Array2BIO: from microarray expression data to functional annotation of co-regulated genes

Background  

There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we have developed Array2BIO, an application that couples several analytical methods into a single web based utility.     

The carbon implications of large‐scale afforestation of agriculturally marginal land with short‐rotation willow in Saskatchewan

Afforestation with short‐rotation coppice (SRC) willow plantations for the purpose of producing bioenergy feedstock was contemplated as one potential climate change mitigation option. The objectives of this study were to assess the magnitude of this mitigation potential by addressing: (i) the land area potentially available for SRC systems in the province of Saskatchewan, Canada; (ii) the potential biomass yields of SRC plantations; and (iii) the carbon implications from such a large‐scale afforestation program. Digital soils and land‐use data were used to identify, map, and group into clusters of similar polygons 2.12 million hectares (Mha) of agriculturally marginal land that was potentially suitable for willow in the Boreal Plains and Prairies ecozones in Saskatchewan. The Physiological Principles in Predicting Growth (3PG) model was calibrated with data from SRC experiments in Saskatchewan, to quantify potential willow biomass yields, and the Carbon Budget Model of the Canadian Forest Sector (CBM‐CFS3), was used to simulate stand and landscape‐level C fluxes and stocks. Short‐rotation willow plantations managed in 3 year rotations for seven consecutive harvests (21 years) after coppicing at Year 1 produced about 12 Mg ha^?1 yr^?1 biomass. The more significant contribution to the C cycle was the cumulative harvest. After 44 years, the potential average cumulative harvested biomass C in the Prairies was 244 Mg C ha^?1 (5.5 Mg C ha^?1 yr^?1) about 20% higher than the average for the Boreal Plains, 203 Mg C ha^?1 (4.6 Mg C ha^?1 yr^?1). This analysis did not consider afforestation costs, rate of establishment of willow plantations, and other constraints, such as drought and disease effects on biomass yield. The results must therefore be interpreted as a biophysical mitigation potential with the technical and economic potential being both lower than our estimates. Nevertheless, short‐rotation bioenergy plantations offer one potential mitigation option to reduce the rate of CO₂ accumulation in the earth's atmosphere and further research is needed to operationalise such a mitigation effort.     

Diversity of free-living ‘naked’ amoeboid organisms

Amoeboid organisms are phylogenetically diverse, some being more closely related to plants or metazoans than to each other. Amoeboid organisms are ecologically successful, having been isolated on all continents, including Antarctica, as well as being the main predators controlling bacterial populations in soil. The classification of these organisms has historically relied upon morphological characteristics. The application of electron microscopy, comparison of enzymic profiles after electrophoretic separation, and analysis of nucleic acid fractions have provided reliable bases for classifying amoeboid organisms. The extent of diversity of these organisms has been recognized, as methods to detect, culture, characterize and identify them has increased. It is reasonable to anticipate that the current 40 000 species of protists will increase substantially as amoeboid organisms are cultivated from poorly accessible niches and from extreme environs.     

Volatile organic compound concentrations and their health risks in various workplace microenvironments

Abstract

Volatile organic compounds (VOCs) are some of the most important pollutants that have adverse effects on human health. In this study, simultaneous indoor and outdoor air samples were collected from four types of microenvironments (restaurants, photocopy centers, dry cleaners, and auto paint shops) in Kocaeli, Turkey in both winter and summer. Twenty-four VOCs were detected using gas chromatography and a flame ionization detector. The aim of the study was to determine the VOC concentrations in various workplaces and investigate associated health risks. Results show that the highest mean total VOC concentrations are in auto paint shops (14,066 µg/m³ in winter, 3441 µg/m³ in summer) followed by dry cleaners, restaurants, and photocopy centers. Total cancer risk was approximately 310 times greater than the acceptable limit in auto paint shops, 44 times greater in restaurants, 42 times greater in dry cleaners, and 17 times greater in photocopy centers. Total hazard quotients were also greater than the acceptable limit in all microenvironments.