Lamellate bodies in the nuclei of dragonfly (odonata) oocytes

Summary Concentrically lamellate spherical bodies have been observed in the oocyte nuclei of the anisopterous dragonflyCordulia aenea. In their ultrastructure, these bodies resemble the cortical granules reported from the cytoplasm of the sea urchin oocytes. The lamellate bodies ofCordulia are compared with other lamellate systems known to exist in nuclei. It is suggested that the nuclear lamellate spheres ofCordulia may be homologous with the somewhat less regular lamellate bodies described from maize microspores.The competent help of MissRiitta Lallukka, M. A., is acknowledged with many thanks. We are grateful to ProfessorsESko Suomalainen andAntti Telkkä for helpful suggestions. Grants for the study have been received from the National Research Council for Sciences, from the University of Helsinki and from the Emil Aaltonen Foundation.     

Unraveling protein interaction networks with near-optimal efficiency

The functional characterization of genes and their gene products is the main challenge of the genomic era. Examining interaction information for every gene product is a direct way to assemble the jigsaw puzzle of proteins into a functional map. Here we demonstrate a method in which the information gained from pull-down experiments, in which single proteins act as baits to detect interactions with other proteins, is maximized by using a network-based strategy to select the baits. Because of the scale-free distribution of protein interaction networks, we were able to obtain fast coverage by focusing on highly connected nodes (hubs) first. Unfortunately, locating hubs requires prior global information about the network one is trying to unravel. Here, we present an optimized 'pay-as-you-go' strategy that identifies highly connected nodes using only local information that is collected as successive pull-down experiments are performed. Using this strategy, we estimate that 90% of the human interactome can be covered by 10,000 pull-down experiments, with 50% of the interactions confirmed by reciprocal pull-down experiments.     

Bayesian search of functionally divergent protein subgroups and their function specific residues

MOTIVATION: The rapid increase in the amount of protein sequence data has created a need for an automated identification of evolutionarily related subgroups from large datasets. The existing methods typically require a priori specification of the number of putative groups, which defines the resolution of the classification solution. RESULTS: We introduce a Bayesian model-based approach to simultaneous identification of evolutionary groups and conserved parts of the protein sequences. The model-based approach provides an intuitive and efficient way of determining the number of groups from the sequence data, in contrast to the ad hoc methods often exploited for similar purposes. Our model recognizes the areas in the sequences that are relevant for the clustering and regards other areas as noise. We have implemented the method using a fast stochastic optimization algorithm which yields a clustering associated with the estimated maximum posterior probability. The method has been shown to have high specificity and sensitivity in simulated and real clustering tasks. With real datasets the method also highlights the residues close to the active site. AVAILABILITY: Software 'kPax' is available at http://www.rni.helsinki.fi/jic/softa.html     

Neighboring Deschampsia flexuosa and Trientalis europaea harbor contrasting root fungal endophytic communities

Fungal endophytic communities and potential host preference of root-inhabiting fungi of boreal forest understory plants are poorly known. The objective of this study was to find out whether two neighboring plant species, Deschampsia flexuosa (Poaceae) and Trientalis europaea (Primulaceae), share similar root fungal endophytic communities and whether the communities differ between two sites. The study was carried out by analysis of pure culture isolates and root fungal colonization percentages. A total of 84 isolates from D. flexuosa and 27 isolates from T. europaea were obtained. The roots of D. flexuosa harbored 16 different isolate types based on macromorphological characteristics, whereas only 4 isolate types were found in T. europaea. The root colonization by dark septate and hyaline septate hyphae correlated with isolate numbers being higher in D. flexuosa compared to T. europaea. The different isolate types were further identified on the basis of internal transcribed spacer sequence and phylogenetic analysis. An isolate type identified as dark septate endophyte Phialocephala fortinii colonized 50 % of the T. europaea and 21 % of the D. flexuosa specimens. In addition, Meliniomyces variabilis, Phialocephala sphaeroides, and Umbelopsis isabellina were found colonizing the grass, D. flexuosa, for the first time and Mycena sp. was confirmed as an endophyte of D. flexuosa. Site-specific differences were observed in the abundance and diversity of endophytic fungi in the roots of both study plants, but the differences were not as predominant as those between plant species. It is concluded that D. flexuosa harbors both higher amount and more diverse community of endophytic fungi in its roots compared to T. europaea.     

Fibrous carrot root responses to irrigation and compaction of sandy and organic soils

Field experiments were performed in Southern Finland on fine sand and organic soil in 1990 and 1991 to study carrot roots. Fall ploughed land was loosened by rotary harrowing to a depth of 20 cm or compacted under moist conditions to a depth of 25–30 cm by three passes of adjacent wheel tracks with a tractor weighing 3 Mg, in April were contiguously applied across the plot before seed bed preparation. Sprinkler irrigation (30 mm) was applied to fine sand when moisture in the 0–15 cm range of soil depth was 50% of plant-available water capacity. For root sampling, polyvinyl chloride (PVC) cylinders (30 × 60 cm) were installed in the rows of experimental plots after sowing, and removed at harvest. Six carrot plants were grown in each of in these soil colums in situ in the field.Fine root length and width were quantified by image analysis. Root length density (RLD) per plant was 0.2–1.0 cm cm^-3 in the 0–30 cm range. The fibrous root system of one carrot had total root lengths of 130–150 m in loose fine sand and 180–200 m in compacted fine sand. More roots were observed in irrigated than non-irrigated soils. In the 0–50 cm range of organic soil, 230–250 m of root length were removed from loosened organic soils and 240–300 m from compacted soils. Specific root surface area (surface area divided by dry root weight) of a carrot fibrous root system averaged 1500–2000 cm² g^-1. Root length to weight ratios of 250–350 m g^-1 effectively compare with the ratios of other species.Fibrous root growth was stimulated by soil compaction or irrigation to a depth of 30 cm, in both the fine sand and organic soils, suggesting better soil water supply in compacted than in loosened soils. Soil compaction increased root diameters more in fine sand than it did in organic soil. Most of the root length in loosened soils (fine sand 90%, organic soil 80%) and compacted soils (fine sand 80%, organic soil 75%) was composed of roots with diameters of approximately 0.15 mm. With respect to dry weight, length, surface area and volume of the fibrous root system, all the measurements gave significant resposes to irrigation and soil compaction. Total root volumes in the 0–50 cm of soil were 4.3 cm³ and 9.8 cm³ in loosened fine sand and organic soils, respectively, and 6.7 cm³ and 13.4 cm³ in compacted sand and organic soils, respectively. In fine sand, irrigation increased the volume from 4.8 to 6.3 cm³.     

Immunologgical self-tolerance in allophenic and embryo-aggregated mice

Allophenic mice, supposedly containing almost equal numbers of cells derived from embryos of mouse strains C57Bl and FVB, were shown in a recent paper to grow the B16 melanoma, a long transplanted tumor of C57Bl origin, much better than did mice of either the parental C57Bl strain or the C57Bl × FVB F1 hybrid. Mice containing smaller proportions of C57Bl cells rejected the tumor. A reconsideration of these suprising data, in light of the current literature, suggests that the better growth of the tumor in the 50-50% allophenics than in the C57Bl parental strain was almost certainly caused by the tumor stimulation engendered by a weak anti-C57Bl immune reaction in the overtly healthy allophenic mice.