SPATIO-TEMPORAL AND FUNCTIONAL STRUCTURE OF THE AMPHIPOD COMMUNITIES OFF SANTOS, SOUTHWESTERN ATLANTIC

The amphipod fauna was employed to investigate a bottom environmental gradient in the continental shelf adjacent to Santos Bay. The constant flow of less saline water from the estuarine complex of the Santos and Sao Vicente rivers besides the seasonal intrusion of the cold saline South Atlantic Central Water (SACW) bring a highly dynamic water regime to the area. Density, distribution, diversity and functional structure of the communities were studied on a depth gradient from 10 to 100 m on two cruises in contrasting seasons, winter 2005 and summer 2006. Twenty-one sediment samples were taken with a 0.09m(2) box corer. Temperature and salinity were measured at each station and an additional surface sediment sample was obtained with the box corer for granulometric and chemical analyses. Sixty species were collected on each survey and higher density values were found in summer. A priori one-way Analysis of Similarities (ANOSIM) indicated the existence of three different groups of amphipods related to the depth gradient: the Coastal group, the Mixed Zone group and the Deep Zone group. The Coastal Zone in both cruises was inhabited by a community presenting low diversity and density, besides high dominance of the infaunal tube-dweller Ampelisca paria; the area around 30 m presented the highest values of all the ecological indicators and the species showed several life styles; the outer area, situated between 50 and 100 m depth in the SACW domain, presented a community characterized by lower diversity and high biomass and density values. A season-depth ANOSIM showed the influence of depth and season for the Coastal and Mixed Zone groups whereas no seasonal difference was obtained for the Deep Zone group. The synergistic effect of the SACW and depth in the first place, followed by physical changes in substrate, seem to be the main factors controlling the fauna's distribution. In addition, the estuarine waters from Santos Bay apparently had no effect on the establishment of the environmental gradient observed on the adjacent shelf. Diversity, distribution, functional groups and trophic conditions of superficial sediments are discussed in the light of the main oceanographic processes present on the southern Brazilian shelf.

APTES-Modified RE2O3:Eu3+ Luminescent Beads: Structure and Properties

Europium-doped lanthanide oxide RE2O3:Eu3+ (RE = Y or Gd) luminescent beads, with a spherical shape and a diameter of 150 +/- 15 nm, have been modified by reaction with 3-aminopropyltriethoxysilane (APTES), in order to introduce reactive amine groups at their surfaces. The direct silanation has resulted in the formation of a nanometric layer at the surface of the beads, with an optimum grafting rate of 0.055 +/- 0.005 mol APTES/mol RE2O3. Fourier transform infrared (FTIR) and X-ray photoelectron (XPS) spectroscopies confirmed the condensation of an organosilane layer, made of cross-linked -O-Si-O-Si- and of groups -O-Si-R (with R = (CH2)(3)NH2 or O-Et). Titration of the accessible amine groups has been performed by simultaneously measuring the luminescence of grafted fluorescein isothiocyanate and that of core particles: there are about 2.3 X 10(4) (2.8 X 10(4)) -NH2 per Y2O3:Eu3+ (Gd2O3:Eu3+) bead. The isoelectronic point was shifted by one pH unit after APTES modification. The surface modification by APTES at least preserved (for Gd2O3:Eu3+) or improved (for Y2O3:Eu3+) the red emission of the beads.

First-principles studies of complex magnetism in Mn nanostructures on the Fe(001) surface

The magnetic properties of Mn nanostructures on the Fe(001) surface have been studied using the noncollinear first-principles real space-linear muffin-tin orbital-atomic sphere approximation method within density-functional theory. We have considered a variety of nanostructures such as adsorbed wires, pyramids, and flat and intermixed clusters of sizes varying from two to nine atoms. Our calculations of interatomic exchange interactions reveal the long-range nature of exchange interactions between Mn-Mn and Mn-Fe atoms. We have found that the strong dependence of these interactions on the local environment, the magnetic frustration, and the effect of spin-orbit coupling lead to the possibility of realizing complex noncollinear magnetic structures such as helical spin spiral and half-skyrmion.

Spectroscopic characterization and crystal structure of cis-Bis(N-(2-benzoyl)-N ',N '-diphenylthioureato-k O-2,S)nickel(II)

The title compound [Ni(C20H15N2OS)(2)] is prepared by the reaction of metal acetate with the corresponding acylthiourea derivative. The complex is characterized by elemental analysis, IR, H-1 and C-13 NMR, and its structure is determined by single crystal X-ray diffraction. The Ni(II) ion is coordinated by the S and O atoms of two N-benzoyl-N',N'-diphenylthiourea ligands in a slightly distorted square-planar coordination geometry. The two O and two S atoms are mutually cis to each other. The substance crystallizes triclinic (P-1 space group) with cell dimensions a = 10.7262(9) , b = 12.938(3) , c = 14.2085(12) , alpha = 74.650(4)A degrees, beta = 78.398(4)A degrees, gamma = 68.200(5)A degrees, and two formula units in the unit cell. The structure is very close to the related N-(2-furoyl) Ni complex reported previously.

Dissecting structure-function-stability relationships of a thermostable GH5-CBM3 cellulase from Bacillus subtilis 168

Cellulases participate in a number of biological events, such as plant cell wall remodelling, nematode parasitism and microbial carbon uptake. Their ability to depolymerize crystalline cellulose is of great biotechnological interest for environmentally compatible production of fuels from lignocellulosic biomass. However, industrial use of cellulases is somewhat limited by both their low catalytic efficiency and stability. In the present study, we conducted a detailed functional and structural characterization of the thermostable BsCe15A (Bacillus subtilis cellulase 5A), which consists of a GH5 (glycoside hydrolase 5) catalytic domain fused to a CBM3 (family 3 carbohydrate-binding module). NMR structural analysis revealed that the Bacillus CBM3 represents a new subfamily, which lacks the classical calcium-binding motif, and variations in NMR frequencies in the presence of cellopentaose showed the importance of polar residues in the carbohydrate interaction. Together with the catalytic domain, the CBM3 forms a large planar surface for cellulose recognition, which conducts the substrate in a proper conformation to the active site and increases enzymatic efficiency. Notably, the manganese ion was demonstrated to have a hyper-stabilizing effect on BsCel5A, and by using deletion constructs and X-ray crystallography we determined that this effect maps to a negatively charged motif located at the opposite face of the catalytic site.

Structure of the haptoglobin-haemoglobin complex

Red cell haemoglobin is the fundamental oxygen-transporting molecule in blood, but also a potentially tissue-damaging compound owing to its highly reactive haem groups. During intravascular haemolysis, such as in malaria and haemoglobinopathies(1), haemoglobin is released into the plasma, where it is captured by the protective acute-phase protein haptoglobin. This leads to formation of the haptoglobin-haemoglobin complex, which represents a virtually irreversible non-covalent protein-protein interaction(2). Here we present the crystal structure of the dimeric porcine haptoglobin-haemoglobin complex determined at 2.9 angstrom resolution. This structure reveals that haptoglobin molecules dimerize through an unexpected beta-strand swap between two complement control protein (CCP) domains, defining a new fusion CCP domain structure. The haptoglobin serine protease domain forms extensive interactions with both the alpha- and beta-subunits of haemoglobin, explaining the tight binding between haptoglobin and haemoglobin. The haemoglobin-interacting region in the alpha beta dimer is highly overlapping with the interface between the two alpha beta dimers that constitute the native haemoglobin tetramer. Several haemoglobin residues prone to oxidative modification after exposure to haem-induced reactive oxygen species are buried in the haptoglobin-haemoglobin interface, thus showing a direct protective role of haptoglobin. The haptoglobin loop previously shown to be essential for binding of haptoglobin-haemoglobin to the macrophage scavenger receptor CD163 (ref. 3) protrudes from the surface of the distal end of the complex, adjacent to the associated haemoglobin alpha-subunit. Small-angle X-ray scattering measurements of human haptoglobin-haemoglobin bound to the ligand-binding fragment of CD163 confirm receptor binding in this area, and show that the rigid dimeric complex can bind two receptors. Such receptor cross-linkage may facilitate scavenging and explain the increased functional affinity of multimeric haptoglobin-haemoglobin for CD163 (ref. 4).

Unraveling the structure of sugarcane bagasse after soaking in concentrated aqueous ammonia (SCAA) and ethanol production by Scheffersomyces (Pichia) stipitis

Abstract Background Fuel ethanol production from sustainable and largely abundant agro-residues such as sugarcane bagasse (SB) provides long term, geopolitical and strategic benefits. Pretreatment of SB is an inevitable process for improved saccharification of cell wall carbohydrates. Recently, ammonium hydroxide-based pretreatment technologies have gained significance as an effective and economical pretreatment strategy. We hypothesized that soaking in concentrated aqueous ammonia-mediated thermochemical pretreatment (SCAA) would overcome the native recalcitrance of SB by enhancing cellulase accessibility of the embedded holocellulosic microfibrils. Results In this study, we designed an experiment considering response surface methodology (Taguchi method, L8 orthogonal array) to optimize sugar recovery from ammonia pretreated sugarcane bagasse (SB) by using the method of soaking in concentrated aqueous ammonia (SCAA-SB). Three independent variables: ammonia concentration, temperature and time, were selected at two levels with center point. The ammonia pretreated bagasse (SCAA-SB) was enzymatically hydrolysed by commercial enzymes (Celluclast 1.5 L and Novozym 188) using 15 FPU/g dry biomass and 17.5 Units of β-glucosidase/g dry biomass at 50°C, 150 rpm for 96 h. A maximum of 28.43 g/l reducing sugars corresponding to 0.57 g sugars/g pretreated bagasse was obtained from the SCAA-SB derived using a 20% v/v ammonia solution, at 70°C for 24 h after enzymatic hydrolysis. Among the tested parameters, pretreatment time showed the maximum influence (p value, 0.053282) while ammonia concentration showed the least influence (p value, 0.612552) on sugar recovery. The changes in the ultra-structure and crystallinity of native SCAA-SB and enzymatically hydrolysed SB were observed by scanning electron microscopy (SEM), x-ray diffraction (XRD) and solid-state 13C nuclear magnetic resonance (NMR) spectroscopy. The enzymatic hydrolysates and solid SCAA-SB were subjected to ethanol fermentation under separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) by Scheffersomyces (Pichia) stipitis NRRL Y-7124 respectively. Higher ethanol production (10.31 g/l and yield, 0.387 g/g) was obtained through SSF than SHF (3.83 g/l and yield, 0.289 g/g). Conclusions SCAA treatment showed marked lignin removal from SB thus improving the accessibility of cellulases towards holocellulose substrate as evidenced by efficient sugar release. The ultrastructure of SB after SCAA and enzymatic hydrolysis of holocellulose provided insights of the degradation process at the molecular level.

Interspecific variation of the bacterial community structure in the phyllosphere of the three major plant components of mangrove forests

Mangrove forests encompass a group of trees species that inhabit the intertidal zones, where soil is characterized by the high salinity and low availability of oxygen. The phyllosphere of these trees represent the habitat provided on the aboveground parts of plants, supporting in a global scale, a large and complex microbial community. The structure of phyllosphere communities reflects immigration, survival and growth of microbial colonizers, which is influenced by numerous environmental factors in addition to leaf physical and chemical properties. Here, a combination of culture-base methods with PCR-DGGE was applied to test whether local or plant specific factors shape the bacterial community of the phyllosphere from three plant species (Avicenia shaueriana, Laguncularia racemosa and Rhizophora mangle), found in two mangroves. The number of bacteria in the phyllosphere of these plants varied between 3.62 x 10(4) in A. schaeriana and 6.26 x 10³ in R. mangle. The results obtained by PCR-DGGE and isolation approaches were congruent and demonstrated that each plant species harbor specific bacterial communities in their leaves surfaces. Moreover, the ordination of environmental factors (mangrove and plant species), by redundancy analysis (RDA), also indicated that the selection exerted by plant species is higher than mangrove location on bacterial communities at phyllosphere.

Spatio-temporal and functional structure of the amphipod communities off Santos, Southwestern Atlantic

The amphipod fauna was employed to investigate a bottom environmental gradient in the continental shelf adjacent to Santos Bay. The constant flow of less saline water from the estuarine complex of the Santos and São Vicente rivers besides the seasonal intrusion of the cold saline South Atlantic Central Water (SACW) bring a highly dynamic water regime to the area. Density, distribution, diversity and functional structure of the communities were studied on a depth gradient from 10 to 100 m on two cruises in contrasting seasons, winter 2005 and summer 2006. Twenty-one sediment samples were taken with a 0.09m² box corer. Temperature and salinity were measured at each station and an additional surface sediment sample was obtained with the box corer for granulometric and chemical analyses. Sixty species were collected on each survey and higher density values were found in summer. A priori one-way Analysis of Similarities (ANOSIM) indicated the existence of three different groups of amphipods related to the depth gradient: the Coastal group, the Mixed Zone group and the Deep Zone group. The Coastal Zone in both cruises was inhabited by a community presenting low diversity and density, besides high dominance of the infaunal tube-dweller Ampelisca paria; the area around 30 m presented the highest values of all the ecological indicators and the species showed several life styles; the outer area, situated between 50 and 100 m depth in the SACW domain, presented a community characterized by lower diversity and high biomass and density values. A season-depth ANOSIM showed the influence of depth and season for the Coastal and Mixed Zone groups whereas no seasonal difference was obtained for the Deep Zone group. The synergistic effect of the SACW and depth in the first place, followed by physical changes in substrate, seem to be the main factors controlling the fauna's distribution. In addition, the estuarine waters from Santos Bay apparently had no effect on the establishment of the environmental gradient observed on the adjacent shelf. Diversity, distribution, functional groups and trophic conditions of superficial sediments are discussed in the light of the main oceanographic processes present on the southern Brazilian shelf.

Variability in light absorption and scattering of phytoplankton in Patagonian waters: Role of community size structure and pigment composition

Intense phytoplankton blooms were observed along the Patagonian shelf-break with satellite ocean color data, but few in situ optical observations were made in that region. We examine the variability of phytoplankton absorption and particulate scattering coefficients during such blooms on the basis of field data. The chlorophyll-a concentration, [Chla], ranged from 0.1 to 22.3 mg m−3 in surface waters. The size fractionation of [Chla] showed that 80% of samples were dominated by nanophytoplankton (N-group) and 20% by microphytoplankton (M-group). Chlorophyll-specific phytoplankton absorption coefficients at 440 and 676 nm, a*ph(440) and a*ph(676), and particulate scattering coefficient at 660 nm, b*p(660), ranged from 0.018 to 0.173, 0.009 to 0.046, and 0.031 to 2.37 m2 (mg Chla)−1, respectively. Both a*ph(440) and a*ph(676) were statistically higher for the N-group than M-group and also considerably higher than expected from global trends as a function of [Chla]. This result suggests that size of phytoplankton cells in Patagonian waters tends to be smaller than in other regions at similar [Chla]. The phytoplankton cell size parameter, Sf, derived from phytoplankton absorption spectra, proved to be useful for interpreting the variability in the data around the general inverse dependence of a*ph(440), a*ph(676), and b*p(660) on [Chla]. Sf also showed a pattern along the increasing trend of a*ph(440) and a*ph(676) as a function of the ratios of some accessory pigments to [Chla]. Our results suggest that the variability in phytoplankton absorption and scattering coefficients in Patagonian waters is caused primarily by changes in the dominant phytoplankton cell size accompanied by covariation in the concentrations of accessory pigments.

Structure of the PilZ-FimXEAL-c-di-GMP complex responsible for the regulation of bacterial type IV pilus biogenesis

Signal transduction pathways mediated by cyclic-bis(3'→5')-dimeric GMP (c-di-GMP) control many important and complex behaviors in bacteria. C-di-GMP is synthesized through the action of GGDEF domains that possess diguanylate cyclase activity and is degraded by EAL or HD-GYP domains with phosphodiesterase activity. There is mounting evidence that some important c-di-GMP-mediated pathways require protein-protein interactions between members of the GGDEF, EAL, HD-GYP and PilZ protein domain families. For example, interactions have been observed between PilZ and the EAL domain from FimX of Xanthomonas citri (Xac). FimX and PilZ are involved in the regulation of type IV pilus biogenesis via interactions of the latter with the hexameric PilB ATPase associated with the bacterial inner membrane. Here, we present the crystal structure of the ternary complex made up of PilZ, the FimX EAL domain (FimXEAL) and c-di-GMP. PilZ interacts principally with the lobe region and the N-terminal linker helix of the FimXEAL. These interactions involve a hydrophobic surface made up of amino acids conserved in a non-canonical family of PilZ domains that lack intrinsic c-di-GMP binding ability and strand complementation that joins β-sheets from both proteins. Interestingly, the c-di-GMP binds to isolated FimXEAL and to the PilZ-FimXEAL complex in a novel conformation encountered in c-di-GMP-protein complexes in which one of the two glycosidic bonds is in a rare syn conformation while the other adopts the more common anti conformation. The structure points to a means by which c-di-GMP and PilZ binding could be coupled to FimX and PilB conformational states