Roles of Tyr122-hydrophobic cluster and K+ binding in Ca2+ -releasing process of ADP-insensitive phosphoenzyme of sarcoplasmic reticulum Ca2+ -ATPase

Tyr(122)-hydrophobic cluster (Y122-HC) is an interaction network formed by the top part of the second transmembrane helix and the cytoplasmic actuator and phosphorylation domains of sarcoplasmic reticulum Ca(2+)-ATPase. We have previously found that Y122-HC plays critical roles in the processing of ADP-insensitive phosphoenzyme (E2P) after its formation by the isomerization from ADP-sensitive phosphoenzyme (E1PCa(2)) (Wang, G., Yamasaki, K., Daiho, T., and Suzuki, H. (2005) J. Biol. Chem. 280, 26508-26516). Here, we further explored kinetic properties of the alanine-substitution mutants of Y122-HC to examine roles of Y122-HC for Ca(2+) release process in E2P. In the steady state, the amount of E2P decreased so that of E1PCa(2) increased with increasing lumenal Ca(2+) concentration in the mutants with K(0.5) 110-320 microm at pH 7.3. These lumenal Ca(2+) affinities in E2P agreed with those estimated from the forward and lumenal Ca(2+)-induced reverse kinetics of the E1PCa(2)-E2P isomerization. K(0.5) of the wild type in the kinetics was estimated to be 1.5 mM. Thus, E2P of the mutants possesses significantly higher affinities for lumenal Ca(2+) than that of the wild type. The kinetics further indicated that the rates of lumenal Ca(2+) access and binding to the transport sites of E2P were substantially slowed by the mutations. Therefore, the proper formation of Y122-HC and resulting compactly organized structure are critical for both decreasing Ca(2+) affinity and opening the lumenal gate, thus for Ca(2+) release from E2PCa(2). Interestingly, when K(+) was omitted from the medium of the wild type, the properties of the wild type became similar to those of Y122-HC mutants. K(+) binding likely functions via producing the compactly organized structure, in this sense, similarly to Y122-HC.     

Germplasm resources research of Toona sinensis with RAPD and isoenzyme analysis

Collected from Chinese mainland, 25 samples of Toona sinensis seed were planted in a standard garden. Three years later, samples were analyzed with random amplified polymorphic DNA (RAPD) and isoenzymes variants of cytochrome oxidase and peroxidases. Results of RAPD and isoenzymes variants were analyzed with software POPGENE32 and SPSS10.0 respectively. Phylogenetic trees were calculated from the clustered result of RAPD and isoenzymes variants. Such additional factors as leaves color, latitude and altitude of original seeds were analyzed at the same time. Our result suggested that a general similarity is concurred with the three analyses as RAPD, isoenzymes variants analysis of peroxidases and cytochrome oxidase. Two clusters can be separated from the sample collected as southern and northern ones. In the evolutionary history, a migrating route in the direction from West-South to East-North and with sequential differentiation in the direction South-North can be decided if only it is true with the argument that Toona sinensis came from tropic Asia, the border of east-north India and Burma.     

Statistical analysis of interface similarity in crystals of homologous proteins

Many proteins function as homo-oligomers and are regulated via their oligomeric state. For some proteins, the stoichiometry of homo-oligomeric states under various conditions has been studied using gel filtration or analytical ultracentrifugation experiments. The interfaces involved in these assemblies may be identified using cross-linking and mass spectrometry, solution-state NMR, and other experiments. However, for most proteins, the actual interfaces that are involved in oligomerization are inferred from X-ray crystallographic structures using assumptions about interface surface areas and physical properties. Examination of interfaces across different Protein Data Bank (PDB) entries in a protein family reveals several important features. First, similarities in space group, asymmetric unit size, and cell dimensions and angles (within 1%) do not guarantee that two crystals are actually the same crystal form, containing similar relative orientations and interactions within the crystal. Conversely, two crystals in different space groups may be quite similar in terms of all the interfaces within each crystal. Second, NMR structures and an existing benchmark of PDB crystallographic entries consisting of 126 dimers as well as larger structures and 132 monomers were used to determine whether the existence or lack of common interfaces across multiple crystal forms can be used to predict whether a protein is an oligomer or not. Monomeric proteins tend to have common interfaces across only a minority of crystal forms, whereas higher-order structures exhibit common interfaces across a majority of available crystal forms. The data can be used to estimate the probability that an interface is biological if two or more crystal forms are available. Finally, the Protein Interfaces, Surfaces, and Assemblies (PISA) database available from the European Bioinformatics Institute is more consistent in identifying interfaces observed in many crystal forms compared with the PDB and the European Bioinformatics Institute's Protein Quaternary Server (PQS). The PDB, in particular, is missing highly likely biological interfaces in its biological unit files for about 10% of PDB entries.     

