SDSL-ESR-based protein structure characterization

As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be seen in the number of protein structures published in the Protein Data Bank. This is especially the case for less-ordered, more hydrophobic and more flexible protein systems. The lack of efficient methods for structure determination calls for urgent development of a new class of biophysical techniques. This work attempts to address this problem with a novel combination of site-directed spin labelling electron spin resonance spectroscopy (SDSL-ESR) and protein structure modelling, which is coupled by restriction of the conformational spaces of the amino acid side chains. Comparison of the application to four different protein systems enables us to generalize the new method and to establish a general procedure for determination of protein structur

Nekton communities of an intertidal creek of an European estuarine brackish marsh

The utilization of an estuarine brackish marsh in the Westerschelde estuary (southwest Netherlands) by fish and crustaceans visiting the intertidal creeks at rising tides was investigated over an 18 mo period. Samples were collected every month over a tidal cycle. A stow net passively fished the nekton migrating in and out of the marsh habitat. Simultaneous measurements of current speed and waterheight allowed for quantification of the catches. Multivariate clustering and ordination techniques were applied to assess temporal changes in the nekton assemblage. A total of 68 fish and crustacean species were caught but only 38 were regular visitors of the marsh creek. The marsh nekton community proved to have a very stable character. Only 40% of the observed variance could be explained. The seasonal appearance of juvenile stages of fish and crustaceans was found to differentiate between spring and summer-autumn communities. The environmental variables measured (i.e. temperature, salinity, oxygen concentration and detritus standing stock) did not correlate well with the observed changes in community structure. The mysid shrimp Neomysis integer dominated the community, both in density and biomass, during most of the year. Early postlarval flounder Pleuronectes flesus characterized the spring nekton assemblage. Early postlarval brown shrimp Crangon crangon was abundant from spring through autumn. In late summer juveniles of seabass Dicentrarchus labrax, common goby Pomatoschistus microps and shore crab Carcinus maenas were typical members of the marsh creek nekton. The hyperbenthic fauna of the marsh was comparable to the hyperbenthos found in the adjacent subtidal parts of the Westerschelde estuary while the epifauna of both areas differed substantially. It is argued that the marsh under study is a nursery ground for only a small number of estuarine inhabitants: C. crangon, P. flesus, C. maenas, P. microps, D. labrax and possibly 2 mullet species. Adult flounder, adult and juvenile common goby, juvenile seabass and the early postlarval brown shrimp all use the creeks as feeding ground, mainly preying upon the creek infauna and mysids. Given the high abundance of hyperbenthic mysid shrimp in the marsh and their presumed role in detritus-based food chains, we believe marsh studies should not refrain from considering this component of the nekton. This is the first study reporting on the nekton use of a European marsh. The need for similar research in other European marshes is stressed

High critical temperature above Tg may contribute to the stability of biological systems

In this study, we characterized the molecular mobility around Tg in sugars, poly-L-lysine and dry desiccation-tolerant biological systems, using ST-EPR, 1H-NMR, and FTIR spectroscopy, to understand the nature and composition of biological glasses. Two distinct changes in the temperature dependence of the rotational correlation time (R) of the spin probe 3-carboxy-proxyl or the second moment (M2) were measured in sugars and poly-L-lysine. With heating, the first change was associated with the melting of the glassy state (Tg). The second change (Tc), at which R abruptly decreased over several orders of magnitude, was found to correspond with the so-called cross-over temperature, where the dynamics changed from solid-like to liquid-like. The temperature interval between Tg and Tc increased in the order of sucrose 50°C, implying that the stability above Tg improved in the same order. These differences in temperature-dependent mobilities above Tg suggest that proteins rather than sugars play an important role in the intracellular glass formation. The exceptionally high Tc of intracellular glasses is expected to provide excellent long-term stability to dry organisms, maintaining a slow molecular motion in the cytoplasm even at temperatures far above Tg

The root/rhizome system of seagrasses: an asset and a burden

Large-scale declines in seagrass vegetation have been frequently observed in recent decades. Many of these declines can be traced to the reduction of light levels in the water column. In this paper, it is argued that the root/rhizome system offers a competitive advantage in nutrient-poor waters, but that it makes the plant vulnerable when changes in water quality lead to reduction of incident light. Seagrasses are capable of exploiting the nutrient stocks of both the water column and the sediment pore water, by leaves and roots, respectively. A survey of the literature shows that the median concentrations of water-column ammonium and phosphate in seagrass beds worldwide are 1.7 and 0.35 mu M, respectively, whereas the same compounds in the pore water of the root zone reach median concentrations of 60 and 6.5 mu M. The dual possibilities for nutrient uptake may underlie the apparent lack of strongly developed nutrient conservation strategies in seagrasses. The possession of roots becomes a disadvantage when the photosynthetically active radiation available to the plants decreases. At saturating light levels, the maximum rate of net photosynthesis (measured as O-2 production) of the leaves typically exceeds leaf respiration (measured as O-2 consumption) about 5 times. In low-light environments, the respiring below-ground biomass (which can greatly exceed the above-ground biomass) can be a considerable burden to the carbon balance of the plant, limiting its survival potential. In addition, secondary and tertiary effects of light reduction involving the roots and rhizomes may undermine plant vitality as well. Leaf photosynthesis is the major source of oxygen for the roots and rhizomes. Hence, decreased photosynthetic activity following light reduction may lead to hypoxic or anoxic conditions in the below-ground organs, presumably making them vulnerable to carbon starvation. A decreased flux of oxygen to the roots and rhizomes also restricts the possibilities for oxidation of sediment sulphide, a known phytotoxin, because release of oxygen into the rhizosphere will diminish. The cascade effects of light reduction which involve the below-ground organs of seagrasses are little studied. More insight into the functioning of the root!rhizome system and into the interactions between this system and the sediment environment is needed to fully understand the vulnerability of seagrasses to light reduction. [KEYWORDS: seagrasses; population declines; roots; rhizomes photosynthesis; respiration; light reduction Zostera-marina-l; san-francisco bay; thalassia-testudinum; cymodocea-nodosa; l eelgrass; syringodium-filiforme; posidonia-oceanica; heterozostera-tasmanica; depth distribution; sulfate-reduction]