Search

The current Finnish public hospitals’ eHealth services are organization-oriented rather than patient-oriented. Patients remain passive and use eHealth services that are designed by private or governmental organizations. Patients had little or no involvement in that process. This paper introduces a novel eHealth Services Model that can be used as a tool to capture the needs of both organizations and patients. Two eHealth services were used to verify and support the validity of the presented model. The first eHealth service features came from an existing Finnish eHealth service that was designed by a Finnish organization. The second eHealth service features have been derived from the collected patients’ feedback. A survey was carried out to compare the selected two eHealth services features. The finding of this paper suggests that an eHealth service with features that capture patients’ needs is favorable against the eHealth service features that came from a Finnish organization. The presented model is a long-term solution that can be utilized in designing and providing the right technologies and services that will continuously satisfy the needs of patients and organizations. publishedVersion

Nitrate input to a river is largely controlled by land use in its catchment. We compared the information carried by the isotopic signatures of nitrate in 12 Baltic rivers, in relation to the vegetation cover, land use, and fertilization of agricultural land of their catchments. We found isotope values in nitrate ranging from −2 to 14‰ for δ15N and 8 to 25‰ for δ18O. The annual variability of riverine nitrate isotope signatures is presented in detail for one Nordic, the Kemijoki, and two southern rivers, the Vistula and Oder. Nordic rivers with relatively pristine vegetation in their catchments show not only low δ15N values and high δ18O-NO3− but also lower annual variability than rivers draining densely populated land. Seasonal signals were found in all the rivers. We used load weighted nitrate isotope data and data from the three major N sources (farmland/sewage, atmospheric deposition and from runoff of pristine soils) to theoretically estimate the shares of nitrate from these sources. The results of an isotope mixing model (IMM-1) agree reasonably well with the same estimates for agricultural land derived from a Global Land Cover (GLC) data base, with a deviation varying from −16% to +26%. The comparison with an emission model (EM) reveals relatively good agreements for intensively used catchments (−18 to +18% deviation). Rather unsatisfactory agreement was found between the IMM-1 and GLC calculations for pristine catchments (−36 to +50% deviation). Advantages and limitations of the tested model are discussed.

Cyanolichens are obligate symbioses between fungi and cyanobacteria. They occur in many types of environments ranging from Arctic tundra and semi-deserts to tropical rainforests. Possibly even a majority of their global species diversity has not yet been described. Symbiotic cyanobacteria provide both photosynthate and fixed nitrogen to the fungal host and the relative importance of these functions differs in different cyanolichens. The cyanobiont can either be the sole photosynthetic partner or a secondary symbiont in addition to a primary green algal photobiont. In addition, the cyanolichen thallus may incorporate a plethora of other microorganisms. The fungal symbionts in cyanolichens are almost exclusively ascomycetes. Nostoc is by far the most commonly encountered cyanobacterial genus. While the cyanobacterial symbionts are presently not readily identifiable to species, molecular methods work well on the generic level and offer practical means for identifying symbiotic cyanobacterial genotypes. The present diversity of lichen cyanobionts may partly reflect the evolutionary effects of their lichen-symbiotic way of life and dispersal.

The degradation of organic matter to CH4 and CO2 was investigated in three different boreal peatland systems in Finland, a mesotrophic fen (MES), an oligotrophic fen (OLI), and an ombrotrophic peat (OMB). MES had similar production rates of CO2 and CH4, but the two nutrient-poor peatlands (OLI and OMB) produced in general more CO2 than CH4. δ13C analysis of CH4 and CO2 in the presence and absence methyl fluoride (CH3F), an inhibitor of acetoclastic methanogenesis, showed that CH4 was predominantly produced by hydrogenotrophic methanogenesis and that acetoclastic methanogenesis only played an important role in MES. These results, together with our observations concerning the collective inhibition of CH4 and CO2 production rates by CH3F, indicate that organic matter was degraded through different paths in the mesotrophic and the nutrient-poor peatlands. In the mesotrophic fen, the major process is canonical fermentation followed by acetoclastic and hydrogenotrophic methanogenesis, while in the nutrient-poor peat, organic matter was apparently degraded to a large extent by a different path which finally involved hydrogenotrophic methanogenesis. Our data suggest that degradation of organic substances in the oligotrophic environments was incomplete and involved the use of organic compounds as oxidants.

To test the reliability of the radiocarbon method for determining root age, we analyzed fine roots (originating from the years 1985 to 1993) from ingrowth cores with known maximum root age (1 to 6 years old). For this purpose, three Scots pine (Pinus sylvestris L.) stands were selected from boreal forests in Finland. We analyzed root 14C age by the radiocarbon method and compared it with the above-mentioned known maximum fine root age. In general, ages determined by the two methods (root 14C age and ingrowth core root maximum age) were in agreement with each other for roots of small diameter (

The genus Diphyscium (Diphysciaceae, Bryophyta) has three species in the Hunan Province of China: D. fulvifolium Mitt., D. mucronifolium Mitt, and D. chiapense D.H. Norris subsp. unipapillosum (Deguchi) T.-Y. Chiang & S.-H. Lin. Diphyscium fulvifolium is clearly the most common species. The other two taxa are reported for the first time from Hunan, and D. chiapense subsp. unipapillosum also from Jiangxi; in China, it was previously known only from Taiwan. The three species are illustrated in line drawings. A previous record of D. foliosum (Hedw.) Mohr was based on a misidentified specimen and the species is thus excluded from the flora of Hunan.

We show that the putative N-peptide binding area in Sec1p domain 1 is important for Mso1p binding and that Mso1p can interact with Sso1p and Sso2p. Our results suggest that Mso1p mimics N-peptide binding to facilitate membrane fusion., Sec1p/Munc18 (SM) family proteins regulate SNARE complex function in membrane fusion through their interactions with syntaxins. In addition to syntaxins, only a few SM protein interacting proteins are known and typically, their binding modes with SM proteins are poorly characterized. We previously identified Mso1p as a Sec1p-binding protein and showed that it is involved in membrane fusion regulation. Here we demonstrate that Mso1p and Sec1p interact at sites of exocytosis and that the Mso1p–Sec1p interaction site depends on a functional Rab GTPase Sec4p and its GEF Sec2p. Random and targeted mutagenesis of Sec1p, followed by analysis of protein interactions, indicates that Mso1p interacts with Sec1p domain 1 and that this interaction is important for membrane fusion. In many SM family proteins, domain 1 binds to a N-terminal peptide of a syntaxin family protein. The Sec1p-interacting syntaxins Sso1p and Sso2p lack the N-terminal peptide. We show that the putative N-peptide binding area in Sec1p domain 1 is important for Mso1p binding, and that Mso1p can interact with Sso1p and Sso2p. Our results suggest that Mso1p mimics N-peptide binding to facilitate membrane fusion.

