Thermal optimality of net ecosystem exchange of carbon dioxide and underlying mechanisms.

• It is well established that individual organisms can acclimate and adapt to temperature to optimize their functioning. However, thermal optimization of ecosystems, as an assemblage of organisms, has not been examined at broad spatial and temporal scales. • Here, we compiled data from 169 globally distributed sites of eddy covariance and quantified the temperature response functions of net ecosystem exchange (NEE), an ecosystem-level property, to determine whether NEE shows thermal optimality and to explore the underlying mechanisms.

Experimental validation of a nonequilibrium model of CO₂ fluxes between gas, liquid medium, and algae in a flat-panel photobioreactor.

Carbon dioxide (CO₂) availability strongly affects the productivity of algal photobioreactors, where it is dynamically exchanged between different compartments, phases, and chemical forms. To understand the underlying processes, we constructed a nonequilibrium mathematical model of CO₂ dynamics in a flat-panel algal photobioreactor. The model includes mass transfer to the algal suspension from a stream of bubbles of CO₂-enriched air and from the photobioreactor headspace.

Behaviour of arsenic in forested catchments following a high-pollution period.

Due to high availability of adsorption sites, forested catchments could be net sinks for pollutant arsenic both during the period of increasing and decreasing pollution. We tested this hypothesis along a north-south pollution gradient in spruce die-back affected areas of Central Europe. For two water years (2007-2008), we monitored As fluxes via spruce-canopy throughfall, open-area precipitation, and runoff in four headwater catchments (Czech Republic).

Structural analysis of natural killer cell receptor protein 1 (NKR-P1) extracellular domains suggests a conserved long loop region involved in ligand specificity.

Receptor proteins at the cell surface regulate the ability of natural killer cells to recognize and kill a variety of aberrant target cells. The structural features determining the function of natural killer receptor proteins 1 (NKR-P1s) are largely unknown. In the present work, refined homology models are generated for the C-type lectin-like extracellular domains of rat NKR-P1A and NKR-P1B, mouse NKR-P1A, NKR-P1C, NKR-P1F, and NKR-P1G, and human NKR-P1 receptors.

The α-galactosidase type A gene aglA from Aspergillus niger encodes a fully functional α-N-acetylgalactosaminidase.

Two genes in the genome of Aspergillus niger, aglA and aglB, have been assigned to encode for α-d-galactosidases variant A and B. However, analyses of primary and 3D structures based on structural models of these two enzymes revealed significant differences in their active centers suggesting important differences in their specificity for the hydrolyzed carbohydrates. To test this unexpected finding, a large screening of libraries from 42 strains of filamentous fungi succeeded in identifying an enzyme from A.

Near-distance imaging spectroscopy investigating chlorophyll fluorescence and photosynthetic activity of grassland in the daily course.

Detection of grassland canopy chlorophyll fluorescence (Chl-F) conducted with an imaging spectroradiometer provided evidence of potential remote sensing estimation of steady-state Chl-F (Chl-F). Daily near-nadir views of extremely high spatial resolution hyperspectral images were acquired from a distance of 4 m for temperate montane grassland in the Czech Republic. Simultaneously, measurements of Chl-F and total chlorophyll content (Chl) were made on a single leaf at ground level were collected.

Metabolic rhythms of the cyanobacterium Cyanothece sp. ATCC 51142 correlate with modeled dynamics of circadian clock.

These experiments aim to reveal the dynamic features that occur during the metabolism of the unicellular, nitrogen fixing cyanobacterium Cyanothece sp. when exposed to diverse circadian forcing patterns (LD 16:8, LD 12:12, LD 8:16, LD 6:6). The chlorophyll concentration grew rapidly from subjective morning when first illuminated to around noon, then remained stable from later in the afternoon and throughout the night.

Crystallization and preliminary crystallographic characterization of the extrinsic PsbP protein of photosystem II from Spinacia oleracea.

Preliminary X-ray diffraction analysis of the extrinsic PsbP protein of photosystem II from spinach (Spinacia oleracea) was performed using N-terminally His-tagged recombinant PsbP protein overexpressed in Escherichia coli. Recombinant PsbP protein (thrombin-digested recombinant His-tagged PsbP) stored in bis-Tris buffer pH 6.00 was crystallized using the sitting-drop vapour-diffusion technique with PEG 550 MME as a precipitant and zinc sulfate as an additive.

