Two-level QSAR network (2L-QSAR) for peptide inhibitor design based on amino acid properties and sequence positions.

In the design of peptide inhibitors the huge possible variety of the peptide sequences is of high concern. In collaboration with the fast accumulation of the peptide experimental data and database, a statistical method is suggested for peptide inhibitor design. In the two-level peptide prediction network (2L-QSAR) one level is the physicochemical properties of amino acids and the other level is the peptide sequence position. The activity contributions of amino acids are the functions of physicochemical properties and the sequence positions. In the prediction equation two weight coefficient sets {ak} and {bl} are assigned to the physicochemical properties and to the sequence positions, respectively. After the two coefficient sets are optimized based on the experimental data of known peptide inhibitors using the iterative double least square (IDLS) procedure, the coefficients are used to evaluate the bioactivities of new designed peptide inhibitors. The two-level prediction network can be applied to the peptide inhibitor design that may aim for different target proteins, or different positions of a protein. A notable advantage of the two-level statistical algorithm is that there is no need for host protein structural information. It may also provide useful insight into the amino acid properties and the roles of sequence positions.

Prediction of protein structural classes using support vector machines.

The support vector machine, a machine-learning method, is used to predict the four structural classes, i.e. mainly alpha, mainly beta, alpha-beta and fss, from the topology-level of CATH protein structure database. For the binary classification, any two structural classes which do not share any secondary structure such as alpha and beta elements could be classified with as high as 90% accuracy. The accuracy, however, will decrease to less than 70% if the structural classes to be classified contain structure elements in common. Our study also shows that the dimensions of feature space 20(2) = 400 (for dipeptide) and 20(3) = 8 000 (for tripeptide) give nearly the same prediction accuracy. Among these 4 structural classes, multi-class classification gives an overall accuracy of about 52%, indicating that the multi-class classification technique in support of vector machines may still need to be further improved in future investigation.

[Zn8(SiO4)(C8H4O4)6]n: the firstborn of a metallosilicate-organic hybrid material family (C8H4O4 = isophthalate).

[Zn8(SiO4)(C8H4O4)6]n (C8H4O4 = isophthalate), synthesized by hydrothermal reaction, possesses a diamondoid framework structure constructed from hexahedron-like Zn8(SiO4) cores and C8H4O4 linkers and remains stable up to 500 degrees C in air, representing the first member of a new class of metallosilicate-organic hybrid materials.

Separation and identification of perchlorinated polycyclic aromatic hydrocarbons and fullerenes (C60, C70) by coupling high-performance liquid chromatography with ultraviolet absorption spectroscopy and atmospheric pressure chemical ionization mass spectrometry.

Simultaneous separation and identification of perchlorinated polycyclic aromatic hydrocarbons (PCPAHs) and fullerenes is of practical interest due to the growth mechanism of fullerenes involved with PCPAHs. Non-aqueous reversed-phase high-performance liquid chromatography (HPLC), with an ODS column and a gradient mobile phase of methanol-ethanol-cyclohexane mixtures, was combined with both rapid-scan ultraviolet spectrometry (UV) and atmospheric pressure chemical ionization mass spectrometry (APCI-MS) for the separation and identification of over 80 PCPAHs as well as fullerenes C60 and C70, that were synthesized in the discharge reaction of chloroform. PCPAH retention was found to depend on the number of aromatic rings and the degree of non-planarity of PCPAH structure. Based on the isotopic pattern of molecular ion or/and quasi-molecular ion peaks in corresponding mass spectra, molecular compositions of the PCPAH products were unambiguously determined. The results obtained from the HPLC-UV-MS analysis not only are helpful for the understanding of the fullerenes formation mechanism, but also contribute to the analytical technique capable of separating and identifying the complicated mixture of PCPAHs and fullerenes.

A novel four base-pair deletion within the Agamma-GLOBin gene promoter associated with slight increase of Agamma expression in adult.

