A von Willebrand factor-binding protein from Staphylococcus lugdunensis

In the present study, a phage display library covering the genome of Staphylococcus lugdunensis, was affinity-selected against von Willebrand factor (vWf). This led to the identification of a gene, vwbl, encoding a putative cell surface protein of 2060 amino acids, denoted vWbl. The deduced protein has an overall organisation typical of staphylococcal cell surface proteins, with an N-terminal signal peptide, and a C-terminal cell wall sorting signal. The vWf-binding part is located in repetitive domains and antibodies against vWbl or vWf can inhibit the binding. Southern blot analysis showed that vwbl was present in the 12 S. lugdunensis strains tested.     

Silanized surfaces for in vitro studies of actomyosin function and nanotechnology applications

We have previously shown that selective heavy meromyosin (HMM) adsorption to predefined regions of nanostructured polymer resist surfaces may be used to produce a nanostructured in vitro motility assay. However, actomyosin function was of lower quality than on conventional nitrocellulose films. We have therefore studied actomyosin function on differently derivatized glass surfaces with the aim to find a substitute for the polymer resists. We have found that surfaces derivatized with trimethylchlorosilane (TMCS) were superior to all other surfaces tested, including nitrocellulose. High-quality actin filament motility was observed up to 6 days after incubation with HMM and the fraction of motile actin filaments and the velocity of smooth sliding were generally higher on TMCS than on nitrocellulose. The actomyosin function on TMCS-derivatized glass and nitrocellulose is considered in relation to roughness and hydrophobicity of these surfaces. The results suggest that TMCS is an ideal substitute for polymer resists in the nanostructured in vitro motility assay. Furthermore, TMCS derivatized glass also seems to offer several advantages over nitrocellulose for HMM adsorption in the ordinary in vitro motility assay.     

SNP typing by apyrase-mediated allele-specific primer extension on DNA microarrays

This study reports the development of a microarray-based allele-specific extension method for typing of single nucleotide polymorphisms (SNPs). The use of allele-specific primers has been employed previously to identify single base variations but it is acknowledged that certain mismatches are not refractory to extension. Here we have overcome this limitation by introducing apyrase, a nucleotide-degrading enzyme, to the extension reaction. We have shown previously that DNA polymerases exhibit slower reaction kinetics when extending a mismatched primer compared with a matched primer. This kinetic difference is exploited in the apyrase-mediated allele-specific extension (AMASE) assay, allowing incorporation of nucleotides when the reaction kinetics are fast but degrading the nucleotides before extension when the reaction kinetics are slow. Here we show that five homozygous variants (14% of the total number of variants) that were incorrectly scored in the absence of apyrase were correctly typed when apyrase was included in the extension reaction. AMASE was performed in situ on the oligonucleotide microarrays using fluorescent nucleotides to type 10 SNPs and two indels in 17 individuals generating approximately 200 genotypes. Cluster analysis of these data shows three distinct clusters with clear-cut boundaries. We conclude that SNP typing on oligonucleotide microarrays by AMASE is an efficient, rapid and accurate technique for large-scale genotyping.     

An experimental test of hybrid resistance to insects and pathogens using Salix caprea, S. repens and their F1 hybrids

The aim of this study was to assess the responses of herbivores and pathogens to hybrid plants under controlled conditions. F1 hybrids and parental species, produced by hand-pollinating willows in the field, were potted and kept in an experimental field under controlled conditions. In 1997, plant growth and survival were measured along with densities of insects and the degree of pathogen infection on the willows. The survival rate was higher for S. repens than for the hybrids and lowest for S. caprea. Densities of the sawflies Pontania pedunculi and P. brigmanii and the leaf-galling midge Iteomyia capreae were higher on hybrids and on S. caprea than on S. repens. The densities of Crepidodera fulvicornis (Chrysomelidae), chrysomelid larvae and the bud-galling midge Dasineura rosaria did not differ between any of the plant categories. Hybrids were more severely infected by rust (Melampsora sp.) than S. caprea and the totally resistant S. repens. Densities of herbivores on hybrid willows were consistent with the dominance hypothesis (i.e. herbivore densities were similar to densities on one of the parental species) or supported the no-difference hypothesis. Furthermore, herbivore densities on hybrid plants were most similar to densities on the more susceptible parent. The breakdown in rust resistance in hybrid plants suggests that resistance traits are severely disrupted by the genetic re-arrangement in hybrids and that this increased susceptibility could select against hybridisation. Received: 17 February 1998 / Accepted: 15 June 1998     

Inter‐annual variation in herring,Clupea harengus,and sprat,Sprattus sprattus,condition in the central Baltic Sea: what gives the tune?

