A truncated mutant of the extrinsic 23-kDa protein that absolutely requires the extrinsic 17-kDa protein for Ca2+ retention in photosystem II

One function of the extrinsic 23-kDa protein in photosystem II (OEC23) is to retain Ca(2+ )and Cl(-), two essential cofactors for photosynthetic oxygen evolution. A truncated mutant of OEC23 (OEC23 Delta19) revealed that 19 residues of the N-terminus of OEC23 were necessary for Ca(2+ )retention but not for its proper interaction with OEC17, the extrinsic 17-kDa protein in photosystem II. The lost ability of OEC23 Delta19 to reconstitute the oxygen-evolving activity was partially restored by OEC17 binding, suggesting the involvement of OEC17 in Ca(2+ )retention in photosystem II.     

Enhanced secretion of tissue plasminogen activator by simultaneous use of retinoic acid and ascorbic acid from tissue cultured gastroepiploic artery

Tissue-type plasminogen activator (tPA) is a key enzyme in the fibrinolysis system and the regulation of its expression has been extensively studied in cultured vascular endothelial cells. Many kinds of supplements including growth factors are needed, however, to keep endothelial cells viable, which leads the culture condition far from the physiological milieu. Using a new device of amorphous calcium phosphate coated culture plate, we succeeded in culturing ring-cut gastroepiploic artery in a basic medium of RPMI 1640 containing 10% fetal calf serum. The overall normal vessel architecture and the antigenicity of von Willebrand factor, tPA and plasminogen activator inhibitor type 1 (PAI-1) were retained for at least 9 days. tPA was constantly secreted into the conditioned medium at least up to day 12. Employing this organ culture technique, we analyzed the effects of two well-known profibrinolytic vitamins of retinoic acid (Vit. A) and ascorbic acid (Vit. C) on the release of tPA and PAI-1. The cultured artery responded well and the tPA secretion was enhanced by factors of 1.5 fold by Vit. A, 1.7 fold by Vit C and 3.2 fold by their combination, whereas none of these stimuli increased PAI-1 secretion. These results suggested that the cultured ring-cut artery retained functional endothelial cells for at least 9 days and was suitable in analyzing the regulatory mechanism of protein synthesis and secretion from the vascular wall. Using this method, vitamins A and C were shown to lead the intravascular condition to a profibrinolytic state.     

Orthogonality of calcium concentration and ability of 4,5-diaminofluorescein to detect NO

We have developed diaminofluoresceins (DAFs) and diaminorhodamines as fluorescent indicators for NO based on the specific reaction of the aromatic vicinal diamines with NO. Among them, 4,5-diaminofluorescein (DAF-2) is widely used for real-time biological imaging of NO in cultured cells or tissues by many researchers. Contrary to a recent report of divalent cation sensitivity and photoactivation of DAF-2 (Broillet, M. C., Randin, O., and Chatton, J. Y. (2001) FEBS Lett. 491, 227-232), our study using NO gas itself reveals that the reaction of DAF-2 and NO is completely independent of Ca2+ and Mg2+ at physiological concentrations. Ca2+ enhances not the conversion of DAF-2 into its fluorescent product (DAF-2 triazole) but the release of NO from NO donors. Therefore it is concluded that DAF-2 can provide reliable information on NO production in biological systems regardless of the dynamic changes of Ca2+ concentration.     

Degradation of car engine base oil by Rhodococcus sp. NDKK48 and Gordonia sp. NDKY76A

Two microorganisms (NDKK48 and NDKY76A) that degrade long-chain cyclic alkanes (c-alkanes) were isolated from soil samples. Strains NDKK48 and NDKY76A were identified as Rhodococcus sp. and Gordonia sp., respectively. Both strains used not only normal alkane (n-alkane) but also c-alkane as a sole carbon and energy source, and the strains degraded more than 27% of car engine base oil (1% addition).     

Efficient information visualization in LCA: approach and examples

Aim, Scope and Background  The data-intensive nature of life cycle assessment (LCA), even for non-complex products, quickly leads to the utilization of various methods of representing the data in forms other than written characters. Up until now, traditional representations of life cycle inventory (LCI) data and environmental impact analysis (EIA) results have usually been based on 2D and 3D variants of simple tables, bar charts, pie charts and x/y graphs. However, these representation methods do not sufficiently address aspects such as representation of life cycle inventory information at a glance, filtering out data while summarizing the filtered data (so as to reduce the information load), and representation of data errors and uncertainty. Main Features  This new information representation approach with its glyph-based visualization method addresses the specific problems outlined above, encountered when analyzing LCA and EIA related information. In particular, support for multi-dimensional information representation, reduction of information load, and explicit data feature propagation are provided on an interactive, computer-aided basis. Results  Three-dimensional, interactive geometric objects, so called OM-glyphs, were used in the visualization method introduced, to represent LCA-related information in a multi-dimensional information space. This representation is defined by control parameters, which in turn represent spatial, geometric and retinal properties of glyphs and glyph formations. All relevant analysis scenarios allowed and valid can be visualized. These consist of combinations of items for the material and energy inventories, environmental items, life cycle phases and products, or their parts and components. Individual visualization scenarios, once computed and rendered on a computer screen, can then interactively be modified in terms of visual viewpoint, size, spatial location and detail of data represented, as needed. This helps to increase speed, efficiency and quality of the assessment performance, while at the same time considerably reducing mental load due to the more structured manner in which information is represented to the human expert. Conclusions  The previous paper in this series discussed the motivation for a new approach to efficient information visualization in LCA and introduced the essential basic principles. This second paper offers more insight into and discussion on technical details and the framework developed. To provide a means for better understanding the visualization method presented, examples have been given. The main purpose of the examples, as already indicated, is to demonstrate and make transparent the mapping of LCA related data and their contexts to glyph parameters. Those glyph parameters, in turn, are used to generate a novel form of sophisticated information representation which is transparent, clear and compact, features which cannot be achieved with any traditional representation scheme. Outlook  Final technical details of this approach and its framework will be presented and discussed in the next paper. Theoretical and practical issues related to the application of this visualization method to the computed life cycle inventory data of an actual industrial product will also be discussed in this next paper.     

Efficient Information Visualization in LCA

Background, Goal and Scope  A complete life cycle assessment (LCA) always requires several itemizations of goal/scope definitions, inventory analysis and impact analysis. This requires the retrieval and collection of inventory information on all processes with which a product or any part of it comes into either direct or indirect contact. As a result, the data required for LCA is vast, uncertain and, therefore, complex. Up until now, unfortunately, and as far as the authors are aware, there has not been much computer-assisted aid available from any of the systems currently used in either academia or industry to support any life cycle (LC) related data representation, other than the traditional methods of tables, xy-graphs, bar charts, pie charts and various 3-D variants of those which are difficult for humans to interpret. Main Features  Benefiting from the synergy of latest developments in both visualization techniques and computer technology, the authors are able to introduce a new information representation approach based on glyphs. These exploit the human perceptual capability for distinguishing spatial structures and shapes presented in different colors and textures. Within this approach, issues of representing life cycle related information at a glance, filtering out data so as to reduce the information load, and representation of data features, such as uncertainty and estimated errors, are targeted. Results  Advanced information visualization, the process which transforms and maps data to a visual representation, employs the glyphs rendered here to create abstract representations of multi-dimensional data sets. Different parameters describing spatial, geometrical and retinal properties of such glyphs, and defining their position, orientation, shape, color, etc., can be used to encode more information in a comprehensible format, thus allowing multiple values to be encoded in those glyph parameters. The natural function of glyphs, linking (mapped) data within a known context with the attributes that in turn control their visualization, is believed capable of providing sufficient functionality to interactively support designers and LCA experts performing life cycle inventory (LCI) information analysis so that they can operate faster and more efficiently than at present. Conclusions  Within this paper, the first of a small series on efficient information visualization in LCA, the motivation for and essential basic principles of the approach are introduced and discussed. With this technique, the essential characteristics of data, relationships, patterns, trends, etc. can be represented in a much better structured and compact manner, thus rendering them clearer and more meaningful. It is hoped that a continuing interest in this work combined with an improved collaboration with industrial partners will eventually provide the grounds for translating this novel approach into an efficient and reliable tool enhancing applied LCA in practice on a broader base. Outlook  More technical details of the approach and its implementation will be introduced and discussed in the following papers, and examples will be offered demonstrating its application and first experimental translation into practice.     

Statistics of trinucleotides in coding sequences and evolution

The aim of this paper is to give measurements indicative of evolutional stages of the species. Two types of statistics of trinucleotides in coding regions are analysed for 27 species. The first one is the codon space, the nucleotide ratio for each of the three codon positions. We apply principal component analysis on this space and extract two principal components faithfully describing the original distribution of the codon space. The first principal component corresponds to the GC content. The second principal component classifies the species into three evolutional groups, Archaea, Bacteria and Eukaryota. The second statistics is the real and theoretical frequency of amino acids. The real frequency of an amino acid in a coding sequence is its frequency in the translated protein. The theoretical frequency is the expected frequency calculated from the ratio of nucleotides. We introduce the discrepancy between these two frequencies as an index of non-randomness of nucleotides in the sequence. This index of non-randomness divides the species into two groups: eukaryotes having smaller non-randomness (i.e. being more random) and prokaryotes having higher non-randomness.