The NCBO OBOF to OWL Mapping

Two of the most significant formats for biomedical ontologies are the Open Biomedical Ontologies Format (OBOF) and the Web Ontology Language (OWL). To make it possible to translate ontologies between these two representation formats, the National Center for Biomedical Ontology (NCBO) has developed a mapping between the OBOF and OWL formats as well as inter-conversion software. The goal was to allow the sharing of tools, ontologies, and associated data between the OBOF and Semantic Web communities.

OBOF does not have a formal grammar, so the NCBO had to capture its intended semantics to map it to OWL.

This official NCBO mapping was used to make all OBO Foundry ontologies available in OWL. 

Availability: This mapping functionality can be embedded into OBO-Edit and Protégé-OWL ontology editors. This software is available at: http://bioontology.org/wiki/index.php/OboInOwl:Main_Pag

Dwarf White Clover Supports Pollinators, Augments Nitrogen in Clover-Turfgrass Lawns, and Suppresses Root-Feeding Grubs in Monoculture but Not in Mixed Swards

The runoff or leaching of nitrogen fertilizers from monoculture turfgrass lawns contri-butes to water pollution, and such lawns are susceptible to insect pests and provide few resources for pollinators. One approach to creating more sustainable lawns is to incorporate white clover (Trifolium repens L.), a nitrogen-fixing legume, into grass seed mixtures or existing turfgrass swards. “Dutch” white clover (DWC), a ubiquitous landrace, forms non-uniform clumps when intermixed with turfgrasses, thus it is often considered to be a lawn weed. Recently, several dwarf varieties of white clover have been selected for their small leaf size and low growth habit, allowing them to tolerate low mowing heights and blend better with grasses. To date, there have been no studies published on the entomological aspects of dwarf clover in pure stands or intermixed with turfgrass. We established field plots with combinations of DWC, two cultivars of dwarf clover, and tall fescue (Schedonorus arundinaceus (Schreb.) Dumort.) in monoculture or mixed swards, and compared the invertebrate communities therein. Predatory arthropods and earthworm numbers were similar in all plot types. The clover monocultures were resistant to white grubs, but the grub densities in the clover–tall fescue dicultures were similar to those found in the pure tall fescue swards. Dwarf clovers and DWC were similarly attractive to bees and supported similar bee assemblages. The tall fescue foliar N content was elevated 17–27% in the dicultures with clovers

Is Alpha-Synuclein Loss-of-Function a Contributor to Parkinsonian Pathology? Evidence from Non-human Primates

Accumulation of alpha-synuclein (α-syn) in Lewy bodies and neurites of midbrain dopamine neurons is diagnostic for Parkinson’s disease (PD), leading to the proposal that PD is a toxic gain-of-function synucleinopathy. Here we discuss the alternative viewpoint that α-syn displacement from synapses by misfolding and aggregation results in a toxic loss-of-function. In support of this hypothesis we provide evidence from our pilot study demonstrating that knockdown of endogenous α-syn in dopamine neurons of nonhuman primates reproduces the pattern of nigrostriatal degeneration characteristic of PD

SOX9 transduction of a human chondrocytic cell line identifies novel genes regulated in primary human chondrocytes and in osteoarthritis

The transcription factor SOX9 is important in maintaining the chondrocyte phenotype. To identify novel genes regulated by SOX9 we investigated changes in gene expression by microarray analysis following retroviral transduction with SOX9 of a human chondrocytic cell line (SW1353). From the results the expression of a group of genes (SRPX, S100A1, APOD, RGC32, CRTL1, MYBPH, CRLF1 and SPINT1) was evaluated further in human articular chondrocytes (HACs). First, the same genes were investigated in primary cultures of HACs following SOX9 transduction, and four were found to be similarly regulated (SRPX, APOD, CRTL1 and S100A1). Second, during dedifferentiation of HACs by passage in monolayer cell culture, during which the expression of SOX9 progressively decreased, four of the genes (S100A1, RGC32, CRTL1 and SPINT1) also decreased in their expression. Third, in samples of osteoarthritic (OA) cartilage, which had decreased SOX9 expression compared with age-matched controls, there was decreased expression of SRPX, APOD, RGC32, CRTL1 and SPINT1. The results showed that a group of genes identified as being upregulated by SOX9 in the initial SW1353 screen were also regulated in expression in healthy and OA cartilage. Other genes initially identified were differently expressed in isolated OA chondrocytes and their expression was unrelated to changes in SOX9. The results thus identified some genes whose expression appeared to be linked to SOX9 expression in isolated chondrocytes and were also altered during cartilage degeneration in osteoarthritis

Northern Bobwhite Response to Control of Red Imported Fire Ants in the Gulf Coast Prairie of Texas

The population decline of northern bobwhite (Colinus virginianus; hereafter, bobwhite) on the Texas Gulf Coast Prairie, USA is largely attributed to habitat loss. However, red imported fire ants (Solenopsis invicta) occur throughout the region and are considered a possible contributing factor to the bobwhite decline. The objectives of our study were to determine the influence of red imported fire ants on bobwhites by comparing bobwhite nest success, survival, and density between sites treated with fire ant bait (treatment) and reference (control) sites. Our study was conducted on 3 private ranches in Goliad and Refugio counties, Texas. Each ranch contained 2 paired experimental units that consisted of a treatment and control site (500 ha each). The treatment sites received an aerial application of fire ant bait (Extinguish® Plus) during April 2018, whereas the control sites were not treated. We estimated mound density by counting fire ant mounds using distance sampling. We used radio-telemetry to monitor bobwhite nest success and survival, and we estimated bobwhite densities using distance sampling via helicopter surveys. Fire ant mound density decreased through time on both treatment and control sites. However, fire ant mound density was lower on treatment sites than control sites, indicating the insecticide was effective at decreasing fire ant mound density. Bobwhite survival, nest success, and density did not statistically differ between control and treated sites either pre-treatment (2017) or post-treatment (2018), but survival and nest success metrics were numerically higher in treated units. Bobwhite survival remained relatively stable in the treatment units 4 weeks after application but decreased in the control units. Following treatment, apparent nest success in the treated units increased by 37.4% while nest success in the control units decreased by 35.2%. Bobwhite populations were low in this ecoregion, which influenced our ability to trap and monitor many bobwhites or monitor many nests. In addition, it may be possible that repeated, annual treatments for fire ants are necessary for a benefit to accrue and be observed in bobwhites. Our results indicate that there may be potential benefits to bobwhites from fire ant reduction that deserve further research attention

Outcomes following surgery and post-operative radiotherapy for perineural spread of head and neck cutaneous squamous cell carcinoma

Background Queensland, Australia, has the highest rates of cutaneous squamous cell carcinoma (SCC). Perineural invasion (PNI) is associated with reduced local control and survival. Methods A retrospective review of a prospective database of patients with clinical PNI from cutaneous SCC of the head and neck (SCCHN) treated with surgery and postoperative radiotherapy (PORT) between 2000 and 2011 and a minimum of 24 months follow-up. Patients were excluded if immunosuppressed, had non-SCC histology, or were treated palliatively. Results Fifty patients (mean age, 60 years) with median follow-up of 50 months were included in this study. A total of 54.8% of known primary tumors had incidental PNI. Ten percent had nodal disease at presentation. MRI neurogram was positive in 95.8%. Recurrence-free survival (RFS) at 5-years was 62%. Five-year disease-specific survival (DSS) and overall survival (OS) were 75% and 64%, respectively. There were no perioperative deaths. Conclusion This report demonstrates that long-term survival is achievable in patients with clinical PNI from cutaneous SCCHN after surgery and PORT