Structural genomics efforts at the Chinese Academy of Sciences and Peking University

Structural genomics efforts at the Chinese Academy of Sciences and Peking University are reported in this article. The major targets for the structural genomics project are targeted proteins expressed in human hematopoietic stem/progenitor cells, proteins related to blood diseases and other human proteins. Up to now 328 target genes have been constructed in expression vectors. Among them, more than 50% genes have been expressed in Escherichia coli, approximately 25% of the resulting proteins are soluble, and 35 proteins have been purified. Crystallization, data collection and structure determination are continuing. Experiences accumulated during this initial stage are useful for designing and applying high-throughput approaches in structural genomics.

Prediction of P-Glycoprotein Substrates by a Support Vector Machine Approach

P-glycoproteins (P-gp) actively transport a wide variety of chemicals out of cells and function as drug efflux pumps that mediate multidrug resistance and limit the efficacy of many drugs. Methods for facilitating early elimination of potential P-gp substrates are useful for facilitating new drug discovery. A computational ensemble pharmacophore model has recently been used for the prediction of P-gp substrates with a promising accuracy of 63%. It is desirable to extend the prediction range beyond compounds covered by the known pharmacophore models. For such a purpose, a machine learning method, support vector machine (SVM), was explored for the prediction of P-gp substrates. A set of 201 chemical compounds, including 116 substrates and 85 nonsubstrates of P-gp, was used to train and test a SVM classification system. This SVM system gave a prediction accuracy of at least 81.2% for P-gp substrates based on two different evaluation methods, which is substantially improved against that obtained from the multiple-pharmacophore model. The prediction accuracy for nonsubstrates of P-gp is 79.2% using 5-fold cross-validation. These accuracies are slightly better than those obtained from other statistical classification methods, including k-nearest neighbor (k-NN), probabilistic neural networks (PNN), and C4.5 decision tree, that use the same sets of data and molecular descriptors. Our study indicates the potential of SVM in facilitating the prediction of P-gp substrates.

[Cloning and sequencing of cytochrome c oxidase II(COII) gene of three species of mosquitoes]

OBJECTIVE

To determine and compare the complete sequence of COII gene from Anopheles sinensis, Aedes albopictus and Culex quinquefasciatus and to identify the molecular homology among these mosquitoes.

METHODS

The recombinant plasmids including COII gene from the three species of mosquitoes were obtained by the T-A cloning technique, and the COII genes were sequenced and analyzed.

RESULTS

The homology of the COII gene nucleotide sequence and the deduced amino acid sequence of COII among the three species of mosquitoes varied from 84.1% to 87.9% and from 85.1% to 89.5%, respectively. The C + G content of COII gene was 23.2%-24.9%, the frequency of transversion higher than that of transition.

CONCLUSION

Aedes albopictus and Culex quinquefasciatus are closely related species at their COII molecular level according to COII gene.

Analysis of zein by matrix-assisted laser desorption/ionization mass spectrometry

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI/MS) was used to analyze the protein composition of corn prolamine (zein). Mass spectra were obtained from commercial zein and zein extracted with aqueous 2-propanol and aqueous ethanol from consumer corn meal. For the commercial zein, three major zein fractions with m/z 26.8k, 24.1k, and 23.4k were clearly seen with two minor fractions (m/z 14.5k and 20.4k) also present. As compared with the results from sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), these three fractions were identified as alpha-zeins (24.1k and 23.4k combined as Z19; 26.8k as Z22). When extracted with 55% aqueous 2-propanol, three alpha-zein fractions with m/z 26.8k, 24.1k, and 23.4k were predominant. When extracted with ethanol, extraction temperature had an effect on the final products. When extracted with 75% aqueous ethanol at room temperature, alpha-zein and some 17-18k species were observed, whereas at 60 degrees C, a small amount of delta-zein was also present. Comparison of the MALDI/MS results with SDS-PAGE and gene sequence analysis shows that the MALDI/MS method is superior to SDS-PAGE in having higher resolution and mass accuracy.

