Effects of sand bar openings on some limnological variables in a hypertrophic tropical coastal lagoon of Brazil

This study describes the spatial and temporal dynamics of several physical, chemical and biological variables in the Grussai lagoon, and their relationship to ephemeral sand bar openings and to a constant in natura waste water input. The spatial variation in pH, dissolved oxygen, electrical conductivity, total alkalinity and nutrients (e.g. soluble reactive silicate, soluble reactive phosphate and ammonium) was associated to the anoxic and nutrient rich groundwater discharge, the development of aquatic macrophytes, the biological activities of phytoplanktonic community and the marine influence. During the period when the sand bar was closed (isolated), the lagoon water was supersaturated with dissolved oxygen and exhibited high values of pH (8–10), total alkalinity (3.000–5.000 μeq l^-1), and chlorophyll a contents (60-300 μg l^-1), and had low values of dissolved nutrients (nearly undetectable). These suggest a biological processes dominance. When the sand bar was opened, there was an enrichment with dissolved inorganic nutrients (e.g. ammonium and soluble reactive phosphorus up to 120 and 5 μM, respectively) and a decrease in pH (below 8), total alkalinity (below 3.000 μeq l^-1) and dissolved oxygen during the initial second to eight days. Subsequently there was a period when the physical and chemical characteristics of seawater prevailed. The lagoon returned chemical to the pre-opening water conditions in a few days (∼ 10–20). This quick return implies highly efficient biological mechanisms. The high levels of chlorophyll a, total nitrogen and phosphorus in the water column indicate a high eutrophication stage in the Grussai lagoon during the sand bar closed periods. This revised version was published online in July 2006 with corrections to the Cover Date.     

Globin and linker sequences of the giant extracellular hemoglobin from the leech Macrobdella decora

A detailed electrospray ionization mass spectrometric study of the 3.5-MDa hexagonal bilayer hemoglobin (HBL Hb) from the pond leech Macrobdella decora has shown it to consist of at least six 17-kDa globin chains, of which two are monomeric and the remaining four occur as disulfide-bonded heterodimers, and three 24-kDa nonglobin linker chains (Weber et al., J. Mol. Biol. 251: 703–720, 1995). The cDNA sequences of the five major constituent chains, globin chains IIA, IIB, B, and C and linker chain L1, are reported here. The globins and linkers share 30%–50% and 20%–30% identity, respectively, with other annelid sequences. Furthermore, IIB and C align with strain A of annelid sequences, whereas IIA and B align with the strain B sequences. Although chains B and C are monomeric, chains IIA and IIB form the main disulfide-bonded dimer. They also have some unusual features: the distal His (E7) is replaced by Phe in IIA, and the highly conserved CD1Phe is replaced by Leu in IIB. In spite of these unusual features, the functional properties of Macrobdella Hb are comparable to those of other HBL Hbs. A phylogenetic analysis of the globin sequences from Macrobdella, the polychaete Tylorrhynchus, the oligochaete Lumbricus, and the vestimentiferan Lamellibrachia, indicates that the two strains originated by gene duplication followed by additional duplication of each of the two strains. The mutation rate of the linkers appeared to be faster than that of the globin chains. The phylogenetic trees constructed using the Maximum Likelihood, Neighbor-Joining and Fitch methods showed the Macrobdella globin sequences to be closest to Lumbricus, in agreement with a view of annelid evolution in which the divergence of the polychaetes occurred before the divergence of the leeches from oligochaetes.     

Molecular mass and chain conformation of carboxymethylated derivatives of beta-glucan from sclerotia of Pleurotus tuber-regium