The Baltic Sea ecosystem has undergone large changes during the last two decades, including a severe reduction in cod and herring biomass but, at the same time, a large increase in sprat abundance. The lower trophic levels of the Baltic Sea also changed due to environmental fluctuations, including variations in salinity and in volume of oxygenated water. In this apparently shifting environment, the conditions of herring and sprat have undergone large inter-annual variations during the past 15–20 years. In this study, we explore how abiotic factors (i.e. salinity and temperature) and biotic factors (biomass of the copepods Pseudocalanus elongatus , Temora longicornis , Acartia spp. and of cladocerans as well as clupeid abundance) in different seasons (May and August) affect clupeid body condition. Our analyses suggest that data of zooplankton biomass and abiotic factors in August have higher predictive power than May data. Although our analysis suggests that salinity (a bottom-up process) has an effect on sprat condition, total abundance of clupeids (a top-down process) is by far the most significant predictor of both herring and sprat condition. The strong correlation between clupeid abundance and total zooplankton biomass points to food competition and to top-down control by herring and sprat on common food resources. Furthermore, clupeid condition co-varied with the changes in the weight of zooplankton in the stomachs, which further suggest food competition being the main mechanism behind the changes in clupeid condition during the last two decades. Hence, our results are not in agreement with most of the current literature that has suggested that clupeid growth is regulated by environmentally mediated bottom-up processes acting on the abundance of copepods. This is, to our knowledge, the first evidence of food resources mediated density-dependent fish growth in a large marine ecosystem.     

A new member of the Balbiani ring multigene family in the dipteran Chironomus tentans consists of a single-copy version of a unit repeated in other gene family members

The known Balbiani ring (BR) multigene family members in the dipteran Chironomus tentans encode salivary gland secretory proteins in the size range between 38 and 1,000 kDa. The proteins interact to form protein fibers used by the aquatic larvae to spin feeding and protective larval tubes or pupation tubes. Here, we describe a new BR multigene family member, the spl7 gene, which codes for an 89-amino-acid-long protein with a relative mobility of 17k. The gene has a high content of charged amino acid residues and consists of two structurally different halves. Five regularly spaced cysteine codons are present in the 5 half while the 3 half contains five proline codons. These two different halves exhibit similarities to the C and SR regions, respectively, which form the tandemly repeated units in the about 40-kb-long BR genes and which also, in different versions, are the building blocks of all genes in the BR multigene family.In this multigene family, encoding interacting structural proteins, the long BR genes with their 125–150 tandemly arranged repeat units as well as the short sp17 gene with its single-copy version of such a repeat unit, have therefore evolved from a common ancestor.Correspondence to: L. Wieslander     

Reversible filamentous growth in the psychrophile Bacillus psychrophilus

At the near-maximum growth temperature of 32.5 °C, the psychrophile Bacillus psychrophilus loses the ability to septate and divide, resulting in the formation of filaments, which are four to six times longer than cells grown at 20 °C. DNA synthesis relative to growth occurs at the same rate both in the filaments at 32.5 °C, (which actually become multi-nucleated) and in normal-size cells at 20 °C, showing that the inhibition of DNA synthesis by the elevated temperature is not the cause of the filamentous growth, as has been found for other microorganisms. Similarly, temperature-sensitive cell-wall mucopeptide synthesis does not appear to be responsible. Reversal of filament production occurs when preformed filaments are incubated at 20 °C. Such reversal, i.e., septation of preformed filaments, requires the de novo synthesis of protein, probably throughout the reversal period.Filamentous cells are more nutritionally demanding than cells at 20 °C, with at least one substrate becoming limiting within 8 hr at 32.5 °C but not at 20 °C. However, such variation in nutritional requirement is not the cause of filament formation. KCl and NaCl stimulate cell division in cells growing at 32.5 °C but not in preformed filaments. Other membrane-active agents such as lysolecithin, dimethyl sulfoxide, ethanol, sodium oleate, and pantoyl lactone do not stimulate septum formation in filaments.     

