Abundance and biomass of phytoplankton in the western part of the Black Sea during the R/V Akademik cruise Ak082001 in August 2001

The dataset is composed of 41 samples from 10 stations. The phytoplankton samples were collected by 5l Niskin bottles attached to the CTD system. The sampling depths were selected according to the CTD profile and the in situ fluorometer readings: surface, temperature, salinity and fluorescence gradients and 1 m above the bottom. At some stations phytoplankton net samples (20 µm mesh-size) were collected to assist species biodiversity examination. The samples (1l sea water) were preserved in 4% buffered to pH 8-8.2 with disodiumtetraborate formaldehyde solution and stored in plastic containers. On board at each station few live samples were qualitatively examined under microscope for preliminary analysis of taxonomic composition and dominant species. The taxon-specific phytoplankton abundance samples were concentrated down to 50 cm**3 by slow decantation after storage for 20 days in a cool and dark place. The species identification was done under light microscope OLIMPUS-BS41 connected to a video-interactive image analysis system at magnification of the ocular 10X and objective - 40X. A Sedgwick-Rafter camera (1ml) was used for counting. 400 specimen were counted for each sample, while rare and large species were checked in the whole sample (Manual of phytoplankton, 2005). Species identification was mainly after Carmelo T. (1997) and Fukuyo, Y. (2000). Total phytoplankton abundance was calculated as sum of taxon-specific abundances. Total phytoplankton biomass was calculated as sum of taxon-specific biomasses. The cell biovolume was determined based on morpho-metric measurement of phytoplankton units and the corresponding geometric shapes as described in detail in (Edier, 1979).

Tree height integrated into pantropical forest biomass estimates

Aboveground tropical tree biomass and carbon storage estimates commonly ignore tree height (H). We estimate the effect of incorporating H on tropics-wide forest biomass estimates in 327 plots across four continents using 42 656 H and diameter measurements and harvested trees from 20 sites to answer the following questions: 1. What is the best H-model form and geographic unit to include in biomass models to minimise site-level uncertainty in estimates of destructive biomass? 2. To what extent does including H estimates derived in (1) reduce uncertainty in biomass estimates across all 327 plots? 3. What effect does accounting for H have on plot- and continental-scale forest biomass estimates? The mean relative error in biomass estimates of destructively harvested trees when including H (mean 0.06), was half that when excluding H (mean 0.13). Power- andWeibull-H models provided the greatest reduction in uncertainty, with regional Weibull-H models preferred because they reduce uncertainty in smaller-diameter classes (?40 cm D) that store about one-third of biomass per hectare in most forests. Propagating the relationships from destructively harvested tree biomass to each of the 327 plots from across the tropics shows that including H reduces errors from 41.8Mgha?1 (range 6.6 to 112.4) to 8.0Mgha?1 (?2.5 to 23.0). For all plots, aboveground live biomass was ?52.2 Mgha?1 (?82.0 to ?20.3 bootstrapped 95%CI), or 13%, lower when including H estimates, with the greatest relative reductions in estimated biomass in forests of the Brazilian Shield, east Africa, and Australia, and relatively little change in the Guiana Shield, central Africa and southeast Asia. Appreciably different stand structure was observed among regions across the tropical continents, with some storing significantly more biomass in small diameter stems, which affects selection of the best height models to reduce uncertainty and biomass reductions due to H. After accounting for variation in H, total biomass per hectare is greatest in Australia, the Guiana Shield, Asia, central and east Africa, and lowest in eastcentral Amazonia, W. Africa, W. Amazonia, and the Brazilian Shield (descending order). Thus, if tropical forests span 1668 million km2 and store 285 Pg C (estimate including H), then applying our regional relationships implies that carbon storage is overestimated by 35 PgC (31?39 bootstrapped 95%CI) if H is ignored, assuming that the sampled plots are an unbiased statistical representation of all tropical forest in terms of biomass and height factors. Our results show that tree H is an important allometric factor that needs to be included in future forest biomass estimates to reduce error in estimates of tropical carbon stocks and emissions due to deforestation.

Agronomic properties of biochars from different manure wastes

Biochar research has focused in the last years in the use of wood or grass derived materials for carbon sequestration. However, manure derived biochar can provide other benefits after soil addition, including nutrient supply. At present, there is an incomplete understanding of pyrolysis on manures. In order to understand the benefits obtained after addition of these types of materials to the soil, an experiment involving the use of different manures and pyrolysis temperatures was performed. Five manure wastes were selected for this experiment: cattle manure (E); cattle manure mixed with straw (EP), chicken manure (G), chicken manure mixed with sawdust (GS) and pig slurry (PC). Unpyrolyzed samples were compared to biochars prepared at 300 and 500?C. Relevant properties for agronomic purposes were determined, including pH, electrical conductivity, nutrient content, metal content, proximate analysis and carbon thermostability. Our results show that biochars tailored for different purposes can be prepared after a careful choice of feedstock and pyrolysis temperature.

The impact of soil salinity on the yield, composition and physiology of the bioenergy grass Miscanthus × giganteus

Funded by OPTIMA Biotechnology & Biological Sciences Research Council (BBSRC) Institute Strategic Programme Energy Grasses & Biorefining. Grant Number: BBS/E/W/10963A01 Defra GIANT LINK

Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases

The 2.15-Å resolution cocrystal structure of EcoRV endonuclease mutant T93A complexed with DNA and Ca2+ ions reveals two divalent metals bound in one of the active sites. One of these metals is ligated through an inner-sphere water molecule to the phosphate group located 3′ to the scissile phosphate. A second inner-sphere water on this metal is positioned approximately in-line for attack on the scissile phosphate. This structure corroborates the observation that the pro-SP phosphoryl oxygen on the adjacent 3′ phosphate cannot be modified without severe loss of catalytic efficiency. The structural equivalence of key groups, conserved in the active sites of EcoRV, EcoRI, PvuII, and BamHI endonucleases, suggests that ligation of a catalytic divalent metal ion to this phosphate may occur in many type II restriction enzymes. Together with previous cocrystal structures, these data allow construction of a detailed model for the pretransition state configuration in EcoRV. This model features three divalent metal ions per active site and invokes assistance in the bond-making step by a conserved lysine, which stabilizes the attacking hydroxide ion nucleophile.

In vitro selection for altered divalent metal specificity in the RNase P RNA

The ribozyme RNase P absolutely requires divalent metal ions for catalytic function. Multiple Mg2+ ions contribute to the optimal catalytic efficiency of RNase P, and it is likely that the tertiary structure of the ribozyme forms a specific metal-binding pocket for these ions within the active-site. To identify base moieties that contribute to catalytic metal-binding sites, we have used in vitro selection to isolate variants of the Escherichia coli RNase P RNA with altered specificities for divalent metal. RNase P RNA variants with increased activity in Ca2+ were enriched over 18 generations of selection for catalysis in the presence of Ca2+, which is normally disfavored relative to Mg2+. Although a wide spectrum of mutations was found in the generation-18 clones, only a single point mutation was common to all clones: a cytosine-to-uracil transition at position 70 (E. coli numbering) of RNase P. Analysis of the C70U point mutant in a wild-type background confirmed that the identity of the base at position 70 is the sole determinant of Ca2+ selectivity. It is noteworthy that C70 lies within the phylogenetically well conserved J3/4-P4-J2/4 region, previously implicated in Mg2+ binding. Our finding that a single base change is sufficient to alter the metal preference of RNase P is further evidence that the J3/4-P4-J2/4 domain forms a portion of the ribozyme’s active site.

An amino acid as a cofactor for a catalytic polynucleotide

Natural ribozymes require metal ion cofactors that aid both in structural folding and in chemical catalysis. In contrast, many protein enzymes produce dramatic rate enhancements using only the chemical groups that are supplied by their constituent amino acids. This fact is widely viewed as the most important feature that makes protein a superior polymer for the construction of biological catalysts. Herein we report the in vitro selection of a catalytic DNA that uses histidine as an active component for an RNA cleavage reaction. An optimized deoxyribozyme from this selection requires l-histidine or a closely related analog to catalyze RNA phosphoester cleavage, producing a rate enhancement of ≈1-million-fold over the rate of substrate cleavage in the absence of enzyme. Kinetic analysis indicates that a DNA–histidine complex may perform a reaction that is analogous to the first step of the proposed catalytic mechanism of RNase A, in which the imidazole group of histidine serves as a general base catalyst. Similarly, ribozymes of the “RNA world” may have used amino acids and other small organic cofactors to expand their otherwise limited catalytic potential.

Toward a quantum-mechanical description of metal-assisted phosphoryl transfer in pyrophosphatase

The wealth of kinetic and structural information makes inorganic pyrophosphatases (PPases) a good model system to study the details of enzymatic phosphoryl transfer. The enzyme accelerates metal-complexed phosphoryl transfer 1010-fold: but how? Our structures of the yeast PPase product complex at 1.15 Å and fluoride-inhibited complex at 1.9 Å visualize the active site in three different states: substrate-bound, immediate product bound, and relaxed product bound. These span the steps around chemical catalysis and provide strong evidence that a water molecule (Onu) directly attacks PPi with a pKa vastly lowered by coordination to two metal ions and D117. They also suggest that a low-barrier hydrogen bond (LBHB) forms between D117 and Onu, in part because of steric crowding by W100 and N116. Direct visualization of the double bonds on the phosphates appears possible. The flexible side chains at the top of the active site absorb the motion involved in the reaction, which may help accelerate catalysis. Relaxation of the product allows a new nucleophile to be generated and creates symmetry in the elementary catalytic steps on the enzyme. We are thus moving closer to understanding phosphoryl transfer in PPases at the quantum mechanical level. Ultra-high resolution structures can thus tease out overlapping complexes and so are as relevant to discussion of enzyme mechanism as structures produced by time-resolved crystallography.

Monitoring the structure of Escherichia coli RNase P RNA in the presence of various divalent metal ions

Lead(II)-induced cleavage can be used as a tool to probe conformational changes in RNA. In this report, we have investigated the conformation of M1 RNA, the catalytic subunit of Escherichia coli RNase P, by studying the lead(II)-induced cleavage pattern in the presence of various divalent metal ions. Our data suggest that the overall conformation of M1 RNA is very similar in the presence of Mg2+, Mn2+, Ca2+, Sr2+ and Ba2+, while it is changed compared to the Mg2+-induced conformation in the presence of other divalent metal ions, Cd2+ for example. We also observed that correct folding of some M1 RNA domains is promoted by Pb2+, while folding of other domain(s) requires the additional presence of other divalent metal ions, cobalt(III) hexamine or spermidine. Based on the suppression of Pb2+ cleavage at increasing concentrations of various divalent metal ions, our findings suggest that different divalent metal ions bind with different affinities to M1 RNA as well as to an RNase P hairpin–loop substrate and yeast tRNAPhe. We suggest that this approach can be used to obtain information about the relative binding strength for different divalent metal ions to RNA in general, as well as to specific RNA divalent metal ion binding sites. Of those studied in this report, Mn2+ is generally among the strongest RNA binders.

A structure-based catalytic mechanism for the xanthine oxidase family of molybdenum enzymes.

The crystal structure of the xanthine oxidase-related molybdenum-iron protein aldehyde oxido-reductase from the sulfate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas (Mop) was analyzed in its desulfo-, sulfo-, oxidized, reduced, and alcohol-bound forms at 1.8-A resolution. In the sulfo-form the molybdenum molybdopterin cytosine dinucleotide cofactor has a dithiolene-bound fac-[Mo, = O, = S, ---(OH2)] substructure. Bound inhibitory isopropanol in the inner compartment of the substrate binding tunnel is a model for the Michaelis complex of the reaction with aldehydes (H-C = O,-R). The reaction is proposed to proceed by transfer of the molybdenum-bound water molecule as OH- after proton transfer to Glu-869 to the carbonyl carbon of the substrate in concert with hydride transfer to the sulfido group to generate [MoIV, = O, -SH, ---(O-C = O, -R)). Dissociation of the carboxylic acid product may be facilitated by transient binding of Glu-869 to the molybdenum. The metal-bound water is replenished from a chain of internal water molecules. A second alcohol binding site in the spacious outer compartment may cause the strong substrate inhibition observed. This compartment is the putative binding site of large inhibitors of xanthine oxidase.

