Crop ontology: integration of standard variables

The Crop Ontology (CO, http://www.cropontology.org/) is a resource of the Integrated Breeding Platform (IBP, http://integratedbreeding.net/) providing breeders with crop specific terms for fieldbook edition and data annotation. Until Mai 2015, a plant phenotype was annotated with 3 CO identifiers for the trait, the method and the scale, respectively. Yet, breeders’ fieldbook and most phenotypic databases are designed to annotate a datapoint with only one identifier. To meet the need of providing one single identifier to an observation variable, the CO and IBP teams have worked on integrating the notion of variable into the CO. This has led to a thorough revision of the structure of the Trait Dictionary (TD) template. The TD template is a user-friendly xls file that is used to submit terms to CO which are then stored in the IBP Breeding Management System and other information systems (NextGen, Agtrials…). The most notable changes to the TD template are the addition of the term type “variable” and the decomposition of a trait into an entity and an attribute so as to formalize the trait definition and to foster the mapping with external ontologies (TO, PO, PATO, CHEBI, EO, PDO, GO…). Guidelines document how to post-compose variables. Along with the partners, the CO and IBP team have been working on formatting and curating the TD of pigeonpea (ICRISAT), cowpea (IITA), wheat (CIMMYT), groundnut (ICRISAT/USDA), yam (IITA), chickpea (ICRISAT), lentil (ICARDA), cassava (IITA), soybean (IITA/USDA), common bean (CIAT), rice (IRRI), pearl millet (ICRISAT), sorghum (CIRAD/ICRISAT), and maize (CIMMYT)

Exposure to naphthalene and β-pinene-derived secondary organic aerosol induced divergent changes in transcript levels of BEAS-2B cells.

The health effects of exposure to secondary organic aerosols (SOAs) are still limited. Here, we investigated and compared the toxicities of soot particles (SP) coated with β-pinene SOA (SOAβPin-SP) and SP coated with naphthalene SOA (SOANap-SP) in a human bronchial epithelial cell line (BEAS-2B) residing at the air-liquid interface. SOAβPin-SP mostly contained oxygenated aliphatic compounds from β-pinene photooxidation, whereas SOANap-SP contained a significant fraction of oxygenated aromatic products under similar conditions. Following exposure, genome-wide transcriptome responses showed an Nrf2 oxidative stress response, particularly for SOANap-SP. Other signaling pathways, such as redox signaling, inflammatory signaling, and the involvement of matrix metalloproteinase, were identified to have a stronger impact following exposure to SOANap-SP. SOANap-SP also induced a stronger genotoxicity response than that of SOAβPin-SP. This study elucidated the mechanisms that govern SOA toxicity and showed that, compared to SOAs derived from a typical biogenic precursor, SOAs from a typical anthropogenic precursor have higher toxicological potency, which was accompanied with the activation of varied cellular mechanisms, such as aryl hydrocarbon receptor. This can be attributed to the difference in chemical composition; specifically, the aromatic compounds in the naphthalene-derived SOA had higher cytotoxic potential than that of the β-pinene-derived SOA