Genome-wide selection of unique and valid oligonucleotides

Functional genomics methods are used to investigate the huge amount of information contained in genomes. Numerous experimental methods rely on the use of oligo- or polynucleotides. Nucleotide strand hybridization forms the underlying principle for these methods. For all these techniques, the probes should be unique for analyzed genes. In addition to being unique for the studied genes, the probes should fulfill a large number of criteria to be usable and valid. The criteria include for example, avoidance of self-annealing, suitable melting temperature and nucleotide composition. We developed a method for searching unique and valid oligonucleotides or probes for genes so that there is not even a similar (approximate) occurrence in any other location of the whole genome. By using probe size 25, we analyzed 17 complete genomes representing a wide range of both prokaryotic and eukaryotic organisms. More than 92% of all the genes in the investigated genomes contained valid oligonucleotides. Extensive statistical tests were performed to characterize the properties of unique and valid oligonucleotides. Unique and valid oligonucleotides were relatively evenly distributed in genes except for the beginning and end, which were somewhat overrepresented. The flanking regions in eukaryotes were clearly underrepresented among suitable oligonucleotides. In addition to distributions within genes, the effects on codon and amino acid usage were also studied.     

Some Factors Causing Mortality among Female Minks during the Puerperium and Lactation Periods

The purpose of this study, in which the farm was used as the statistical unit, was to find factors affecting mink mortality under farm conditions. Mortality was hypothesised to be affected by factors including, among others, variables describing the amount (level) and variation in composition and quality of the feed. Other explanatory variables applied in the study included farm size and age. Factor analyses were performed for variables of feed composition and quality in order to condense the variable information and to facilitate the selection of explanatory variables. This report presents a preliminary regression model for female mink mortality factors describing feed level and variation, and farm size, as explanatory variables. The regression model emphasized among other factors the importance of a constant albumin quality and a constant energy level.     

Non-native Fish Occurrence and Biomass in 1943 Western Palearctic Lakes and Reservoirs and their Abiotic and Biotic Correlates

Invasion of non-native species is considered a major threat to global biodiversity. Here we present a comprehensive overview of the occurrence, richness and biomass contribution of non-native fish species in 1943 standing water bodies from 14 countries of the Western Palearctic, based on standardised fish catches by multi-mesh gillnetting. We expected strong geographical gradients to emerge in the occurrence of non-natives. We further hypothesised that the contribution by non-natives to the local fish community biomass was correlated with local richness and the trophic level of native and non-native species. Non-native fish species occurred in 304 of 1943 water bodies (16%). If the average number of occupied water bodies per country was weighted by number of water bodies per country, the grand mean occurrence of non-natives in Western Palearctic water bodies was 10%. Exotic (non-native to the Palearctic) and translocated (non-native only to parts of the Palearctic) species were found in 164 (8.4%) or 235 (12.1%) of the water bodies, respectively. The occurrence and local richness of non-native fish species increased with temperature, precipitation and lake area and were substantially higher in reservoirs than in natural lakes. High local biomass contributions of non-native species were strongly correlated with low richness of native species and high richness of non-native species, whereas the trophic level of the fish species had only a weak effect. Single non-native species rarely dominated community biomass, but high biomass contributions and thus strong community and ecosystem impacts can be expected if several non-native species accumulate in a water body.     

A colcemid-sensitive mechanism involved in regulation of chromosome movements during meiotic pairing

Active movements of the chromosomes may be needed in the process, where homologous chromosomes find each other during the meiotic pairing. Because the components of the cytoskeleton are generally believed to be responsible for all movements in living nonmuscle cells, we have analyzed the regulation of the movements of zygotene chromosomes in the male rat by using specific inhibitors of the assembly of the various components of the cytoskeleton. — Colcemid, an inhibitor of microtubule formation, completely inhibited the chromosome movements in vitro at a concentration of 1 g/ml. This was associated with a damage of the nuclear envelope revealed by the electron microscopic analysis. Another inhibitor of microtubule formation, vinblastine, was ineffective below the level of general toxicity (100 g/ml). A specific microfilament inhibitor, cytochalasin B was similarly ineffective. — The findings suggest the presence of a specific colcemid-sensitive mechanism in the nuclear envelope of the zygotene spermatocytes, which regulates the movements of the chromosomes during meiotic pairing.     

Dye permeability and alkaline phosphatase activity of testicular capillaries in the postnatal rat

Summary Staining of testicular and epididymal tissues after intravenous, intraperitoneal or subcutaneous administration of a number of dyes was investigated in rats at different stages of postnatal development. After light green injections heavy staining of both testis and epididymis was visible to the naked eye in neonatal animals up to the age of 10 days, while in rats over 15 days old no appreciable staining of the testis could be seen, although the caput epididymis was strongly coloured. From 3–8 hours after subcutaneous acriflavine administration, the nuclei in the blood vessel walls of the testis, as well as the nuclei in the rete testis, tubuli efferentes and caput epididymis, fluoresced in all age groups. The nuclei of the interstitial and tubular cells were stained intensely until the age of 5 days. Thereafter the intensity gradually diminished until the age of 20 days, when no nuclear fluorescence was visible in the seminiferous tubules and even the interstitial nuclei fluoresced weakly or not at all.The histochemical alkaline phosphatase activity of the testicular capillaries was studied by Gomori's method, using fresh and postfixed cryostat sections from postnatal rat testes. The testicular capillaries exhibited appreciable activity at the age of 10 days.On the basis of the present and previous observations on the permeability of the testicular capillaries, the existence of a blood-testis barrier in the puberal and adult rat testis is suggested.Development of the blood-testis barrier and the alkaline phosphatase activity of the testicular capillaries are suggested to reflect general vascular maturation at the beginning of puberty in the rat.Supported by grants from Yrjö Jahnsson's Foundation and P. O. Klingendahl Foundation.     

