Stochastic boundary molecular dynamics simulation of L-ribose in the active site of Actinoplanes missouriensis xylose isomerase and its Val135Asn mutant with improved reaction rate

We used molecular dynamics simulations to study how a non-natural substrate, L-ribose, interacts with the active site of Actinoplanes missouriensis xylose isomerase. The simulations showed that L-ribose does not stay liganded in the active site in the same way as D-xylose, in which the oxygens O2 and O4 are liganded to the metal M1. The oxygen O4 of L-ribose moved away from the metal M1 to an upside down position. Furthermore, the distances of the carbons C1 and C2 of L-ribose to the catalytic metal M2 were higher than in the case of D-xylose. These findings explain the extremely low reaction rate of xylose isomerase with L-ribose. The mutation V135N close to the C5-OH of the substrate increased the reaction efficiency 2- to 4-fold with L-ribose. V135N did not affect the reaction with D-xylose and L-arabinose, whereas the reaction with D-glucose was impaired, probably due to a hydrogen bond between Asn-135 and the substrate. When L-ribose was the substrate, Asn-135 formed a hydrogen bond to Glu-181. As a consequence, O4 of L-ribose stayed liganded to the metal M1 in the V135N mutant in molecular dynamics simulations. This explains the decreased K(m) of the V135N mutant with L-ribose.     

Phytoplankton community responses to nutrient and iron enrichment under different nitrogen to phosphorus ratios in the northern Baltic Sea

The impact of nutrient enrichment on the phytoplankton community structure, and particularly cyanobacteria, was studied in a 3-week mesocosm experiment conducted in August 2001 in the Archipelago Sea, a part of the northern Baltic Sea. The factorial design experiment included daily additions of nitrogen (N) and phosphorus (P) at two mass ratios, 1N:1P and 7N:1P, respectively, additions of iron (Fe) and a synthetic chelator, ethylenediaminetetraacetic acid (EDTA). The floating enclosures (400 l) were sampled for analyses of phytoplankton biomass and community structure, phytoplankton primary production, chlorophyll a, nutrients, and hepatotoxins. Chlorophyll a concentration, phytoplankton biomass and primary production increased most in the 7N:1P treatment. The increase was mainly due to an abundant growth of chlorophytes (Dictyosphaerium subsolitarium, Kirchneriella spp., Monoraphidium contortum, and Oocystis spp.), pennate diatoms (especially Nitzschia spp.), dinophytes and the chroococcalean cyanobacterium Synechococcus sp. The nutrient enrichments had no effect on the total biomass of N₂-fixing cyanobacteria. Nevertheless, the biomass of Anabaena spp. was highest in the enrichments with a low N/P ratio. Chlorophyll a concentration and total phytoplankton biomass were not affected by Fe or EDTA, but Fe alone had a positive effect on the chlorophyte Kirchneriella sp. The N₂-fixing cyanobacteria Aphanizomenon sp. responded positively to Fe alone and to both Fe and EDTA added together. The hepatotoxin concentration increased during the experiment, but no clear responses to nutrient enrichments were found. Our study showed species-specific responses to nutrient enrichments among the N₂-fixing cyanobacteria. Although the total phytoplankton production was not Fe-limited; the availability of Fe clearly affected the phytoplankton community structure.     

Scales of horizontal patchiness in chlorophyll a, chemical and physical properties of landfast sea ice in the Gulf of Finland (Baltic Sea)

Horizontal variation of first-year landfast sea ice properties was studied in the Gulf of Finland, the Baltic Sea. Several scales of variation were considered; a number of arrays with core spacings of 0.2, 2 and 20 m were sampled at different stages of the ice season for small-scale patchiness. Spacing between these arrays was from hundreds of meters to kilometers to study mesoscale variability, and once an onshore–offshore 40-km transect was sampled to study regional scale variability. Measured variables included salinity, stable oxygen isotopes (¹⁸O), chlorophyll a (chl-a), nutrients and dissolved organic carbon. On a large scale, a combination of variations in the under-ice water salinity (ice porosity), nutrient supply and the stage of ice development control the build-up of ice algal biomass. At scales of hundreds of meters to kilometers, there was significant variability in several parameters (salinity, chl-a, snow depth and ice thickness). Analyses of the data from the arrays did not show evidence of significant patchiness at scales <20 m for algal biomass. The results imply that the sampling effort in Baltic Sea ice studies should be concentrated on scales of hundreds of meters to kilometers. Using the variations observed in the study area, the estimate for depth-integrated algal biomass in landfast sea ice in the Gulf of Finland (March 2003) is 5.5±4.4 mg chl-a m^–2.     

