Homology modeling and evolutionary trace analysis of superoxide dismutase from extremophile Acidithiobacillusferrooxidans

The gene sod in Acidithiobacillus ferrooxidans may play a crucial role in its tolerance to the extremely acidic, toxic and oxidative environment of bioleaching. For insight into the anti-toxic mechanism of the bacteria, a three-dimensional (3D) molecular structure of the protein encoded by this gene was built by homology modeling techniques, refined by molecular dynamics simulations, assessed by PROFILE-3D and PROSTAT programs and its key residues were further detected by evolutionary trace analysis. Through these procedures, some trace residues were identified and spatially clustered. Among them, the residues of Asn38, Gly103 and Glu161 are randomly scattered throughout the mapped structure; interestingly, the other residues are all distinctly clustered in a subgroup near Fe atom. From these results, this gene can be confirmed at 3D level to encode the Fe-depending superoxide dismutase and subsequently play an anti-toxic role. Furthermore, the detected key residues around Fe binding site can be conjectured to be directly responsible for Fe binding and catalytic function.     

Homology modeling and docking studies of IscS from extremophile Acidithiobacillusferrooxidans

The gene iscS-3 from Acidithiobacillus ferrooxidans may play a central role in the delivery of sulfur to a variety of metabolic pathways in this organism. For insight into the sulfur metabolic mechanism of the bacteria, an integral three-dimensional (3D) molecular structure of the protein encoded by this gene was built by homology modeling techniques, refined by molecular dynamics simulations, assessed by PROFILE-3D and PROSTAT programs and further used to search bind sites, carry out flexible docking with cofactor pyridoxal 5′-phosphate(PLP) and substrate cysteine and hereby detect its key residues. Through these procedures, the detail conformations of PLP-IscS(P-I) and cysteine-PLP-IscS(C-P-I) complexes were obtained. In P-I complex, the residues of Lys208, His106, Thr78, Ser205, His207, Asp182 and Gln185 have large interaction energies and/or hydrogen bonds fixation with PLP. In C-P-I complex, the amino group in cysteine is very near His106, Lys208 and PLP, the interaction energies for cysteine with them are very high. The above results are well consistent with those experimental facts of the homologues from other sources. Interestingly, the four residues of Glu105, Glu79, Ser203 and His180 in P-I docking and the residue of Lys213 in C-P-I docking also have great interaction energies, which are fitly conservation in IscSs from all kinds of sources but have not been identified before. From these results, this gene can be confirmed at 3D level to encode the iron-sulfur cluster assembly protein IscS and subsequently play a sulfur traffic role. Furthermore, the substrate cysteine can be presumed to be effectively recruited into the active site. Finally, the above detected key residues can be conjectured to be directly responsible for the bind and/or catalysis of PLP and cysteine.     

Bioleaching of sphalerite by Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans cultured in 9K medium modified with pyrrhotite

Elective culture of Acidithiobacillus ferrooxidans and Acidithiobacillus thiooxidans in 9K medium modified with pyrrhotite was studied. Bioleaching of flotation concentrate of sphalerite by the selected bacteria was carried out. The results show that the microorganisms cultured by pyrrhotite are a mixture of Acidithiobacillusferrooxidans and Acidithiobacillus thiooxidans, of which the capability to oxidize ferrous to ferric irons is enhanced by the high mass ratio of Fe to S in pyrrhotite. Three pyrrhotite samples were separated into various parts with corresponding S/Fe ratios by magnetic separation and were used to culture the elective bacteria as the substrate. The association of the cultures could provide a more rapid and complete oxidation of sphalerite than that of bacteria cultivated by conventional methods.     

Isolation and characterization of Acidithiobacillus caldus from several typical environments in China

Six strains of moderately thermophilic sulfur-oxidizing bacteria were isolated from several different typical environments in China. The identities of the isolates were confirmed by analyses of their 16S rRNA genes, and some key physiological traits. The isolates are Gram negative, rod-shaped bacteria, their optimal temperature and pH value for growth are 45-50 ℃ and 2.5-3.5 respectively. They are autotrophic and used＇elemental sulfur, sodium thiosulfate and potassium tetrathionate as electron donor, while a little glucose stimulated their growth. 16S rDNA sequences analysis reveals that the strains are phylogenetically clustered to Acidithiobacillus caldus.     