We studied a Chinese family and revealed 5.4% and 3.2% fetal hemoglobin (HbF) with advantageously Agamma type in the mother and the daughter, respectively, using alkali denaturation assay and urea-Triton-acrylamide gel electrophoresis and high-performance liquid chromatography. The father's HbF was less than 0.5%. Large deletion was not observed within the beta-globin gene cluster by restriction endonuclease mapping. Characterization by the polymerase chain reaction (PCR) and DNA sequencing demonstrated the mother is a homozygote with a novel four base-pair "AAGC" (-226 to -223) deletion within the Agamma-globin gene promoter and the daughter is a heterozygote with this deletion. The deletion was not detected in the father. No any mutations were identified in the Ggamma promoter of all the subjects studied. We propose that the small deletion is associated with the slight increase of Agamma gene expression in adult.

Separation and identification of perchlorinated polycyclic aromatic hydrocarbons by high-performance liquid chromatography and ultraviolet absorption spectroscopy.

High-performance liquid chromatography (HPLC) was coupled with ultraviolet absorption spectroscopy (UV) for the simultaneous separation and identification of a series of perchlorinated polycyclic aromatic hydrocarbons, such as perchlorobenzene (C6Cl6), perchloronaphthalene (C10Cl8), perchlorobiphenyl (C12Cl10), perchloroanthracene (C14Cl10), perchlorophenanthrene (C14C10), perchloroacenaphthylene (C12Cl8), perchloropyrene (C16Cl10) and perchlorofluoranthene (C16Cl10). HPLC was performed on an ODS column using methanol-hexane (80:20) as mobile phase at a flow-rate of 1.0 ml/min. UV absorption spectra of the elutes were detected in the region of 210-350 nm.

Purification of virus like particles from yeast cells using aqueous two-phase systems.

Aqueous two-phase systems have been used for the separation and purification of recombinant virus-like particles (VLPs) from a yeast cell homogenate. Systems have been evaluated on the basis of their ability to separate VLPs from cell debris and from contaminating proteins. Two strategies are proposed for VLP separation, both involve the use of two PEG/salt aqueous two-phase systems. For separation of VLPs from cell debris systems composed of PEG 400 or 600 and (NH4)2SO4 or PEG 4000/MgSO4 can be used and for separation of VLPs from proteins PEG 4000/(NH4)2SO4 or MgSO4 and Na2SO4 are effective. The molecular weight of the PEG used and the use of additional salts (e.g. NaCl) greatly influence the effectiveness of the systems.

Determination of age-related changes of cytochrome P-450 sensitive to mepyramine in rat hepatic microsomes.

The cytochrome P-450 (Cyt P-450) sensitive to mepyramine (HP-450) in liver microsome is a protein that possesses properties of both H1 receptor and cytochrome P-450. We used [3H]mepyramine radioligand binding assay and enzymological technique to study the kinetic properties of HP-450 and Cyt P-450. Age-related changes in the Bmax, Kd of HP-450 and Cyt P-450 in rat hepatic microsome were demonstrated. The levels of Bmax for both HP-450 and the Cyt P-450 dramatically increased in the postnatal period from the second to the eighth week, and reached maximum steady status during the eighth to tenth week. The values of Bmax of HP-450 correlated well with the content of Cyt P-450 in rat liver microsome (r = 0.625). The affinity of HP-450 (Kd) decreased with the growth of rats during postnatal. No sexual-related difference was observed in this experiment.

Selective release of recombinant protein particles (VLPs) from yeast using a pure lytic glucanase enzyme.

We have used a pure lytic glucanase enzyme to selectively release recombinant 60 nm protein particles (virus like particles or VLPs) from yeast cells. Although the protease components of the lytic enzyme complexes were found to degrade the VLPs, purified glucanase enzymes from these complexes (derived from Cytophaga sp. and Oerskovia sp.) produced cell lysis without degradation and released the VLPs in the absence of mercaptoethanol, a reducing agent commonly used in cell lysis. The Oerskovia glucanase enzyme released the recombinant protein particles selectively as it only produced ca. 17% cell lysis compared to the use of the total lytic enzyme preparation. The use of osmotic supports did not improve the recovery of VLPs, however, treatment of the enzymatically lysed pellet with Triton X-100 did increase the amount of VLPs released. This 'selectivity', which results in the release of the recombinant particles with only a fraction of contaminating proteins, represents an improvement over presently used mechanical or enzymatic cell disruption processes.

Differential product release (DPR) of proteins from yeast: a new technique for selective product recovery from microbial cells.