Biological dosimetry of complex ion radiation fields

We report on a set of cell survival experiments performed in complex field combinations of therapeutic 12C ion beams. CHO cells were exposed to the superposition of two or three fields of 12C ions arranged in a similar way to real patient treatments. Two-dimensional survival distributions were measured and compared with the predictions of the TRiP98 treatment planning system. Good agreement was found in general. In particular the method of tissue sparing using dose ramps could be verified.

Exact representation of crossover of transitions from first order to second order in the Potts model for rumor transmission

The L-state Potts model for rumor is the N-spin chain describing how a simple rumor transmitted by N recreant rumormongers is aggrandized. The studied rumor is represented mathematically by a simple proposition with the universal quantifier, which again is represented geometrically by a point in a proposition space. During the transmission, such a proposition is changed with the change of the rumor, which has individual number N0 at the beginning of the transmission. Correspondingly, the point expressing the proposition may start from an arbitrary site at the proposition space, and then it shifts in the space. Thus, a spin sum of the Potts model corresponds to a walk of a point in the proposition space and spin configuration's numbers is given by enumerating the corresponding walks. The concept of the lattice path in combinatorial mathematics is introduced and the exact series representation of the configuration's numbers is given. The partition function exhibits the transition of the chain and critical equivalent inverse temperature beta(c) is determined. Moreover, there is a crossover value of the individual number, N00. The model has a first-order transition when N0<N00 and a second-order one when N0>N00.

Attenuation of N-methyl-D-aspartate-mediated cytoplasmic vacuolization in primary rat hippocampal neurons by mood stabilizers

Recent post-mortem and brain imaging studies suggest that decreased neuronal and glial densities may account for cell loss in vulnerable brain regions such as the hippocampus and the frontal cortex in patients with bipolar disorder. Investigations into the mechanisms of action of mood stabilizers suggest that these drugs may regulate the expression of neuroprotective genes and protect against excitotoxicity. In this study, we characterized the ultrastructural appearance of rat hippocampal neurons pretreated with mood stabilizers and then exposed to the glutamate receptor agonist N-methyl-D-aspartate. Using transmission electron microscopy we found that rat hippocampal neurons exposed to 0.5 mM N-methyl-D-aspartate for 10 min produced more cytoplasmic vacuolization than in control neurons. Chronic treatment with mood stabilizers, lithium, valproate or carbamazepine for 7 days at therapeutically relevant concentrations fully attenuated N-methyl-D-aspartate-mediated cytoplasmic vacuolization. These results suggest that inhibition of neurotoxicity may be involved in the action of mood stabilizers.

Activity difference between alpha-COOH and beta-COOH in N-phosphorylaspartic acids

N-phosphorylamino acids are chemically active species that have many biomimic activities. alpha-COOH in amino acids and peptides behaviors rather differently than beta-COOH in many biochemical processes and takes a more important role in the origin of life. Activity differences between alpha-COOH and beta-COOH in the peptide formation of phosphoryl amino acids are studied by 1D, 2D NMR techniques and by ab initio and density functional theory (DFT) calculations in this paper. Phosphoryl dipeptide is formed directly from phosphoryl aspartic acids without any coupling reagents. Only the alpha-dipeptide ester is observed by 1D (1)H, (13)C, and (31)P NMR and 2D NMR. In the ab initio and DFT calculations, the pentacoordinate phosphorane intermediates containing five-membered rings are predicted to be more favored than those with six-membered rings. Both the experimental results and the theoretical calculations suggest that only the alpha-COOH group is activated by N-phosphorylation in N-phosphorylaspartic acid under mild conditions.

Valproate inhibits oxidative damage to lipid and protein in primary cultured rat cerebrocortical cells

Valproate is often prescribed as a long-term therapeutic mood stabilizing agent for individuals with bipolar disorder. Although research suggests that this drug may produce a neuroprotective effect, its neuroprotective mechanism is not yet clear. The purpose of this study was to determine if valproate provides a neuroprotective effect against damage caused by oxidative stress in primary cultured rat cerebral cortical cells. We found that chronic treatment with valproate at therapeutically relevant concentrations for 7 days inhibited lipid peroxidation and protein oxidation induced by treatment with 0.25 mM oxidant FeCl(3) for 90 min, indicating that valproate inhibits oxidative damage to lipid and protein. Our results suggest that chronic treatment with valproate may protect neuronal cells from damage caused by oxidative stress and that neuroprotection from oxidative damages may be involved in the mechanism of action of valproate. Supporting this possibility are recent findings that chronic treatment with valproate increased the expression of endoplasmic reticulum stress protein GRP78 and antiapoptotic factor bcl-2 in rat cerebral cortex. Since GRP78 binds Ca(2+) and folds damaged protein, bcl-2 stabilizes mitochondrial transmembrane potential and inhibits cytochrome C release, and both GRP78 and bcl-2 have been shown to inhibit oxyradical accumulation, together these findings indicate that valproate may target one or more of these processes in order to produce neuroprotective effects.

