Expressionview: visualization of quantitative trait loci and gene-expression data in Ensembl

We present here a software tool for combined visualization of gene-expression data and quantitative trait loci (QTL). The application is implemented as an extension to the Ensembl project and caters for a direct transition from microarray experiments of gene or protein expression levels to the genomic context of individual genes and QTL. It supports the visualization of gene clusters and the selection of functional candidate genes in the context of research on complex traits.     

Mapping of Homologous Interaction Sites in the Hepatitis B Virus Core Protein

Hepatitis B virus consists of an outer envelope and an inner capsid, or core, that wraps around the small genome plus the viral replication enzyme. The icosahedrally symmetric nucleocapsid is assembled from multiple dimeric subunits of a single 183-residue capsid protein, which must therefore contain interfaces for monomer dimerization and for dimer multimerization. The atomic structure of the protein is not known, but electron microscopy-based image reconstructions suggested a hammerhead shape for the dimer and, very recently, led to a tentative model for the main chain trace. Here we used a combination of interaction screening techniques and functional analyses of core protein variants to define, at the primary sequence level, the regions that mediate capsid assembly. Both the two-hybrid system and the pepscan technique identified a strongly interacting region I between amino acids (aa) 78 and 117 that probably forms part of the dimer interface. Surprisingly, mutations in this region, in the context of a C-terminally truncated but assembly-competent core protein variant, had no detectable effect on assembly. By contrast, mutations in a second region, bordered by aa 113 and 143, markedly influenced capsid stability, strongly suggesting that this region II is the main contributor to dimer multimerization. Based on the electron microscopic data, it must therefore be located at the basal tips of the dimer, experimentally supporting the proposed main chain trace.     

Stomatocysts of Mallomonas hamata and M. heterospina (Mallomonadaceae, Synurophyceae) from South Swedish lakes

The stomato cysts of Mallomonas hamata and M. heterospina are described from lakes in South Sweden. These Mallomonas species develop cysts of similar appearance, size and form. Cyst formation for Mallomonas hamata was recorded at temperature 10–11°C and pH 5.9 and for M. heterospina at temperatures 4.2–11°C and pH 7.4. The cysts of M. hamata and M. heterospina are ovoid and easy to recognize, even with light microscopy, but difficult to distinguish from another. Thus their value as paleoindicators is limited, even if the two species have preference for waters of different nutrient and pH status.     

Assessing fragmentation and disturbance of west Kenyan rainforests by means of remotely sensed time series data and landscape metrics

Biodiversity in tropical rainforests is heavily influenced by land use/cover change (LUCC), but so far there have been few LUCC studies conducted in Africa. We present several methods that make use of remotely sensed data and landscape metrics and allow for assessment of the development of land cover and thus forest fragmentation and disturbance over a substantial period of time. The study covers Kakamega Forest and its associated forest areas in western Kenya, over the last 30 years. The accuracy of a supervised multispectral classification of Landsat time series data encompassing seven time steps between 1972 and 2001 is numerically assessed using ground truth reference data considering the 2001 time step. Here, buffering the forest areas by 1 km, highest user's accuracies for the forest classes ‘near natural + old secondary forest’ (87.50%), ‘secondary forest’ (80.00%) and ‘bushland/shrubs’ (81.08%) are revealed. Images of a spatially distributed fragmentation index derived from the land cover time series by applying a three by 3 pixel‐sized moving window to determine forest pixels’ adjacency, highlight trends in forest fragmentation, e.g. the splitting into two separate forests along the Yala/Ikuywa corridor. Calculations of mean fragmentation indices for the Biodiversity Monitoring Transect Analysis in Eastern Africa (BIOTA‐East Africa) focus research areas are used to evaluate the fragmentation index and to demonstrate its potential to extrapolate (e.g. biological) field findings in space and time. Here we argue for a correlation of the fragmentation indices results not only with forest management regimes, but with population distribution and accessibility (e.g. by roads). A cluster analysis applying the isodata‐algorithm on the classification results of all seven times steps allows for a rapid visual assessment of the distinct pattern of typical land cover development trends since 1972. This reveals that parts of Kakamega Forest have experienced severe forest loss while others, especially in the north‐east, show signs of succession.     

Importance of intermediate disturbances for the species composition and diversity of phytoplankton in two very different Berlin lakes

Species composition and diversity of phytoplankton were studied for several years in two lakes which differ with respect to mixing conditions and nutrient limitation: Schlachtensee regularly stratifies very stably. In contrast, size and wind-exposure predispose Lake Tegel to deeper mixing; additionally, stratification is artificially destabilized by aeration. As the duration of aeration was varied, the study period includes interannual changes in mixing conditions. For both lakes, it also covers trophic change due to restoration; this was especially pronounced in Schlachtensee.Results show that mixing conditions affect species composition on two levels: on a superordinate level, lake morphology or hydrology govern stability of stratification and susceptibility to perturbation, and hence the extent to which motile species can develop. In Schlachtensee, species with some means of actively seeking preferred depths usually dominated during summer stratification: Planktothrix agardhii during the hypertrophic phase, and flagellates since restoration. In contrast, in Lake Tegel deeper mixing as a generally prevailing condition favored non-motile species. Their seasonal pattern was remarkably constant from year to year. Although changes in the extent of mixing were pronounced during the four years studied (1987–1990), these were within a range that affected species composition only slightly: in summer, cyanobacteria and diatoms represented climax species whose dominance was not offset by additional, weather-induced increases of turbulence.On a subordinate level, and within the constraints set by nutrient limitation as well as by grazing pressure, small-scale changes in mixing conditions caused by meteorological cycles were shown to strongly affect species composition and in consequence diversity: Results for the fouryear post-restoration study period at Schlachtensee show that considerable interannual variations of species composition and diversity can be attributed to variations in the frequency of meteorological changes. In accordance with the intermediate disturbance hypothesis (IDH), diversity was lowest during 1989, the year with the longest and most pronounced cycles of fair weather (14 to 27 fair days on end). However, the mechanism for this was rarely a decline of diversity caused by competitive exclusion within single long phases of stable conditions, as conceived by the intermediate disturbance hypothesis. Instead, diversity responded to changes in mixing conditions with a variety of patterns — often with low values during phases of increased mixing and with high values under quiescent conditions, especially during the first calm days just after increased mixing. Thus, not disturbance as such, but rather the rate of change between phases of disturbance and quiescence appears to determine the frequency of high diversity indices.In Lake Tegel, high diversity indices were somewhat more frequent in 1989, the year during which thermal stratification was most stable. For species adapted to frequent or continuous mixing, interjected calm phases with unusually high stability of thermal stratification may represent a disturbance of accustomed conditions. Thus, in turbulent Lake Tegel, meteorological cycles appear to act in reversal to the IDH, in a sense which may be termed intermediate quiescence hypothesis.Phosphorus limitation due to successful restoration was found to decrease winter and vernal diversity in Schlachtensee. Presumably, without nutrient constraints, new populations could grow more rapidly in response to the rapid changes of physical parameters during this season. In contrast, restoration has increased summer diversity, as phosphorus concentrations no longer allow the virtual monocultures of Planktothrix agardhii which prevailed previously. In Lake Tegel, the reduction of phosphorus concentration down to 60 µg/l P in 1989 limited biomass, but this level was still too high to significantly alter species composition or diversity.     

Zur Rhabdomstruktur des Auges vonPieris brassicae L. (Insecta,Lepidoptera)

Zusammenfassung Die Anordnung der Microvilli im Rhabdom vonPieris brassicae L. wurde elektronenmikroskopisch untersucht und schematisch dargestellt. — Dieses Rhabdom ist zweireihig und gebändert. Sein außergewöhnlicher Habitus, seine Querschnittstypen 1 und 2 mit den im Winkel abwechselnden Microvillibündeln zweier sich gegenüberliegender Sehzellen im distalen Bereich werden im Gegensatz zu der einfach rechtwinklig orientierten Microvillibündelung im proximalen Rhabdombereich schematisch wiedergegeben. Die funktionelle Bedeutung dieser Rhabdomstruktur wird diskutiert. Außerdem werden die Rhabdome vonPieris brassicae undPieris protodice miteinander verglichen.

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Rhabdomstructure of the eye ofPieris brassicae L. (Insecta, Lepidoptera)

Summary The orientation of microvilli in the rhabdom ofPieris brassicae L. has been examined using electronmicroscopy and presented schematically. This rhabdom is tiered and banded. Its exceptional morphology, its transsectional types 1 and 2 where the microvilli-bundles of two opposing cells alternate at angle in its distal region are presented (diagrammatically) in contrast to the simple microvilli-bundles which are positioned at right angles within the proximal rhabdom. — The functional significance of this rhabdom-structure is discussed. A comparison was also made between the ultrastructure of rhabdoms ofPieris brassicae and that ofPieris protodice.

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Mit Unterstützung der Deutschen Forschungsgemeinschaft und der Stiftung Volkswagenwerk

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Herrn Prof. Dr. Dr. h.c. H. Autrum danke ich für kritische Durchsicht des Manuskripts, Frau G. Schwarz für gewissenhafte technische Mitarbeit und Frl. F. Althaus für die graphische Darstellung.     

Growth and malnutrition in Ethiopia

This article focuses on anthropometric parameters as height for age, weight for age and weight for height, which are among the most used tools for assessing well-being of infants and children. Such data have been collected between 1992--1993 from samples of infants and children aged between 2 and 10 years from urban and rural areas of Ethiopia. Similar to many other reports from developing countries the great amount of malnourished children is preoccupying as reflected by about 15% of children below the 5th centile of weight for height and about 53% of children below the 5th centile of height for age and about 45% below the 5th centile of weight for age.     

Nuclear ribosomal DNA and karyotypes indicate a NW African origin of South American Hypochaeris (Asteraceae, Cichorieae)

Hypochaeris has a disjunct distribution, with more than 15 species in the Mediterranean region, the Canary Islands, Europe, and Asia, and more than 40 species in South America. Previous studies have suggested that the New World taxa have evolved from ancestors similar to the central European H. maculata. Based on internal transcribed spacer (ITS) sequences and fluorescence in situ hybridization (FISH) with 5S and 18S-25S rDNA of the previously overlooked Hypochaeris angustifolia from Moyen Atlas, Morocco, we show that it is sister to the entire South American group. A biogeographic analysis supports the hypothesis of long-distance dispersal from NW Africa across the Atlantic Ocean for the origin of the South American taxa rather than migration from North America, through the Panamian land bridge, followed by subsequent extinction in North America. With the assumption of a molecular clock, the trans-Atlantic dispersal from NW Africa to South America is roughly estimated to have taken place during Pliocene or Pleistocene.