Species–area relationships across four trophic levels – decreasing island size truncates food chains

That larger areas will typically host more diverse ecological assemblages than small ones has been regarded as one of the few fundamental ‘laws’ in ecology. Yet, area may affect not only species diversity, but also the trophic structure of the local ecological assemblage. In this context, recent theory on trophic island biogeography offers two clear‐cut predictions: that the slope of the species–area relationship should increase with trophic rank, and that food chain length (i.e. the number of trophic levels) should increase with area. These predictions have rarely been verified in terrestrial systems. To offer a stringent test of key theory, we focused on local food chains consisting of trophic specialists: plants, lepidopteran herbivores, and their primary and secondary parasitoids. For each of these four trophic levels, we surveyed species richness across a set of 20 off‐shore continental islands spanning a hundred‐fold range in size. We then tested three specific hypotheses: that species richness is affected by island size, that the slope of the species–area curve is related to trophic rank, and that such differences in slope translate into variation in food chain length with island size. Consistent with these predictions, estimates of the species–area slope steepened from plants through herbivores and primary parasitoids to secondary parasitoids. As a result of the elevated sensitivity of top consumers to island size, food chain length decreased from large to small islands. Since island size did not detectably affect the ratio between generalists and specialists among either herbivores (polyphages vs oligophages) or parasitoids (idiobionts vs koinobionts), the patterns observed seemed more reflective of changes in the overall number of nodes and levels in local food webs than of changes in their linking structure. Overall, our results support the trophic‐level hypothesis of island biogeography. Per extension, they suggest that landscape modification may imperil food web integrity and vital biotic interactions.     

Cloning,purification, kinetic and anion inhibition studies of a recombinant β-carbonic anhydrase from the Atlantic salmon parasite platyhelminth Gyrodactylus salaris

A β-class carbonic anhydrase (CA, EC 4.2.1.1) was cloned from the genome of the Monogenean platyhelminth Gyrodactylus salaris, a parasite of Atlantic salmon. The new enzyme, GsaCAβ has a significant catalytic activity for the physiological reaction, CO₂ + H₂O ⇋ HCO₃⁻ + H⁺ with a k_cat of 1.1 × 10⁵ s⁻¹ and a k_cat/K_m of 7.58 × 10⁶ M⁻¹ × s⁻¹. This activity was inhibited by acetazolamide (K_I of 0.46 µM), a sulphonamide in clinical use, as well as by selected inorganic anions and small molecules. Most tested anions inhibited GsaCAβ at millimolar concentrations, but sulfamide (K_I of 81 µM), N,N-diethyldithiocarbamate (K_I of 67 µM) and sulphamic acid (K_I of 6.2 µM) showed a rather efficient inhibitory action. There are currently very few non-toxic agents effective in combating this parasite. GsaCAβ is subsequently proposed as a new drug target for which effective inhibitors can be designed.     

Monitoring of in vivo function of superparamagnetic iron oxide labelled murine dendritic cells during anti-tumour vaccination

Dendritic cells (DCs) generated in vitro to present tumour antigens have been injected in cancer patients to boost in vivo anti-tumour immune responses. This approach to cancer immunotherapy has had limited success. For anti-tumour therapy, delivery and subsequent migration of DCs to lymph nodes leading to effective stimulation of effector T cells is thought to be essential. The ability to non-invasively monitor the fate of adoptively transferred DCs in vivo using magnetic resonance imaging (MRI) is an important clinical tool to correlate their in vivo behavior with response to treatment. Previous reports of superparamagnetic iron oxides (SPIOs) labelling of different cell types, including DCs, have indicated varying detrimental effects on cell viability, migration, differentiation and immune function. Here we describe an optimised labelling procedure using a short incubation time and low concentration of clinically used SPIO Endorem to successfully track murine DC migration in vivo using MRI in a mouse tumour model. First, intracellular labelling of bone marrow derived DCs was monitored in vitro using electron microscopy and MRI relaxometry. Second, the in vitro characterisation of SPIO labelled DCs demonstrated that viability, phenotype and functions were comparable to unlabelled DCs. Third, ex vivo SPIO labelled DCs, when injected subcutaneously, allowed for the longitudinal monitoring by MR imaging of their migration in vivo. Fourth, the SPIO DCs induced the proliferation of adoptively transferred CD4(+) T cells but, most importantly, they primed cytotoxic CD8(+) T cell responses to protect against a B16-Ova tumour challenge. Finally, using anatomical information from the MR images, the immigration of DCs was confirmed by the increase in lymph node size post-DC injection. These results demonstrate that the SPIO labelling protocol developed in this study is not detrimental for DC function in vitro and in vivo has potential clinical application in monitoring therapeutic DCs in patients with cancer.