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.     

Growth kinetics of Thiobacillus ferrooxidans in bioelectrochemical cell

Thiobacillus ferrooxidans might be the most important bacteria used in biometallurgy. The foundation way of its growth process is oxidizing ferrous in order to obtain energy needed for metabolism, but the variation of ferrous concentration and mixed potential of the culture media would have crucial effect on the bacteria growth. Based on the characteristics of Thiobacillus ferroxidans growth and redox potential of ferric and ferrous, an electrochemical cell was designed conventionally to study growth rule and the relationship between redox potential and bacteria growth was built up, and some growth kinetics of Thiobacillus ferrooxidans were elucidated. It demonstrates that the variation of open potential of electrochemical cell ΔE shows the growth tendency of Thiobacillus ferrooxidans, at the initial growth stage, the value of δE increases slowly, when at logistic growth stage, it increases drastically, and the growth rate of bacteria is linear with the oxidation rate of ferrous. The bacteria growth kinetics model is proposed using Monod and Michealis-Menten equation, and the kinetics parameters are got. The consistence of the measured and the calculated results proves that it is proper to use the proposed kinetics model and the electrochemical cell method to describe the growth rule of Thiobacillus ferrooxidans. Foundation item: Project (50204001) supported by the National Science Foundation of China     

Adsorption characteristics of thiobacillus ferrooxidans on surface of sulfide minerals

By using thiobacillus ferroxidans (T. f) from Qixiashan, Hubei Province, China, the adsorption characteristics of T. f on surface of sulfide mineral were studied. The influences of adsorption time, pH value, temperature, initial inoculated concentration of bacteria, concentration of sulfide mineral powder, and variety of minerals on the adsorption characteristics were firstly investigated by using the ninhydrin colorimetric method, and the changes of contact angles and Zeta potentials of mineral surface during the bacterial adsorption were then determined. The results show that when the leaching experiments are performed for a long time from several days to a month, the maximal quantity of adsorption of T f on the surface of pyrite is obtained under the following conditions: leaching for 20 d, pH value in range of 1–2 and temperature at 30 °C, respectively; when the bio-leaching experiments are performed for a shorter leaching time, the maximal quantity of adsorption is obtained under the conditions: bio-leaching for 2 h, at 2.4×10⁷ cell/mL of initial inoculated bacteria concentration, and at 10% of mineral powder concentration; and the adsorption quantities are different from one sulfide mineral to another, and the adsorption of T. f on the surface of sulfide minerals includes three phases: increasing phase, stationary phase and decreasing phase. Foundation item: Project(50321402) supported by the National Natural Science Foundation of China; project (2004CB619204) supported by the National Key Fundamental Research and Development Program of China     

嗜酸性硫杆菌脱除废镀铝膜表面铝的工艺参数及效果研究

镀铝膜袋是电子产品等的常用包装物,使用量大,废弃后铝影响了塑料膜的循环使用.由于缺乏有效和低成本的方法,镀铝膜中的金属铝未完全从镀铝膜中提取出来.因此,需开发新的方法来提高铝塑分离效率,降低成本,提高废镀铝膜的再生利用率.通过利用嗜酸菌的产酸能力等作用溶解铝进行铝塑分离,对包装用废镀铝膜表面铝进行微生物浸出实验研究,探...     

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.     

Thermodynamics and kinetics analysis of in-situ synthesizing AIN

AIN powders were prepared by in-situ synthesis technique. It is a reaction of binary molten Al−Mg alloys with highly pure nitrogen. It was confirmed through thermodynamics calculation that Mg element in Al−Mg alloys can decrease oxygen content in the reacting system. Thus, nitridation reaction can be performed to form AIN. Moreover, an analysis of kinetics shows that the nitridation reaction of Al−Mg alloys can be accelerated and transferred rapidly with the increment of Mg content.     

Component analysis of volatile oil from Illicium Verum Hook. f.

Volatile oil was extracted from Illicium Verum Hook. f. by using steam distillation. 41 kinds of compounds were separated and identified by GC/MS, and their relative contents were determined by normalization method. Among 41 identified compounds, there are 14 hydrocarbon components and 22 oxygenated hydrocarbon derivatives, and a small amount of nitrogenous compounds. The main component is anethole, accounting for 76.23%, and the other components such as anisyl acetone, anisaldehyde, p-allylanisole, p-cumic aldehyde and p-allylpen take up more than 10%. Foundation item: Science Foundation of Education for Hunan Province (No. 00C324) Biography of the first author: YAN Jian-hui, associate professor, doctorate candidate, born in 1958, majoring in applied chemistry.     