Reconsideration of the catalytic center and mechanism of mammalian paraoxonase/arylesterase.

For three decades, mammalian paraoxonase (A-esterase, aromatic esterase, arylesterase; PON, EC 3.1.8.1) has been thought to be a cysteine esterase demonstrating structural and mechanistic homologies with the serine esterases (cholinesterases and carboxyesterases). Human, mouse, and rabbit PONs each contain only three cysteine residues, and their positions within PON have been conserved. In purified human PON, residues Cys-41 and Cys-352 form an intramolecular disulfide bond and neither could function as an active-center cysteine. Highly purified, enzymatically active PON contains a single titratable sulfhydryl group. Thus, Cys-283 is the only probable candidate for an active-center cysteine. Through site-directed mutagenesis of the human cDNA, Cys-283 was replaced with either serine (C283S) or alanine (C283A). The expressed C283 (wild-type) enzyme was inactivated by para-hydroxymercuribenzoate, but the C283S and C283A mutant enzymes were not inactivated. C283A and C283S mutant enzymes retained both paraoxonase and arylesterase activities, and the Km values for paraoxon and phenyl acetate were similar to those of the wild type. Clearly, residue Cys-283 is free in active PON, but a free sulfhydryl group is not required for either paraoxonase or arylesterase activities. Consequently, it is necessary to examine other models for the active-site structure and catalytic mechanism of PON.

Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase.

Escherichia coli RuvC protein is a specific endonuclease that resolves Holliday junctions during homologous recombination. Since the endonucleolytic activity of RuvC requires a divalent cation and since 3 or 4 acidic residues constitute the catalytic centers of several nucleases that require a divalent cation for the catalytic activity, we examined whether any of the acidic residues of RuvC were required for the nucleolytic activity. By site-directed mutagenesis, we constructed a series of ruvC mutant genes with similar amino acid replacements in 1 of the 13 acidic residues. Among them, the mutant genes with an alteration at Asp-7, Glu-66, Asp-138, or Asp-141 could not complement UV sensitivity of a ruvC deletion strain, and the multicopy mutant genes showed a dominant negative phenotype when introduced into a wild-type strain. The products of these mutant genes were purified and their biochemical properties were studied. All of them retained the ability to form a dimer and to bind specifically to a synthetic Holliday junction. However, they showed no, or extremely reduced, endonuclease activity specific for the junction. These 4 acidic residues, which are dispersed in the primary sequence, are located in close proximity at the bottom of the putative DNA binding cleft in the three-dimensional structure. From these results, we propose that these 4 acidic residues constitute the catalytic center for the Holliday junction resolvase and that some of them play a role in coordinating a divalent metal ion in the active center.

Gene for the catalytic subunit of the human DNA-activated protein kinase maps to the site of the XRCC7 gene on chromosome 8.

The DNA-activated serine/threonine protein kinase (DNA-PK) is composed of a large (approximately 460 kDa) catalytic polypeptide (DNA-PKcs) and Ku, a heterodimeric DNA-binding component (p70/p80) that targets DNA-PKcs to DNA. A 41-kbp segment of the DNA-PKcs gene was isolated, and a 7902-bp segment was sequenced. The sequence contains a polymorphic Pvu II restriction enzyme site, and comparing the sequence with that of the cDNA revealed the positions of nine exons. The DNA-PKcs gene was mapped to band q11 of chromosome 8 by in situ hybridization. This location is coincident with that of XRCC7, the gene that complements the DNA double-strand break repair and V(D)J recombination defects (where V is variable, D is diversity, and J is joining) of hamster V3 and murine severe combined immunodeficient (scid) cells.