Testate amoebae community analysis as a tool to assess biological impacts of peatland use

As most ecosystems, peatlands have been heavily exploited for different human purposes. For example, in Finland the majority is under forestry, agriculture or peat mining use. Peatlands play an important role in carbon storage, water cycle, and are a unique habitat for rare organisms. Such properties highlight their environmental importance and the need for their restoration. To monitor the success of peatland restoration sensitive indicators are needed. Here we test whether testate amoebae can be used as a reliable bioindicator for assessing peatland condition. To qualify as reliable indicators, responses in testate amoebae community structure to ecological changes must be stronger than random spatial and temporal variation. In this study, we simultaneously assessed differences between the effects of seasonality, intermediate scale spatial variation and land uses on living testate amoebae assemblages in natural, forested and restored peatlands. We expected the effects of seasonality on testate amoebae communities to be less pronounced than those of land use and within site variation. On average, natural sites harboured the highest richness and density, while the lowest numbers were found at forestry sites. Despite small changes observed in taxa dominance and differences in TA community structure between seasons and years at some sites, spatial heterogeneity, temperature, pH, nor water table depth seemed to significantly affect testate amoebae communities. Instead, observed differences were related to type of land use, which explained 75% of the community variation. Our results showed that testate amoebae community monitoring is a useful tool to evaluate impacts of human land use on boreal peatlands.     

Genetics of microenvironmental sensitivity of body weight in rainbow trout (Oncorhynchus mykiss) selected for improved growth

Microenvironmental sensitivity of a genotype refers to the ability to buffer against non-specific environmental factors, and it can be quantified by the amount of residual variation in a trait expressed by the genotype's offspring within a (macro)environment. Due to the high degree of polymorphism in behavioral, growth and life-history traits, both farmed and wild salmonids are highly susceptible to microenvironmental variation, yet the heritable basis of this characteristic remains unknown. We estimated the genetic (co)variance of body weight and its residual variation in 2-year-old rainbow trout (Oncorhynchus mykiss) using a multigenerational data of 45,900 individuals from the Finnish national breeding programme. We also tested whether or not microenvironmental sensitivity has been changed as a correlated genetic response when genetic improvement for growth has been practiced over five generations. The animal model analysis revealed the presence of genetic heterogeneity both in body weight and its residual variation. Heritability of residual variation was remarkably lower (0.02) than that for body weight (0.35). However, genetic coefficient of variation was notable in both body weight (14%) and its residual variation (37%), suggesting a substantial potential for selection responses in both traits. Furthermore, a significant negative genetic correlation (-0.16) was found between body weight and its residual variation, i.e., rapidly growing genotypes are also more tolerant to perturbations in microenvironment. The genetic trends showed that fish growth was successfully increased by selective breeding (an average of 6% per generation), whereas no genetic change occurred in residual variation during the same period. The results imply that genetic improvement for body weight does not cause a concomitant increase in microenvironmental sensitivity. For commercial production, however, there may be high potential to simultaneously improve weight gain and increase its uniformity if both criteria are included in a selection index.     

CD marker expression profiles of human embryonic stem cells and their neural derivatives,determined using flow-cytometric analysis,reveal a novel CD marker for exclusion of pluripotent stem cells

Human embryonic stem cells (hESCs) are pluripotent cells that can differentiate into neural cell lineages. These neural populations are usually heterogeneous and can contain undifferentiated pluripotent cells that are capable of producing teratomas in cell grafts. The characterization of surface protein profiles of hESCs and their neural derivatives is important to determine the specific markers that can be used to exclude undifferentiated cells from neural populations. In this study, we analyzed the cluster of differentiation (CD) marker expression profiles of seven undifferentiated hESC lines using flow-cytometric analysis and compared their profiles to those of neural derivatives. Stem cell and progenitor marker CD133 and epithelial adhesion molecule marker CD326 were more highly expressed in undifferentiated hESCs, whereas neural marker CD56 (NCAM) and neural precursor marker (chemokine receptor) CD184 were more highly expressed in hESC-derived neural cells. CD326 expression levels were consistently higher in all nondifferentiated hESC lines than in neural cell derivatives. In addition, CD326-positive hESCs produced teratomas in SCID mouse testes, whereas CD362-negative neural populations did not. Thus, CD326 may be useful as a novel marker of undifferentiated hESCs to exclude undifferentiated hESCs from differentiated neural cell populations prior to transplantation.     

