Computer simulation of human iodothyronine deiodinase single-chain antibody

Iodothyronine plays a major role in growth, basic metabolism and organ formation. It has an extremely limited source in the body. In this thesis, we designed iodothyronine(T4) as hapten. Then a single chain antibody displayed on phange was obtained from a human phage displaying a single chain antibody library. The specific genes of E3 was subcloned in P-5E vector. According to its amino acid sequences, we simulate its three dimention structure by computer. It has never been reported in PDB.

Automorphism group algorithm in computer-aided structure elucidation

It is necessary to generate automorphism group of chemical graph in computer-aided structure eluciation. In this paper, an algorithm is developed by all-path topological symmetry algorithm to build automorphism group of chemical graph. A comparison of several topological symmetry algorithm reveals that all-path algorthm can yield correct of class of chemical graph. It lays a foundation for ESESOC system for computer-aided structure elucidation.

Study on speciation of Pr(III) in human blood plasma by computer simulation

Speciation of Pr(III) in human blood plasma has been investigated by computer simulation. The speciation and distribution of Pr(III) has been obtained. It has been found that most of Pr(III) is bound to phosphate and to form precipitate. The results obtained-are in accord with experimental observations.

Studies on insoluble species of Gd (III) in human blood plasma by computer simulation

The insoluble species of Gd (III) in human blood plasma were investigated by computer simulation. The distribution of the Gd (I) species was obtained. It was found that most of the Gd (III) ions were bound to phosphate to form precipitate GdPO4 at the concentration of 1. 000 x 10(-7) mol/L and when the concentration of the Gd (III) increased to 3. 750 x 10(-4) mol/L, in excess of the concentration of phosphate, the Gd (III) ions were bound to carbonate to form another kind of precipitate, Gd-2 (CO3)(3).

Tb(III) speciation in human blood plasma by computer simulation

A multi-phase model was developed and Tb(III) speciation in human blood plasma was studied. At a concentration below 3.744x 10(-4) mol/L (or at the concentration), Tb(III) is mostly bound to phosphate to form precipitate of TbPO4. As the concentration of Tb(III) increases, phosphate is exceeded and another kind of precipitate of Tb-2(CO3)(3) appears. Among soluble Tb(III) species, Tb(III) mainly distribute in [Tb (Tf)] at low concentration and in [Tb (HSAA, [Tb-2 (Tf)], [Th (IgG)], [Tb (Lactate)](2+), [Tb (CitArgH)] and free Tb(III) at high concentration.

Study on effect of Gd (III) speciation on Ca (II) speciation in human blood plasma by computer simulation

Ca (II) speciation and effect of Gd (III) speciation on Ca (II) speciation in human blood plasma were studied by computer simulation. [CaHCO3](-) is a predominant compound species of Ca (II). Gd (III) can compete with Ca (II) for biological molecules. The presence of Gd (III) results in a increase of concentration of free Ca (II) and a decrease of concentration of Ca (II) compounds.

Computer perception of topological symmetry by all-paths algorithm

During the development of our ESESOC system (Expert System for the Elucidation of the Structures of Organic Compounds), computer perception of topological symmetry is essential in searching for the canonical description of a molecular structure, removing the irredundant connections in the structure generation process, and specifying the number of peaks in C-13- and H-1-NMR spectra in the structure evaluation process. In the present paper, a new path identifier is introduced and an algorithm for detection of topological symmetry from a connection table is developed by the all-paths method. (C) 1999 Elsevier Science B.V. All rights reserved.

Structure and Conformation of 2,3,6, 7,10,11-hexakispentyloxytriphenylene by TEM and Computer Simulation

Experimental electron diffraction patterns and high resolution images were used to determine the space group and unit cell dimensions of 2,3,6,7,10,11-hexakispentyloxytriphenylene. Subsequently the molecular conformation was calculated by energy minimized package in Cerius2. Using this method, we got the HPT crystal structure: space group: P6/mmm; lattice type: hexogonal; the lattice parameters are a = b = 20.3 angstrom, c = 3.52 angstrom, = = 90 degrees, = 120 degrees. The core of HPT is not perpendicular to the column. The angle between a axis and HPT core plane is 9 degrees which cannot be seen in b-c projection. The simulated ED patterns and HREM images are good agreement with the experimental ED patterns and HREM images.

Study on computer perception of topological symmetry

A new algorithm for computer perception of topological symmetry is proposed. A node library containing various kinds of nodes is built, and the index number of the library is used as initial atom class identifier (CI) to discriminate the different types of non-hydrogen atoms. The path index (PI) and ringindex (RI) are calculated from the CI, and the global topological enviroment is defined as the sum of PIs and RIs. The topological symmetry can be detected by the iterative calculation of the global topological enviroment.