Characterization of tricalcium phosphate solubilization by Stenotrophomonas maltophilia YC isolated from phosphate mines

The phosphate solubilizing characteristics of a strain YC, which was isolated from phosphate mines (Hubei, China), were studied in National Botanical Research Institute’s phosphate (NBRIP) growth medium containing tricalcium phosphate (TCP) as sole phosphorus (P) source. The strain YC is identified as Stenotrophomonas maltophilia (S. maltophilia) based upon the results of morphologic, physiological and biochemical characteristics and 16S rRNA sequences analysis. The results show that the strain S. maltophilia YC can solubilize TCP and release soluble P in NBRIP growth medium. A positive correlation between concentration of soluble P and population of the isolate and a negative correlation between concentration of soluble P and pH in the culture medium are observed from statistical analysis results. Moreover, gluconic acid is detected in the culture medium by HPLC analysis. It indicates that the isolate can release gluconic acid during the solubilizing experiment, which causes acidification of the culture medium and then TCP solubilization. S. maltophilia YC has a maximal TCP solubilizing capability when using maltose as carbon source and ammonium nitrate as nitrogen source, respectively, in NBRIP growth medium. Foundation item: Project(2004CB619201) supported by the Major State Basic Research and Development Program of China; Project(Z200515002) supported by the Key Project Foundation of the Education Department of Hubei Province, China; Project(GCP200801) supported by the Open Research Fund of Key Laboratory for Green Chemical Process of Ministry of Education, China; Project(Q200811) supported by the Youths Science Foundation of Wuhan Institute of Technology, China     

Delay-independent decentralized H ∞ control for multi-channel discrete-time systems with uncertainties

A robust decentralized H∞ control problem was considered for uncertain multi-channel discrete-time systems with time-delay. The uncertainties were assumed to be time-invariant, norm-bounded, and exist in the system, the time-delay and the output matrices. Dynamic output feedback was focused on. A sufficient condition for the multi-channel uncertain discrete time-delay system to be robustly stabilizable with a specified disturbance attenuation level was derived based on the theorem of Lyapunov stability theory. By setting the Lyapunov matrix as block diagonal appropriately according to the desired order of the controller, the problem was reduced to a linear matrix inequality （LMI） which is sufficient to existence condition but much more tractable. An example was given to show the efficiency of this method.     

First-principles lattice stability of Fe, Ru and Os

Lattice constants, total energies and densities of states of transition metals Fe, Ru and Os with BCC, FCC and HCP structures were calculated by the GGA+PBE functional and the ultrasoft pseudo-potential plane wave method, and compared with those of the first-principles projector augmented wave (PAW) method, CALPHAD method and experimental data. The results show that the lattice stability of this work is ΔG ^BCC-HCP>ΔG ^FCC-HCP>0, agreeing well with those of PAW method in the first-principles and CALPHAD method except for BCC-Fe. And the densities of state of HCP-Ru and Os have an obvious character of stable phase, agreeing completely with the results of the total energy calculations. Further analyses of atomic population show that the transition rate of electrons from s to p state for HCP, FCC and BCC crystals increases from Fe to Os, and a stronger cohesion, a higher cohesive energy or a more stable lattice between atoms of heavier metals are formed. Foundation item: Project(20070533118) supported by the Doctoral Discipline Foundation of Ministry of Education of China; Projects(50471058, 50271085) supported by the National Natural Science Foundation of China; Project supported by the Postdoctoral Foundation of Central South University, China     

Trace and minor element geochemistry of Xiangdong tungsten deposits

Geochemical characteristics of trace and minor elements in some strata of geosynclinal tectonic layer, platform tectonic layer, in granite of Diwa stage, altered rocks and wolframite in the Xiangdong Tungsten Mine are systematically studied. Enrichment of W, Sn and Cu in geosynclinal tectonic layer could be one part of mineralization. Different types of alteration might result in variance of distribution of the same trace or minor element.m _Nb/m _Ta andm _Mn/m _Fe ratios, contents of Nb and Ta in wolramite vary with vein groups’ location. Project supported by the National Natural Science Foundation of China Synopsis of the first author Chen Zilong, associate professor, born in Oct. 1962. obtained Ph. D degree in 1993. Speciality: Experimental Geochemistry.     

μ Analysis and μ synthesis for nonlinear robust control systems

A μ analysis and μ synthesis method for nonlinear robust control systems was presented. The nonlinear robust control problem using μ method was described. By means of the nonlinear state feedback and state coordinates transformation, many uncertain nonlinear systems can be transformed as a linear fractional transformation (LFT) on the generalized plant and the uncertainty. Based on the LFT, a linear robust controller can be obtained by the D-K iteration and then a corresponding nonlinear robust control law is constructed. An example was given in the paper. Project supported by the National Natural Science Foundation of China Synopsis of the first author Wu Min, professor, Ph. D, born in 1963, majoring in complex industrial process control, robust control, nonlinear control and expert control.     

Influence of CYP3A5 polymorphism on tacrolimus blood concentrations in renal transplant patients

Objective Tacrolimus is an immunosuppressive drug with narrow therapeutic range and wide interindividual variation in its pharmacokinetics. Tacrolimus is a substrate of cytochrome P450(CYP)3A5. The aim of this study was to evaluate whether the A6986G polymorphism is associated with tacrolimus concentration /dose ratio. Methods Fifty-two Chinese renal transplant patients were enrolled in this study. Their body weight, dosage and concentration of tacrolimus were observed. CYP3A5 genotype was determined by polymerase chain reaction followed by restriction fragment length polymorphism analysis. Results A significant association was found between tacrolimus levels per dose/kg/d and CYP3A5 gene A6986G polymorphism (P<0.001). The CYP3A5 * 3 * 3 patients have a significantly higher tacrolimus level/dose than CYP3A5 * 1 * 1 and CYP3A5 * 1 * 3. Conclusions CYP3A5 gene A6986G polymorphism is associated with tacrolimus pharmacokinetics and dose requirements. Pharmacogenetic methods could be employed prospectively to help the dose selection and to individualize immunosuppressive therapy according to the result. Foundation item: Project (03GZ3072) supported by the Science and Technology Department of Hunan Province; project (2004035206) supported by the China Postdoctoral Foundation and project (30300383) supported by the National Natural Sciences Foundation of China     

Isolation and characterization of YNTC-1, a novel Alicyclobacillus sendaiensis strain

A heterotrophic acidothermophilic bacterial strain, YNTC-1, was isolated from an acidic hot spring in Tengchong, Yunan, China. YNTC-1 grows at pH value of 1.5-8.0 and temperature of 40-70 ℃, with optimal pH and temperature at 3.0 and 55 ℃, respectively. The cells of the strain are in shape of short rod, with 1.0-1.2 μm in length and 0.7-0.8 μm in diameter, and with distinct spores at both poles of each cell. The predominant fatty acids in cellular membrane of the strain are C18：1 ω7c. 16s rRNA gene analysis reveals that this strain is closely related to Alicyclobacillus sendaiensis, with over 99% sequence similarity. Based on phenotypic and genotypic analyses, YNTC-1 is identified as a member ofA. sendaiensis. Considering some important morphological and biochemical differences between strain YNTC-1 and A. sendaiensis ATCC 27009T, YNTC-1 may be proposed to be a novel subspecies of A. sendaiensis. However, this viewpoint has to be confirmed by further studies. Co-bioleaching of pyrite and chalcopyrite with strain YN22, Sulfobacillus thermosulfidooxidans, shows that strain YNTC-1 has no evident influence on bioleaching rates of these two sulphide minerals.     