Simple traits among diaspore weight/number, plant height and ability of vegetative propagation.

Several expected correlations among followed internal plant traits were confirmed using the dataset of 492 herbaceous species from the temporal zone of Central Europe. Average diaspore weight (seed mass), reproductive capacity of population (number of produced diaspores), species height, and ability of lateral spread were the plant traits considered. The evident correlations were confirmed among all investigated traits: (i) The reproductive capacity of population negatively correlated with diaspore weight, plant height, and vegetative propagation.

Structure of the motor subunit of type I restriction-modification complex EcoR124I.

Type I restriction-modification enzymes act as conventional adenine methylases on hemimethylated DNAs, but unmethylated recognition targets induce them to translocate thousands of base pairs before cleaving distant sites nonspecifically. The first crystal structure of a type I motor subunit responsible for translocation and cleavage suggests how the pentameric translocating complex is assembled and provides a structural framework for translocation of duplex DNA by RecA-like ATPase motors.

Hydrogen peroxide removal with magnetically responsive Saccharomyces cerevisiae cells.

Hydrogen peroxide (HP) is a promising chemical sanitizer for use in the food industry. Its residues have to be decomposed, usually using an enzyme process employing catalase. In order to offer an inexpensive biocatalyst and to simplify subsequent manipulation, we have prepared magnetically responsive alginate beads containing entrapped Saccharomyces cerevisiae cells and magnetite microparticles.

Comparison of photosynthetic induction and transient limitations during the induction phase in young and mature leaves from three poplar clones.

We tested the hypothesis that leaf age affects photosynthetic induction, because conductance to CO2 diffusion usually decreases with increasing leaf age. Photosynthetic inductions, primarily determined by the light modulation of Rubisco activity and stomatal opening, were investigated in both young and mature leaves, as defined by leaf plastochron index (LPI), from three poplar clones: Populus alba L., P.

A photobioreactor system for precision cultivation of photoautotrophic microorganisms and for high-content analysis of suspension dynamics.

Small-scale photobioreactors for cultivation of photoautotrophic microbes are required for precise characterization of the growth parameters of wild-type and engineered strains of these organisms, for their screening, and for optimization of culture conditions. Here, we describe the design and use of a flat-cuvette photobioreactor that allows accurate control of culture irradiance, temperature, pH, and gas composition combined with real-time monitoring by a built-in fluorometer and densitometer. The high-power LED light source generates precise irradiance levels that are programmed by user-designed protocols.

Annual variation of the steady-state chlorophyll fluorescence emission of evergreen plants in temperate zone.

Remotely sensed passive chlorophyll fluorescence emission has a potential to become one of the major global-scale reporter signals on vegetation performance and stress. In contrast to the actively probed parameters such as maximal (F') or minimal (F') emission, the steady-state chlorophyll fluorescence, Chl-F, (F' > Chl-F > F') has not been adequately studied. Using fluorescence imaging of leaves, we explored the modulation of Chl-F by actinic irradiance and by temperature in laboratory, as well as the changes that occurred in three coniferous and broadleaf plant species grown in field.

Seasonal variation in CO2 efflux of stems and branches of Norway spruce trees.

Background And Aims: Stem and branch respiration, important components of total forest ecosystem respiration, were measured on Norway spruce (Picea abies) trees from May to October in four consecutive years in order (1) to evaluate the influence of temperature on woody tissue CO2 efflux with special focus on variation in Q10 (change in respiration rate resulting from a 10 degrees C increase in temperature) within and between seasons, and (2) to quantify the contribution of above-ground woody tissue (stem and branch) respiration to the carbon balance of the forest ecosystem.

Methods: Stem and branch CO2 efflux were measured, using an IRGA and a closed gas exchange system, 3-4 times per month on 22-year-old trees under natural conditions. Measurements of ecosystem CO2 fluxes were also determined during the whole experiment by using the eddy covariance system.

Structure of the dimeric N-glycosylated form of fungal beta-N-acetylhexosaminidase revealed by computer modeling, vibrational spectroscopy, and biochemical studies.

