalline array templating, except that the bead array in this case is a cubic array of nonionic micelles. The use of particles as templates in making core-shell and hollow microgel beads is described, as is the use of membrane pores as another illustration of confinement templating

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology.

BACKGROUND: The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. RESULTS: We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. CONCLUSIONS: The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl

A joint geochemical–geophysical record of time-dependent mantle convection south of Iceland

The North Atlantic V-Shaped Ridges (VSRs) provide a spatially extensive and clear record of unsteady mantle convective circulation over >40 My>40 My. VSRs are diachronous ridges of thick crust formed with a periodicity of ∼5 My∼5 My along the Mid Atlantic Ridge, south of Iceland. We present data from a set of dredged basalt samples that shows chemical variation associated with two complete VSR crustal thickness cycles where they intersect the Mid Atlantic Ridge. The new dataset also records chemical variation associated with a VSR crustal thickness cycle along a plate spreading flow-line. Inverse correlations between crustal thickness and both incompatible trace element concentrations and incompatible element ratios such as Nb/Y and La/Sm are observed. Geochemical and crustal thickness observations can be matched using a time-dependent mid-ocean ridge melting model with a basal boundary condition of sinusoidally varying potential temperature. Our observations and models suggest that VSRs are generated when hot patches are carried up the plume stem beneath SE Iceland and spread radially outward within the asthenosphere. These patches are then drawn upward into the melting region when passing beneath the Mid Atlantic Ridge. The geometry of the VSRs and the size of the dynamically supported swell suggest that the Iceland Plume is the strongest plume in the Earth at present, with a volume flux of View the MathML source49±14 km3yr−1

Representing kidney development using the gene ontology.

Gene Ontology (GO) provides dynamic controlled vocabularies to aid in the description of the functional biological attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). Here we describe collaboration between the renal biomedical research community and the GO Consortium to improve the quality and quantity of GO terms describing renal development. In the associated annotation activity, the new and revised terms were associated with gene products involved in renal development and function. This project resulted in a total of 522 GO terms being added to the ontology and the creation of approximately 9,600 kidney-related GO term associations to 940 UniProt Knowledgebase (UniProtKB) entries, covering 66 taxonomic groups. We demonstrate the impact of these improvements on the interpretation of GO term analyses performed on genes differentially expressed in kidney glomeruli affected by diabetic nephropathy. In summary, we have produced a resource that can be utilized in the interpretation of data from small- and large-scale experiments investigating molecular mechanisms of kidney function and development and thereby help towards alleviating renal disease

P04-45. Characterization of the plasma cell repertoire in acute HIV-1 infection (AHI)

Analysis of immunoglobulin (Ig) VH and VL genes derived from sorted single B cells is a powerful technology for definition of Ig repertoires to viral infections. The purpose of this study was to characterize the Ig repertoire of plasma cells/plasmablasts (PCs) in subjects early on after HIV transmission

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.

BACKGROUND: A systems biology approach to cardiac physiology requires a comprehensive representation of how coordinated processes operate in the heart, as well as the ability to interpret relevant transcriptomic and proteomic experiments. The Gene Ontology (GO) Consortium provides structured, controlled vocabularies of biological terms that can be used to summarize and analyze functional knowledge for gene products. METHODS AND RESULTS: In this study, we created a computational resource to facilitate genetic studies of cardiac physiology by integrating literature curation with attention to an improved and expanded ontological representation of heart processes in the Gene Ontology. As a result, the Gene Ontology now contains terms that comprehensively describe the roles of proteins in cardiac muscle cell action potential, electrical coupling, and the transmission of the electrical impulse from the sinoatrial node to the ventricles. Evaluating the effectiveness of this approach to inform data analysis demonstrated that Gene Ontology annotations, analyzed within an expanded ontological context of heart processes, can help to identify candidate genes associated with arrhythmic disease risk loci. CONCLUSIONS: We determined that a combination of curation and ontology development for heart-specific genes and processes supports the identification and downstream analysis of genes responsible for the spread of the cardiac action potential through the heart. Annotating these genes and processes in a structured format facilitates data analysis and supports effective retrieval of gene-centric information about cardiac defects. Circ Genom Precis Med 2018 Feb; 11(2):e001813