LIGAND database for enzymes, compounds and reactions

LIGAND is a composite database consisting of three sections and containing the information of chemical substances, chemical reactions and enzymes that catalyze reactions. The COMPOUND section is a collection of metabolic compounds, as well as macromolecules, chemical elements and other chemical substances in a living cell. The ENZYME section is a collection of all known enzymatic reactions, together with the information of enzyme molecules, classified according to the EC (Enzyme Commission) numbers. The REACTION section is a new addition to the database containing metabolic reactions that appear in the pathway diagrams of the KEGG/PATHWAY database and/or in the ENZYME section. The LIGAND database can be accessed through the WWW (http://www.genome.ad.jp/dbget/ligand.html) or may be downloaded by anonymous FTP (ftp://kegg.genome.ad. jp/molecules/ligand).     

Investigation of a Monte Carlo model for chemical reactions

Many new technologies are being developed to improve the efficiency and productivity of nursing staff. A key to the success of these technologies is acceptance by nurses. Davis' constructs of perceived ease of use and perceived usefulness were developed to measure the acceptance of computer systems. This article presents a discussion on nursing acceptance of computer systems, reviews the development of the perceived ease of use and perceived usefulness measures, and reports findings of a study based on these constructs along with attitude of bedside-computer systems. Results of the study showed that nurses in general are accepting of bedside-computer technology.     

Chemical modification and chemical cross-linking for protein/enzyme stabilization

The developmental competence of bovine follicular oocytes that had been meiotically arrested with the phosphokinase inhibitor 6-dimethylaminopurine (6-DMAP) was studied. After 24 h in vitro culture with 2 mM 6-DMAP, 85 +/- 12% of the oocytes were at the germinal vesicle stage compared to 97 +/- 3% at the start of culture (P > 0.05). After release of the 6-DMAP inhibition, followed by 24 h IVM, 82 +/- 18% were at MII stage, compared with 93 +/- 7% in the control group (P > 0.05). The 6-DMAP oocytes displayed a much higher frequency of abnormal MII configurations than the control oocytes (67% vs 23%; P < 0.0001). In addition spontaneous oocyte activation was more frequent than among control oocytes (5% vs 0.3%; P 0.0006). After IVF of 6-DMAP oocytes, normal fertilization was lower (76 +/- 8% vs 89 +/- 7%; P < 0.01), oocyte activation higher (11 +/- 5% vs 2 +/- 2%; P < 0.01), and polyspermy slightly but not significantly higher (8 +/- 7% vs 4 +/- 4%; P > 0.05), compared with the control group. Cleavage was lower (61 +/- 13% vs 81 +/- 6%; P < 0.001), as well as day 8 blastocyst formation (17 +/- 7% vs 36 +/- 8%; P < 0.001). The MII kinetics was different for 6-DMAP and control oocytes. Maximum MII levels were reached at 22 h IVM in both groups, but 50% MII was reached at 17 h in 6-DMAP oocytes, compared to 20 h in control oocytes. Ultrastructure of MII oocytes was similar in the two groups, but in 6-DMAP oocytes the ooplasmic vesicle pattern at GV was at a more advanced stage than in control oocytes. In conclusion, 6-DMAP exposure of GV oocytes prior to IVM induce asynchronous cytoplasmic maturation, leading to aberrant MII kinetics. Thus, at the time of insemination a smaller cohort of oocytes will be at the optimal stage for normal fertilization and subsequent blastocyst development.     

Shock-induced chemical reactions and synthesis of nickel aluminides

Chemical reactions in Ni and Al powder mixtures, initiated by the passage of shock waves, are used for the synthesis of nickel aluminides. Mechanistic investigations reveal that the extent of these shock-induced chemical reactions and the type (stoichiometry) of shock-synthesized compound formed depend on shock-loading conditions and the initial powder particle morphology. More intense shock conditions and irregular powder morphology assist in attaining an intimately (mechanically) mixed and activated closed-packed mass, thereby favoring bulk chemical reactions and resulting in the synthesis of compounds. While the Ni₃Al compound is the preferred reaction product at lower shock conditions, more intense shock conditions favor the formation of the equiatomic B2-phase NiAl compound (having highest melting temperature and highest heat of reaction in contrast to other nickel aluminides), in spite of the starting powders mixed in a volumetric ratio corresponding to the Ni₃Al compound. This paper is based on a presentation made in the symposium “Reaction Synthesis of Materials” presented during the TMS Annual Meeting, New Orleans, LA, February 17–21, 1991, under the auspices of the TMS Powder Metallurgy Committee.     

Kinetic treatment of chemical reactions in emulsion metallurgy

Chemical reactions in emulsion metallurgy often take place under transistoric phase contact without mixing within the extracting phase, especially if the phase is finely dispersed. A kinetic treatment of this type of reaction is presented. Limiting cases which correspond to near to – and far from – equilibrium are discussed. Three examples: 1. manganese oxidation in the basic oxygen converter, 2. hot metal desulphurization by lime or calcium carbide, and 3. seperation of hydrogen from liquid steel by inert gas bubbling are calculated. In the case of manganese oxidation, the reaction at the droplets proceeds almost until the equilibrium, whereas in the case of desulphurization the reaction is far from equilibrium. The separation of hydrogen is described by somewhat different equations compared to the other two cases, as the hydrogen reaction obeys Sievert's law and the bubble size changes with change of ferrostatic pressure.     

Visualization of electronic properties of molecules in chemical reactions

Modern computational methods allow for the tracking of entire chemical reactions, ranging from initial reactants, through transition states, and to the final products. They also permit the computation of a variety of properties that can change as the reaction proceeds from start to finish. Visualization of these reactions is often difficult and usually limited to static displays of specific steps along the reaction paths. This article describes a program, Reaction Viewer, that we have developed to visualize a chemical reaction dynamically. The article also describes the use of this program to see the movement of electrons and other electronic effects, as well as steric ramifications during the reaction.     

KEYnet: a keywords database for biosequences functional organization

KEYnet is a database where gene and protein names are hierarchically structured. Particular care has been devoted to the search and organisation of synonyms. The structuring is based on biological criteria in order to assist the user in the data search and to minimise the risk of loss of information. Links to the EMBL data library by the entry name and the accession number have been implemented. KEYnet is available through the World Wide Web at the following site: http://www.ba.cnr.it/keynet.html. Recently KEYnet has incorporated specific gene name classifications, which can be browsed starting from the above-mentioned KEYnet home page: the Mitochondrial Gene Names classification and the Rat Gene Names classification. KEYnet database has also been structured in a flatfile format and can be queried through SRS (http://bio-www.ba.cnr.t:8000/srs).     

Melt penetration and chemical reactions in 16 industrial aluminum carbon cathodes

The study shows examples of the distribution of melt components in spent carbon cathodes from 16 industrial aluminum electrolysis cells shut down after 10 to 2534 days. The concentration of the phases was determined by quantitative X-ray diffraction (XRD), and the distribution was found by analyzing series of samples from several vertical cores from each cathode. The results show that the analysis is useful for characterizing phases in spent potlining, and the detailed distribution graphs are suitable for comparing different parts of a cathode, or different cathodes. The composition of the melt in the 16 cathodes changed systematically over time, and the stages in the evolution, the effect of the cathode material type, and the effect of the melt on the lining are discussed.     

Effect of the bubble size and chemical reactions on slag foaming

Slag foams have been investigated with smaller bubbles than those used in the previous studies.^[5,6,7] The bubbles were generated by argon gas injection with the nozzle of multiple small orifices and by the slag/metal interfacial reaction of FeO in the slag with carbon in the liquid iron. The foam stability in terms of the foam index for a bath-smelting type of slag (CaO-SiO₂-Al₂O₃-FeO) was determined for different bubble sizes. The average diameter of bubbles in the foam was measured by an X-ray video technique. When the foam was generated by the slag/metal interfacial reaction at 1450 °C, it was found that the average bubble diameter varied from less than 1 to more than 5 mm as a function of the sulfur activity in the carbon-saturated liquid iron. The foam index was found to be inversely proportional to the average bubble diameter. A general correlation is obtained by dimensional analysis in order to predict the foam index from the physical properties of the liquid slag and the average size of the gas bubbles in the foam. Formerly Graduate Student and Research Associate, Department of Materials Science and Engineering, Carnegie Mellon University.     

A strategy for database interoperation

To realize the full potential of biological databases (DBs) requires more than the interactive, hypertext flavor of database interoperation that is now so popular in the bioinformatics community. Interoperation based on declarative queries to multiple network-accessible databases will support analyses and investigations that are orders of magnitude faster and more powerful than what can be accomplished through interactive navigation. I present a vision of the capabilities that a query-based interoperation infrastructure should provide, and identify assumptions underlying, and requirements of, this vision. I then propose an architecture for query-based interoperation that includes a number of novel components of an information infrastructure for molecular biology. These components include a knowledge base that describes relationships among the conceptualizations used in different biological databases, a module that can determine the DBs that are relevant to a particular query, a module that can translate a query and its results from one conceptualization to another, a collection of DB drivers that provide uniform physical access to different database management systems, a suite of translators that can interconvert among different database schema languages, and a database that describes the network location and access methods for biological databases. A number of the components are translators that bridge the heterogeneities that exist between biological DBs at several different levels, including the conceptual level, the data model, the query language, and data formats.     

Penetration and chemical reactions in carbon cathodes during aluminum electrolysis: part i. laboratory experiments

Penetration of metallic sodium and salt melt into cathodic carbon materials was studied in a laboratory aluminum electrolysis cell. Variables were cryolite ratio, current density, N₂ or Ar atmosphere, degree of graphitization, and strain on the carbon samples. The carbon sample was analyzed by optical and electron microscopy, ash analysis, sodium detection by phenolphtalein, density, and X-ray diffraction (XRD). The developed XRD technique proved especially useful and allowed quantitative determination of concentration profiles for the crystallized compounds. Sodium was found to be the primary penetration agent and its velocity and saturation concentration increased with increased cryolite ratio of the melt and decreased graphitization of the carbon material. Sodium was found to be important as a wetting agent facilitating melt penetration. Al₄C₃ was not present within the pores of the carbon material. Melt penetration was enhanced by polarization and formation of nitrogen compounds. NaCN was formed directly from the elements and was destabilized by the advancing melt. In nitrogen atmosphere, A1N was the major nitrogen component and was formed within the melt phase. Formerly with the Institute of Inorganic Chemistry, The Norwegian Institute of Technology     

CNBr/formic acid reactions of methionine- and trifluoromethionine-containing lambda lysozyme: probing chemical and positional reactivity and formylation side reactions by mass spectrometry

The cyanogen bromide (CNBr)/formic acid cleavage reactions of wild-type and trifluoromethionine (TFM)-containing recombinant lambda lysozyme were studied utilizing ESI and MALDI mass spectrometry. Detailed analysis of the mass spectra of reverse-phase HPLC-purified cleavage fragments produced from treatment of the wild-type and labeled proteins with CNBr indicated cleavage solely of methionyl peptide bonds with no observation of cleavage at TFM. N-Acetyl-TFM was also found to be resistant to reaction with CNBr, in contrast to N-acetyl-methionine. The analysis also indicated differential reactivity among the three methionine positions in the wild-type enzyme. Additionally, formylation of intact enzyme as well as peptide fragments were observed and characterized and indicated that serine, threonine, as well as C-terminal homoserine side chains are partially formylated under standard cleavage protocols.     

SPEM: a parser for EMBL style flat file database entries

SUMMARY: We present a set of Perl modules for the flexible and robust parsing and editing of EMBL/SWISS-PROT databases. AVAILABILITY: The Web page at http://www.sanger.ac. uk/Software/PerlModule/ provides information about downloading the SPEM and PrEMBL modules, and provides links to documentation and example code.     

HOMSTRAD: a database of protein structure alignments for homologous families

We describe a database of protein structure alignments for homologous families. The database HOMSTRAD presently contains 130 protein families and 590 aligned structures, which have been selected on the basis of quality of the X-ray analysis and accuracy of the structure. For each family, the database provides a structure-based alignment derived using COMPARER and annotated with JOY in a special format that represents the local structural environment of each amino acid residue. HOMSTRAD also provides a set of superposed atomic coordinates obtained using MNYFIT, which can be viewed with a graphical user interface or used for comparative modeling studies. The database is freely available on the World Wide Web at: http://www-cryst.bioc.cam. ac.uk/-homstrad/, with search facilities and links to other databases.     

A mutation spectra database for bacterial and mammalian genes: 1998

This database consists of over 24 000 mutations in 18 viral, bacterial, yeast or mammalian genes. The data are grouped as sets of DNA base sequence changes or spectra caused by a particular mutagen under defined conditions. The spectra are available on the World Wide Web at http://info.med.yale.edu/mutbase/ in two formats; in text format that can be browsed on-line or downloaded for use with a text editor and in dBASEIII format for use, after downloading, by relational database programs or by spreadsheets. Researchers are encouraged to submit DNA sequence changes to a suitable mutation database such as ours. A data entry program, MUTSIN, can be retrieved from this site. MUTSIN diagrams each mutation on the computer screen and alerts the user to any discrepancies.