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.     

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.     

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.     

Simultaneous identification of soyasaponins and isoflavones and quantification of soyasaponin Bb in soy products,using liquid chromatography/electrospray ionization-mass spectrometry

A method has been developed for simultaneous identification of soyasaponins and soy isoflavones in soy products, based on liquid chromatography/electrospray ionization-mass spectrometry (LC/ESI-MS). Soy-based nutraceutical products were analyzed by LC/ESI-MS with detection of protonated and sodiated molecular ions, as well as characteristic fragment ions for these compounds. Soy isoflavones were characterized by a strong protonated molecular ion in addition to corresponding [aglycone + H](+) ions. Monitoring the soyasaponin-specific protonated aglycone and dehydrated aglycone ions throughout the chromatogram provided a unique fingerprint for soyasaponin content in the samples. This mass spectrometric fingerprint also allowed immediate classification of the soyasaponin analytes as group A or B soyasaponins, based on the unique masses of aglycone ions observed for each class. Quantification of soyasaponin B(b) in soy-derived materials, based on the use of a purified soyasaponin B(b) standard and a glycyrrhizin internal standard, has been accomplished.     

Analysis of a Secreted Aspartic Peptidase Disruption Mutant of Glomerella cingulata

Peptidases have been implicated in the pathogenicity of fungi that cause disease in plants. Expression of the secreted aspartic peptidase gene (gcsap), of a Glomerella cingulata isolate pathogenic on apples, is induced during appressorium formation. To determine whether the secreted aspartic peptidase (GcSAP) is essential to pathogenicity, gcsap was disrupted using a vector containing a 637 bp fragment of genomic DNA that encodes the sequence spanning the two active site aspartic acid (Asp) residues. To ensure that the truncated gcsap gene products could not have residual peptidase activity the codons for the active site residues Asp¹¹² and Asp²⁹⁷ were both mutated to histidine residues. Both PCR and Southern analysis confirmed disruption of gcsap. Neither gcsap mRNA nor GcSAP activity was detected in the disruption mutant. Pathogenicity tests on fruit from three apple cultivars showed that GcSAP was not required for pathogenicity. The disruption mutant grew on medium containing protein as the sole source of nitrogen because G. cingulata secretes a previously undetected peptidase(s). A serine peptidase that had a pH optimum between pH 7.0 and 8.0 and a K _m of 0.25 mM for the synthetic substrate succinyl-Ala–Ala–Pro–Phe-p-nitroanilide was identified.