Seven water-insoluble (1 --> 3)-beta-D-glucan fractions TM8-1 to TM8-7 with weight-average molecular mass M(w) ranged from 2.22 to 77.4 x 10(4) obtained from the sclerotia of Pleurotus tuber-regium were carboxymethylated to produce the water-soluble fractions CTM8-1 to CTM8-7 with M(w) ranged from 3.87 to 87.8 x 10(4). The degree of substitution (DS) of CTM8 fractions was analyzed by ir and elemental analysis (EA) to be 0.3-0.68. The M(w) and the intrinsic viscosity [eta] of the CTM8 fractions were measured by size-exclusion chromatography combined with multiangle laser light scattering (SEC-MALLS), MALLS, and viscometry in phosphate buffer solution (PBS) at 37 degrees C. The dependencies of [eta] and radius of gyration (z) (1/2) on M(w) for the CTM8 samples were found to be [eta] = (8.82 +/- 0.03) x 10(-3) M(w)(0.78 +/- 0.04) (cm(3) g(-1)) and (z) (1/2) = (3.09 +/- 0.05) x 10(-3) M(w)(0.75 +/- 0.06) (nm) in the M(w) range from 3.87 x 10(4) to 53.2 x 10(4). Based on current theories for wormlike chain model, the conformational parameters of the CTM8 were obtained to be 790 (nm(-1)) for M(L), 9.6 (nm) for q, which were higher than those of the native TM8 fractions, suggesting a more extended flexible chain of CTM8 in PBS. On the whole, the CTM8 fractions showed higher antitumor activity than their corresponding TM8 fractions. In view of data from molecular parameters and bioactivity, the antitumor activity of the CTM8 fractions may be correlated to its water solubility and relatively extended chain.     

Molecular modeling of glycosyltransferases involved in the biosynthesis of blood group A,blood group B,Forssman, and iGb3 antigens and their interaction with substrates

A terminal alpha1-3 linked Gal or GalNAc sugar residue is the common structure found in several oligosaccharide antigens, such as blood groups A and B, the xeno-antigen, the Forssman antigen, and the isogloboside 3 (iGb3) glycolipid. The enzymes involved in the addition of this residue display strong amino acid sequence similarities, suggesting a common fold. From a recently solved crystal structure of the bovine alpha3-galactosyltransferase complexed with UDP, homology modeling methods were used to build the four other enzymes of this family in their locked conformation. Nucleotide-sugars, the Mn2+ ion, and oligosaccharide acceptors were docked in the models. Nine different amino acid regions are involved in the substrate binding sites. After geometry optimization of the complexes and analysis of the predicted structures, the basis of the specificities can be rationalized. In the nucleotide-sugar binding site, the specificity between Gal or GalNAc transferase activity is due to the relative size of two clue amino acids. In the acceptor site, the presence of up to three tryptophan residues define the complexity of the oligosaccharide that can be specifically recognized. The modeling study helps in rationalizing the crystallographic data obtained in this family and provides insights on the basis of substrate and donor recognition.     

Effects of Exotic Plant Invasions on Soil Nutrient Cycling Processes

Although it is generally acknowledged that invasions by exotic plant species represent a major threat to biodiversity and ecosystem stability, little attention has been paid to the potential impacts of these invasions on nutrient cycling processes in the soil. The literature on plant–soil interactions strongly suggests that the introduction of a new plant species, such as an invasive exotic, has the potential to change many components of the carbon (C), nitrogen (N), water, and other cycles of an ecosystem. I have reviewed studies that compare pool sizes and flux rates of the major nutrient cycles in invaded and noninvaded systems for invasions of 56 species. The available data suggest that invasive plant species frequently increase biomass and net primary production, increase N availability, alter N fixation rates, and produce litter with higher decomposition rates than co-occurring natives. However, the opposite patterns also occur, and patterns of difference between exotics and native species show no trends in some other components of nutrient cycles (for example, the size of soil pools of C and N). In some cases, a given species has different effects at different sites, suggesting that the composition of the invaded community and/or environmental factors such as soil type may determine the direction and magnitude of ecosystem-level impacts. Exotic plants alter soil nutrient dynamics by differing from native species in biomass and productivity, tissue chemistry, plant morphology, and phenology. Future research is needed to (a) experimentally test the patterns suggested by this data set; (b) examine fluxes and pools for which few data are available, including whole-site budgets; and (c) determine the magnitude of the difference in plant characteristics and in plant dominance within a community that is needed to alter ecosystem processes. Such research should be an integral component of the evaluation of the impacts of invasive species.     

Effect of constituting amino acid residue numbers on molecularly imprinted chiral recognition sites

In the present study, the effect of constituting amino acid residue numbers of oligopeptide derivatives, which are candidate materials to construct molecular recognition sites, on chiral recognition ability was investigated. Chiral recognition sites were formed from oligopeptide derivatives, of which constituting amino acid residue numbers were three to six, by adopting an alternative molecular imprinting. It was made clear that the number four, in other words, the tetrapeptide derivative, is the best candidate material to form a chiral recognition site.     

