Informatics and quantitative analysis in biological imaging

Biological imaging is now a quantitative technique for probing cellular structure and dynamics and is increasingly used for cell-based screens. However, the bioinformatics tools required for hypothesis-driven analysis of digital images are still immature. We are developing the Open Microscopy Environment (OME) as an informatics solution for the storage and analysis of optical microscope image data. OME aims to automate image analysis, modeling, and mining of large sets of images and specifies a flexible data model, a relational database, and an XML-encoded file standard that is usable by potentially any software tool. With this design, OME provides a first step toward biological image informatics.     

Mutations in U4atac snRNA, a component of the minor spliceosome, in the developmental disorder MOPD I

Small nuclear RNAs (snRNAs) are essential factors in messenger RNA splicing. By means of homozygosity mapping and deep sequencing, we show that a gene encoding U4atac snRNA, a component of the minor U12-dependent spliceosome, is mutated in individuals with microcephalic osteodysplastic primordial dwarfism type I (MOPD I), a severe developmental disorder characterized by extreme intrauterine growth retardation and multiple organ abnormalities. Functional assays showed that mutations (30G>A, 51G>A, 55G>A, and 111G>A) associated with MOPD I cause defective U12-dependent splicing. Endogenous U12-dependent but not U2-dependent introns were found to be poorly spliced in MOPD I patient fibroblast cells. The introduction of wild-type U4atac snRNA into MOPD I cells enhanced U12-dependent splicing. These results illustrate the critical role of minor intron splicing in human development.     

Occurrence and infectivity of arbuscular mycorrhizal fungi in some norwegian soils influenced by heavy metals and soil properties

Mycorrhizae are ubiquitous symbiosis which can mediate uptake of some plant nutrients. In polluted soils they could be of great importance in heavy metal availability and toxicity to plants. Mycorrhizae have also been reported to protect plants against toxic metals. We investigated the occurrence and infectivity of arbuscular mycorrhizal (AM) spores as affected by heavy metal levels and other soil properties in Norwegian soils collected from heavy metal polluted, high natural background and non-polluted areas. Spore numbers, mycorrhizal infectivity and spore germination of indigenous mycorrhizal fungi and of a reference strain (Glomus mosseae) in soils showed lower values in two soils with high metal concentrations and in one soil with a low pH. Mycorrhizal infectivity was negatively correlated with extractable metals. Spore number and mycorrhizal infectivity in a soil with naturally high heavy metal content were not different to in non-polluted soils, and indigenous AM fungi appeared more tolerant to metals than those in non-polluted soils. Mycorrhizal infectivity, expressed as MSI₅₀ values, was significantly correlated (r′=0.89, P< 0.05) with the percentage of germinating G. mosseae spores in the soils. However, the number of spores per volume of soil was not significantly correlated with infectivity or spore germination of the reference strain. The spore germination method is discussed as a bioassay of heavy metal toxicity in soil.     

Effect of cultivation and within-field differences in soil conditions on feral Helianthus annuus growth in ridge-tillage maize

Differences in weed population dynamics with respect to within-field heterogeneity are not well documented despite increasing interest in site-specific management of agro-ecosystems. The focus of this study was to determine if mechanical weed management (cultivation) and/or soil factors help to explain observed within-field distributions of feral common sunflower (Helianthus annuus L.). The ridges and furrows created by the ridge–tillage system adds additional microsites to existing spatial heterogeneity for soil characteristics such as soil organic carbon (SOC) concentration. Experimental areas were selected on the basis of naturally high or low SOC concentration. Cultivation resulted in 100% mortality of H. annuus seedlings growing in the middle of furrows. Cultivation of pre-emergence herbicide treated and no-herbicide ridges resulted in small but statistically significant ( = 0.05) reductions in seedling survival. No differences were detected in H. annuus canopy height, stem diameter, stem length, or vegetative biomass between high and low SOC environments. Neither total reproductive biomass (P = 0.49) nor the biomass of flowers near physiological maturity (an estimate of fecundity; P = 0.59) were affected by SOC environment. Late season H. annuus lodging was observed to reduce reproductive biomass. Juvenile plants that survived mechanical weed control efforts grew and produced reproductive biomass similarly across SOC environments. The lack of difference in vegetative and reproductive characteristics between high and low SOC environments suggests that SOC (or the edaphic conditions associated with greater or lesser SOC level) was not critical in contributing to the observed distribution of H. annuus from juvenile to flowering stages of growth within well-fertilized, irrigated agricultural habitats.     

The relationship between local extinctions of grassland butterflies and increased soil nitrogen levels

In contrast to many other western European countries, the knowledge about trends in the Swedish butterfly fauna is poor. We studied the effects of habitat and species characteristics on species turnover in 13 grassland sites in southern Sweden by comparing species richness and compositions at two separate occasions with an interval of 21 years. The mean number of species per site decreased from 30 to 24, with a large variation between sites. The number of extinctions was highest in sites where the proportion of trees and shrubs had increased most, but there was no detectable effect of area or of the composition of landscapes surrounding the sites. Areas protected as nature reserves had lost as many species as unprotected areas had, indicating both the importance of proper management of nature reserves and that nature reserves alone may not be enough to inhibit regional extinction of butterfly species. Species dependent on nutrient-poor conditions tended to decrease while species dependent on nutrient-rich conditions tended to increase, indicating a negative effect of increased soil nitrogen levels resulting from active fertilizing of pastures and/or atmospheric nitrogen deposition. A regular monitoring program could show whether our results are representative for Sweden or Northern Europe.