Toward pyrosequencing on surface-attached genetic material by use of DNA-binding luciferase fusion proteins

Mutation detection and single-nucleotide polymorphism genotyping require screening of large samples of materials and therefore the importance of high-throughput DNA analysis techniques is significant. Pyrosequencing is a four-enzyme bioluminometric DNA sequencing technology based on the sequencing-by-synthesis principle. Currently, the technique is limited to simultaneous analysis of 96 or 384 samples. Earlier, attempts to increase the sample capacity were made using micromachined filter chamber arrays where parallel analyses of nanoliter samples could be monitored in real time. We have developed a strategy for specific immobilization of the light-producing enzyme luciferase to the DNA template within a reaction chamber. By this approach, luciferase is genetically fused to a DNA-binding protein (Klenow polymerase or Escherichia coli single-stranded DNA-binding (SSB) protein) and to a purification handle (Z(basic)). The proteins are produced in E. coli and purified using cation and anion exchange chromatography with removal of Z(basic). The produced proteins have been analyzed using an assay for complete primer extension of DNA templates immobilized on magnetic beads detected by pyrosequencing chemistry. Results from these experiments show that the proteins bind selectively to the immobilized DNA and that their enzymatic domains were active. Z(basic)-SSB-luciferase produced the highest signal in this assay and was further exploited as enzymatic reagent for DNA sequencing.     

Distribution and oviposition preference of galling sawflies in arctic Canada

The distribution and ecology of insects in arctic regions are poorly known. The aim of this study was to determine the distribution of galling sawflies in the Canadian arctic and their oviposition preference. The Swedish Tundra Northwest 1999 expedition visited 17 sites in the Canadian arctic. We determined the occurrence of galling sawflies at all the sites and studied the oviposition preference of two leaf-galling sawflies, Eupontania arctica and Pontania nivalis, on Salix reticulata and S. glauca, respectively. Galling sawflies were abundant at only one site, the mainland site at Ivvavik National Park. Only a few galls in total were found at the remaining sites, suggesting that galling sawflies are rare in the higher arctic, and potential explanations for this pattern are discussed. Shoots with leaf galls were longer than shoots without galls on both S. reticulata and S. glauca. These differences could not be explained by a higher number of leaves on longer shoots. This suggests that long shoots are preferred by sawflies because of faster development and better survival of larvae on long shoots.     

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.     

Requirement for far-red light to maintain secondary needle extension growth in northern but not southern populations of Pinus sylvestris (Scots pine)

Extension growth of secondary needles is under photoperiodic control in Pinus sylvestris . To test for the effects of far-red light on maintaining this extension growth, seedlings of six populations originating from latitudes between 57° and 67°N were raised for 11 weeks in continuous incandescent (metal halogen) light at 300 µmol m⁻² s⁻¹ and 20°C and then transferred at the same temperature to a daily regime of 8 h incandescent light (230 µmol m⁻² s⁻¹) followed by a 16 h day extension with cool white fluorescent light (40 µmol m⁻² s⁻¹, R/FR ratio 7.5) or with incandescent lamps (20 µmol m⁻² s⁻¹, R/FR ratio 2.0). For the seedlings from the three populations north of 64°, needle extension growth over 42 days in the FR-poor day extension treatment was lower by up to 40% than in the FR-rich day extension treatment, whereas for the seedlings from the three southern populations the needle extension growth was similar in both day extension treatments. The requirement for FR in day extensions is characteristic of 'light-dominant' photoperiodic control mechanisms. It appears that P. sylvestris changes from dark-dominant night timekeeping to light-dominant day timekeeping with increasing latitude, as with the photoperiodic control of budset in Picea abies .     

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     

Photoperiodic reactions in conifer species

In Picea abies seedlings the critical night length for bud-set was determined for provenances from different latitudes, longitudes and altitudes within the natural range of the species. The clinal variation of this character was demonstrated. Inheritance studies indicated that this character is controlled by many genes with predominantly additive effects. In seedlings of Pinus sylvestris and Pinus contorta, growth cessation and bud-set took place in all light regimes, thus, even under continuous illumination. A photoperiodic optimum for height growth was determined. The photoperiodic influence on such characters as recurrent flushing of shoots, needle growth, dry matter production and frost resistance was demonstrated for northern and southern populations of the two Pinus species. Shorter nights were needed to induce a particular photoperiodic response in the northern populations as compared with those from the south. The importance of reliable phenological characters for assessing frost hardiness in provenance and progeny trials by means of early tests, is discussed.