DNA alignment and Bayesian trees of partial sequences of COI, COIII and the haemocyanin functional unit f-g of 28 octopod species

Background: Octopods have successfully colonised the world's oceans from the tropics to the poles. Yet, successful persistence in these habitats has required adaptations of their advanced physiological apparatus to compensate impaired oxygen supply. Their oxygen transporter haemocyanin plays a major role in cold tolerance and accordingly has undergone functional modifications to sustain oxygen release at sub-zero temperatures. However, it remains unknown how molecular properties evolved to explain the observed functional adaptations. We thus aimed to assess whether natural selection affected molecular and structural properties of haemocyanin that explains temperature adaptation in octopods. Results: Analysis of 239 partial sequences of the haemocyanin functional units (FU) f and g of 28 octopod species of polar, temperate, subtropical and tropical origin revealed natural selection was acting primarily on charge properties of surface residues. Polar octopods contained haemocyanins with higher net surface charge due to decreased glutamic acid content and higher numbers of basic amino acids. Within the analysed partial sequences, positive selection was present at site 2545, positioned between the active copper binding centre and the FU g surface. At this site, methionine was the dominant amino acid in polar octopods and leucine was dominant in tropical octopods. Sites directly involved in oxygen binding or quaternary interactions were highly conserved within the analysed sequence. Conclusions: This study has provided the first insight into molecular and structural mechanisms that have enabled octopods to sustain oxygen supply from polar to tropical conditions. Our findings imply modulation of oxygen binding via charge-charge interaction at the protein surface, which stabilize quaternary interactions among functional units to reduce detrimental effects of high pH on venous oxygen release. Of the observed partial haemocyanin sequence, residue 2545 formed a close link between the FU g surface and the active centre, suggesting a role as allosteric binding site. The prevalence of methionine at this site in polar octopods, implies regulation of oxygen affinity via increased sensitivity to allosteric metal binding. High sequence conservation of sites directly involved in oxygen binding indicates that functional modifications of octopod haemocyanin rather occur via more subtle mechanisms, as observed in this study.

Zooplankton abundance and biomass along transects seaward from the coastline of the White Sea in August 2006 and 2007

Distribution patterns of water temperature, salinity, current velocities, suspended matter concentration, bottom contour, and zooplankton abundance were studied in relation to marine-riverine interactions and tide/ebb phases for coast lines of different configurations in the White Sea during cruises of R/V Ekolog (August of 2006 and 2007). Significant difference in manifestation of combined effect of marine and riverine impacts (estuarine concave relief) and only marine impact (open-sea straight line portion) was observed. This results in both variations in sea water level and distribut patterns of suspended matter and zooplankton.

Inorganic and organic geochemistry and sediment descriptions at DSDP Hole 93-603B