Purification and characterization of extracellular chitinase from a novel strain Aspergillus fumigatus CS-01

Twelve samples derived from different locations in south central area of China are treated by enrichment and spread-plate technique for initial screening. Seven chitinase-producing strains are isolated. The chitinase present in the culture supernatant of strain CS-01 possesses the maximum activity of 0.118 U/mL. Analysis of the morphological feature and the ITS rDNA sequence reveals that strain CS-01 belongs to Aspergillus fumigatus. Production of the chitinase is regulated by a inducible way and the maximum activity appears at 36 h in colloidal chitin culture. Purification of the chitinase is carried out by salting out, gel filtrate chromatography and anion exchange chromatography sequentially. Native-PAGE and SDS-PAGE indicate that the chitinase from A. fumigatus CS-01 is a monomer with the relative molecular mass estimated to be 4.50×10⁴. Its maximum activity appears at pH 5 and 55 °C. The chitinase is stable at pH 4.0–7.5 and below 45 °C. Foundation item: Projects(50621063, 50674101) supported by the National Natural Science Foundation of China     

基于15N质量平衡法研究养殖消化废水中氨氮的去除机理

为避免养猪场消化废水对环境造成的污染,利用微藻去除消化废水中营养物质的二次处理方法受到了广泛关注。采用¹⁵N质量平衡法研究了鞘藻去除氨氮的主要机理,重点研究了鞘藻生长与氨氮去除的关系以及氨氮去除的主要途径。经高压灭菌后的消化废水在鞘藻培养期的氨氮去除率为96.2%,鞘藻特定生长率为0.04~0.15;稀释后的原消化废水氨氮的去除率为94.1%,鞘藻特定生长率为-0.14~0.13。通过曝气的汽提效应对氨的去除有显著的促进作用,尤其在高pH值试验条件下更有利于脱氨。¹⁵N同位素质量平衡分析表明,原始消化废水中存在的细菌对氨氮的去除影响小,在鞘藻培养期去除原消化废水中氨氮的主要途径是鞘藻的吸收和气体的损失,分别占总氮量的40.97%和32.59%。氨氮的去除与主要影响因素间的回归和通径分析表明,要提高氨氮去除率,需要提高鞘藻Chl-a含量和DO浓度,同时限制或保持pH值在弱碱性状态。     

Comparative analysis of chemical components between barks and leaves of Eucommia ulmoides Oliver

The chemical components of the essential oils in the barks and leaves of Eucommia ulmoides Oliver were analyzed and compared by chromatograms and mass spectra technique, heuristic evolving latent projections (HELP), alternative moving window factor analysis (AMWFA) algorithms and normalization method based on the peak areas; the flavones in the barks and leaves of Eucommia ulmoides Oliver were separated on an ODS column by gradient elution carried out with the flow phase consisting of water, methanol and phosphoric acid (0.1%), and their contents were quantitatively determined by standard curve method and diode array detection (DAD) at 362 nm. The results show that 68 and 73 compounds respectively from essential oils of the barks and leaves of Eucommia ulmoides Oliver are identified, and there are 33 mutual compounds among 108 compounds determined. The total contents of these volatile components of the two samples possess 92.9% and 97.75% of the gross of the relevant essential oils, respectively; the contents of the rutin, quercetin and kaempferol in the barks and leaves of Eucommia ulmoides Oliver are 0.016 9, 0.003 6, 0.002 1 and 0.064 4, 0.030 2, 0.010 0 mg/g, respectively, and the determination recoveries are 95.2%–106.2%. The comparative analysis shows that for the barks and leaves of Eucommia ulmoides Oliver, there are significant differences in their components of the relevant essential oils and flavones. Foundation item: Project(20235020) supported by the National Natural Science Foundation of China     

Fractionation and characterization of polysaccharides from cyanobacterium Spirulina （Arthrospira） maxima in nitrogen-limited batch culture

By a sequentially selective extraction procedure, polysaccharides (PS) from cyanobacterium Spirulina (Arthrospira) maxima that can be bio-functionally healthy components were fractionated in four parts including the culture medium (PSCM), the external layers of the cell (PSEL), the cell wall (PSCW) and storage granules (PSSG). The four fractionated parts of polysaccharides were characterized by gas-liquid chromatography (GLC) equipped with FID and fused-silica capillary column (15 m×0.53 mm i. d.). The contents of PSCM, PSEL, PSCW and PSSG were about 2.0%, 2.6%, 10.0% and 52.0% to cell dry matter, respectively. Glucose was almost the only monosaccharide in PSSG and PSCW and most predominant in PSEL, while in PSCM, xylose, rhamnose and glucose were the main ones. Two uronic acids represented by glucuronic acid and galacturoic acid, six neutral monosaccharides including fucose, rhamnose, xylose, mannose, galactose and glucose, and two possible unidentified sugars were found in PSEL and PSCM. These data are valuable for the selective productions of high-added value sugars from Spirulina. Foundation item: Scholarship for Ph. D at FPMs, Belgium Biography of the first author: NIE Zhen-yuan, Engineer in biomedicine, born in 1963, majoring in biotechnology and bioengineering.