This study aimed at examining whether plant species of varying resource quality give rise to a fungal- or bacterial-based energy channel in the plants' rhizosphere, when planted in soil, in which the plant species naturally occur. In an 18-month large-scale laboratory mesocosm experiment, two plant species (Holcus lanatus and Lotus corniculatus) producing labile litter and two plant species (Picea abies and Calluna vulgaris) producing recalcitrant litter were placed in the same mesocosm. This allowed the decomposer biota (microbes, protozoa, nematodes, collembolans, and enchytraeid worms) to freely choose their preferred plant rhizosphere. Because a fungal-based energy channel is in theory regarded to retain nutrients better in the soil than a bacterial-based energy channel, water was collected underneath the plant species and analyzed for its nutrient (N and P) content. In general, the number of soil biota groups responding significantly to the plant treatment increased with time. Soil microbes were the first group to react, but the ability of the plants to boost a clearly fungal- or bacterial-based energy channel was generally weak. However, at the end of the study, a higher fungal-to-bacterial biomass ratio was found beneath Calluna than beneath the other plant treatments. Of the secondary consumers, nematodes were the most responsive group, with total number and especially plant parasites being more abundant beneath Lotus than beneath Picea and Calluna indicating a root-based energy channel to persist under the legume. Protozoa, enchytraeid worms and collembolans responded weakly and inconsistently to plant treatment. Liberation of plant-available nutrients was plant-dependent. Towards the end of the study, less nitrate and phosphate leached through the Picea soils than through the control, which indicates a more effective nutrient retention to take place under this plant species. We found that plant species can, in a relatively short time, modify the composition of the soil decomposer community. However, no consistent evidence for the plant-soil systems developing to separated detritus energy channels emerged, we found a clearly separated root energy channel under the legume L. corniculatus.

Northern plants have to cope with a wide range of overwintering conditions, as the depth and physical properties of snow show high spatial variation in the Arctic. The overwintering of lingonberry (Vaccinium vitis-idaea) was studied in a reciprocal transplantation experiment between two sub-Arctic microhabitats in northern Finland. The experiment was set up in the autumn, and physiological traits related to overwintering were measured at the time of snowmelt in the following spring. The origin of the plants was not a significant source of variation for most of the traits measured, whereas major differences were observed between the two sites. Plants that overwintered at an exposed site above the treeline showed high relative winter damage, assessed by the electrolyte leakage of the leaves. No severe winter damage was observed in the plants that overwintered under a moderate snowpack at a sheltered birch forest site. These plants were able to maintain their photosynthetic capacity through the winter. A low capacity of photosystem II and a very low capacity of CO2 uptake were characteristic of the exposed site, where low temperatures and high irradiation predominate during late winter. However, photosynthetic capacity was recovered within a few days when the plants were kept under favourable conditions after the field experiment. The content of nonstructural carbohydrates was low, probably because of high respiratory losses under the snow. This short-term study suggests that lingonberry, which occupies a wide range of microhabitats in the present climate, may thrive even if the overwintering conditions change as a result of climatic warming.

Reactive oxygen species (ROS) have important functions in plant stress responses and development. In plants, ozone and pathogen infection induce an extracellular oxidative burst that is involved in the regulation of cell death. However, very little is known about how plants can perceive ROS and regulate the initiation and the containment of cell death. We have identified an Arabidopsis thaliana protein, GRIM REAPER (GRI), that is involved in the regulation of cell death induced by extracellular ROS. Plants with an insertion in GRI display an ozone-sensitive phenotype. GRI is an Arabidopsis ortholog of the tobacco flower-specific Stig1 gene. The GRI protein appears to be processed in leaves with a release of an N-terminal fragment of the protein. Infiltration of the N-terminal fragment of the GRI protein into leaves caused cell death in a superoxide-and salicylic acid-dependent manner. Analysis of the extracellular GRI protein yields information on how plants can initiate ROS-induced cell death during stress response and development. Reactive oxygen species (ROS) have important functions in plant stress responses and development. In plants, ozone and pathogen infection induce an extracellular oxidative burst that is involved in the regulation of cell death. However, very little is known about how plants can perceive ROS and regulate the initiation and the containment of cell death. We have identified an Arabidopsis thaliana protein, GRIM REAPER (GRI), that is involved in the regulation of cell death induced by extracellular ROS. Plants with an insertion in GRI display an ozone-sensitive phenotype. GRI is an Arabidopsis ortholog of the tobacco flower-specific Stig1 gene. The GRI protein appears to be processed in leaves with a release of an N-terminal fragment of the protein. Infiltration of the N-terminal fragment of the GRI protein into leaves caused cell death in a superoxide-and salicylic acid-dependent manner. Analysis of the extracellular GRI protein yields information on how plants can initiate ROS-induced cell death during stress response and development. Reactive oxygen species (ROS) have important functions in plant stress responses and development. In plants, ozone and pathogen infection induce an extracellular oxidative burst that is involved in the regulation of cell death. However, very little is known about how plants can perceive ROS and regulate the initiation and the containment of cell death. We have identified an Arabidopsis thaliana protein, GRIM REAPER (GRI), that is involved in the regulation of cell death induced by extracellular ROS. Plants with an insertion in GRI display an ozone-sensitive phenotype. GRI is an Arabidopsis ortholog of the tobacco flower-specific Stig1 gene. The GRI protein appears to be processed in leaves with a release of an N-terminal fragment of the protein. Infiltration of the N-terminal fragment of the GRI protein into leaves caused cell death in a superoxide-and salicylic acid-dependent manner. Analysis of the extracellular GRI protein yields information on how plants can initiate ROS-induced cell death during stress response and development.

"Single-nucleotide polymorphisms (SNPs) in the 30 region of myosin IXB (MYO9B) gene have recently been reported to associate with different inflammatory or autoimmune diseases. We monitored for the association of MYO9B variants to multiple sclerosis (MS) in four Northern European populations. First, 18 SNPs including 6 SNPs with previous evidence for association to immune disorders, were tested in 730 Finnish MS families, but no linkage or family-based association was observed. To ensure the power to detect variants with a modest effect size, we further analyzed 10 variants in 899 Finnish cases and 1325 controls, and in a total of 1521 cases and 1476 controls from Denmark, Norway and Sweden, but found no association. Our results thereby do not support a major function of the tested MYO9B variants in MS. European Journal of Human Genetics (2009) 17, 840-843; doi: 10.1038/ejhg.2008.251; published online 14 January 2009" "Single-nucleotide polymorphisms (SNPs) in the 30 region of myosin IXB (MYO9B) gene have recently been reported to associate with different inflammatory or autoimmune diseases. We monitored for the association of MYO9B variants to multiple sclerosis (MS) in four Northern European populations. First, 18 SNPs including 6 SNPs with previous evidence for association to immune disorders, were tested in 730 Finnish MS families, but no linkage or family-based association was observed. To ensure the power to detect variants with a modest effect size, we further analyzed 10 variants in 899 Finnish cases and 1325 controls, and in a total of 1521 cases and 1476 controls from Denmark, Norway and Sweden, but found no association. Our results thereby do not support a major function of the tested MYO9B variants in MS. European Journal of Human Genetics (2009) 17, 840-843; doi: 10.1038/ejhg.2008.251; published online 14 January 2009" "Single-nucleotide polymorphisms (SNPs) in the 30 region of myosin IXB (MYO9B) gene have recently been reported to associate with different inflammatory or autoimmune diseases. We monitored for the association of MYO9B variants to multiple sclerosis (MS) in four Northern European populations. First, 18 SNPs including 6 SNPs with previous evidence for association to immune disorders, were tested in 730 Finnish MS families, but no linkage or family-based association was observed. To ensure the power to detect variants with a modest effect size, we further analyzed 10 variants in 899 Finnish cases and 1325 controls, and in a total of 1521 cases and 1476 controls from Denmark, Norway and Sweden, but found no association. Our results thereby do not support a major function of the tested MYO9B variants in MS. European Journal of Human Genetics (2009) 17, 840-843; doi: 10.1038/ejhg.2008.251; published online 14 January 2009"