About one hundred samples of sediments and rocks recovered in Hole 603B were analyzed for type, abundance, and isotopic composition of organic matter, using a combination of Rock-Eval pyrolysis, C-H-N-S elemental analysis, and isotope-ratio mass spectrometry. Concentrations of major, minor, and trace inorganic elements were determined with a combination of X-ray fluorescence and induction-coupled plasma spectrometry. The oldest strata recovered in Hole 603B (lithologic Unit V) consist of interbedded light-colored limestones and marlstones, and black calcareous claystones of Neocomian age. The inorganic and organic geochemical results suggest a very terrigenous aspect to the black claystones. The organic geochemical results indicate that the limestones and marlstones contain a mixture of highly degraded marine and terrestrial organic matter. Comparison of the Neocomian carbonates at Site 603 with those on the other side of the North Atlantic, off Northwest Africa at Site 367, shows that the organic matter at Site 367 contains more marine organic matter, as indicated by higher pyrolysis hydrogen indices and lighter values of d13C. Comparison of inorganic geochemical results for the carbonate lithologies at Site 603 with those for carbonate lithologies at Site 367 suggests that the Site 603 carbonates may contain clastic material from both North American and African sources. The black claystones at Site 603, on the other hand, probably were derived almost entirely from North American clastic sources. Lithologic Unit IV overlying the Neocomian carbonates, consists of interbedded red, green, and black claystones. The black claystones at Site 603 contain more than ten times the organic carbon concentration of the interbedded green claystones. The average concentration of organic carbon in the black claystones (2.8%), however, is low relative to most mid-Cretaceous black claystones and shales in the Atlantic, particularly those found off Northwest Africa. The geochemical data all suggest that the organic matter in the black claystones is more abundant but generally more degraded than the organic matter in the green claystones, and that it was derived mainly from terrestrial sources and deposited in oxygenated bottom waters. The increased percentage of black claystone beds in the upper Cenomanian section, and the presence of more hydrogen-rich organic matter in this part of the section, probably resulted from the increased production and accumulation of marine organic matter that is represented worldwide near the Cenomanian/Turonian boundary in deep-sea and land sections. A few upper Cenomanian black claystone samples that have hydrogen indices > 150 also contain particularly high concentrations of V and Zn. Most samples of black claystone, however, are not particularly metal-rich compared with other black claystones and shales. Compared with red claystones from lithologic Unit IV, the green and black claystones are enriched in many trace transition elements, especially V, Zn, Cu, Co, and Pb. The main difference between the "carbonaceous" claystones of lithologic Unit IV and "variegated" or "multicolored" claystones of the overlying Upper Cretaceous to lower Tertiary Unit III is the absence of black claystone beds. As observed at several other sites (105 and 386), the multicolored claystones at Site 603 are somewhat enriched in several trace transition elements-especially Cu, Ni, and Cr-relative to most deep-sea clays. The multicolored claystones are not enriched in Fe and Mn, and therefore are not "metalliferous" sediments in the sense of those found at several locations in the eastern Pacific. The source of the slightly elevated concentrations of transition metals in the multicolored claystones probably is upward advection and diffusion of metals from the black claystones of the underlying Hatteras Formation. The red, orange, and green claystone beds of lithologic Unit II (Eocene), like those of Unit III, really represent a continuation of deposition of multicolored claystone that began after the deposition of the Neocomian carbonates. The color of the few black beds that occur within this unit results from high concentrations of manganese oxide rather than high concentrations of organic matter.

Pore-water chemistry of ODP sites 111-677 and 111-678

Sites 677 and 678 were drilled on ODP Leg 111 to test hypotheses about the nature and pattern of hydrothermal circulation on a mid-ocean ridge flank. Together with earlier results from DSDP Site 501/504 and several heatflow and piston coring surveys covering a 100-km**2 area surrounding the three drill sites, they confirm that hydrothermal circulation persists in this 5.9-m.y.-old crust, both in basement and through the overlying sediments (Langseth et al., 1988, doi:10.2973/odp.proc.ir.111.102.1988). Profiles of sediment pore-water composition with depth at the three drill sites show both vertical and horizontal gradients. The shapes of the profiles and their variation from one site to another result from a combination of vertical and horizontal diffusion, convection, and reaction in the sediments and basement. Chemical species that are highly reactive in the siliceous-calcareous biogenic sediments include bicarbonate (alkalinity), ammonium, sulfate, manganese, calcium, strontium, lithium, silica, and possibly potassium. Reactions include bacterial sulfate reduction, mobilization of Mn2+, precipitation of CaCO3, and recrystallization of calcareous and siliceous oozes to chalk, limestone, and chert. Species with profiles more affected by reaction in basaltic basement than in the sediments include Mg, Ca, Na, K, and oxygen isotopes. Reaction in basement at 60?C and at higher temperatures has produced a highly altered basement formation water that is uniform in composition over distances of several kilometers. As inferred from the composition of the basal sediment pore water at the three sites, this uniformity extends from up flow zone to downflow zone in basement and the sediments. It exists in spite of large variations in heat flow and depth to basement, apparently as a result of homogenization by hydrothermal circulation in basement. Profiles for chlorinity, Na, Mg, and other species in the sediment pore waters confirm that Site 678, drilled on a localized heatflow high identified by Langseth et al. (1988), is a site of long-lived upwelling of warm water from basement through the sediments at velocities of 1 to 2 mm/yr. The upflow through the anomalously thin sediments is apparently localized above an uplifted fault block in basement. This site and other similar sites in the survey area give rise to lateral diffusion and possibly flow through the sediments, which produces lateral gradients in sediment pore-water composition at sites such as 501/504. The complementary pore-water profiles at the low-heatflow Site 677 2 km to the south indicate that downflow is occurring through the sediments there, at comparable rates of 1 to 2 mm/yr.