Solving the heart mechanics equations with Newton and quasi Newton methods--a comparison

The non-linear elasticity equations of heart mechanics are solved while emulating the effects of a propagating activation wave. The dynamics of a 1 cm(3) slab of active cardiac tissue was simulated as the electrical wave traversed the muscular heart wall transmurally. The regular Newton (Newton-Raphson) method was compared to two modified Newton approaches, and also to a third approach that delayed update only of some selected Jacobian elements. In addition, the impact of changing the time step (0.01, 0.1 and 1 ms) and the relative non-linear convergence tolerance (10(-4), 10(-3) and 10(-2)) was investigated. Updating the Jacobian only when slow convergence occurred was by far the most efficient approach, giving time savings of 83-96%. For each of the four methods, CPU times were reduced by 48-90% when the time step was increased by a factor 10. Increasing the convergence tolerance by the same factor gave time savings of 3-71%. Different combinations of activation wave speed, stress rate and bulk modulus revealed that the fastest method became relatively even faster as stress rate and bulk modulus was decreased, while the activation speed had negligible influence in this respect.     

Molecular cloning and characterization of a cDNA encoding poplar UDP-glucose dehydrogenase,a key gene of hemicellulose/pectin formation

Plant UDP-glucose dehydrogenase (UGDH) is an important enzyme in the formation of hemicellulose and pectin, the components of newly formed cell walls. A cDNA clone (Ugdh) corresponding to UGDH was isolated from a cDNA library prepared from cambial zone of poplar (Populus tremula x tremuloides). Within the 1824-nucleotide (nt)-long clone, an open reading frame encoded a protein of 481 amino acids (aa), with a calculated molecular weight of 53.1 kDa. The derived aa sequence showed 90% and 63% identity with UGDHs from soybean and bovine liver, respectively, and had highly conserved aa motifs believed to be of importance for nt binding and catalytic efficiency. In poplar, the Ugdh corresponds to one or two genes, as found by genomic Southern analysis. The gene was expressed predominantly in differentiating xylem and young leaves, with little expression in the phloem zone of the stem. The expression pattern matched that of UGDH protein, as found by immunoblotting. In leaves, the Ugdh expression was upregulated by a short-term feeding with sucrose, sorbitol and polyethylene glycol, and this effect was to some extent mimicked by light exposure. The data suggest that Ugdh is regulated via an osmoticum-dependent pathway, possibly related to the availability of osmotically active carbohydrate precursors to UDP-glucose, a substrate of UGDH.     

Extensive linkage disequilibrium in small human populations in Eurasia

The extent of linkage disequilibrium (LD) was studied in two small food-gathering populations—Evenki and Saami—and two larger food-producing populations—Finns and Swedes—in northern Eurasia. In total, 50 single-nucleotide polymorphisms (SNPs) from five genes were genotyped using real-time pyrophosphate DNA sequencing, whereas 14 microsatellites were genotyped in two X-chromosomal regions. In addition, hypervariable region I of the mtDNA was sequenced to shed light on the demographic history of the populations. The SNP data, as well as the microsatellite data, reveal extensive levels of LD in Evenki and Saami when compared to Finns and Swedes. mtDNA-sequence variation is compatible with constant population size over time in Evenki and Saami but indicates population expansion in Finns and Swedes. Furthermore, the similarity between Finns and Swedes in SNP allele- and haplotype-frequency distributions indicate that these two populations may share a recent common origin. These findings suggest that populations such as the Evenki and the Saami, rather than the Finns, may be particularly suited for the initial coarse mapping of common complex diseases.