A Fuzzy Logic Model to Describe the Cyanobacteria Nodularia spumigena Blooms in the Gulf of Finland, Baltic Sea

A fuzzy logic model to describe the seasonal evolution of Nodularia spumigena blooms in the Gulf of Finland was built and calibrated on the basis of monitoring data. The model includes three phosphate sources: excess phosphate after the annual spring bloom and parameterised phosphate transport to the upper mixed layer by turbulent mixing and upwelling events. Surface layer temperature and wind mixing form the physical conditions controlling the growth of N. spumigena. Model simulations revealed that phosphate input caused by turbulent mixing and upwelling have to be taken into account to achieve the best fit with observed data. Testing the fuzzy model for early prediction of maximum N. spumigena biomass about a month before the usual occurrence of blooms, gave good results. The potential use of the model for prediction of bloom risk at a certain location along the Estonian or Finnish coast was tested. The bloom transport velocities used in the fuzzy model were pre-calculated by a 3D numerical circulation model for different wind regimes.     

Fungal associates of <Emphasis Type="Italic">Pyrola rotundifolia</Emphasis>, a mixotrophic Ericaceae,from two Estonian boreal forests

Pyrola rotundifolia (Ericaceae, Pyroleae tribe) is an understorey subshrub that was recently demonstrated to receive considerable amount of carbon from its fungal mycorrhizal associates. So far, little is known of the identity of these fungi and the mycorrhizal anatomy in the Pyroleae. Using 140 mycorrhizal root fragments collected from two Estonian boreal forests already studied in the context of mixotrophic Ericaceae in sequence analysis of the ribosomal DNA internal transcribed spacer region, we recovered 71 sequences that corresponded to 45 putative species in 19 fungal genera. The identified fungi were mainly ectomycorrhizal basidiomycetes, including Tomentella, Cortinarius, Russula, Hebeloma, as well as some ectomycorrhizal and/or endophytic ascomycetes. The P. rotundifolia fungal communities of the two forests did not differ significantly in terms of species richness, diversity and nutritional mode. The relatively high diversity retrieved suggests that P. rotundifolia does not have a strict preference for any fungal taxa. Anatomical analyses showed typical arbutoid mycorrhizae, with variable mantle structures, uniseriate Hartig nets and intracellular hyphal coils in the large epidermal cells. Whenever compared, fungal ultrastructure was congruent with the molecular identification. Similarly to other mixotrophic and autotrophic pyroloids in the same forests, P. rotundifolia shares its mycorrhizal fungal associates with surrounding trees that are likely a carbon source for pyroloids.     

Potential applications of equine genomics in dissecting diseases and fertility

Following the recent development of high-resolution gene maps and generation of several basic tools and resources to use them in analyzing traits that are economically important to horse owners, genome analysis in horses is witnessing a shift towards developing an ability to analyze complex traits. The likelihood of this happening in the very near future is great, mainly because of the recent availability of the whole genome sequence in the horse. The latter has triggered the development of novel tools like SNP-chip and expression arrays that will permit rapid genome-wide analysis. While these tools will be used for a range of multi-factorial disease traits, attempts are underway to develop focused tools that can target reproduction, fertility and sex determination. For this, a catalog of sex and reproduction related (SRR) genes is being developed in horses. A recently developed dense map of the horse Y chromosome will provide genes that are expressed exclusively in males and, therefore, have an impact on stallion fertility. Overall, these advances in equine genome analysis hold promise for improved diagnosis and treatment of various conditions in horses.     

Abiotic factors influencing cyanobacterial bloom development in the Gulf of Finland (Baltic Sea)

Blooms of cyanobacteria are a recurrent phenomenon in the Baltic Sea, including the Gulf of Finland. The spatial extension, duration, intensity and species composition of these blooms varies widely between years. Alg@line data collected regularly from ferries as well as weather service and marine monitoring data from 1997 to 2005 are analysed to determine the main abiotic factors influencing the intensity and species composition of cyanobacterial blooms in the Gulf of Finland. It is demonstrated that the development of the Nodularia spumigena Mertens bloom is highly dependent on weather conditions such as photosynthetically active radiation and water temperature. Nutrient conditions, especially the surplus of phosphorus (according to Redfield ratio) related to the pre-bloom upwelling events in the Gulf, affect the intensity of Aphanizomenon sp. (L.) Ralfs blooms. Differences in bloom timing and duration indicate that, if the preconditions (like nutrient ratio/concentration and weather conditions) for bloom formation are favourable, then the Aphanizomenon bloom starts earlier, the overall bloom period is longer and the Nodularia peak might appear in a wider time window. Handling editor: K. Martens     