Winner-Take-All Contention of Innovation under Globalization: A Simulation Analysis and East Asia's Empirics

This paper sets out to examine how innovation enhances export competitiveness: The proposition that export volume becomes enhanced as more productivity-enhancing innovation is captured by the exporting economy is the focus of this study. From a Schumpeterian perspective, innovation can be characterized by continuous creation and subsequent diffusion of newer technologies on the basis of the exporters' existing capital stock. Then we highlight the theoretical possibility that concentration of innovative activities in a small group of "winner" economies would lead to larger shares of "winner" economies' exports of innovation-active commodities than those commodities for which technology involved is already mature. The world's export data corroborates this theoretical prediction overall, and a focus upon East Asia has revealed the region's increasing resort to technology-intensive commodity sectors, which has presumably been enabled through attracting technology-bearing inward foreign direct investment. Considering the overall gains from innovation, acceleration of full "cycle" of innovation and imitation might be a desirable option.

A closer look at the diffusion of ChinaGAP

To enhance Chinese agricultural production, improve food quality, build consumer trust, and encourage the export of agricultural products, the Chinese government designed the Chinese version of Good Agricultural Practice (ChinaGAP) based on the main principles of the GlobalGAP combining the current Chinese agricultural production situation. This paper studies the characteristics of the ChinaGAP and focusing on the diffusion of the standard using qualitative analysis. Relevant policy recommendations are given based on the Chinese agricultural production status. Previous studies mainly focused on the role of the government. However this paper makes specific suggestions to particular stakeholders in the standard making and diffusion process.

Influence of termal fluctuations in radiation damage cascade production and defect dynamics in tungsten

The detailed study of the deterioration suffered by the materials of the components of a nuclear facility, in particular those forming part of the reactor core, is a topic of great interest which importance derives in large technological and economic implications. Since changes in the atomic-structural properties of relevant components pose a risk to the smooth operation with clear consequences for security and life of the plant, controlling these factors is essential in any development of engineering design and implementation. In recent times, tungsten has been proposed as a structural material based on its good resistance to radiation, but still needs to be done an extensive study on the influence of temperature on the behavior of this material under radiation damage. This work aims to contribute in this regard. Molecular Dynamics (MD) simulations were carried out to determine the influence of temperature fluctuations on radiation damage production and evolution in Tungsten. We have particularly focused our study in the dynamics of defect creation, recombination, and diffusion properties. PKA energies were sampled in a range from 5 to 50 KeV. Three different temperature scenarios were analyzed, from very low temperatures (0-200K), up to high temperature conditions (300-500 K). We studied the creation of defects, vacancies and interstitials, recombination rates, diffusion properties, cluster formation, their size and evolution. Simulations were performed using Lammps and the Zhou EAM potential for W

IFE Plant Technology Overview and contribution to HiPER proposal

HiPER is the European Project for Laser Fusion that has been able to join 26 institutions and signed under formal government agreement by 6 countries inside the ESFRI Program of the European Union (EU). The project is already extended by EU for two years more (until 2013) after its first preparatory phase from 2008. A large work has been developed in different areas to arrive to a design of repetitive operation of Laser Fusion Reactor, and decisions are envisioned in the next phase of Technology Development or Risk Reduction for Engineering or Power Plant facilities (or both). Chamber design has been very much completed for Engineering phase and starting of preliminary options for Reactor Power Plant have been established and review here.

Detecting reliable gene interactions by a hierarchy of Bayesian network classifiers

The main purpose of a gene interaction network is to map the relationships of the genes that are out of sight when a genomic study is tackled. DNA microarrays allow the measure of gene expression of thousands of genes at the same time. These data constitute the numeric seed for the induction of the gene networks. In this paper, we propose a new approach to build gene networks by means of Bayesian classifiers, variable selection and bootstrap resampling. The interactions induced by the Bayesian classifiers are based both on the expression levels and on the phenotype information of the supervised variable. Feature selection and bootstrap resampling add reliability and robustness to the overall process removing the false positive findings. The consensus among all the induced models produces a hierarchy of dependences and, thus, of variables. Biologists can define the depth level of the model hierarchy so the set of interactions and genes involved can vary from a sparse to a dense set. Experimental results show how these networks perform well on classification tasks. The biological validation matches previous biological findings and opens new hypothesis for future studies

Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein-ligand interactions. We present here a computational study of protein-ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries inmolecular dynamics calculations, we computed Poisson- Boltzmann electrostatic potentials, solvation energies, properties of the protein-ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein-lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity.