Prediction of membrane proteins based on classification of transmembrane segments

The number of transmembrane segments often corresponds to a structural or functional class of membrane proteins such as to seven-transmembrane receptors and six-transmembrane ion channels. We have developed a new prediction method to detect the membrane protein class that is defined by the number of transmembrane segments, as well as to locate the transmembrane segments in the amino acid sequence. Each membrane protein class is represented by a model of ordering different types of transmembrane segments. Specifically, we have classified the transmembrane segments in known membrane proteins into five groups (types) using the Mahalanobis distance with the average hydrophobicity and the periodicity of hydrophobicity as a measure of similarity. The discriminant functions derived for these groups were then used to detect transmembrane segments and to match with the models for one- to fourteen-spanning membrane proteins and for globular proteins. Using the test data set of 89 membrane proteins whose transmembrane positions are known by experimental evidence, 61.8% of the proteins and 85.1% of the transmembrane segments were correctly predicted. Because of the new feature to predict membrane protein classes, the method should be useful in the functional assignment of genomic sequences.     

Measurements and thermodynamic modeling of the solubility of squalene in supercritical carbon dioxide

The solubility of squalene in supercritical carbon dioxide (SC-CO₂) was measured and it was analyzed together with the values obtained by Catchpole and von Kamp (1997). The results showed that the experimental values obtained in this work agreed with the order of magnitude of those reported in the literature and correlated well with the Chrastil equation. The thermodynamic modeling using the Peng–Robinson equation of state only correlated well with the experimental values obtained when the critical properties and acentric factor reported by Ruivo et al. (2004) were used. The values predicted for the solubility of squalene in SC-CO₂ using modeling employing the GC-EOS, were only of the same order of magnitude as the experimental values for pressures below 200 bar, and its performance was influenced by the value of the critical hard sphere diameter.     

Steam absorption process of water/LiBr system inside vertical small bore pipes

In a previous paper, a numerical model for absorption within vertical pipes was proposed and compared with the experiments. Agreements were good for pipes with an OD 28–15 mm but at 10 mm pipe experiments fell below the predicted values. For smaller diameters, the difference between the surface area of the falling liquid film and that of the outer surface of the pipe is not negligible and the thickness of the liquid film is also not negligible. In this paper a new model is formulated in cylindrical coordinates and experiments using pipes with 9.52 mm and 7 mm OD are done. Smooth pipes and two kinds of internally finned pipes, originally developed and used to enhance the heat transfer characteristics of the evaporator and condenser of a refrigerator using HFC as refrigerant, are tested in the experiments. The absorption performance is enhanced by 30% when compared to the smooth pipes, but the difference between the finned pipes is small. © 2004 Wiley Periodicals, Inc. Heat Trans Asian Res, 34(1): 18–28, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/htj.20040     

Steam absorption into films of lithium bromide solution falling over horizontal pipes arranged in a vertical column

Absorber of a water/LiBr absorption chiller is made up of horizontal tube banks, and its improvement is needed to get higher COP. To clarify the absorption process in these tube banks, a single row of horizontal pipe column is studied experimentally and analytically. The analytical model proposed in a previous paper is further changed to a conservative form according to the method of Shyy. It is confirmed that the mass balance of water is kept exactly by the present procedure. As for total absorption rate for the pipe column, the agreement between experiment and numerical calculations is fairly good except for the cases of 8 to 10 pipes at a lower flow rate. The roughed pipes with different knurls on their surface were also tested experimentally and it was found that a knurl height of 0.5 mm was the most effective in absorption enhancement. © 2001 Scripta Technica, Heat Trans Asian Res, 30(6): 451–462, 2001     

Moderation of oxonate-induced hyperuricemia in rats via the ingestion of an ethanol-soluble fraction of a shark cartilage proteolytic digest

A shark cartilage proteolytic digest was fractionated by selective extraction with 75% ethanol. Peptides in the digest were recovered in the 75% ethanol-soluble fraction. The ethanol-soluble fraction showed lower viscosity and higher solubility in water than the crude digest. Oxonate-induced hyperuricemia in rat was suppressed by the oral administration of the ethanol-soluble fraction of the digest (1 g/kg body weight/day) for 28 days. Single administration of the ethanol-soluble fraction also reduced blood uric acid level in a dose-dependent manner. Administration of the ethanol-soluble fraction of the digest (1 g/kg body weight/day) significantly increased serum inhibitory activity against xanthine oxidase, whereas the ethanol-soluble fraction had no in vitro xanthine oxidase inhibitory activity. These facts suggest that peptides in the ethanol-soluble fraction might be converted into smaller peptides with xanthine oxidase inhibitory activity during digestion, absorption, and metabolism.     

A comparative analysis of ABC transporters in complete microbial genomes

The ABC transporter is a major class of cellular translocation machinery in all bacterial species encoded in the largest set of paralogous genes. The operon structure is frequently found for the genes of three molecular components: the ATP-binding protein, the membrane protein, and the substrate-binding protein. Here, we developed an "ortholog group table" by comparison and classification of known and putative ABC transporters in the complete genomes of seven microorganisms. Our procedure was to first search and classify the most conserved ATP-binding protein components by the sequence similarity and then to classify the entire transporter units by examining the similarity of the other components and the conservation of the operon structure. The resulting 25 ortholog groups of ABC transporters were well correlated with known functions. Through the analysis, we could assign substrate specificity to hypothetical transporters, predict additional transporter operons, and identify novel types of putative transporters. The ortholog group table was also used as a reference data set for functional assignment in four additional genomes. In general, the ABC transporter operons were strongly conserved despite the extensive shuffling of gene locations in bacterial evolution. In Synechocystis, however, the tendency of forming operons was clearly diminished. Our result suggests that the ancestral ABC transporter operons may have arisen early in evolution before the speciation of bacteria and archaea.     

The RoboCup Soccer Server and CMUnited Clients: Implemented Infrastructure for MAS Research

The RoboCup Soccer Server and associated client code is a growing body of software infrastructure that enables a wide variety of multiagent systems research. The Soccer Server is a multiagent environment that supports 22 independent agents interacting in a complex, real-time environment. AI researchers have been using the Soccer Server to pursue research in a wide variety of areas, including real-time multiagent planning, real-time communication methods, collaborative sensing, and multiagent learning. This article describes the current Soccer Server and the champion CMUnited soccer-playing agents, both of which are publically available and used by a growing research community. It also describes the ongoing development of FUSS, a new, flexible simulation environment for multiagent research in a variety of multiagent domains.