Global biogeography of the ectomycorrhizal /sebacina lineage (Fungi,Sebacinales) as revealed from comparative phylogenetic analyses

Compared with plants and animals, large‐scale biogeographic patterns of microbes including fungi are poorly understood. By the use of a comparative phylogenetic approach and ancestral state reconstructions, we addressed the global biogeography, rate of evolution and evolutionary origin of the widely distributed ectomycorrhizal (EcM) /sebacina lineage that forms a large proportion of the Sebacinales order. We downloaded all publicly available internal transcribed spacer (ITS) sequences and metadata and supplemented sequence information from three genes to construct dated phylogenies and test biogeographic hypotheses. The /sebacina lineage evolved 45–57 Myr ago that groups it with relatively young EcM taxa in other studies. The most parsimonious origin for /sebacina is inferred to be North American temperate coniferous forests. Among biogeographic traits, region and biome exhibited stronger phylogenetic signal than host family. Consistent with the resource availability (environmental energy) hypothesis, the ITS region is evolving at a faster rate in tropical than nontropical regions. Most biogeographic regions exhibited substantial phylogenetic clustering suggesting a strong impact of dispersal limitation over a large geographic scale. In northern Holarctic regions, however, phylogenetic distances and phylogenetic grouping of isolates indicate multiple recent dispersal events.     

Body movements and their role as triggers of heartbeats in pupae of the Colorado potato beetle Leptinotarsa decemlineata

Rhythmic body movements and their role as triggers of intermittent heartbeats were studied in pupae of Leptinotarsa decemlineata Say. Heartbeats and body movements were recorded simultaneously by means of an optical method (infra‐red cardiography) combined with respirometry. IR‐cardiography allows heartbeats and body movements to be distinguished on the basis of their different rates (40–80 min^?1 and 4–8 min^?1, respectively) and amplitude. In the mid‐interecdysial period, abdominal movements in the pupae were always accompanied by heart activity beginning after the first 5–12 abdominal strokes. Simultaneous periods of abdominal movements and heartbeats lasted 2–5 min, while the intervening pause ranged from 40 to 72 min at 24°C. Experiments of forced heart activity showed that a slight external tactile stimulus (prodding once with a single hair), applied prior to an expected heartbeat bout, evoked abdominal movements followed soon afterwards by contractions of the dorsal vessel. Repeated prodding with a hair evoked body rotating movements (1–3 strokes) at any time with heartbeats starting at the first movement. We surmise that rhythmic body movements play an active role in the triggering of heart activity in pupae according to the principle of cardiac reflex response. This is a possible mechanism for synchronizing periods of heart activity with periods of rhythmic body movements. Haemolymph circulation in pupae is favoured when heartbeat bouts are accompanied by active body movements.     

Large-scale production of dsRNA and siRNA pools for RNA interference utilizing bacteriophage phi6 RNA-dependent RNA polymerase

The discovery of RNA interference (RNAi) has revolutionized biological research and has a huge potential for therapy. Since small double-stranded RNAs (dsRNAs) are required for various RNAi applications, there is a need for cost-effective methods for producing large quantities of high-quality dsRNA. We present two novel, flexible virus-based systems for the efficient production of dsRNA: (1) an in vitro system utilizing the combination of T7 RNA polymerase and RNA-dependent RNA polymerase (RdRP) of bacteriophage 6 to generate dsRNA molecules of practically unlimited length, and (2) an in vivo RNA replication system based on carrier state bacterial cells containing the 6 polymerase complex to produce virtually unlimited amounts of dsRNA of up to 4.0 kb. We show that pools of small interfering RNAs (siRNAs) derived from dsRNA produced by these systems significantly decreased the expression of a transgene (eGFP) in HeLa cells and blocked endogenous pro-apoptotic BAX expression and subsequent cell death in cultured sympathetic neurons.     

Low genetic polymorphism in the re-introduced Eurasian beaver (Castor fiber) population in Finland: implications for conservation

Mammal Research - Reduction of genetic diversity can lead to reduced fitness of species, such as the loss of adaptability to changing environments. The native Eurasian beaver (Castor fiber) was...     

Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.