Template synthesis and adsorption properties of chitosan salicylal Schiff bases

To improve the adsorption properties of chemically modified chitosan, the chelating resin of salicylal chitosan Schiff bases was prepared by the template cross-linking method using Cu(Ⅱ) as template ion and ethylene glycol bisglycidyl ether as cross-linking agent in microwave, and was characterized by IR. The adsorption capacity and selectivity coefficient of the chemically modified chitosan for Cu(Ⅱ), Fe(Ⅲ) and Zn(Ⅱ) were investigated, respectively. The results show that the adsorption capacity of the resin 2.73 mmol/g for Cu(Ⅱ) is bigger than that for other two metal ions, 0.22 mmol/g for Fe(Ⅲ), and 0.42 mmol/g for Zn(Ⅱ), and the selectivity coefficients are as follows: KCu(Ⅱ)/Fe(Ⅲ)=12.4, KCu(Ⅱ)/Zn(Ⅱ)=6.5.     

Non-fragile delay-dependent H ∞ control of linear time-delay system with uncertainties in state and control input

The problem of designing a non-fragile delay-dependent H∞ state-feedback controller was investigated for a linear time-delay system with uncertainties in state and control input. First, a recently derived integral inequality method and Lyapunov-Krasovskii stability theory were used to derive new delay-dependent bounded real lemmas for a non-fragile state-feedback controller containing additive or multiplicative uncertainties. They ensure that the closed-loop system is internally stable and has a given H∞ disturbance attenuation level. Then, methods of designing a non-fragile H∞ state feedback controller were presented. No parameters need to be tuned and can be easily determined by solving linear matrix inequalities. Finally, the validity of the proposed methods was demonstrated by a numerical example with the asymptotically stable curves of system state and controller output under the initial condition of x（0）=[1 0 -1]^T and h=0.8 time-delay boundary.     

Synthesis and photophysical and electrochemical properties of new cyclometalated platinum complex containing oxadiazole ligand

A new cyclometalated platinum complex containing 2, 5-bis（naphthalene-1-yl）-1,3,4-oxadiazole ligand was synthesized and characterized. The UV-Vis absorptions and photoluminescent properties of the ligand and its platinum complex were investigated A characteristic metal-ligand charge transfer absorption peak at 439 nm in the UV spectrum and a strong emission peak at 625 nm in the photoluminescence spectrum were observed for this complex in dichloromethane. Cyclic voltammtry （CV） analysis shows that the EHOMO （energy level of the highest occupied molecular orbital） and ELUMO （energy level of the lowest unoccupied molecular orbital） of the platinum complex are about -5.69 and -3.25 eV, respectively, indicating that the oxadiazole-based platinum complex has a potential application in electrophosphorescent devices used as a red-emitting material.     

Scanner external calibration algorithm based on fixed point in robot remanufacturing system

This paper deals with the scanner exterior calibration algorithm when the scanner is arranged by the robot and the object scanned is fixed on a rotate device in the Robot Remanufacturing System. The method of calibrating the relationship between the scanner coordinate and the robot Tool₀, such as the rotation, R _x , R_y, R_z, and the transformation X, Y, Z is studied. The data of Tool₀ can be directly obtained from the relationship with the robot base-coordinate. So, the coordinate relationship between the scanner coordinate and the robot base coordinate can be easily gotten. This paper explains the basic algorithm theory, computing method, data collecting process and the resulted data in detail. The calibration algorithm is deduced under the orthogonal coordinate. Foundation item: Project (50075086; 50235030) supported by the National Natural Science Foundation of China; Project (413270103) supported by National Basic Research Foundation of China; Project (2000-476) supported by the Ministry of Education for the Outstanding Teachers     

Isolation, identification and characterization of cadmium-resistant Pseudomonas aeruginosa strain E1

Strain E₁ with resistance to 18 mmol/L cadmium (Cd), isolated from Cd-contaminated soil was identified by morphological observation, biochemical and physiological characterization and 16S rDNA sequence analysis. The resistance to heavy metals Cd, Cu, Co, Mn, Pb, Zn and 12 antibiotics was examined. The ability of removing Cd from solution was studied. The characterizations show that strain E₁ is affiliated to Pseudomonas aeruginosa (P. aeruginosa). Strain E₁ has high resistance to heavy metals and the order is found to be Cd>Mn>Zn>Cu>Pb>Co in solid media. Strain E₁ also exhibits the resistance to 12 antibiotics. Both living and non-living cells of strain E₁ can remove Cd from solution, and living cell has better biosorption than non-living cell. Foundation item: Project (50621063) supported by the National Natural Science Foundation of China; Project (2004CB619204) supported by the Major State Basic Research and Development Program of China     

Isolation of Leptospirillum ferriphilum by single-layered solid medium

According to physiological and biochemical characteristics of Leptospirillum ferriphilum,a strain of object bacteria was isolated successfully.Bacteria were enriched by selective liquid medium and plated on designed single-layered agar solid medium.Colony was cultured and bacteria were collected.The morphologies of the object bacteria were observed using crystal violet staining,scanning electron microscope(SEM)and transmission electron microscope(TEM).The result of 16S rDNA identification shows that this bacterium belongs to Leptospirillum ferriphilum and it is named as Leptospirillum ferriphilum strain D1.These results indicate that this new single-layered agar solid medium is efficient and simple for isolation of Leptospirillum ferriphilum.Additionally,physiological-biochemical characteristics show that the optimum initial pH value and its growth temperature are 1.68 and 40 ℃,respectively.The culture of it is used to leach a complex concentrate chalcopyrite,the leaching efficiencies of copper and iron are 1.93 % and 13.74 %,respectively,and it is more effective than the A.ferrooxidans culture in the leaching of the complex concentrate chalcopyrite.     

A utility-optimal backoff algorithm for wireless sensor networks

A novel backoff algorithm in CSMA/CA-based medium access control (MAC) protocols for clustered sensor networks was proposed. The algorithm requires that all sensor nodes have the same value of contention window (C _W ) in a cluster, which is revealed by formulating resource allocation as a network utility maximization problem. Then, by maximizing the total network utility with constrains of minimizing collision probability, the optimal value of C _W (W _opt) can be computed according to the number of sensor nodes. The new backoff algorithm uses the common optimal value W _opt and leads to fewer collisions than binary exponential backoff algorithm. The simulation results show that the proposed algorithm outperforms standard 802.11 DCF and S-MAC in average collision times, packet delay, total energy consumption, and system throughput. Foundation item: Project(60772088) supported by the National Natural Science Foundation of China     

Coating of Fe, Ni on α-alumina microspheres by heterogeneous precipitation

1INTRODUCTION Themagneticmetal coatedceramicoxides,core shellstructuralcompositematerials,inwhichthinmetallicfilmsarecoatedonaceramicoxide matrixwithmicrometerparticlesizes,areattrac tiveduetothecombinationofthefunctionalchar acteristicsofmetalsandmechanicalpropertiesoftheceramicmatrix.Theceramic basedtransition metal coated,core shellcompositessuchasNi coatedAl2O3[1],Fe coatedAl2O3[2],FeNi coated Al2O3[3]orCoFe coatedSiO2[4],havebeenfoundtoexhibitinterestingfunctionalperformancesdue…     

Microscopic phase-field simulation for coarsening behavior of L12 and DO22 phases of Ni75Cr x Al25? x alloy

Based on the microscopic phase-field dynamic model and the microelasticity theory, the coarsening behavior of L1₂ and DO₂₂ phases in Ni₇₅Cr _x Al_25−x alloy was simulated. The results show that the initial irregular shaped, randomly distributed L1₂ and DO₂₂ phases are gradually transformed into cuboidal shape with round corner, regularly aligned along directions [100] and [001], and highly preferential selected microstructure is formed during the later stage of precipitation. The elastic field produced by the lattice mismatch between the coherent precipitates and the matrix has a strong influence on the coarsening kinetics, and there is no linear relationship between the cube of the average size of precipitates and the aging time, which does not agree with the results predicted by the classical Lifshitz-Slyozov-Wagner. The coarsening processes of L1₂ and DO₂₂ phases are retarded in elastically constrained system. In the concurrent system of L1₂ and DO₂₂ phases, there are two types of coarsening modes: the migration of antiphase domain boundaries and the interphase Ostwald ripening. Foundation item: Project(50671084) supported by the National Natural Science Foundation of China; Project(20070420218) supported by China Postdoctoral Science Foundation