As part of the effort to find better cellulases for bioethanol production processes, we were looking for novel GH‐7 family cellobiohydrolases, which would be particularly active on insoluble polymeric substrates and participate in the rate‐limiting step in the hydrolysis of cellulose. The enzymatic properties were studied and are reported here for family 7 cellobiohydrolases from the thermophilic fungi Acremonium thermophilum, Thermoascus aurantiacus, and Chaetomium thermophilum. The Trichoderma reesei Cel7A enzyme was used as a reference in the experiments. As the native T. aurantiacus Cel7A has no carbohydrate‐binding module (CBM), recombinant proteins having the CBM from either the C. thermophilum Cel7A or the T. reesei Cel7A were also constructed. All these novel acidic cellobiohydrolases were more thermostable (by 4–10°C) and more active (two‐ to fourfold) in hydrolysis of microcrystalline cellulose (Avicel) at 45°C than T. reesei Cel7A. The C. thermophilum Cel7A showed the highest specific activity and temperature optimum when measured on soluble substrates. The most effective enzyme for Avicel hydrolysis at 70°C, however, was the 2‐module version of the T. aurantiacus Cel7A, which was also relatively weakly inhibited by cellobiose. These results are discussed from the structural point of view based on the three‐dimensional homology models of these enzymes.

Whether sediments act as sinks or sources of nutrients depends partly on the oxygen conditions at the seafloor. Laboratory experiments on coastal Gulf of Finland (Baltic Sea) sediment tested the sensitivity of denitrification to a 2 wk anoxia exposure and subsequent reoxidation of the bottom waters. At the same time we followed the rapidly (1 d) and more slowly (9 d) emerging changes in different forms of sediment P after oxic conditions were restored. The total denitrification rate (Dtot) did not change during anoxic incubation, but shifted from coupled nitrification-denitrification (Dn) towards water column nitrate dependence (Dw). As the Dn rate did not decrease at the same rate as the Dw rate increased, the overall effect of 2 wk exposure to anoxia was an increase in Dtot rate. Nitrification was enhanced in the manipulated sediment compared to natural conditions, despite anoxia. Anoxia quickly caused a release of dissolved P from its 2 most labile forms. The effect was readily reversible, but in nature the replenishment of oxygen stores is usually linked to an intense mixing of the water column, and it is possible that part of the P released during anoxia reaches the productive layer. In our experiments, anoxia affected P cycling more than N cycling. Whether sediments act as sinks or sources of nutrients depends partly on the oxygen conditions at the seafloor. Laboratory experiments on coastal Gulf of Finland (Baltic Sea) sediment tested the sensitivity of denitrification to a 2 wk anoxia exposure and subsequent reoxidation of the bottom waters. At the same time we followed the rapidly (1 d) and more slowly (9 d) emerging changes in different forms of sediment P after oxic conditions were restored. The total denitrification rate (Dtot) did not change during anoxic incubation, but shifted from coupled nitrification-denitrification (Dn) towards water column nitrate dependence (Dw). As the Dn rate did not decrease at the same rate as the Dw rate increased, the overall effect of 2 wk exposure to anoxia was an increase in Dtot rate. Nitrification was enhanced in the manipulated sediment compared to natural conditions, despite anoxia. Anoxia quickly caused a release of dissolved P from its 2 most labile forms. The effect was readily reversible, but in nature the replenishment of oxygen stores is usually linked to an intense mixing of the water column, and it is possible that part of the P released during anoxia reaches the productive layer. In our experiments, anoxia affected P cycling more than N cycling. Whether sediments act as sinks or sources of nutrients depends partly on the oxygen conditions at the seafloor. Laboratory experiments on coastal Gulf of Finland (Baltic Sea) sediment tested the sensitivity of denitrification to a 2 wk anoxia exposure and subsequent reoxidation of the bottom waters. At the same time we followed the rapidly (1 d) and more slowly (9 d) emerging changes in different forms of sediment P after oxic conditions were restored. The total denitrification rate (Dtot) did not change during anoxic incubation, but shifted from coupled nitrification-denitrification (Dn) towards water column nitrate dependence (Dw). As the Dn rate did not decrease at the same rate as the Dw rate increased, the overall effect of 2 wk exposure to anoxia was an increase in Dtot rate. Nitrification was enhanced in the manipulated sediment compared to natural conditions, despite anoxia. Anoxia quickly caused a release of dissolved P from its 2 most labile forms. The effect was readily reversible, but in nature the replenishment of oxygen stores is usually linked to an intense mixing of the water column, and it is possible that part of the P released during anoxia reaches the productive layer. In our experiments, anoxia affected P cycling more than N cycling.

Benthic processes were measured at a coastal deposition area in the northern Baltic Sea, covering all seasons. The N-2 production rates, 90-400 mu mol N m(-2) d(-1), were highest in autumn-early winter and lowest in spring. Heterotrophic bacterial production peaked unexpectedly late in the year, indicating that in addition to the temperature, the availability of carbon compounds suitable for the heterotrophic bacteria also plays a major role in regulating the denitrification rate. Anaerobic ammonium oxidation (anammox) was measured in spring and autumn and contributed 10% and 15%, respectively, to the total N-2 production. The low percentage did, however, result in a significant error in the total N-2 production rate estimate, calculated using the isotope pairing technique. Anammox must be taken into account in the Gulf of Finland in future sediment nitrogen cycling research. Benthic processes were measured at a coastal deposition area in the northern Baltic Sea, covering all seasons. The N-2 production rates, 90-400 mu mol N m(-2) d(-1), were highest in autumn-early winter and lowest in spring. Heterotrophic bacterial production peaked unexpectedly late in the year, indicating that in addition to the temperature, the availability of carbon compounds suitable for the heterotrophic bacteria also plays a major role in regulating the denitrification rate. Anaerobic ammonium oxidation (anammox) was measured in spring and autumn and contributed 10% and 15%, respectively, to the total N-2 production. The low percentage did, however, result in a significant error in the total N-2 production rate estimate, calculated using the isotope pairing technique. Anammox must be taken into account in the Gulf of Finland in future sediment nitrogen cycling research. Benthic processes were measured at a coastal deposition area in the northern Baltic Sea, covering all seasons. The N-2 production rates, 90-400 mu mol N m(-2) d(-1), were highest in autumn-early winter and lowest in spring. Heterotrophic bacterial production peaked unexpectedly late in the year, indicating that in addition to the temperature, the availability of carbon compounds suitable for the heterotrophic bacteria also plays a major role in regulating the denitrification rate. Anaerobic ammonium oxidation (anammox) was measured in spring and autumn and contributed 10% and 15%, respectively, to the total N-2 production. The low percentage did, however, result in a significant error in the total N-2 production rate estimate, calculated using the isotope pairing technique. Anammox must be taken into account in the Gulf of Finland in future sediment nitrogen cycling research.

The swarming behaviour of a Baltic littoral mysid shrimp, Neomysis integer, was studied both in the presence and absence of a predator (European perch, Perca fluviatilis L.). I performed two kinds of laboratory experiments. First, the swarming tendency of mysids and the effect of swarm size on swarm choice were studied. Second, the ingestion rate of mysids was measured when feeding alone versus in a swarm. The results indicate that N. integer actively join swarms. The avoidance of the perch by N. integer individuals was stronger when there was a swarm present. Larger swarms were preferred over smaller ones regardless of presence or absence of the predator. The overall feeding rate was similar when feeding alone and in swarm, but predator cues reduced feeding rate only when the mysids were feeding alone. This study demonstrates the capability of N. integer to assess predation risk and social context and alter their behaviour accordingly.

Study of the Plantaginaceae for the Flora Mesoamericana project has resulted in five lectotypifications, a new combination in Rhodochiton, and the discovery of a new species of Tetranema from Honduras. This species, Tetranema michaelfayanum, is described here, a key to the species of Tetranema is provided, and the T. roseum complex is discussed.

Non

Mitochondrial DNA (mtDNA) sequence variants segregate in mutation and tissue-specific manners, but the mechanisms remain unknown. The segregation pattern of pathogenic mtDNA mutations is a major determinant of the onset and severity of disease. Using a heteroplasmic mouse model, we demonstrate that Gimap3, an outer mitochondrial membrane GTPase, is a critical regulator of this process in leukocytes. Gimap3 is important for T cell development and survival, suggesting that leukocyte survival may be a key factor in the genetic regulation of mtDNA sequence variants and in modulating human mitochondrial diseases., Author Summary Mitochondria are essential cellular organelles, which contain their own small circular genome in mammals. The mitochondrial genome is maternally inherited and encodes proteins critical for aerobic energy production. Mutations in mitochondrial DNA can lead to disruptions in aerobic energy production, which manifest as a wide spectrum of human clinical disorders. These mutations can segregate in mitotic and post-mitotic tissues, so that the proportion of the mutant genome can change with age, thereby affecting the clinical onset and severity of disease. The mechanisms regulating mtDNA segregation in mammals are not understood. We have used a mouse model of mtDNA segregation to elucidate the molecular basis of this process. Here, we demonstrate that the gene, Gimap3, can regulate mtDNA segregation in mouse white blood cells. This is the first gene identified to regulate mtDNA segregation in mammals, which is also an important factor in cell survival. Future work on this protein will provide critical insight into the pathways that regulate mitochondrial DNA in white blood cells, an important factor in the pathogenesis of human mitochondrial DNA mutations.

Background Uukuniemi virus (UUKV) belongs to the Phlebovirus genus in the family Bunyaviridae. As a non-pathogenic virus for humans UUKV has served as a safe model bunyavirus in a number of studies addressing fundamental questions such as organization and regulation of viral genes, genome replication, structure and assembly. The present study is focused on the oligomerization of the UUKV nucleocapsid (N) protein, which plays an important role in several steps of virus replication. The aim was to locate the domains involved in the N protein oligomerization and study the process in detail. Results A set of experiments concentrating on the N- and C-termini of the protein was performed, first by completely or partially deleting putative N-N-interaction domains and then by introducing point mutations of amino acid residues. Mutagenesis strategy was based on the computer modeling of secondary and tertiary structure of the N protein. The N protein mutants were studied in chemical cross-linking, immunofluorescence, mammalian two-hybrid, minigenome, and virus-like particle-forming assays. The data showed that the oligomerization ability of UUKV-N protein depends on the presence of intact α-helices on both termini of the N protein molecule and that a specific structure in the N-terminal region plays a crucial role in the N-N interaction(s). This structure is formed by two α-helices, rich in amino acid residues with aromatic (W7, F10, W19, F27, F31) or long aliphatic (I14, I24) side chains. Furthermore, some of the N-terminal mutations (e.g. I14A, I24A, F31A) affected the N protein functionality both in mammalian two-hybrid and minigenome assays. Conclusions UUKV-N protein has ability to form oligomers in chemical cross-linking and mammalian two-hybrid assays. In mutational analysis, some of the introduced single-point mutations abolished the N protein functionality both in mammalian two-hybrid and minigenome assays, suggesting that especially the N-terminal region of the UUKV-N protein is essential for the N-N interaction.

Background Caspases are a family of proteases that have central functions in programmed cell death (apoptosis) and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins, and at present almost 400 caspase substrates are known. There are several methods developed to predict caspase cleavage sites from individual proteins, but currently none of them can be used to predict caspase cleavage sites from multiple proteins or entire proteomes, or to use several classifiers in combination. The possibility to create a database from predicted caspase cleavage products for the whole genome could significantly aid in identifying novel caspase targets from tandem mass spectrometry based proteomic experiments. Results Three different pattern recognition classifiers were developed for predicting caspase cleavage sites from protein sequences. Evaluation of the classifiers with quality measures indicated that all of the three classifiers performed well in predicting caspase cleavage sites, and when combining different classifiers the accuracy increased further. A new tool, Pripper, was developed to utilize the classifiers and predict the caspase cut sites from an arbitrary number of input sequences. A database was constructed with the developed tool, and it was used to identify caspase target proteins from tandem mass spectrometry data from two different proteomic experiments. Both known caspase cleavage products as well as novel cleavage products were identified using the database demonstrating the usefulness of the tool. Pripper is not restricted to predicting only caspase cut sites, but it gives the possibility to scan protein sequences for any given motif(s) and predict cut sites once a suitable cut site prediction model for any other protease has been developed. Pripper is freely available and can be downloaded from http://users.utu.fi/mijopi/Pripper. Conclusions We have developed Pripper, a tool for reading an arbitrary number of proteins in FASTA format, predicting their caspase cleavage sites and outputting the cleaved sequences to a new FASTA format sequence file. We show that Pripper is a valuable tool in identifying novel caspase target proteins from modern proteomics experiments.

Background The SROs (SIMILAR TO RCD-ONE) are a group of plant-specific proteins which have important functions in stress adaptation and development. They contain the catalytic core of the poly(ADP-ribose) polymerase (PARP) domain and a C-terminal RST (RCD-SRO-TAF4) domain. In addition to these domains, several, but not all, SROs contain an N-terminal WWE domain. Results SROs are present in all analyzed land plants and sequence analysis differentiates between two structurally distinct groups; cryptogams and monocots possess only group I SROs whereas eudicots also contain group II. Group I SROs possess an N-terminal WWE domain (PS50918) but the WWE domain is lacking in group II SROs. Group I domain structure is widely represented in organisms as distant as humans (for example, HsPARP11). We propose a unified nomenclature for the SRO family. The SROs are able to interact with transcription factors through the C-terminal RST domain but themselves are generally not regulated at the transcriptional level. The most conserved feature of the SROs is the catalytic core of the poly(ADP-ribose) polymerase (PS51059) domain. However, bioinformatic analysis of the SRO PARP domain fold-structure and biochemical assays of AtRCD1 suggested that SROs do not possess ADP-ribosyl transferase activity. Conclusions The SROs are a highly conserved family of plant specific proteins. Sequence analysis of the RST domain implicates a highly preserved protein structure in that region. This might have implications for functional conservation. We suggest that, despite the presence of the catalytic core of the PARP domain, the SROs do not possess ADP-ribosyl transferase activity. Nevertheless, the function of SROs is critical for plants and might be related to transcription factor regulation and complex formation.

Background Environmental noise is ubiquitous in population growth processes, with a well acknowledged potential to affect populations regardless of their sizes. It therefore deserves consideration in population dynamics modelling. The usual approach to incorporating noise into population dynamical models is to make some model parameter(s) (typically the growth rate, the carrying capacity, or both) stochastic and responsive to environment fluctuations. It is however still unclear whether including noise in one or/and another parameter makes a difference to the model performance. Here we investigated this issue with a focus on model fit and predictive accuracy. To do this, we developed three population dynamical models of the Ricker type with the noise included in the growth rate (Model 1), in the carrying capacity (Model 2), and in both (Model 3). We generated several population time series under each model, and used a Bayesian approach to fit the three models to the simulated data. We then compared the model performances in fitting to the data and in forecasting future observations. Results When the mean intrinsic growth rate, r, in the data was low, the three models had roughly comparable performances, irrespective of the true model and the level of noise. As r increased, Models 1 performed best on data generated from it, and Model 3 tended to perform best on data generated from either Models 2 or Model 3. Model 2 was uniformly outcompeted by the other two models, regardless of the true model and the level of noise. The correlation between the deviance information criterion (DIC) and the mean square error (MSE) used respectively as measure of fit and predictive accuracy was broadly positive. Conclusion Our results suggested that the way environmental noise is incorporated into a population dynamical model may profoundly affect its performance. Overall, we found that including noise in one or/and another parameter does not matter as long as the mean intrinsic growth rate, r, is low. As r increased, however, the three models performed differently. Models 1 and 3 broadly outperformed Model 2, the first having the advantage of being simple and more computationally tractable. A comforting result emerging from our analysis is the broad positive correlation between MSEs and DICs, suggesting that the latter may also be informative about the predictive performance of a model.

An actin-regulated importin α/β-dependent extended bipartite NLS directs nuclear import of MRTF-A The transcriptional coactivator MRTF-A/Mal binds G-actin, which sequesters it in the cytoplasm. In this study, Treisman and colleagues identify an unusual bipartite nuclear localisation signal in MRTF-A, and show that importin α/β-mediated import through this NLS is directly inhibited by G-actin binding., Myocardin-related transcription factors (MRTFs) are actin-regulated transcriptional coactivators, which bind G-actin through their N-terminal RPEL domains. In response to signal-induced actin polymerisation and concomitant G-actin depletion, MRTFs accumulate in the nucleus and activate target gene transcription through their partner protein SRF. Nuclear accumulation of MRTFs in response to signal is inhibited by increased G-actin level. Here, we study the mechanism by which MRTF-A enters the nucleus. We show that MRTF-A contains an unusually long bipartite nuclear localisation signal (NLS), comprising two basic elements separated by 30 residues, embedded within the RPEL domain. Using siRNA-mediated protein depletion in vivo, and nuclear import assays in vitro, we show that the MRTF-A extended bipartite NLS uses the importin (Imp)α/β-dependent import pathway, and that import is inhibited by G-actin. Interaction of the NLS with the Impα–Impβ heterodimer requires both NLS basic elements, and is dependent on the Impα major and minor binding pockets. Binding of the Impα–Impβ heterodimer to the intact MRTF-A RPEL domain occurs competitively with G-actin. Thus, MRTF-A contains an actin-sensitive nuclear import signal.

The nuclear ribosomal locus coding for the large subunit is represented in tandem arrays in the plant genome. These consecutive gene blocks, consisting of several regions, are widely applied in plant phylogenetics. The regions coding for the subunits of the rRNA have the lowest rate of evolution. Also the spacer regions like the internal transcribed spacers (ITS) and external transcribed spacers (ETS) are widely utilized in phylogenetics. The fact, that these regions are present in many copies in the plant genome is an advantage for laboratory practice but might be problem for phylogenetic analysis. Beside routine usage, the rDNA regions provide the great potential to study complex evolutionary mechanisms, such as reticulate events or array duplications. The understanding of these processes is based on the observation that the multiple copies of rDNA regions are homogenized through concerted evolution. This phenomenon results to paralogous copies, which can be misleading when incorporated in phylogenetic analyses. The fact that non-functional copies or pseudogenes can coexist with ortholougues in a single individual certainly makes also the analysis difficult. This article summarizes the information about the structure and utility of the phylogenetically informative spacer regions of the rDNA, namely internal- and external transcribed spacer regions as well as the intergenic spacer (IGS).

The capercaillie has been negatively affected by the loss of mature forests. However, forestry creates young plantations offering a superabundant food supply for moose. Using two spatial scales, we tested whether the landscape-level environmental requirements of the capercaillie and moose differ. We compared the spatial association between the abundances of the two species in 50- × 50-km grids and, using a set of regression models, analyzed how it was affected by various land use variables in five regions of Finland. Both species were generally most abundant in the same grid cells. Moreover, the association between abundance and several landscape variables was very similar for both species. Forest cover had a positive impact on both species in Eastern and South-Western Finland. Only in Western Finland was the capercaillie more positively associated with older forest than the moose. Human impact variables were negatively related to both capercaillie and moose abundance in Eastern and South-Western Finland, the effect being stronger for capercaillie. In Northern Finland, human impact turned positive. Our results highlight that, on broad landscape and regional scales, we might not need to make trade-offs in management decisions concerning capercaillie and moose. While considering regional land use planning, the primary goal for both species seems to be to secure large areas of forest, preferably at a distance from human settlement.

In Finland, Capercaillie (Tetrao urogallus) populations have a history of serious decrease starting from the mid-20th century. The decline is temporally in line with the expansion of modern forestry practices that created major changes in the landscape. We used tetraonid route-censuses from 18 forestry board districts and Finnish forest inventories (data on forest stand structure) to analyze the decline in 1965–1988. We used information theoretical model selection to evaluate a set of log-linear second order autoregressive models, allowing for spatially correlated process errors. The average trend throughout the country corresponded to an annual decline of 4.01% (mean of local trends) ± 0.24% (SEM), parallel to a half-life of 17 years. The decline was surprisingly uniform throughout the country (SD = 1.01%) and most parsimoniously explained by a geographically constant log-linear trend. At the large scale of observation applied here, population trends could not be explained by the proportional increase of younger forest age classes (

beta-Catenin is a multifunctional protein involved in both signalling by secreted factors of Wnt family and regulation of the cellular architecture. We show that beta-catenin stabilization in mouse midbrain-rhombomere 1 region leads to robust up-regulation of several Wnt signalling target genes, including Fgf8. Suggestive of direct transcriptional regulation of the Fgf8 gene, beta-catenin stabilization resulted in Fgf8 up-regulation also in other tissues, specifically in the ventral limb ectoderm. Interestingly, stabilization of beta-catenin rapidly caused down-regulation of the expression of Wnt1 itself, suggesting a negative feedback loop. The changes in signal molecule expression were concomitant with deregulation of anterior-posterior and dorso-ventral patterning. The transcriptional regulatory functions of beta-catenin were confirmed by beta-catenin loss-of-function experiments. Temporally controlled inactivation of beta-catenin revealed a cell-autonomous role for beta-catenin in the maintenance of cell-type specific gene expression in the progenitors of midbrain dopaminergic neurons. These results highlight the role of beta-catenin in establishment of neuroectodermal signalling centers, promoting region-specific gene expression and regulation of cell fate determination.

Background A molecular population genetics understanding is central to the study of ecological and evolutionary functional genomics. Population genetics identifies genetic variation and its distribution within and among populations, it reveals the demographic history of the populations studied, and can provide indirect insights into historical selection dynamics. Here we use this approach to examine the demographic and selective dynamics acting of a candidate gene involved in plant-insect interactions. Previous work documents the macroevolutionary and historical ecological importance of the nitrile-specifier protein (Nsp), which facilitated the host shift of Pieridae butterflies onto Brassicales host plants ~80 Myr ago. Results Here we assess the microevolutionary dynamics of the Nsp gene by studying the within and among-population variation at Nsp and reference genes in the butterfly Pieris rapae (Small Cabbage White). Nsp exhibits unexpectedly high amounts of amino acid polymorphism, unequally distributed across the gene. The vast majority of genetic variation exists within populations, with little to no genetic differentiation among four populations on two continents. A comparison of synonymous and nonsynonymous substitutions in 70 randomly chosen genes among P. rapae and its close relative Pieris brassicae (Large Cabbage White) finds Nsp to have a significantly relaxed functional constraint compared to housekeeping genes. We find strong evidence for a recent population expansion and no role for strong purifying or directional selection upon the Nsp gene. Conclusions The microevolutionary dynamics of the Nsp gene in P. rapae are dominated by recent population expansion and variation in functional constraint across the repeated domains of the Nsp gene. While the high amounts of amino acid diversity suggest there may be significant functional differences among allelic variants segregating within populations, indirect tests of selection could not conclusively identify a signature of historical selection. The importance of using this information for planning future studies of potential performance and fitness consequences of the observed variation is discussed.

BackgroundThe U12-type spliceosome is responsible for the removal of a subset of introns from eukaryotic mRNAs. U12-type introns are spliced less efficiently than normal U2-type introns, which suggests a rate-limiting role in gene expression. The Drosophila genome contains about 20 U12-type introns, many of them in essential genes, and the U12-type spliceosome has previously been shown to be essential in the fly.Methodology/principal findingsWe have used a Drosophila line with a P-element insertion in U6atac snRNA, an essential component of the U12-type spliceosome, to investigate the impact of U12-type introns on gene expression at the organismal level during fly development. This line exhibits progressive accumulation of unspliced U12-type introns during larval development and the death of larvae at the third instar stage. Surprisingly, microarray and RT-PCR analyses revealed that most genes containing U12-type introns showed only mild perturbations in the splicing of U12-type introns. In contrast, we detected widespread downstream effects on genes that do not contain U12-type introns, with genes related to various metabolic pathways constituting the largest group.Conclusions/significanceU12-type intron-containing genes exhibited variable gene-specific responses to the splicing defect, with some genes showing up- or downregulation, while most did not change significantly. The observed residual U12-type splicing activity could be explained with the mutant U6atac allele having a low level of catalytic activity. Detailed analysis of all genes suggested that a defect in the splicing of the U12-type intron of the mitochondrial prohibitin gene may be the primary cause of the various downstream effects detected in the microarray analysis.

The outstanding levels of knowledge attained today in the research on animal communication, and the new available technologies to study visual, vocal and chemical signalling, allow an ever increasing use of information theory as a sophisticated tool to improve our knowledge of the complexity of animal communication. Some considerations on the way information theory and intraspecific communication can be linked are presented here. Specifically, information theory may help us to explore interindividual variations in different environmental constraints and social scenarios, as well as the communicative features of social vs. solitary species. © 2010 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.

Midbrain GABAergic neurons regulate multiple aspects of behavior and play important roles in psychiatric and neurological disease. These neurons constitute several anatomical and functional subpopulations, but their molecular heterogeneity and developmental regulatory mechanisms are poorly understood. Here we have studied the involvement of the proneural gene Ascl1 in the development of the midbrain GABAergic neurons. Analysis of Ascl1 mutant mice demonstrated highly region-specific requirements for Ascl1 for development of different GABAergic neuron subpopulations. Ascl1 is dispensable for the development of the ventral-most midbrain GABAergic neurons associated with dopaminergic nuclei substantia nigra pars reticulata (SNpr) and ventral tegmental area (VTA) GABAergic neurons. In the ventrolateral midbrain, loss of Ascl1 results in markedly delayed neurogenesis in the midbrain domains m3–m5. Within this region, Ascl1 has a unique role in m4, where it also regulates glutamatergic neurogenesis. Our results suggest that the m3–m5 midbrain neuroepithelium gives rise to the GABAergic neuron groups located in the midbrain reticular formation and ventrolateral periaqueductal gray. In contrast to m3–m5, Ascl1 is absolutely required in the dorsal midbrain domains m1–m2, for generation of the GABAergic neurons populating the superior and inferior colliculi as well as dorsal periaqueductal gray. These studies demonstrate different molecular regulatory mechanisms for the distinct midbrain GABAergic neuron subpopulations. Also, our results have implications on understanding the origins of the various midbrain GABAergic neuron groups in the embryonic neuroepithelium.

Background The Saccharomyces cerevisiae syntaxin1 homologues Sso1p and Sso2p perform an essential function in membrane fusion in exocytosis. While deletion of either SSO1 or SSO2 causes no obvious phenotype in vegetatively grown cells, deletion of both genes is lethal. In sporulating diploid S. cerevisiae cells only Sso1p, but not Sso2p, is needed for membrane fusion during prospore membrane formation. Mass spectrometry and in vivo labeling data suggest that serines 23, 24, and 79 in Sso1p and serines 31 and 34 in Sso2p can be phosphorylated in vivo. Here we set out to assess the contribution of phosphorylation on Sso protein in vivo function. Principal Findings Different mutant versions of SSO1 and SSO2 were generated to target the phosphorylation sites in Sso1p and Sso2p. Basal or overexpression of phospho-mimicking or putative non-phosphorylated Sso1p or Sso2p mutants resulted in no obvious growth phenotype. However, S79A and S79E mutations caused a mild defect in the ability of Sso1p to complement the temperature-sensitive growth phenotype of sso2-1 sso1Δ cells. Combination of all mutations did not additionally compromise Sso1p in vivo function. When compared to the wild type SSO1 and SSO2, the phosphoamino acid mutants displayed similar genetic interactions with late acting sec mutants. Furthermore, diploid cells expressing only the mutant versions of Sso1p had no detectable sporulation defects. In addition to sporulation, also pseudohyphal and invasive growth modes are regulated by the availability of nutrients. In contrast to sporulating diploid cells, deletion of SSO1 or SSO2, or expression of the phospho-mutant versions of SSO1 or SSO2 as the sole copies of SSO genes caused no defects in haploid or diploid pseudohyphal and invasive growth. Conclusions The identified phosphorylation sites do not significantly contribute to the in vivo functionality of Sso1p and Sso2p in S. cerevisiae.

Background Ecological immunology has focused on the costs of investment in immunocompetence. However, understanding optimal resource allocation to immune defence requires also identification of its benefits, which are likely to occur only when parasites are abundant. Methodology We manipulated the abundance of parasitic hen fleas in blue tit (Cyanistes caeruleus) nests, and supplemented their hosts, the nestlings, with methionine (a sulphur amino acid enhancing cell-mediated immunity) during day 3–6. We found a significant interaction between these two experimental factors on the development of immune defences and growth rates. Only in parasitized nests did methionine supplementation boost immune (PHA) response, and did nestling with experimentally increased immunocompetence show a relatively faster growth rate than control nestlings between days 6–9. Hence, the allocation of resources into immune defence and its growth-benefits are apparent only in presence of parasites. The main cost of methionine-induced increased allocation to the immune system was an increase in mortality, independently of ectoparasites. Nestlings in all treatments compensated initial growth reduction and all reached equal body size at day 16 (just prior to fledging), indicating a lack of long-term benefits. In addition, methionine treatment tended (P = 0.09) to lower circulating plasma immunoglobulin levels, possibly indicating a trade-off between the cell-mediated and humoral components of the immune system. Conclusions We found no strong benefits of an increased investment in immunocompetence in a parasite-rich environment. Any deviation from the growth trajectory (due to changes in allocation induced by methionine) is largely detrimental for survival. Hence, while costs are apparent identifying the benefits of investment in immunocompetence during ontogeny is challenging.

Pfam is a widely used database of protein families and domains. This article describes a set of major updates that we have implemented in the latest release (version 24.0). The most important change is that we now use HMMER3, the latest version of the popular profile hidden Markov model package. This software is approximately 100 times faster than HMMER2 and is more sensitive due to the routine use of the forward algorithm. The move to HMMER3 has necessitated numerous changes to Pfam that are described in detail. Pfam release 24.0 contains 11,912 families, of which a large number have been significantly updated during the past two years. Pfam is available via servers in the UK (http://pfam.sanger.ac.uk/), the USA (http://pfam.janelia.org/) and Sweden (http://pfam.sbc.su.se/).

Rimbachia leucobryi, a small pleurotoid agaric, is described as new to science. The species grew on living stems of Leucobryum sanctum in lowland rainforest. It is characterised by lamellate hymenophore, hymenial cystidia and small, ellipsoid spores. Pterygellus armeniacus, a bright-coloured stipitate stereoid species, is reported as new to Indonesia. The two species are illustrated.

Although little is known about the relationship between aboveground and belowground biota and ecosystem services in urban soils, the scarce data suggests that plant coverage has a key role in influencing the urban C and N cycles. Plant litter quality and quantity have been addressed as one the major factors determining the rate of nutrient and organic carbon cycling in urban soils. However, the land-use history of urban soils, frequency of disturbances and abiotic-biotic conditions may largely contribute to the effects of aboveground biota on decomposition process. Here we studied the decomposition process of different litter types (labile and recalcitrant litter) in two structurally and chemically divergent urban soils (landfill sandy soil and richer park soil). At both of these urban sites, a reciprocal litter placement experiment was performed to distinguish the effects between plant coverage (plant treatment) and litter type on litter decomposition processes. As hypothesized, labile litter decomposed faster than recalcitrant litter at both urban soil types. Urban soil type however, had a clear impact on degradation rate of the litter: all litter types decomposed at higher rates in park soil with higher organic matter and soil moisture content. Unexpectedly, the plant treatment did not affect the degradation rate of the litter although it did have a significant influence on the abundance of litter-inhabiting Collembola in landfill soil. Our study suggests potentially higher carbon retention in urban soils under recalcitrant litter producing plants in comparison to plant-soil systems with labile-litter producing plants.

Non

Background How new forms arise in nature has engaged evolutionary biologists since Darwin's seminal treatise on the origin of species. Transposable elements (TEs) may be among the most important internal sources for intraspecific variability. Thus, we aimed to explore the temporal dynamics of several TEs in individual genotypes from a small, marginal population of Aegilops speltoides. A diploid cross-pollinated grass species, it is a wild relative of the various wheat species known for their large genome sizes contributed by an extraordinary number of TEs, particularly long terminal repeat (LTR) retrotransposons. The population is characterized by high heteromorphy and possesses a wide spectrum of chromosomal abnormalities including supernumerary chromosomes, heterozygosity for translocations, and variability in the chromosomal position or number of 45S and 5S ribosomal DNA (rDNA) sites. We propose that variability on the morphological and chromosomal levels may be linked to variability at the molecular level and particularly in TE proliferation. Results Significant temporal fluctuation in the copy number of TEs was detected when processes that take place in small, marginal populations were simulated. It is known that under critical external conditions, outcrossing plants very often transit to self-pollination. Thus, three morphologically different genotypes with chromosomal aberrations were taken from a wild population of Ae. speltoides, and the dynamics of the TE complex traced through three rounds of selfing. It was discovered that: (i) various families of TEs vary tremendously in copy number between individuals from the same population and the selfed progenies; (ii) the fluctuations in copy number are TE-family specific; (iii) there is a great difference in TE copy number expansion or contraction between gametophytes and sporophytes; and (iv) a small percentage of TEs that increase in copy number can actually insert at novel locations and could serve as a bona fide mutagen. Conclusions We hypothesize that TE dynamics could promote or intensify morphological and karyotypical changes, some of which may be potentially important for the process of microevolution, and allow species with plastic genomes to survive as new forms or even species in times of rapid climatic change.

For studies on the fern family Tectariaceae for the Flora of China, four species previously treated as Ctenitopsis need new combinations in Tectaria. The new combinations are proposed here and information on their types is provided.

Species specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm’ region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined. Non

The family Neckeraceae is composed of three distinct clades, of which two, i.e. the Neckera and Thamnobryum clades, are well defined. The third clade, consisting of species belonging to Caduciella, Curvicladium, Handeliobryum, Himantocladium, Homaliodendron, Hydrocryphaea, Neckera, Neckeropsis, Pinnatella, Shevockia and Taiwanobryum, is the focus of this study. Based on sequence data from the trnS-rps4-trnT-trnL-trnF plastid cluster and the rpl16 intron as well as from nuclear ITS1&2, the phylogenetic relationships of these genera are reconstructed. The nearest relatives of this clade are resolved shedding more light on the evolution of the family. The generic composition of the clade and its individual genera are discussed; polyphyly requires redefinition of Pinnatella, Neckeropsis and Homaliodendron. The positions of Touwia and Homalia within the family are addressed in an additional analysis based on more extensive sequence data, and the corresponding new combinations are made. Several further taxonomic changes are proposed, including Circulifolium gen. nov., comprising the former Homaliodendron exiguum and H. microdendron.

Molecular techniques have revealed that avian mating systems are more diverse and complex than previously thought. We used microsatellite markers to determine genetic parentage, the prevalence of extrapair paternity and quasi-parasitism (i.e. situations where a male's extrapair mate lay in his nest) in a socially monogamous population of three-toed woodpeckers (Picoides tridactylus) in southern Finland. A total of 129 adults and nestlings, representing 5–9 families annually from 2004–2007, were genotyped at up to ten microsatellite loci. The results of genetic assignment tests confirmed that monogamous parentage characterized the majority (84.6%, 22/26) of broods, and that most (93.8%, 75/80) nestlings were the offspring of their social parents. Two of 80 nestlings (2.5%) in two of 26 broods (7.7%) were sired by extrapair males and quasi-parasitism occurred in 3.8% (3/80) of nestlings and 7.7% (2/26) of broods. Hence, the levels of extrapair parentage were low, possibly because both genetic polygyny and polyandry are constrained by the high paternal effort required for parental care. The co-occurrence of low levels of extrapair paternity and quasi-parasitism are discussed in light of ecological and behavioural factors characterizing the species biology.

Background Plant Receptor-like/Pelle kinases (RLK) are a group of conserved signalling components that regulate developmental programs and responses to biotic and abiotic stresses. One of the largest RLK groups is formed by the Domain of Unknown Function 26 (DUF26) RLKs, also called Cysteine-rich Receptor-like Kinases (CRKs), which have been suggested to play important roles in the regulation of pathogen defence and programmed cell death. Despite the vast number of RLKs present in plants, however, only a few of them have been functionally characterized. Results We examined the transcriptional regulation of all Arabidopsis CRKs by ozone (O3), high light and pathogen/elicitor treatment - conditions known to induce the production of reactive oxygen species (ROS) in various subcellular compartments. Several CRKs were transcriptionally induced by exposure to O3 but not by light stress. O3 induces an extracellular oxidative burst, whilst light stress leads to ROS production in chloroplasts. Analysis of publicly available microarray data revealed that the transcriptional responses of the CRKs to O3 were very similar to responses to microbes or pathogen-associated molecular patterns (PAMPs). Several mutants altered in hormone biosynthesis or signalling showed changes in basal and O3-induced transcriptional responses. Conclusions Combining expression analysis from multiple treatments with mutants altered in hormone biosynthesis or signalling suggest a model in which O3 and salicylic acid (SA) activate separate signaling pathways that exhibit negative crosstalk. Although O3 is classified as an abiotic stress to plants, transcriptional profiling of CRKs showed strong similarities between the O3 and biotic stress responses.

Individuals with a particular variant of the gene phosphoglucose isomerase (Pgi) have been shown to have superior dispersal capacity and fecundity in the Glanville fritillary butterfly (Melitaea cinxia), raising questions about the mechanisms that maintain polymorphism in this gene in the field. Here, we investigate how variation in thePgigenotype affects female and male life history under controlled conditions. The most striking effect is the longer lifespan of genotypes with high dispersal capacity, especially in non-reproducing females. Butterflies use body reserves for somatic maintenance and reproduction, but different resources (in thorax versus abdomen) are used under dissimilar conditions, with some interactions with thePgigenotype. These results indicate life-history trade-offs that involve resource allocation and genotype×environment interactions, and these trade-offs are likely to contribute to the maintenance ofPgipolymorphism in the natural populations.

Chloroplast NADPH-thioredoxin reductase (NTRC) belongs to the thioredoxin systems that control crucial metabolic and regulatory pathways in plants. Here, by characterization of T-DNA insertion lines of NTRC gene, we uncover a novel connection between chloroplast thiol redox regulation and the control of photoperiodic growth in Arabidopsis (Arabidopsis thaliana). Transcript and metabolite profiling revealed severe developmental and metabolic defects in ntrc plants grown under a short 8-h light period. Besides reduced chlorophyll and anthocyanin contents, ntrc plants showed alterations in the levels of amino acids and auxin. Furthermore, a low carbon assimilation rate of ntrc leaves was associated with enhanced transpiration and photorespiration. All of these characteristics of ntrc were less severe when plants were grown under a long 16-h photoperiod. Transcript profiling revealed that the mutant phenotypes of ntrc were accompanied by differential expression of genes involved in stomatal development, chlorophyll biosynthesis, chloroplast biogenesis, and circadian clock-linked light perception systems in ntrc plants. We propose that NTRC regulates several key processes, including chlorophyll biosynthesis and the shikimate pathway, in chloroplasts. In the absence of NTRC, imbalanced metabolic activities presumably modulate the chloroplast retrograde signals, leading to altered expression of nuclear genes and, ultimately, to the formation of the pleiotrophic phenotypes in ntrc mutant plants.

Habitat instability has an important influence on species' occurrence and community composition. For freshwater arthropods that occur in ephemeral rock pools, the most drastic habitat instabilities are droughts and the intermittent availability of water. However, although the desiccation of a rock pool is detrimental for planktonic populations, it may also bring certain benefits: the exclusion of predators or parasites, for example, or the coexistence of otherwise competitively exclusive species. The commonness of drought resistant resting stages in many aquatic organisms shows the ecological significance of droughts. We measured daily evaporation in 50 rock pools inhabited by three Daphnia species D. magna, D. longispina and D. pulex over one summer. Daily evaporation and ultimately desiccation showed significantly seasonally influenced correlation with pool surface area, presence of vegetation, ambient temperature, wind and standardized evaporation measures. We used the estimates from this analysis to develop a simulation model to predict changes in the water level in 530 individual pools on a daily basis over a 25-year period. Eventually, hydroperiod lengths and desiccation events could be predicted for all of these rock pools. We independently confirmed the validity of this simulation by surveying desiccation events in the 530 rock pools over a whole season in 2006. In the same 530 rock pools, Daphnia communities had been recorded over the 25 years the simulation model considered. We correlated pool-specific occupation lengths of the three species with pool-specific measures of desiccation risk. Occupation lengths of all three Daphnia species were positively correlated with maximum hydroperiod length and negatively correlated with the number of desiccation events. Surprisingly, these effects were not species-specific.