Background: Fungal beta-N-acetylhexosaminidases catalyze the hydrolysis of chitobiose into its constituent monosaccharides. These enzymes are physiologically important during the life cycle of the fungus for the formation of septa, germ tubes and fruit-bodies. Crystal structures are known for two monomeric bacterial enzymes and the dimeric human lysosomal beta-N-acetylhexosaminidase.

E-photosynthesis: a comprehensive modeling approach to understand chlorophyll fluorescence transients and other complex dynamic features of photosynthesis in fluctuating light.

Plants are exposed to a temporally and spatially heterogeneous environment, and photosynthesis is well adapted to these fluctuations. Understanding of the complex, non-linear dynamics of photosynthesis in fluctuating light requires novel-modeling approaches that involve not only the primary light and dark biochemical reactions, but also networks of regulatory interactions. This requirement exceeds the capacity of the existing molecular models that are typically reduced to describe a partial process, dynamics of a specific complex or its particular dynamic feature.

Induction of photosynthesis and importance of limitations during the induction phase in sun and shade leaves of five ecologically contrasting tree species from the temperate zone.

We examined the principal differences in photosynthetic characteristics between sun and shade foliage and determined the relative importance of biochemical and stomatal limitations during photosynthetic induction. Temperate-zone broadleaf and conifer tree species, ranging widely in shade tolerance, were investigated from one locality in the Czech Republic. The study species included strongly shade-tolerant Abies alba Mill.

Timing of dispersal: effect of ants on aphids.

Mutualists can affect many life history traits of their partners, but it is unclear how this translates into population dynamics of the latter. Ant-aphid associations are ideal for studying this question, as ants affect aphids, both positively (e.g.

GC-MS-MS analysis of bacterial fatty acids in heavily creosote-contaminated soil samples.

Phospholipid fatty acid profiles of soil samples enable rapid and reproducible measurement and characterization of the dominant soil microbial communities. When extensive polycyclic aromatic hydrocarbon (PAH) pollution is present in the soil it is very difficult, or even impossible, to distinguish specific fatty acids in GC-MS chromatograms in full-scan mode, because of the PAHs which, because of their lipophilic character, are co-extracted with the lipids. Selected ions in the samples were scanned in MS-MS mode to eliminate the aromatic hydrocarbon signals and obtain clear chromatograms of the fatty acids.

Case study of combinatorial imaging: what protocol and what chlorophyll fluorescence image to use when visualizing infection of Arabidopsis thaliana by Pseudomonas syringae?

Localized infection of a plant can be mapped by a sequence of images capturing chlorophyll fluorescence transients in actinic light. Choice of the actinic light protocol co-determines fluorescence contrast between infected leaf segment and surrounding healthy tissue. Frequently, biology cannot predict with which irradiance protocol, in which fluorescence image of the sequence, and in which segment of the image there will be the highest contrast between the healthy and infected tissue.

Spatial distribution of dental fluorosis in roe deer (Capreolus capreolus) from North Bohemia (Czech Republic) and its relationships with environmental factors.

We assessed the spatial variation of fluoride load on the local ecosystem in the Czech part of the Ore Mountains region and its southern foothills - a heavily polluted part of Europe's "Black Triangle" region. Dental fluorosis in roe deer (Capreolus capreolus) served as a biomarker of fluoride exposure and thus as an indicator of environmental pollution by fluoride. The mean dental lesion index of fluorosis (DLI) calculated from the analyzed mandibles of wild roe deer (>or=2 years of age) was assigned to the hunting ground from which the specimens originated and classified into one of the eight fluorosis categories.

Structure and dynamics of the N-terminal loop of PsbQ from photosystem II of Spinacia oleracea.

Infrared and Raman spectroscopy were applied to identify restraints for the structure determination of the 20 amino acid loop between two beta-sheets of the N-terminal region of the PsbQ protein of the oxygen evolving complex of photosystem II from Spinacia oleracea by restraint-based homology modeling. One of the initial models has shown a stable fold of the loop in a 20 ns molecular dynamics simulation that is in accordance with spectroscopic data. Cleavage of the first 12 amino acids leads to a permanent drift in the root means square deviation of the protein backbone and induces major structural changes.