A novel method has been developed for the separation of bioproducts from yeast cells. The method uses a combination of physical, chemical, and biological agents such as lytic enzymes, osmotic supports, and spheroplast stabilizers. Using this technique, products (proteins and enzymes) can be released from specific cell locations at different process states; it has thus been celled differential product release (DPR). The wall-associated proteins are released first and the lytic enzyme is removed together with the wall proteins at this stage. Secondly, the cytosol products are released by a mild procedure during which the organelles remained intact. Finally, the organelle proteins are solubilized. In each stage, specific proteins are released while others are kept inside the different cell compartments. This method can be used with relatively high yeast concentrations (up to 145 g dry wt/L) and gives higher product recoveries and much higher selectivity than mechanical disruption.

Release of 3H-5-hydroxytryptamine by amiflamine and related phenylalkylamines from rat occipital cortex slices.

In the present study amiflamine and other related reversible monoamine oxidase-A (MAO-A) inhibitory phenylalkylamines were examined in vitro for their ability to induce release of 3H-5-hydroxytryptamine (3H-5-HT) from rat occipital cortex slices. The slices were preincubated with 3H-5-HT 0.1 mumol/l in the presence of the irreversible MAO inhibitor pargyline 50 mumol/l and then continuously superfused. The effects were compared with those of the 5-HT releaser p-chloroamphetamine (pCA), the reversible MAO-inhibitor alpha-ethyltryptamine and the 5-HT uptake inhibitor citalopram. Amiflamine, some related compounds and alpha-ethyltryptamine which in vivo after transport by the 5-HT uptake mechanism preferentially inhibit MAO within the serotonergic neurons caused a Ca2+-independent release of 3H-5-HT. Some transported compounds, particularly NBF 027 were, however, very weak releasers of 5-HT. This release and that induced by pCA was prevented by citalopram in the superfusion medium. FLA 365, FLA 417 and FLA 1088, which are not transported into the neurons, were poor releasers of 5-HT. It is concluded that compounds which were effective releasers of 5-HT in vitro were those that are transported into the serotonergic neurons by the 5-HT carrier in vivo and has in addition an ability to mobilise vesicular 5-HT.

Identification of base substitutions in the promoter regions of the A gamma- and G gamma-globin genes in A gamma- (or G gamma-) beta+-HPFH heterozygotes using the DNA-amplification-synthetic oligonucleotide procedure.

DNA amplification combined with hybridization with 32P-labeled synthetic oligonucleotide probes has been used to identify base substitutions in the 5' promoter region of the A gamma globin gene in members of eleven families from China, Sardinia, Canada, and the United States who had a heterozygosity for the A gamma-beta+-hereditary persistence of fetal hemoglobin (HPFH), and in members of six black families with a possible G gamma-beta+-HPFH heterozygosity. All three known A gamma types were observed, ie, the British type (-198, T----C), the Chinese type (-196, C----T), and the Green type (-117, G----A); the latter has been found in a black family. Of the six families with G gamma-beta+-HPFH, three had C----G at -202 and none T----C -175. Conditions for hybridization of amplified DNA with the specific probes are provided and the usefulness of the technique is discussed. The increase in numbers of A gamma(G gamma)-beta+-HPFH heterozygotes with specific base substitutions greatly enhances the probability of a direct correlation between these substitutions and the increase in the production of a specific gamma chain.

Dopamine turnover and glutamate decarboxylase activity in the rat brain after acute and chronic treatment with raclopride, a dopamine D2-selective antagonist.

The effect of acute and chronic (94, 141 and/or 199 days) oral treatment of rats with the dopamine D2-selective antagonist raclopride (0, 5, 15, 45 and 135 mumol/kg) upon the turnover of dopamine in the striatum and limbic system and upon the activity of glutamate decarboxylase (GAD) in the s. nigra, striatum and frontal cortex has been investigated. A dose-dependent tolerance to the effect of raclopride on the turnover of dopamine was observed after chronic treatment, although the degree of tolerance was marginal at the 5 and 15 mumol/kg doses. Acute treatment with raclopride was without effect on the activity of GAD in the s. nigra, striatum or frontal cortex, whereas chronic (199 days) treatment with 45 mumol/kg of raclopride produced an increase in the activity of GAD in the s. nigra and striatum.