Efficient and accurate treatment of electron correlations with Correlation Matrix Renormalization theory.

We present an efficient method for calculating the electronic structure and total energy of strongly correlated electron systems. The method extends the traditional Gutzwiller approximation for one-particle operators to the evaluation of the expectation values of two particle operators in the many-electron Hamiltonian. The method is free of adjustable Coulomb parameters, and has no double counting issues in the calculation of total energy, and has the correct atomic limit. We demonstrate that the method describes well the bonding and dissociation behaviors of the hydrogen and nitrogen clusters, as well as the ammonia composed of hydrogen and nitrogen atoms. We also show that the method can satisfactorily tackle great challenging problems faced by the density functional theory recently discussed in the literature. The computational workload of our method is similar to the Hartree-Fock approach while the results are comparable to high-level quantum chemistry calculations.

Metals on graphene: correlation between adatom adsorption behavior and growth morphology.

We present a systematic study of metal adatom adsorption on graphene by ab initio calculations. The calculations cover alkali metals, sp-simple metals, 3d and group 10 transition metals, noble metals, as well as rare earth metals. The correlation between the adatom adsorption properties and the growth morphology of the metals on graphene is also investigated. We show that the growth morphology is related to the ratio of the metal adsorption energy to its bulk cohesive energy (E(a)/E(c)) and the diffusion barrier (ΔE) of the metal adatom on graphene. Charge transfer, electric dipole and magnetic moments, and graphene lattice distortion induced by metal adsorption would also affect the growth morphologies of the metal islands. We also show that most of the metal nanostructures on graphene would be thermally stable against coarsening.

Prediction of RNA-binding proteins by voting systems.

It is important to identify which proteins can interact with RNA for the purpose of protein annotation, since interactions between RNA and proteins influence the structure of the ribosome and play important roles in gene expression. This paper tries to identify proteins that can interact with RNA using voting systems. Firstly through Weka, 34 learning algorithms are chosen for investigation. Then simple majority voting system (SMVS) is used for the prediction of RNA-binding proteins, achieving average ACC (overall prediction accuracy) value of 79.72% and MCC (Matthew's correlation coefficient) value of 59.77% for the independent testing dataset. Then mRMR (minimum redundancy maximum relevance) strategy is used, which is transferred into algorithm selection. In addition, the MCC value of each classifier is assigned to be the weight of the classifier's vote. As a result, best average MCC values are attained when 22 algorithms are selected and integrated through weighted votes, which are 64.70% for the independent testing dataset, and ACC value is 82.04% at this moment.

Imiquimod simultaneously induces autophagy and apoptosis in human basal cell carcinoma cells.

BACKGROUND: Imiquimod shows antitumour activity through the stimulation of cell-mediated immunity in vivo. Recent studies have shown that imiquimod promotes apoptosis in melanoma cells and induces autophagy in macrophage cell lines. OBJECTIVES: To evaluate the imiquimod-induced apoptosis, autophagy and their relationship in a basal cell carcinoma (BCC) cell line. METHODS: Cell viability was determined by XTT test. Apoptosis was evaluated by DNA content assay, annexin V/propidium iodide staining assay and terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick-end labelling assay. Autophagy was determined by LC3 immunoblotting, EGFP-LC3 puncta formation and quantification of acidic vesicular organelles with acridine orange staining. The temporal and spatial differences of imiquimod-induced apoptosis and autophagy were examined by immunoblotting and simultaneously monitored by staining the EGFP-LC3 transfected cells with caspase 3 fluorogenic substrate. We inhibited the apoptosis and autophagy by pancaspase inhibitor and siRNA for Beclin 1 or Atg5, respectively, to evaluate the interplay between imiquimod-induced apoptosis and autophagy. RESULTS: We found that imiquimod induces autophagy and apoptosis in BCC cells in a time- and dose-dependent manner. Imiquimod not only induced EGFP-LC3 puncta formation for autophagy, but also simultaneously activated an apoptotic caspase cascade in the same cells. Both apoptosis and autophagy induced by imiquimod cooperate to cause BCC cell death. However, inhibition of imiquimod-induced apoptosis increased the strength of autophagy, and inhibition of imiquimod-induced autophagy further promoted cell apoptosis. CONCLUSIONS: This study not only demonstrates that imiquimod can directly induce autophagy and apoptosis in BCC cells, but also shows the cooperation and coordination between these two processes to induce cell death.

Suitable reference gene selection for different strains and developmental stages of the carmine spider mite, Tetranychus cinnabarinus, using quantitative real-time PCR.

Reference genes are used as internal controls in gene expression studies, but their expression levels vary according to tissue types and experimental treatments. Quantitative real-time PCR (qPCR) is the most sensitive technique for transcript quantification provided that gene transcription patterns are normalized to an evaluated reference gene. In this study, the suitability of eight commonly used genes (ß-actin, 5.8SrRNA, α-TUB, GAPDH, RPL13a, RPS18, TBP, SDHA) were cloned and investigated to find the most stable candidates for normalizing real-time PCR data generated from the four different strains (abamectin-resistant, fenpropathrin-resistant, omethoate-resistant, and susceptible strains) and different developmental stages (eggs, protonymphs, nymphs, and adults) of carmine spider mite, Tetranychus cinnabarinus (Boisduval) (Acarina: Tetranychidae). The stability of gene expression was assessed using two different analysis programs, geNorm and NormFinder. Using these analyses, RPS18 and 5.8SrRNA had the most stable expression regardless of the four different strains, whereas RPS18 and α-TUB were expressed most stably in different developmental stages.

Molecular characterization and expression of three heat shock protein70 genes from the carmine spider mite, Tetranychus cinnabarinus (Boisduval).

Three heat shock protein 70 (Hsp70) cDNAs were isolated from the carmine spider mite, Tetranychus cinnabarinus. They were tentatively named as TCHsp70-1, TCHsp70-2 and TCHsp70-3. Structural analyses showed that all of the three TCHsp70 cDNAs held the full open reading frame (ORF). Putative protein sequences and a phylogenetic tree suggested that TCHsp70-1 and TCHsp70-3 were cytoplasm HSP70 and TCHsp70-2 was endoplasmic reticulum HSP70. Comparison of deduced amino acid sequences of TCHsp70-1 and TCHsp70-3 showed 84.78% identity, TCHsp70-1 and TCHsp70-2 showed 57.33% identity, TCHsp70-2 and TCHsp70-3 showed 58.26% identity. Real-time comparative quantitative PCR revealed that the relative expression of TCHsp70-2 was lower than TCHsp70-1 and TCHsp70-3 at each temperature tested. TCHsp70-1 and TCHsp70-3 shared a similar expression pattern after cold and heat shock compared with their expression at normal temperature (26 degrees C), but the mRNA expression of TCHsp70-1 was significantly higher and lower than that of TCHsp70-3 at cold and heat shock temperatures (except for 34 degrees C), respectively. This result possibly indicated the expression patterns of TCHsp70 were affected by their location in different cellular compartments. The results also indicated that three TCHsp70s, especially TCHsp70-1 and TCHsp70-3, may play an important role in mediating tolerance to cold, thermal stress for Tetranychus cinnabarinus.

Oxidation pattern of small silicon oxide clusters: structures and stability of Si6On (n = 1-12).

We have performed systematic ab initio calculations to study the structures and stability of Si(6)O(n)() clusters (n = 1-12) in order to understand the oxidation process in silicon systems. Our calculation results show that oxidation pattern of the small silicon cluster, with continuous addition of O atoms, extends from one side to the entire Si cluster. Si atoms are found to be separated from the pure Si cluster one-by-one by insertion of oxygen into the Si-O bonds. From fragmentation energy analyses, it is found that the Si-rich clusters usually dissociate into a smaller pure Si clusters (Si(5), Si(4), Si(3), or Si(2)), plus oxide fragments such as SiO, Si(2)O(2), Si(3)O(3), Si(3)O(4), and Si(4)O(5). We have also studied the structures of the ionic Si(6)O(n)(+/-) (n = 1-12) clusters and found that most of ionic clusters have different lowest-energy structures in comparison with the neutral clusters. Our calculation results suggest that transformation Si(6)O(n)+(a) + O --> Si(6)O(n+1)+(a) should be easier.

Dynamics of the trimeric AcrB transporter protein inferred from a B-factor analysis of the crystal structure.

The Escherichia coli AcrB multidrug transporter recognizes a wide range of toxic chemicals and actively extrudes them from cells. The molecular basis of multidrug transport in AcrB remains unknown. Herein, we describe normal mode analyses to study important regions for drug recognition and extrusion in this transporter. Based on the X-ray structure of AcrB, an elastic network model has been able to correct errors arising from crystal imperfection in the experimental B-factors. The results allow us to understand the functional dynamics of this membrane protein. It is expected that this technique can be applied to other membrane proteins with known structures.

Structure and stability of oxygen adsorption on Si(n) (n = 5-10) clusters.

The structures, binding energies, and electronic properties of one oxygen atom (O) and two oxygen atoms (2O) adsorption on silicon clusters Si(n) with n ranging from 5 to 10 are studied systematically by ab initio calculations. Twelve stable structures are obtained, two of which are in agreement with those reported in previous literature and the others are new structures that have not been proposed before. Further investigations on the fragmentations of Si(n)O and Si(n)O2 (n = 5-10) clusters indicate that the pathways Si(n)O --> Si(n-1) + SiO and Si(n)O2 --> Si(n-2) + Si2O2 are most favorable from thermodynamic viewpoint. Among the studied silicon oxide clusters, Si8O, Si9O, Si5O2 and Si8O2 correspond to large adsorption energies of silicon clusters with respect to O or 2O, while Si8O, with the smallest dissociation energy, has a tendency to separate into Si7 + SiO. Using the recently developed quasi-atomic minimal-basis-orbital method, we have also calculated the unsaturated valences of the neutral Si(n) clusters. Our calculation results show that the Si atoms which have the largest unsaturated valences are more attractive to O atom. Placing O atom right around the Si atoms with the largest unsaturated valences usually leads to stable structures of the silicon oxide clusters.

Potential energy surfaces of SimOn cluster formation and isomerization.

The reaction paths for formation and isomerization of a set of silica SimOn (m = 2,3, n = 1-5) nanoclusters have been investigated using second-order perturbation theory (MP2) with the 6-31G(d) basis set. The MP2/6-31G(d) calculations have predicted singlet ground states for all clusters excluding Si3O2. The total energies of the most important points on the potential energy surfaces (PES) have been determined using the completely renormalized (CR) singles and doubles coupled cluster method including perturbative triples, CR-CCSD(T) with the cc-pVTZ basis set. Although transition states have been located for many isomerization reactions, only for Si3O3 and Si3O4 have some transition states been found for the formation of a cluster from the separated reactants. In all other cases, the process of formation of SimOn clusters appears to proceed without potential energy barriers.

Molecule intrinsic minimal basis sets. I. Exact resolution of ab initio optimized molecular orbitals in terms of deformed atomic minimal-basis orbitals.

A method is presented for expressing the occupied self-consistent-field (SCF) orbitals of a molecule exactly in terms of chemically deformed atomic minimal-basis-set orbitals that deviate as little as possible from free-atom SCF minimal-basis orbitals. The molecular orbitals referred to are the exact SCF orbitals, the free-atom orbitals referred to are the exact atomic SCF orbitals, and the formulation of the deformed "quasiatomic minimal-basis-sets" is independent of the calculational atomic orbital basis used. The resulting resolution of molecular orbitals in terms of quasiatomic minimal basis set orbitals is therefore intrinsic to the exact molecular wave functions. The deformations are analyzed in terms of interatomic contributions. The Mulliken population analysis is formulated in terms of the quasiatomic minimal-basis orbitals. In the virtual SCF orbital space the method leads to a quantitative ab initio formulation of the qualitative model of virtual valence orbitals, which are useful for calculating electron correlation and the interpretation of reactions. The method is applicable to Kohn-Sham density functional theory orbitals and is easily generalized to valence MCSCF orbitals.

Molecule intrinsic minimal basis sets. II. Bonding analyses for Si4H6 and Si2 to Si10.

The method, introduced in the preceding paper, for recasting molecular self-consistent field (SCF) or density functional theory (DFT) orbitals in terms of intrinsic minimal bases of quasiatomic orbitals, which differ only little from the optimal free-atom minimal-basis orbitals, is used to elucidate the bonding in several silicon clusters. The applications show that the quasiatomic orbitals deviate from the minimal-basis SCF orbitals of the free atoms by only very small deformations and that the latter arise mainly from bonded neighbor atoms. The Mulliken population analysis in terms of the quasiatomic minimal-basis orbitals leads to a quantum mechanical interpretation of small-ring strain in terms of antibonding encroachments of localized molecular-orbitals and identifies the origin of the bond-stretch isomerization in Si4H6. In the virtual SCF/DFT orbital space, the method places the qualitative notion of virtual valence orbitals on a firm basis and provides an unambiguous ab initio identification of the frontier orbitals.

Effect of chain connectivity on the structure of Lennard-Jones liquid and its implicationon statistical potentials for protein folding.

Statistical contact potentials and bead-spring models have been widely used for computational studies of protein folding. However, there has been speculation that systematic error may arise in the contact energy calculations when the statistical potentials are deduced under the assumption that the chain connectivity in proteins can be ignored. To address this issue, we have performed molecular-dynamics simulations to study the structure and dynamics of a simple liquid system in which the beads are either connected or unconnected with springs. Results from the present study provide useful information for assessing the accuracy of the statistical potentials for protein structure simulations.

Trans-activation of heparanase promoter by ETS transcription factors.

The remodeling of extracellular matrix (ECM) is an important process required for cancer cells to turn into invasive and metastatic cancer cells. To dissolve the protein components of ECM, matrix metalloproteinases are some of the essential enzymes. Another ECM remodeling enzyme is the heparanase (Hpa) that digests the heparin sulfate component of the matrix. In metastatic cancer cells the Hpa gene is upregulated. To investigate the mechanism of why Hpa was upregulated in metastatic cancer cells, the regulatory sequence of heparanase gene was isolated and its function analysed in metastatic breast cancer cells. We found there are four ETS transcription factor binding sites. Two of them flanking the transcription initiation of the Hpa gene are nonfunctional, whereas two others are highly functional and responded to exogenously added ETS transcription factors. Mutation of these two ETS binding sites abolished the transcriptional activation of Hpa promoter by ETS transcription factors. Among four transcription factors tested (ETS1, ETS2, PEA3, and ER81), ETS1 and ETS2 are more potent in transactivating the human Hpa gene. Furthermore, dominant-negative ETS transcription factors failed to transactivate Hpa promoter and could abrogate the function of wild-type transcription factor in transactivation activity of ETS transcription factors on the Hpa promoter. These results suggest that ETS transcription factors play an important role in tumor invasion and metastasis by modulating the remodeling of ECM.

Structural organization of the human neuronal nitric oxide synthase gene (NOS1).

Neuronal nitric oxide (NO) synthase, localized to human chromosome 12, uniquely participates in diverse biologic processes; neurotransmission, the regulation of body fluid homeostasis, neuroendocrine physiology, control of smooth muscle motility, sexual function, and myocyte/myoblast biology, among others. Restriction enzyme mapping, subcloning, and DNA sequence analysis of bacteriophage- and yeast artificial chromosome-derived human genomic DNA indicated that the mRNA for neuronal NO synthase is dispersed over a minimum of 160 kilobases of human genomic DNA. Analysis of intron-exon splice junctions predicted that the open reading frame is encoded by 28 exons, with translation initiation and termination in exon 2 and exon 29, respectively. Determination of transcription initiation sites in brain poly(A) RNA with primer extension analysis and RNase protection revealed a major start site 28 nucleotides downstream from a TATA box. Sequence inspection of 5'-flanking regions revealed potential cis-acting DNA elements: AP-2, TEF-1/MCBF, CREB/ATF/c-Fos, NRF-1, Ets, NF-1, and NF-kappa B-like sequences. Diversity appears to represent a major theme apparent upon analysis of human neuronal NO synthase mRNA transcripts. A microsatellite of the dinucleotide variety was detected within the 3'-untranslated region of exon 29. Multiple alleles were evident in normal individuals indicating the existence of allelic mRNA sequence variation. Characterization of variant human neuronal NO synthase cDNAs indicated the existence of casette exon 9/10 and exon 10 deletions as examples of structural mRNA diversity due to alternative splicing. The latter deletion of a 175-nucleotide exon introduces a frame-shift and premature stop codon indicating the potential existence of a novel NH2 terminus protein. In summary, analysis of the human neuronal NO synthase locus reveals a complex genomic organization and mRNA diversity that is both allelic and structural.

[Six semi-sold media methods for detecting motility of gram negative bacilli].

Motility is recognized as a significant biological character of certain bacteria, and is used as a fundamental basis of classification in many taxonomic systems. We compared wet mount method, semi-solid medium method and flagella stain method to evaluate the motility activity of 538 Enterobacteriaceae and 300 glucose non-fermentative gram negative bacilli. The results showed a sensitivity of 100% in flagella stain, Gilardi medium, Mueller Hinton semisolid medium and sulfide-indole-motility (SIM) medium (Difco); 99.6% in SIM (Kyokuto) and SIM (BBL); 99.3% in motility test medium (BBL) and 97% in wet mount. Motile Enterobacteriaceae grow well, and turbidity changes clearly and is easy to interpret. Motile glucose nonfermentative gram negative bacilli grow so lightly and rapidly diffuse throughout the medium and are hardly to interpret. It is better to use colorless Gilardi medium and Mueller Hinton semi-solid medium and to read within 4-8 hours or 24 hours. The advantages of the semi-solid medium method are particularly evident in teaching schedules and routine testing, because the results are cumulative, macroscopic, highly sensitive, and easy to manipulate.

[The relation of vasoactive intestinal peptide and acute hypoxia].

In order to observe the effect of acute hypoxia on release of vasoactive intestinal peptide (VIP), the plasma VIP content was determined in anesthetized dogs by a specific radioimmunoassay technique during acute hypoxia. Blood gases and hemodynamics were monitored simultaneously. After inhalation of 10% oxygen. the plasma VIP levels elevated along with decrease in PaO2 and increase in pulmonary artery pressure. The plasma concentration of VIP in the portal vein increased significantly from 106 +/- 21 pg/ml before hypoxia to 173 +/- 36 pg/ml 15 minutes after the onset of hypoxia (P less than 0.01). The difference of arterio-venous VIP content increased from -3 +/- 6 pg/ml before hypoxia to +9 +/- 7 pg/ml after inhalation of 10% oxygen for 30 minutes. The results suggested that VIP was released from the gastrointestinal tract as well as from the lung in case of hypoxia and pulmonary hypertension. It is considered that the release of VIP may be an adaptive and compensatory response, promoting vasodilation and perfusion in vital organs.

The establishment of rat hybridoma cell lines secreting McAb against strains of potato virus Y and analysis of its stability.

The rat splenocytes immunized with potato virus Y (PVYn) and ratmyeloma (IR983) were fused by PEG (M. W.1450). Three kinds of stable hybridoma cell lines secreting specific monoclonal antibodies (McAbs) were derived. One kind of the cell lines producing McAbs reacts to PVYn specifically. Another reacts to PVYo specifically. The third one reacts to both of the two strains. Tested by the methods of sandwich-ELISA and indirect-ELISA, all kinds of McAbs did not react to seven plant viruses: tobacco mosaic (TMV), cucumber mosaic (CMV), tobacco tech (TEV), alfalfa mosaic (AMV), turnip mosaic (TuMV), potato leaf roll (PLRV), potato virus X (PVX). The biological properties of the hybridoma cell lines and the McAbs were tested.