Impacts of nutrient enrichment and sediment on phytoplankton community structure in the northern Baltic Sea

A three-week mesocosm experiment was conducted in order to study the effects of bottom sediment and nutrient enrichment on phytoplankton and zooplankton community structure in the Archipelago Sea, northern Baltic Sea. The transparent polyethylene enclosures included the whole water column and varied in volume from 30 to 40 m³. There were two types of enclosures: some with natural sediment as a bottom and others with a plastic bottom. The experiment was a 2 × 2 factorial design with presence of sediment and nutrient enrichment as treatment factors. Both the sediment presence and nutrient enrichment significantly increased water nutrient concentrations and the rate of primary production. However, external nutrient enrichment and the presence of sediment stimulated the growth of different phytoplankton groups, indicating that the effect of sediment was not related to nutrient fluxes alone, but involved more complex interactions. External nutrient enrichment was primarily channelled to picoplanktonic cyanobacteria, the biomass of which increased four- to fivefold due to enrichment. The presence of sediment increased the biomass of cryptophytes, chrysophytes and prasinophytes, but decreased the biomass of N₂-fixing cyanobacteria. Zooplankton biomass increased during the experiment, but was not affected by the treatments. The study shows that sediment plays a significant role in phytoplankton dynamics, underlining the importance of including sediment in shallow-water mesocosm experiments. Handling editor: J. Padisak     

Farmland carabid beetle communities at multiple levels of spatial scale

Carabid beetle communities were studied at three levels of spatial scale, i.e. within fields (three sets of traps, mean distance 15 m), between fields (five fields within 1 km from each other) and between patches of farmland (four study areas 4-8 km from each other). We compared carabid assemblages sampled on five crop types in each study area, i.e. ley. set-aside, spring cereal, potato, and sugar beet. Because of small sample sizes, only the community composition was studied within fields with a DCA ordination, but the differences were small. Analyses of species richness, activity density, community composition as revealed by DCA ordinations, dominance structure, diversity, and evenness showed that carabid communities varied significantly among patches of farmland but not between fields with different crops within the patches. Only the communities of potato fields were found lo resemble each other. Only five carabid beetle species showed a preference for crops, and twelve species favoured some study areas. We conclude that the effect of spatial scale should be emphasised in further studies as it seems that carabid beetles may be very localised even in agricultural habitats.     

Survival of male Tengmalm’s owls increases with cover of old forest in their territory

The loss and fragmentation of forest habitats have been considered to pose a worldwide threat to the viability of forest-dwelling animals, especially to species that occupy old forests. We investigated whether the annual survival of sedentary male Tengmalm’s owls Aegolius funereus was associated with the cover of old coniferous forests in Finland. Survival and recapture probabilities varied annually with density changes in populations of the main prey (Microtus voles). When this variation was controlled for, and relationships between survival and proportions of the three different forest age classes (old-growth, middle-aged, and young) were modeled separately, the old-growth model was the most parsimonious. Survival increased with the cover of old forest, although the extent of old forest within owl territories was relatively small (mean ∼12%, range 2–37%). This association, however, varied among years and appeared especially in years of increasing vole abundance. At such times, old forests may sustain high populations of bank voles Clethrionomys glareolus, shrews and small passerines. In addition, old forests may serve as refuges against large avian predator species, such as Ural owls Strix uralensis and goshawks Accipiter gentilis. Our results suggest that changes in habitat quality created by agriculture and forestry may have the potential to reduce adult survival, an essential component of fitness and population viability.     

No effects of short-term GSM mobile phone radiation on cerebral blood flow measured using positron emission tomography

The present study investigated the effects of 902.4 MHz Global System for Mobile Communications (GSM) mobile phone radiation on cerebral blood flow using positron emission tomography (PET) with the ¹⁵O‐water tracer. Fifteen young, healthy, right‐handed male subjects were exposed to phone radiation from three different locations (left ear, right ear, forehead) and to sham exposure to test for possible exposure effects on brain regions close to the exposure source. Whole‐brain [¹⁵O]H₂O–PET images were acquired 12 times, 3 for each condition, in a counterbalanced order. Subjects were exposed for 5 min in each scan while performing a simple visual vigilance task. Temperature was also measured in the head region (forehead, eyes, cheeks, ear canals) during exposure. The exposure induced a slight temperature rise in the ear canals but did not affect brain hemodynamics and task performance. The results provided no evidence for acute effects of short‐term mobile phone radiation on cerebral blood flow. Bioelectromagnetics 33:247–256, 2012. © 2011 Wiley Periodicals, Inc.