ADME-AP: a database of ADME associated proteins

Drug absorption, distribution, metabolism and excretion (ADME) often involve interaction of a drug with specific proteins. Knowledge about these ADME-associated proteins is important in facilitating the study of the molecular mechanism of disposition and individual response as well as therapeutic action of drugs. It is also useful in the development and testing of pharmacokinetics prediction tools. Several databases describing specific classes of ADME-associated proteins have appeared. A new database, ADME-associated proteins (ADME-AP), is introduced to provide comprehensive information about all classes of ADME-associated proteins described in the literature including physiological function of each protein, pharmacokinetic effect, ADME classification, direction and driving force of disposition, location and tissue distribution, substrates, synonyms, gene name and protein availability in other species. Cross-links to other databases are also provided to facilitate the access of information about the sequence, 3D structure, function, polymorphisms, genetic disorders, nomenclature, ligand binding properties and related literatures of each protein. ADME-AP currently contains entries for 321 proteins and 964 substrates.

Sequence-specific assignments of proton NMR resonance peaks and analysis of secondary structural elements of LC1, a novel antibacterial polypeptide

LC1 is a type of novel antibacterial polypeptide secreted by a Bacillus subtilis strain. It consists of 47 residues. Using bioengineering, LC1 was expressed in E.coli DH5alpha by using recombinant plasmid PBVAB16. By means of two-dimensional DQF-COSY, TOCSY and NOESY spectroscopies, protons of all 47 residues are identified. The studies show that the secondary structures of LC1 are principally anti-parallel beta sheets and extended conformations. It was speculated that there may be a hydrophobic core around Trp(23) in its three-dimensional structure.

Attenuated lapinized chinese strain of classical swine fever virus: complete nucleotide sequence and character of 3'-noncoding region

The complete nucleotide sequence including precise 5'- and 3'-terminal non-coding regions (NCRs) of the attenuated lapinized Chinese strain (HCLV) of Classical Swine Fever Virus (CSFV) was determined from overlapping cDNA clones constructed by separated RT-PCR and rapid amplification of cDNA ends (RACE) methods. The genomic RNA of the HCLV strain consists of 12.310 nucleotides (nts) including 374 nts and 242nts in the 5'- and 3'-NCRs, respectively. It contains one large open reading frame (ORF) encoding a polyprotein of 3,898 amino acids with a calculated molecular weight of 437.6 kDa. There is one notable insertion of 12 continuous nts, CTTTTTTCTTTT in the 3'-NCR of HCLV genomic cDNA when compared with its parental virulent Shimen strain. Sequence alignment of partial 3'-NCR reveals two groups of CSFV vaccine strains carrying similar T-rich insertions at different positions in this region. Computer-predicted secondary structures suggest that T-rich insertion greatly change the structures and thus decrease the promoter functions of 3'-NCRs during the replications of these two groups of CSFV vaccine strains.

[Studies of mtDNA haplotype polymorphism of Rongcheng population in China]

The loss of one copy of two 9-bp repeats in mtDNA non-coding region V is often found in Asia and Pacific populations. Two hundred and ten samples from Rongcheng county, Shandong province were detected with the deletion frequency of 12.4%. A distribution map of frequencies of mtDNA 9-bp deletion among Asian and Pacific population was made with reference to other published data. Further discussion was made for the hypotheses of affinity and original model of those populations. PCR-RFLP was conducted to obtain the mtDNA polymorphism information in five other mtDNA regions except the 9-bp deletion in 95 samples. Twenty-seven different mtDNA haplotypes were found, and the relationships among these haplotypes have been analyzed by using MEGA2.0 and PHYLIP 3.57. Two new RFLP sites caused by point mutation were also found, which have not been reported in Chinese populations.

Photorefractive polymers sensitized by two-photon absorption

We demonstrate the recording of holograms and their nondestructive readout in a photorefractive polymer, using two-photon absorption. Sensitivity is provided by the excitation of the electroactive chromophore with femtosecond pulses, followed by charge injection into the photoconducting poly(N -vinylcarbazole) matrix. The holograms can be fully erased with a pulsed laser source but are insensitive to cw laser beams with the same wavelength. Studies of the field and intensity dependence of the diffraction efficiency indicate that the holograms are formed through the photorefractive effect.

Molecular scaffold of a new pokeweed antifungal peptide deduced by 1H nuclear magnetic resonance

The antifungal peptide from seeds of Phytolacca americana (Pokeweed), designated PAFP-S hereinafter, is a recently found cationic peptide which consists of 38 amino acid residues and exhibits a broad spectrum of antifungal activity, including inhibition of certain saprophytic fungi and some plant pathogens. The secondary structure and three cysteine pairings have been investigated by 1H NMR analysis. The results show that the molecular scaffold of PAFP-S features a triple-stranded antiparallel beta-sheet knotted by a typical disulfide bridge motif, which characterizes the knottin fold. CD spectroscopy indicates a high stability of the molecule in solution. Therefore, PAFP-S should be a new member of the knottin structural family and the first antifungal peptide that adopts the knottin-like fold.

Stimulation of beta 1 integrin induces tyrosine phosphorylation of vascular endothelial growth factor receptor-3 and modulates cell migration

Interactions between integrins and tyrosine kinase receptors can modulate a variety of cell functions. We observed a cooperative interaction between the beta(1) integrin and vascular endothelial growth factor receptor-3 (VEGFR-3 or Flt4) that appeared to be required for cell migration. By using VEGFR-3-transfected 293 cells (293/VEGFR-3) or primary dermal microvascular endothelial cells (DMEC), we found that stimulation with either soluble or immobilized extracellular matrix (ECM) proteins, collagen or fibronectin (FN), resulted in the increased tyrosine phosphorylation of VEGFR-3 in the absence of a cognate ligand. This increased tyrosine phosphorylation of VEGFR-3 was diminished by pretreatment with a blocking antibody against the beta(1) integrin. Cross-linking with anti-beta(1) integrin antibody induced a similar degree of tyrosine phosphorylation of VEGFR-3. Stimulation with collagen or FN induced an association between beta(1) integrin and VEGFR-3 in both 293/VEGFR-3 and primary DMEC cells. Collagen or FN-induced tyrosine phosphorylation of VEGFR-3 was inhibited by treatment with cytochalasin D, an inhibitor of actin polymerization. Collagen or FN was able to induce the migration of 293/VEGFR-3 or DMEC cells to a limited extent. However, migration was dramatically enhanced when a gradient of the cognate ligand, VEGF-D, was added. VEGF-D failed to induce cell migration in the absence of ECM proteins. Introducing a mutation at the kinase domain of VEGFR-3 or treatment with blocking antibody against either VEGFR-3 or beta(1) integrin inhibited cell migration induced by ECM and VEGF-D, indicating that signals from both beta(1) integrin and VEGFR-3 are required for this cell function.

Gene expression differences in bipolar disorder revealed by cDNA array analysis of post-mortem frontal cortex

Previous studies have implicated a number of biochemical pathways in the etiology of bipolar disorder (BD). However, the precise abnormalities underlying this disorder remain to be established. To investigate novel factors that may be important in the pathophysiology of BD, we utilized cDNA expression arrays to examine differences in expression of up to 1200 genes known to be involved in potentially relevant biochemical processes. This investigation was undertaken in post-mortem samples of frontal cortex tissue from patients with BD and matched controls, obtained (n = 10/group) from the Stanley Foundation Neuropathology Consortium. Results include significant (greater than 35% change in signal intensity) differences between BD and controls in a number of genes (n = 24). Selected targets were analyzed by RT-PCR, which confirmed a decrease in transforming growth factor-beta1 (TGF-beta 1), and an increase in both caspase-8 precursor (casp-8) and transducer of erbB2 (Tob) expression in BD. We further observed a significant decrease of TGF-beta 1 mRNA levels in BD by RT-PCR in individual post-mortem samples. Given the neuroprotective role attributed to this inhibitory cytokine, our results suggest that the down-regulation of TGF-beta 1 may lead to various neurotoxic insults potentially involved in the etiology of certain mood disorders.

[Anterior lumbar interbody fusion of canine with allograft cortical ring plus autogenous cancellus]

OBJECTIVE

To prove the biological characteristics of spinal intervertebral fusion with allograft cortical ring plus autogenous cancellus from iliac bone (called as composite ring).

METHODS

Eight hybrid dogs were adopted in the study. The composite ring and autogenous tri-cortical blocks were implanted into the intervertebral space of dogs respectively. The intervertebral discs were removed before implantation. The fusion segments were evaluated by x-ray, histological examinations at 1, 2, 4 and 6 months after operation to compare the healing status of two implants.

RESULTS

The X-ray film and histological examination showed the lumbar interbody was fused after 4 months of operation in composite ring group, while the autogenous iliac bone blocks fused with peripheral bone tissue after 6 months of operation. Composite ring healed more quickly and completely, showed different osteogenesis behavior compared with that of massive allografts.

CONCLUSION

Composite ring can promote the fusion of intervertebral body and can be used as a potential material for spinal surgery.

Solution structure of PAFP-S: a new knottin-type antifungal peptide from the seeds of Phytolacca americana

The three-dimensional solution structure of PAFP-S, an antifungal peptide extracted from the seeds of Phytolacca americana, was determined using 1H NMR spectroscopy. This cationic peptide contains 38 amino acid residues. Its structure was determined from 302 distance restraints and 36 dihedral restraints derived from NOEs and coupling constants. The peptide has six cysteines involved in three disulfide bonds. The previously unassigned parings have now been determined from NMR data. The solution structure of PAFP-S is presented as a set of 20 structures using ab initio dynamic simulated annealing, with an average RMS deviation of 1.68 A for the backbone heavy atoms and 2.19 A for all heavy atoms, respectively. For the well-defined triple-stranded beta-sheet involving residues 8-10, 23-27, and 32-36, the corresponding values were 0.39 and 1.25 A. The global fold involves a cystine-knotted three-stranded antiparallel beta-sheet (residues 8-10, 23-27, 32-36), a flexible loop (residues 14-19), and four beta-reverse turns (residues 4-8, 11-14, 19-22, 28-32). This structure features all the characteristics of the knottin fold. It is the first structural model of an antifungal peptide that adopts a knottin-type structure. PAFP-S has an extended hydrophobic surface comprised of residues Tyr23, Phe25, Ile27, Tyr32, and Val34. The side chains of these residues are well-defined in the NMR structure. Several hydrophilic and positively charged residues (Arg9, Arg38, and Lys36) surround the hydrophobic surface, giving PAFP-S an amphiphilic character which would be the main structural basis of its biological function.

Increased hippocampal BDNF immunoreactivity in subjects treated with antidepressant medication

BACKGROUND

The cAMP signaling pathway, and its downstream neurotrophic factor BDNF, are major targets of antidepressant medications. Abnormalities in this pathway have previously been reported in postmortem brain of subjects with mood disorders. This study was designed to test whether the diagnosis of a mood disorder, or treatment with an antidepressant or mood stabilizer was associated with changes in hippocampal BDNF in postmortem brain.

METHODS

Frozen postmortem anterior hippocampus sections were obtained from the Stanley Foundation Neuropathology Consortium. Tissue from subjects with major depression, bipolar disorder, schizophrenia and nonpsychiatric control subjects were stained for BDNF using immunohistochemistry.

RESULTS

Increased BDNF expression was found in dentate gyrus, hilus and supragranular regions in subjects treated with antidepressant medications at the time of death, compared with antidepressant-untreated subjects. Furthermore, there was a trend toward increased BDNF expression in hilar and supragranular regions in depressed subjects treated with antidepressants, compared with the subjects not on these medications at the time of death.

CONCLUSIONS

These findings are consistent with recent studies measuring CREB levels in this same subject sample, and support current animal and cellular models of antidepressant function.

