The reactive metabolite target protein database (TPDB) – a web-accessible resource

BACKGROUND: The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To understand the mechanisms of cytotoxic responses it may be important to know which proteins become adducted and whether some may be common targets of multiple toxins. The literature of this field is widely scattered but expanding rapidly, suggesting the need for a comprehensive, searchable database of reactive metabolite target proteins. DESCRIPTION: The Reactive Metabolite Target Protein Database (TPDB) is a comprehensive, curated, searchable, documented compilation of publicly available information on the protein targets of reactive metabolites of 18 well-studied chemicals and drugs of known toxicity. TPDB software enables i) string searches for author names and proteins names/synonyms, ii) more complex searches by selecting chemical compound, animal species, target tissue and protein names/synonyms from pull-down menus, and iii) commonality searches over multiple chemicals. Tabulated search results provide information, references and links to other databases. CONCLUSION: The TPDB is a unique on-line compilation of information on the covalent modification of cellular proteins by reactive metabolites of chemicals and drugs. Its comprehensiveness and searchability should facilitate the elucidation of mechanisms of reactive metabolite toxicity. The database is freely available a

Identifying the problem weeds of rice-based systems along the inland-valley catena in the southern Guinea Savanna, Africa

While weeds generally are considered as the most important overarching production constraints in inland-valley cropping systems in West Africa, little is known about species' associations with environmental and crop management factors. Weed species' associations with seasonal and environmental factors, such as their position on the catena, soils and cropping systems, were studied during two seasons (dry and wet) in 45 arable fields of three inland valleys in south-western Benin, Africa. The three most dominant weed species were Dactyloctenium aegyptium, Commelina benghalensis and Digitaria horizontalis on the inland-valley crests (uplands), Ludwigia hyssopifolia, Corchorus aestuans and Ludwigia octovalvis on the sloping hydromorphic fringes and Leersia hexandra, Ipomoea aquatica and Fimbristylis ferruginea in the valley bottoms (lowlands). Echinochloa colona, Cleome viscosa and Talinum triangulare were the three most dominant species in the dry-season crops (maize or vegetables) and Leer. hexandra, I. aquatica and Sphenoclea zeylanica were the three most dominant species in the wet-season crop (rice). Ageratum conyzoides, Synedrella nodiflora and D. horizontalis were observed throughout the catena. Problem weeds in inland-valley agro-ecosystems are those that combine a high frequency with a high submergence tolerance and ecological plasticity, C4 grasses, perennial C3 species with persistent root structures and broad-leaved species with high propagation rates. Weed management strategies that are aimed at increasing the resilience of rice-based cropping systems in the inland valleys of the southern Guinea Savanna of Africa should address the categories of problem species that were identified in this study. This can be done best by following an integrated approach, including the use of more weed-competitive cultivars and rotation crops