Conformational behavior of chondroitin and chondroitin sulfate in relation to their physical properties as inferred by molecular modeling

Chondroitin and chondroitin sulfates belong to the family of glycosaminoglycans. They are most widely distributed in animal tissues, where they are involved in structural functions and in cell-cell communication. Their basic structures consist of a disaccharidic repeating unit of beta-D-glucuronic acid (GlcA) and 2-acetamido-2-deoxy-beta-D-galactose (GalNAc), this latter being sulfated at different positions. Molecular mechanics has been applied to calculate the adiabatic energy maps for each of the constituting disaccharides of chondroitin, chondroitin 4-sulfate, and chondroitin 6-sulfate using the MM3 force field. Based on these maps, higher levels of structural organization have been simulated. On one hand, the disordered state is studied through a Metropolis-based algorithm; the resulting chains present a behavior of semirigid polymers, with an order of stiffness: chondroitin 4-sulfate > chondroitin > chondroitin 6-sulfate. On the other hand, the exploration of the stable ordered forms leads to numerous helical conformations of comparable energies. Several of these conformations correspond to the experimentally observed ones. The ability of coordination with cations has also been explored, resulting in a preferential stereospecificity for calcium ions when compared to sodium ions.     

Simulating structural and thermodynamic properties of carcinogen-damaged DNA

A pair of stereoisomeric covalent adducts to guanine in double-stranded DNA, derived from the reaction of mutagenic and tumorigenic metabolites of benzo[a]pyrene, have been well characterized structurally and thermodynamically. Both high-resolution NMR solution structures and an array of thermodynamic data are available for these 10S (+)- and 10R (-)-trans-anti -[BP]-N(2)-dG adducts in double-stranded deoxyoligonucleotides. The availability of experimentally well-characterized duplexes containing these two stereoisomeric guanine adducts provides an opportunity for evaluating the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method for computing thermodynamic properties from molecular dynamics ensembles. We have carried out 3-ns molecular dynamics simulations, using NMR solution structures as the starting models for the 10S (+)- and 10R (-)-trans-anti-dG adducts in a DNA duplex 11-mer using AMBER 6.0. We employed the MM-PBSA method to compute the free energies, enthalpies, and entropies of the two adducts. Our complete thermodynamic analysis agrees quite well with the full experimental thermodynamic characterization of these adducts, showing essentially equal stabilities of the two adducts. We also calculated the nuclear Overhauser effect (NOE) distances from the molecular dynamics trajectories, and compared them against the experimental NMR-derived NOE distances. Our results showed that the simulated structures are in good agreement with the NMR experimental NOE data. Furthermore, the molecular dynamics simulations provided new structural and biological insights. Specifically, the puzzling observation that the BP aromatic ring system in the 10S (+)-trans-anti-dG adduct is more exposed to the aqueous solvent than the 10R (-)-trans-anti-dG adduct, is rationalized in terms of the adduct structures. The structural and thermodynamic features of these stereoisomeric adducts are also discussed in relation to their reported low susceptibilities to nucleotide excision repair.     

Epidermal anatomy of Barthelopteris germarii from the Upper Carboniferous and Lower Permian of France and Germany

The epidermal anatomy of Barthelopteris germarii, a late Paleozoic seed fern, is described on the basis of material from the Upper Stephanian of Central France. A number of features are described for the first time for this species. Some have never been reported for late Paleozoic pteridosperms. Although our material is in most respects very similar to previously described material of B. germarii from Germany, there are also some striking differences, especially the peltate glandular trichomes that are very common in the French but completely absent in the German material. Their presence is most probably an ecological adaptation as in many modern plants. This and other epidermal and gross-morphological features (e.g., the presence of papillae on subsidiary cells of the stomata, anastomosing venation) indicate that B. germarii was well adapted to stressed conditions. Of more general interest is the preservation of the material. There appears to exist a clear relationship between the preservation of anticlinal walls and the thickness of the parenchymatic mesophyll; anticlinal walls are very well preserved where parenchyma was thin. Therefore, the absence of anticlinal walls in fossil cuticles, which has often been used as a taxonomic character, is not necessarily a primary feature.