The pig as a model for excisional skin wound healing: characterization of the molecular and cellular biology, and bacteriology of the healing process

A pig model of wound healing was developed by excision of 2-cm-diameter full thickness skin in young Yorkshire pigs. The results indicated that wound re-epithelialization in this animal model took an average of 20 days. Analysis of cellular change was assessed by use of DNA quantification and determination of apoptotic cells in tissue sections. The results indicate that RNA and DNA contents paralleled each other throughout the healing process, and observed changes in the pattern of RNA and DNA content of the scar tissues were consistent with cell loss due to apoptosis in this model. Expression of mRNA for relevant genes was assessed by use of semiquantitative reverse transcription-polymerase chain reaction (RT-PCR) analysis, using porcine specific primer sets and RNA isolated from normal skin and specimens obtained at various times after wounding. The mRNA values for tumor necrosis factor-alpha (TNF-alpha), connective tissue growth factor (CTGF), insulin-like growth factor II (IGF-II), and decorin were significantly high at specific times after wounding, but mRNA values for the transcription factors (c-fos and c-jun) were significantly decreased. Quantitative bacteriologic results indicated that the total bacterial count in this animal model reached 10(9) colony-forming units (CFU)/g, with the highest value at post-wounding day 7, and Pseudomonas aeruginosa and Staphylocococci aureus were the most common bacteria detected in this model. Further definition of this model should identify unique points in the healing process, and such information could lead to development of therapeutic interventions to improve skin wound healing.

Determination of retinoids in human serum, tocopherol and retinyl acetate in pharmaceuticals by RP-LC with electrochemical detection

A liquid chromatography with a electrochemical detector method has been developed of the quantitative measurement for the three retinoids in human serum (13-cis and all-trans retinoic acid and retinol), as well as tocopherol acetate, retinyl acetate and retinol in pharmaceuticals. The detection cell consisted of a glassy carbon electrode held at 1.0 V versus an Ag/AgCl reference electrode. The maximum electrochemical signal was obtained with a supporting electrolyte containing 92% methanol 0.1 M acetate buffer (pH 4.72) as the mobile phase. The quantification limits are 0.5, 0.2, 0.4, 0.5, 0.8 and 0.8 ng for tocopherol acetate, all-trans-RA, 13-cis-RA, retinol, retinal and retinyl acetate, respectively. The electrooxidation process is applied for the simultaneous quantitative determination of retinoids in human serum. Comparison with results obtained from HPLC-UV shows agreement.

Physician control of pediatric antimicrobial use in Beijing, China, and its rural environs

BACKGROUND

Antibiotic resistance is recognized as an increasing problem in China. It is widely believed that because antibiotics are available without a prescription, changing physician prescribing behaviors will not decrease inappropriate usage. This study identified the sources of antibiotics and the important influence that physicians have on antibiotic use by children in one region of China.

METHODS

Trained medical professionals surveyed parents of children attending several kindergartens in urban Beijing and rural Gu'An, Hebei County. Parents completed a questionnaire concerning the children's recent illnesses, care-seeking patterns and antibiotic use. The team also observed hospital- and non-hospital-based pharmacy purchases of antibiotics for children, assessed the proportion accompanied by a prescription and then interviewed parents about factors influencing those purchases.

RESULTS

Of 241 urban and 143 rural kindergarten parents, 76 to 82% usually obtained children's antibiotics from a hospital pharmacy (with a prescription). For 84% the first source of care was usually a physician (primarily western medicine, sometimes traditional Chinese medicine). Only 5% of antibiotics were obtained from independent vendors without prior physician consultation. Among 229 observed antibiotic purchases 72% occurred at hospital-based facilities, even after longer observation times at nonhospital pharmacies. Prescriptions accompanied all hospital-based antibiotic purchases, contrasting with 18% of nonhospital transactions (P < 0.001). Together 86% of parents self-reported that the observed purchase stemmed from a doctor's recommendation.

CONCLUSIONS

Doctors directly and indirectly controlled the majority of antibiotic usage for childhood illnesses in Beijing and Gu'An (Hebei County). Physician education and implementation of treatment guidelines might substantially reduce inappropriate antimicrobial usage and help prevent antimicrobial resistance in this region.