Protein Ontology: A controlled structured network of protein entities

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments

Marrying Social Media Approaches and Space Flight Control: Eight Years at SpaceOps

Three previous SpaceOps papers [1-3] - published in 2010, 2012 (honored by the Conference as a "Best Paper"), and 2014 - have discussed paths to using social media concepts and techniques to enhance space flight controller effectiveness by a) reducing clutter of nonverbal communications (e.g., visual flow with minimal headers and shared content instead of multiple copies), b) moving some voice communication to non-verbal transmission (virtually eliminating "say again" requests because non-verbal comm can be re-read), thus making remaining voice comm easier to focus on, and c) reducing short-term and long-term flight stress on flight control personnel. This paper shows how Marshall Space Flight Center's (MSFC) ISS Payload Operations Integration Center (POIC) is realizing the above goals via the Communications Dashboard (CommDash) software suite deployed in 2017 (including enhancements to the Console Log Tool (CoLT) discussed in earlier papers). Two larger-scope benefits spawned by CommDash evolution are also chronicled: a) emergence of an Agile Software Development (ASD) process adapted to the not-always-nimble environment of government projects, and b) the sprouting of a Human Factors Engineering (HF or HFE) community of practice within MSFC's Payload and Mission Operations Division (PMOD)

“some kind of thing it aint us but yet its in us”: David Mitchell, Russell Hoban, and metafiction after the millennium

This article appraises the debt that David Mitchell’s Cloud Atlas owes to the novels of Russell Hoban, including, but not limited to, Riddley Walker. After clearly mapping a history of Hoban’s philosophical perspectives and Mitchell’s inter-textual genre-impersonation practice, the article assesses the degree to which Mitchell’s metatextual methods indicate a nostalgia for by-gone radical aesthetics rather than reaching for new modes of its own. The article not only proposes several new backdrops against which Mitchell’s novel can be read but also conducts the first in-depth appraisal of Mitchell’s formal linguistic replication of Riddley Walker

Morphometric and structural analysis of Florida manateespermatozoa

Sperm characteristics, such as sperm morphology and sperm morphometry areimportant in assessing sperm quality. This is especially important for the man-agement and conservation of endangered and exotic species, like the Floridamanatee, where information of this nature is extremely limited. In this study,we fill this knowledge gap to better understand the reproductive physiology ofFlorida manatees by conducting the first extensive analysis of sperm mor-phometry and ultrastructure. Sperm were retrieved from the vas deferens ofnine recently deceased Florida manatees. Computer-aided sperm morphologyanalysis (CASMA) was used for morphometric analysis and laser-scanningconfocal microscopy and electron microscopy were used for structural andultrastructural characterization

Development and Field Validation of an Environmental DNA (eDNA) Assay for Invasive Clams of the Genus Corbicula

Early detection is imperative for successful control or eradication of invasive species, but many organisms are difficult to detect at the low abundances characteristic of recently introduced populations. Environmental DNA (eDNA) has emerged as a promising invasive species surveillance tool for freshwaters, owing to its high sensitivity to detect aquatic species even when scarce. We report here a new eDNA assay for the globally invasive Asian clam Corbicula fluminea (Müller, 1774), with field validation in large lakes of western North America. We identified a candidate primer pair for the Cytochrome c oxidase subunit 1 (COI) gene for C. fluminea. We tested it for specificity via qPCR assay against genomic DNA of the target species C. fluminea, and synthetic DNA gBlocks for other non-target species within and outside of the genus Corbicula. Our best identified primer amplifies a 208-bp fragment for C. fluminea and several closely related species within the genus, but was specific for these non-native Asian clams relative to native mollusks of western North America. We further evaluated this assay in application to eDNA water samples for the detection of C. fluminea from four lakes in California and Nevada, United States, where the species is known to occur (including Lake Tahoe) relative to seven lakes where it has never been observed. Our assay successfully detected C. fluminea in all four lakes with historic records for this species, and did not detect C. fluminea from the seven lakes without known populations. Further, the distribution of eDNA detections within Lake Tahoe generally matched the known, restricted distribution of C. fluminea in this large lake. We conclude from this successful field validation that our eDNA assay for C. fluminea will be useful for researchers and managers seeking to detect new introductions and potentially monitor population trends of this major freshwater invader and other closely related members of its genus

Widespread occurrence of two carbon fixation pathways in tubeworm endosymbionts: lessons from hydrothermal vent associated tubeworms from the Mediterranean Sea

Vestimentiferan tubeworms (siboglinid polychaetes) of the genus Lamellibrachia are common members of cold-seep faunal communities and have also been found at sedimented hydrothermal vent sites in the Pacific. As they lack a digestive system, they are nourished by chemoautotrophic bacterial endosymbionts growing in a specialized tissue called the trophosome. Here we present the results of investigations of tubeworms and endosymbionts from a shallow hydrothermal vent field in the Western Mediterranean Sea. The tubeworms, which are the first reported vent-associated tubeworms outside the Pacific, are identified as Lamellibrachia anaximandri using mitochondrial ribosomal and cytochrome oxidase I gene sequences. They harbor a single gammaproteobacterial endosymbiont. Carbon isotopic data, as well as the analysis of genes involved in carbon and sulfur metabolism indicate a sulfide-oxidizing chemoautotrophic endosymbiont. The detection of a hydrogenase gene fragment suggests the potential for hydrogen oxidation as alternative energy source. Surprisingly, the endosymbiont harbors genes for two different carbon fixation pathways, the Calvin-Benson-Bassham (CBB) cycle as well as the reductive tricarboxylic acid (rTCA) cycle, as has been reported for the endosymbiont of the giant vent tubeworm Riftia pachyptila. In addition to RubisCO genes we detected ATP citrate lyase (ACL, the key enzyme of the rTCA cycle) type II gene sequences using newly designed primer sets. Comparative investigations with additional tubeworm species (Lamellibrachia luymesi, Lamellibrachia sp. 1, Lamellibrachia sp. 2, Escarpia laminata, Seepiophila jonesi) from multiple cold seep sites in the Gulf of Mexico revealed the presence of acl genes in these species as well. Thus, our study suggests that the presence of two different carbon fixation pathways, the CBB cycle and the rTCA cycle, is not restricted to the Riftia endosymbiont, but rather might be common in vestimentiferan tubeworm endosymbionts

Protein Ontology: Enhancing and scaling up the representation of protein entities

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities