[Bioinformatics-based identification of the key genes associated with prostate cancer].

OBJECTIVE: To identify the key genes associated with the pathogenesis of PCa using the bioinformatics approach for a deeper insight into the molecular mechanisms underlying the development and progression of PCa. METHODS: The microarray datasets GSE70770, GSE32571 and GSE46602 were downloaded from the Gene Expression Omnibus (GEO) database, and differentially expressed genes (DEG) in the normal prostate tissue and PCa were identified with the GEO2R tool, followed by functional enrichment analysis. A protein-protein interaction (PPI) network of DEGs was constructed by STRING and visualized with the Cytoscape software. RESULTS: A total of 235 DEGs were identified, including 61 up-regulated and 174 down-regulated genes, which were mainly enriched in focal adhesion kinase (FAK), ECM-receptor interaction, and other signaling pathways. From the PPI network were screened out 12 highly connected hub genes, including MYH11, TPM1, TPM2, SMTN, MYL9, VCL, ACTG1, CNN1, CALD1, ACTC1, MYLK and SORBS1, which were shown by hierarchical cluster analysis to be capable of distinguishing prostate cancer from non-cancer tissue. CONCLUSIONS: A total of 235 DEGs and 12 hub genes were identified in this study, which may contribute to a further understanding of the molecular mechanisms of the development and progression of PCa, and provide new candidate targets for the diagnosis and treatment of the malignancy.

Self-powered, ultrasensitive, flexible tactile sensors based on contact electrification.

Tactile/touch sensing is essential in developing human-machine interfacing and electronic skins for areas such as automation, security, and medical care. Here, we report a self-powered triboelectric sensor based on flexible thin-film materials. It relies on contact electrification to generate a voltage signal in response to a physical contact without using an external power supply. Enabled by the unique sensing mechanism and surface modification by polymer-nanowires, the triboelectric sensor shows an exceptional pressure sensitivity of 44 mV/Pa (0.09% Pa(-1)) and a maximum touch sensitivity of 1.1 V/Pa (2.3% Pa(-1)) in the extremely low-pressure region (<0.15 KPa). Through integration of the sensor with a signal-processing circuit, a complete tactile sensing system is further developed. Diverse applications of the system are demonstrated, explicitly indicating a variety of immediate uses in human-electronics interface, automatic control, surveillance, remote operation, and security systems.

[Quantification of class 1 integrase gene expression of Pseudomonas aeruginosa in biofilm].

OBJECTIVE: To study the molecular mechanism of integron related gene transfer in biofilm and aqueous culture of P. aeruginosa by investigating the expression level of intI1 mRNA in class 1 integron positive strains. METHODS: A competitive reverse transcription-PCR (cRT-PCR) method was designed to quantify class 1 integrase mRNA production in two clinical P. aeruginosa strains called PA10 and PA39 when they were grown in biofilms and planktonic culture. In brief, competitive DNA (cDNA) was obtained via PCR from the genomic DNA of class 1 integron positive strains. Then the competitive RNA (cRNA) was amplified from the cDNA. Finally the serials diluted cRNA were mixed separately with the total RNA extracted from the biofilm and planktonic culture of P. aeruginosa and the competitive RT-PCR were conducted. After electrophoresis, the expression level of intI1 mRNA was quantified by comparing with the amount of the cDNA. RESULTS: The PA10 and PA39 strains produced intI1 mRNA both in their biofilms and planktonic cells. Furthermore the expression levels of intI1 mRNA from the two strains were of approximation in their biofilm and plankton stage respectitively, while the quantities of intI1 mRNA expression in their biofilm stage were about 15 times higher than those in their planktonic stage. CONCLUSION: The integrase gene is up-regulated at mRNA level in P. aeruginosa biofilm, which may be one of the reseans for the spread of antibiotic resistance and the formation of multidrug resistance.

[Establishing a real-time PCR assay for anatid herpesvirus 1].

OBJECTIVES: To develop a real-time quantitative PCR assay to detect duck plague virus (DPV) for the rapid diagnosis of DPV infection, the investigation of its nosogenesis and the screening of effective antiviral drugs. METHODS: The primer and probe were designed according to the gene sequence of DPV DNA polymerase gene. To establish a standard curve, a plasmid containing 125 bp PCR product was constructed and severed as a positive control. The TaqMan based real-time PCR method was adopted and compared with the traditional PCR approach in sensitivity, reliability and specificity. RESULTS: A good linear correlation was demonstrated in the standard curve for the real-time PCR assay within the range from 2.3 x 10 to 2.3 x 10(5) copies. A minimum of 23 positive plasmids could be detected, indicating a good sensitivity of the assay. The coefficients of variance (CVs) were 1.22-6.69 and 2.09-8.84 for the intra-assay and inter-assay tests respectively, indicating a good reliability. No amplification products were found for DNA from other pathogens, indicating a good specificity. The comparative study proved that the TaqMan technology was much more sensitive than traditional PCR assay. CONCLUSION: The real-time quantitative PCR assay for DPV DNA has good sensitivity, specificity and reliability.

[The cloning and expression of rhlR, a quorum sensing gene in Pseudomonas aeruginosa PAO1, and a study of its effect on bacterial clearance rate in mouse lung].

OBJECTIVE: To inquire about the molecular characteristics of rhlR, a Quorum Sensing gene in Pseudomonas aeruginosa (P. aeruginosa) PAO1, and to explore the immunogenicity of RhlR protein in mouse. METHODS: The rhlR gene of PAO1 was amplified by PCR and cloned into pGEX4T-1 plasmid. The recombination was expressed in E. coli BL21 (DE3) and analyzed by SDS-PAGE and Western blotting. The fusion protein (GST-RhlR) was purified by GST purification Kit and the purified protein was used to immunize mice. P. aeruginosa PA0315 was injected into mouse lung to explore the immuno-protection of the protein. RESULTS: The 726 bp DNA fragment of rhlR was amplified from PAO1 general DNA. The restriction enzyme map showed that the inserted part of rhlR-pGEX4T-1 was successfully constructed and the gene was 100% homologous to rhlR in GenBank. The recombinant plasmid expressed a 54 kDa fusion protein (rhlR-GST) in E. coli BL21 (DE3) after induction by IPTG. The fusion protein could be recognized by mouse polyvalent antiserum against P. aeruginosa. The results showed that the bacterial clearance rate in mouse lung was 86. 92% in rhlR groups and 49.44% in the control group. CONCLUSION: A 54 kDa protein (RhlR-GST) has been successfully expressed in E. coli BL21 (DE3). The RhlR could increase the bacterial clearance rate in mouse lung and may serve as immunoprotective antigen to develop the genetic engineering vaccine.

[Quantification for biofilm formation of pseudomonas aeruginosa isolates and their genotypic analysis].

OBJECTIVE: To probe the correlation between the ability of biofilm formation of Pseudomonas aeruginosa isolates and their genotypes. METHODS: Forty-eight Pseudomonas aeruginosa isolates were tested for their biofilm formation with a modified microtiter test and were analyzed by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR). The percent similarity between their genetic fingerprints and cluster analysis was performed and worked out using computer software. RESULTS: Forty-eight Pseudomonas aeruginosa isolates demonstrated different abilities of biofilm formation in vitro. And the 48 isolates with different abilities of biofilm formation showed different genotypes in fingerprints by ERIC-PCR. Among the 48 isolates of Pseudomonas aeruginosa tested, five clusters (A, B, C, D, E), were identified at the 17% genetic similarity level. The isolates with strong ability of biofilm formation were in D cluster at the 42% genetic similarity level. CONCLUSION: Most of the 48 PA isolates tested formed strong biofilm, and their genotypes were of correlation.

The action of Pseudomonas aeruginosa biofilms in intrinsic drug resistance.

BACKGROUND: There is a growing interest in studying the relationship between intrinsic resistance and biofilms resistance to drugs. However, the relationship still remains unclear in the macroscopic bacterial growth. Our study is to illuminate the change of bacterial drug resistance of gyrA mutant and active efflux pump during the development of Pseudomonas aeruginosa (P. aeruginosa) biofilms. METHODS: The strains of type II topoisomerase gene mutant (gyrA mutant) and multidrug resistance (MDR) efflux pump were clinical isolates and detected by polymerase chain reaction (PCR). The process of bacterial biofilms development was observed by scanning electron microscope. Triparental mating experiments were performed to transfer report gene of green fluorescent protein (GFP) into P. aeruginosa biofilms strains and followed by analysis of bacterial survival rate between intrinsic resistance and biofilms resistance. RESULTS: The fluorescent strains with pGFPuv could develop mature biofilms on Teflon surface. Before a period of 72 hours, the survival rate of biofilms bacteria and intrinsic resistance strains in ciprofloxacin solution was significantly different (P < 0.05). The survival number of intrinsic resistance strains (gyrA mutation and active efflux pump) was illustriously higher than biofilm strain in the initial stage of biofilms development. After 72 hours incubation, there was no clearly difference between mutants and biofilms strains in the survival rate (P > 0.05). The carbonyl cyanide m-chlorophenylhydrazone and azithromycin could significantly reduce the drug resistance of biofilm strains and efflux pump strains. CONCLUSIONS: In the development of P. aeruginosa biofilms, the strains of gyrA mutation and MDR efflux could be conferred with new level of drug resistance. When co-cultured mutated strains with biofilm strains, biofilms may play a major role in bacterial resistance. But after 72 hours incubation (a mature biofilms had been developed), there was no clearly difference between the number of mutant strains and biofilm strains.

Synthesis and quantitative structure-activity relationships study for phenylpropenamide derivatives as inhibitors of hepatitis B virus replication.

A series of new phenylpropenamide derivatives containing different substituents was synthesized, characterized and evaluated for their anti-hepatitis B virus (HBV) activities. The quantitative structure-activity relationships (QSAR) of phenylpropenamide compound have been studied. The 2D-QSAR models, based on DFT and multiple linear regression analysis methods, revealed that higher values of total energy (TE) and lower entropy (S(Ó©)) enhanced the anti-HBV activities of the phenylpropenamide molecules. Predictive 3D-QSAR models were established using SYBYL multifit molecular alignment rule. The optimum models were all statistically significant with cross-validated and conventional coefficients, indicating that they were reliable enough for activity prediction.

[Experimental study on the antiviral mechanism of Ceratostigma willmattianum against herpes simplex virus type 1 in vitro].

OBJECTIVE: To study the antiviral effect and mechanisms of the liquid extract from Ceratostigma willmattianum against herpes simplex virus type 1 (HSV-1) in vitro. METHOD: C. willmattianum in various concentration was applied to different steps of HSV-1 replication cycle. 50% Tissue culture infective dose (TCID50), cytopathic effect (CPE), MTT staining method, dot blotting and Northern blotting analysis were used to estimate index of antiviral activity. RESULT: 50% Toxic concentration (TC50) was 1077 mg x L(-1), IC50 29.46 mg x L(-1) and therapeutic index (TI) 36.56 in C. willmattianum. TC50 330 mg x L(-1), 50% Inhibiting concentration (IC50) 9.12 mg x L(-1) and TI 36.18 in ACV by MTT staining method. The liquid extract from C. willmattianum had remarkable effect on inhibiting HSV-1 in vitro. Ceratostigma could interfere absorption of HSV-1 to Vero cells to prevent HSV-1 infectivity, inhibit HSV-1 gD DNA replication and HSV-1 gD mRNA expression. CONCLUSION: C. willmattianum possesses strong anti-HSV-1 activity in vitro. The antiviral mechanisms are related to inhibiting virus absorption, HSV-1 gD gene replication and HSV-1 gD gene transcription.

Spin-Hamiltonian parameters for the tetragonal Gd(M)3+-F(i)- centers in CaF(2) and SrF(2) crystals.

The spin-Hamiltonian parameters (g factors g(//), g(⊥) and zero-field splittings b(2)(0), b(4)(0), b(4)(4), b(6)(0), b(6)(4)) of the tetragonal Gd(M)(3+)-F(i)(-) centers in CaF(2) and SrF(2) crystals at T≈1.8K are calculated from the diagonalization (of energy matrix) method based on the one-electron crystal field mechanism. In the calculations, the crystal field parameters used are estimated from the superposition model with the reported defect structural data obtained from the analyses of superhyperfire interaction constants at the same temperature. The calculated results are in reasonable agreement with the experimental values. It appears that the above defect structural data reported in the previous paper are suitable and the diagonalization (of energy matrix) method is effective to the studies of spin-Hamiltonian parameters for 4f(7) ions in crystals.

An aqueous extract of Yunnan Baiyao inhibits the quorum-sensing-related virulence of Pseudomonas aeruginosa.

Yunnan Baiyao is a famous Chinese medicine that has long been directly applied to wounds to reduce bleeding, pain, and swelling without causing infection. However, little is known about its ability to prevent infection. The present study aimed to assess in vitro the anti-virulence activity of an aqueous extract of Yunnan Baiyao (YBX) using Pseudomonas aeruginosa as a pathogenic model. We found that a sub-MIC (2.5 mg/ml) of YBX can efficiently interfere with the quorum-sensing (QS) signaling circuit. Real-time polymerase chain reaction analysis showed that a sub-MIC of YBX down-regulated the transcriptions of lasR, lasI, rhlR, and rhlI, which resulted in global attenuation of QS-regulated virulence activities, such as biofilm formation, and secretion of LasA protease, LasB elastase and pyocyanin. Further, YBX reduced the motility of P. aeruginosa related to QS, and impaired the formation of biofilms. These results suggest that YBX may possess global inhibitory activity against the virulence of P. aeruginosa and that YBX may also exhibit antimicrobial activity in vivo. The present study suggests that Yunnan Baiyao represents a potential source for isolating novel, safe, and efficacious antimicrobial agents.

Studies of the spin-Hamiltonian parameters and defect structures for Gd3+ ions in zircon-structure silicates MSiO4 (M=Zr, Hf, Th).

The spin-Hamiltonian parameters (g factors g∥, g⊥ and zero-field splittings b2(0), b4(0), b4(4), b6(0), b6(4)) for 4f7 ion Gd3+ at the tetragonal M4+ site of zircon-structure silicates MSiO4 (M=Zr, Hf, Th) are calculated from a diagonalization (of energy matrix) method. The Hamiltonian concerning this energy matrix contains the free-ion, crystal-field interaction and Zeeman interaction terms and the 56×56 energy matrix is constructed by considering the ground multiplet 8S7/2 and the excited multiplets 6L7/2 (L=P, D, F, G, H, I). The defect structures of Gd3+ centers in the three MSiO4 crystals are yielded from the calculation. The results are discussed.

A study of the spin-Hamiltonian parameters for the trigonal Sm3+ center in La2Mg3(NO3)(12)·24H2O crystal.

This paper reports a theoretical calculation of spin-Hamiltonian parameters (g factors g//, g⊥ and hyperfine structure constants 147A//, 147A⊥, 149A//, 149A⊥) for 147Sm3+ and 149Sm3+ isotopes in the trigonal La3+ site of La2Mg3(NO3)(12)·24H2O crystal from a diagonalization (of energy matrix) method. In the method, the Hamiltonian concerning the energy matrix includes the Zeeman and hyperfine interaction terms and so there is no perturbation calculation in it. The crystal-field parameters in the energy matrix are calculated using the superposition model, in which the structural data of 12-fold coordinated site rather than those of the incorrect 6-fold coordinated site given in the previous paper are applied. The calculated results are in reasonable agreement with the experimental results. The results are discussed.

A theoretical study on the temperature dependence of zero-field splitting for the tetragonal Cr3+ center in MgO crystal.

This paper reports a detailed theoretical calculation of the temperature dependence of zero-field splitting D (characterized by ΔD(T)=D(T)-D(0)) for the tetragonal Cr3+ center in MgO crystal by considering both the static contribution due to the thermal expansion of Cr3+ center and the vibrational contribution caused by electron-phonon (including the acoustic and optical phonons) interaction. The vibrational contribution due to the acoustic phonon is calculated using the long-wave approximation similar to the study on the specific heat of crystals and that due to optical phonon is estimated using the single-phonon model. The calculated results are in reasonable agreement with the experimental values. From the calculation, it is found that the static contribution ΔDstat(T) (which is often regarded as very small and is neglected in the previous papers) is larger than the vibrational contribution ΔDvib(T) and so the reasonable studies of temperature dependence of zero-field splitting should take both the static and the vibrational contributions into account.

Spin-Hamiltonian parameters and defect structure for the rhombic Dy3+ center in AgCl crystal.

Based on the defect model that the rhombic Dy(3+) center in AgCl crystal is formed by substitutional Dy3+ ion associated with two nearest Ag+ vacancies (VAg) along the <110> and <110> axes owing to charge compensation, the spin-Hamiltonian parameters (g factors gi and hyperfine structure constants 161Ai and 163Ai, where i=x, y, z) of this rhombic Dy3+ center are calculated from a diagonalization (of energy matrix) method. In the method, the Zeeman (or magnetic) and hyperfine interaction terms are attached to the classical Hamiltonian used in the calculation of crystal-field energy levels and a 66×66 energy matrix concerning this Hamiltonian is constructed by taking all the ground-term multiplets 6HJ (J=15/2, 13/2, 11/2, 9/2, 7/2, 5/2) into account. The calculated results (g factors gi and average |A(161Dy3+)| and |A(163Dy3+)|) are in reasonable agreement with the experimental values. From the calculations, the above defect model of rhombic Dy3+ center is confirmed, the defect structure of this Dy3+ center (characterized by the displacement of Cl- ligand caused by VAg) is obtained and the components of hyperfine structure constants Ai(161Dy3+) and Ai(163Dy3+) are predicted. The results are discussed.

Studies of the spin-Hamiltonian parameters and the Jahn-Teller distortions for tetragonal Cu(H(2)O)(6)(2+) clusters in trigonal A(2)Mg(3)(NO(3))(12).24H(2)O (A=La, Bi) crystals.

The anisotropic and isotropic spin-Hamiltonian parameters (g factors and hyperfine structure constants) of tetragonal Cu(H(2)O)(6)(2+) clusters due, respectively, to the static and dynamic Jahn-Teller effects for Cu(2+) in trigonal A(2)Mg(3)(NO(3))(12).24H(2)O (A=La, Bi) crystals are calculated from the high-order perturbation formulas based on the cluster approach. In the approach, the admixture between the d orbitals of 3d(n) ion and the p orbitals of ligand ion via covalence effect is considered. All of the calculated results are in agreement with the experimental values. The tetragonal elongations (characterized by DeltaR=R(parallel)-R( perpendicular)) of Cu(H(2)O)(6)(2+) cluster due to the Jahn-Teller effect in A(2)Mg(3)(NO(3))(12).24H(2)O crystals are acquired from the calculations. The results are discussed.

Investigations of the optical spectra and EPR g factors for the tetragonal Cu2+ centers in trigonal ZnCO3 crystal.

Two distinctive theoretical methods, the complete diagonalization (of energy matrix) method (CDM) and the perturbation theory method (PTM), are employed to calculate the optical band positions and EPR g factors g(||), g(perpendicular) for the tetragonal Cu(2+) centers in trigonal ZnCO(3) crystal. The results from the two methods coincide and are also in good agreement with the experimental values. So both the CDM and PTM are adequate for the investigations of optical and EPR data for d(9) ions in crystals. The tetragonal distortion due to the static Jahn-Teller effect for the tetragonal Cu(2+) centers in trigonal Zn(2+) site of ZnCO(3) is also acquired from the calculations. The results are discussed.

Studies of the EPR parameters and defect models for three Er3+ impurity centers in ThO2 crystals.

The electron paramagnetic resonance (EPR) parameters (g factors and hyperfine structure constants of the ground state, and g factors of the first excited state) of three (one cubic and two trigonal) Er(3+) centers in fluoride-type ThO(2) crystal are studied from a diagonalization (of energy matrix) method. In the method, the Zeeman and hyperfine interaction terms are added to the classical Hamiltonian, and a 52 x 52 energy matrix concerning the ground multiplet (4)I(15/2) and the first to third excited multiplets (4)I(13/2), (4)I(11/2) and (4)I(9/2) is established for a 4f(11) ion in trigonal crystal field and under an external magnetic field. From the studies, the EPR parameters for three Er(3+) centers in ThO(2) are reasonably explained, the defect models for the two trigonal Er(3+) centers suggested in the previous paper are confirmed and the defect structures of the two trigonal centers are obtained. The results are discussed.

Investigation of the spin-Hamiltonian parameters for the trigonal U5+ center in CaF2 crystal.

The spin-Hamiltonian parameters (g factor g(//), g(perpendicular) and hyperfine structure constants A(//), A(perpendicular)) of the trigonal U(5+) center in CaF(2) crystal have been calculated from the complete diagonalization (of energy matrix) method (CDM) for 5f(1) ions in trigonal crystal field and under an external magnetic field. In the calculation, the crystal-field parameters are estimated from the superposition model. From the calculations, these spin-Hamiltonian parameters are reasonably explained, and the defect model (i.e., the trigonal U(5+) center is attributed to U(5+) substituting for Ca(2+) in CaF(2) with six F(-) ions replaced by O(2-) and the other two F(-) sites vacant because of charge compensation) given in the previous paper is confirmed. The results are discussed.