ALGORITHM FOR COMPUTER PERCEPTION OF TOPOLOGICAL SYMMETRY

For the exhaustive and irredundant generation of candidate structures in ESESOC (Expert System for the Elucidation of the Structures of Organic Compounds), a new algorithm for computer perception of topological equivalence classes of the nodes (non-hydrog

IMPEDANCE STUDY OF THE INTERFACES BETWEEN LITHIUM, POLYANILINE, LITHIUM-DOPED MNO2 AND MODIFIED POLY(ETHYLENE OXIDE) ELECTROLYTE

Impedance study was carried out for the interfaces between lithium, polyaniline (PAn), lithium-doped MnO2 and modified poly(ethylene oxide) (PEO) electrolyte under various' conditions. The interfacial charge-transfer resistances R(ct) on PEO/PAn, R(ct) on PEO/LiMn2O4 increase with depth-of-discharge and decrease after the charge of the cell containing modified PEO as electrolyte. The charge-transfer resistance R(ct) on PEO/PAn is higher than R(ct) on PEO/LiMn2O4 under the same condition, since inserted species and mechanism are different for both cases. In the case of PAn, an additional charge-transfer resistance might be related to the electronic conductivity change in discharge/charge potential range, as it was evident from a voltammetry curve. With increasing cycle numbers, the charge-transfer resistance increases gradually. The impedance results also have shown that at low frequency the diffusion control is dominant in the process of the charge and discharge of Li/PEO/PAn or Li/PEO/LiMn2O4 cell. The diffusion coefficients have been calculated from impedance data.

ANESTHETIC LIDOCAINE AND DICAINE TRANSFER ACROSS LIQUID LIQUID INTERFACES

Lidocaine transfer across the water/1,2-dichloroethane and the water/nitrobenzene interfaces has been investigated by chronopotentiometry with linear current scanning and cyclic voltammetry. The irreversible hydrolysis occurring in the phase transfer of dicaine at the water/nitrobenzene interface is discussed.

Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin

Identification of protein interaction interfaces is very important for understanding the molecular mechanisms underlying biological phenomena. Here, we present a novel method for predicting protein interaction interfaces from sequences by using PAM matrix (PIFPAM). Sequence alignments for interacting proteins were constructed and parsed into segments using sliding windows. By calculating distance matrix for each segment, the correlation coefficients between segments were estimated. The interaction interfaces were predicted by extracting highly correlated segment pairs from the correlation map. The predictions achieved an accuracy 0.41-0.71 for eight intraprotein interaction examples, and 0.07-0.60 for four interprotein interaction examples. Compared with three previously published methods, PIFPAM predicted more contacting site pairs for 11 out of the 12 example proteins, and predicted at least 34% more contacting site pairs for eight proteins of them. The factors affecting the predictions were also analyzed. Since PIFPAM uses only the alignments of the two interacting proteins as input, it is especially useful when no three-dimensional protein structure data are available.

Behavioral responses of tilapia (Oreochromis niloticus) to acute fluctuations in dissolved oxygen levels as monitored by computer vision

Behavioral and ventilatory parameters have the possibility of predicting the stress state of fish in vivo and in situ. This paper presents a new image-processing algorithm for quantifying the average swimming speed of a fish school in an aquarium. This method is based on the alteration in projected area caused by the movement of individual fish during frame sequences captured at given time intervals. The image enhancement method increases the contrast between fish and background, and is thus suitable for use in turbid aquaculture water. Behavioral parameters (swimming activity and distribution parameters) and changes in ventilation frequency (VF) of tilapia (Oreochromis niloticus) responded to acute fluctuations in dissolved oxygen (DO) which were monitored continuously in the course of normoxia, falling DO level, maintenance of hypoxia (three levels of 1.5, 0.8 and 0.3 mg l(-1)) and subsequent recovery to normoxia. These parameters responded sensitively to acute variations in DO level; they displayed significant changes (P < 0.05) during severe hypoxia (0.8 and 0.3 mg l(-1) level) compared with normoxic condition, but there was no significant difference under conditions of mild hypoxia (1.5 mg l(-1) level). There was no significant difference in VF between two levels of severe hypoxia 0.8 and 0.3 mg l(-1) level during the low DO condition. The activity and distribution parameters displayed distinguishable differences between the 0.8 and 0.3 mg l(-1) levels. The behavioral parameters are thus capable of distinguishing between different degrees of severe hypoxia, though there were relatively large fluctuations. (c) 2006 Elsevier B.V. All rights reserved.

Use of computer-assisted sperm analysis (CASA) to evaluate the quality of cryopreserved sperm in red seabream (Pagrus major)

In the present study, the quality of post-thaw sperm of red seabream Pagrus major frozen with 6-24% DMSO was investigated. The motility, average path velocity and fertilizing capacity of fresh and their corresponding post-thaw sperm were examined for evaluation of the post-thaw sperm motion characteristics and its association with fertilizing capacity. An analysis of sperm motility before and after cryopreservation has been performed using computer-assisted sperm analysis (CASA). For post-thaw sperm frozen with 12-21% DMSO, the percentages of motile sperm were not significantly (P > 0.05) changed 10 s after activation. Moreover, the main motility pattern and swimming velocity of the motile post-thaw sperm were not significantly (P > 0.05) changed and the progressive linear motion was still the dominant pattern. However, the total motility of post-thaw sperm (72.3 +/- 6.3%) 30 s after activation was (P < 0.05) lower than the corresponding fresh sperm (82.7 +/- 7.2%). Additionally, the fertilizing capacity of post-thaw sperm was investigated with a standardized sperm to egg ratio 500:1. There is a linear regression relationship between the percentage of motile post-thaw sperm and fertilizing capability. These data demonstrate that 12-21% DMSO can provide good protection to the sperm during the freezing-thawing process. (c) 2006 Elsevier B.V. All rights reserved.