海水盐离子对耐盐粘球菌生长和发育的影响

黄褐粘球菌 (Myxococcusfulvus)HW 1菌株是分离自海水样品的耐盐粘细菌 ,能够在海水 (盐浓度为3.8% )或稀释海水条件下生长。随着生长环境中海水浓度的提高 ,HW 1在生长与分化发育上表现出不同于陆地粘细菌的特性。对海水中主要盐离子的进一步分析表明 ,Na+ 对HW 1生长有抑制作用 ,当Ca2 + 超过海水中浓度时对HW 1生长抑制最为明显 ,而Mg2 + 对HW 1生长几乎没有抑制作用 ,但能促进子实体的形成。海水盐成分中SO42 -,K+ 和不含K+ 的其它盐组合都能导致孢子抗热能力的提高。     

Proteomic analysis of different fractions in M. tuberculosis culture]

To provide a basis of molecular genetic analysis of M. tubereulosis, the proteomic profiling was prompted. M. tuberculosis H37RV was cultured in Sauton medium at 37 degrees C for 3 weeks, harvested and fractionated into three portions: suspension filtration proteins(A), cytosol proteins(B) and membrane proteins(C). These fractions were analyzed by pH3-10 IPG gradient and SDS-PAGE. The silver-stained technigue and gel images were used. Then the image was transfered into 2-DE gel analysis Software. A part of protein sports of expression level higher from the culture filtrate fraction were identified by peptide mass fingerprinting. A total of 907, 884 and 681 protein sports were observed for A. B. C fractions in M. tuberculosis H37RV, respectively. Distribution of proteins mass for 3 fractions were principally similar, About 70.5-74.4 per cent were distributed in the ranges of Mr 10-49 kD.pI of the proteins for A, B fractions were pricipally similar, About 80.9-83.5 per cent were distributed in the ranges of pH 3.0-6.4, But the number of protein sports for C fraction distributed in the ranges of pH 7.6-10.0 were more than A, B fractions. The number of protein sports of expression level higher for A, B and C fractions were 71(7.8%), 242(27.4%), 19 (2.8%), respectively. 90 pen cent from them, pH of the proteins were distributed in the ranges of pH 3.0-6.4. 73.1 per cent for proteins mass of C fraction were distributed in the ranges of 10 kD-49 kD, which were more than A, B fractions. Nine of the proteins identified ih this study appeared to be homology or putative fanction proteins, but another five proteins were unknown. The proteomic profiling of different fractions in M. tuberculosis obtained in here will be provide a basis for detailed analysis of biology functions of the proteins.     

海岛棉GbRLCK10基因克隆及表达分析

该研究以拟南芥抗逆基因At1g67520为探针,利用海岛棉ESTs数据库,通过电子克隆获得海岛棉RLCK家族基因GbRLCK10,解析该基因组结构,并结合qRT-PCR技术分析该基因mRNA的组织表达特征以及在不同胁迫诱导下的表达模式,为揭示RLCK家族基因在海岛棉中的表达调控及作用机制提供理论依据。结果显示:(1)获得海岛棉类受体胞质激酶(RLCK)基因,其开放阅读框(ORF)为1 179bp,编码392个氨基酸,具有典型的Serine/Threonine结构域,属于RLCK家族,与GaRLCK10(XP_017604046.1)亲缘关系较近,命名为GbRLCK10(登录号2022184),且该基因由5个外显子和4个内含子组成。(2)实时荧光定量(qRT-PCR)检测显示,GbRLCK10基因在抗病品种‘新海21’和感病品种‘新海14’的根、茎、叶中均有表达;当黄萎病菌诱导后,GbRLCK10基因在抗病品种中对于病原菌的响应时间早于感病品种,且对黄萎病菌响应更强烈,推测该基因参与棉花对黄萎病的响应;盐(NaCl)、干旱(PEG-6000)处理‘新海21’后,GbRLCK10基因在NaCl处理下响应时间要早于PEG-6000处理,但对PEG-6000处理响应更强烈;分别用4种激素处理‘新海21’后,GbRLCK10均能被诱导表达,且在水杨酸(SA)处理后表现为先增加后下降再增加趋势,在乙烯(ET)处理后表达量为持续上升趋势,在茉莉酸甲酯(MeJA)处理后呈先升高然后下降的趋势,但GbRLCK10基因对赤霉素(GA3)响应不明显。研究表明,GbRLCK10基因具有RLCK基因家族典型特征,该基因随黄萎病菌、NaCl、干旱、激素处理时间推移而发生变化,推测GbRLCK10基因可能参与了棉花对黄萎病菌、NaCl、干旱、激素胁迫的应答反应,但其功能仍需进一步研究。     

Effect of concentration and temperature on the rheological behavior of collagen solution

Dynamic viscoelastic properties of collagen solutions with concentrations of 0.5-1.5% (w/w) were characterized by means of oscillatory rheometry at temperatures ranging from 20 to 32.5 degrees C. All collagen solutions showed a shear-thinning flow behavior. The complex viscosity exhibited an exponential increase and the loss tangent decreased with the increase of collagen concentration (C(COL)) when the C(COL)> or =0.75%. Both storage modulus (G') and loss modulus (G') increased with the increase of frequency and concentration, but decreased with the increase of temperature and behaved without regularity at 32.5 degrees C. The relaxation times decreased with the increase of temperature for 1.0% collagen solution. According to a three-zone model, dynamic modulus of collagen solutions showed terminal-zone and plateau-zone behavior when C(COL) was no more than 1.25% or the stated temperature was no more than 30 degrees C. The concentrated solution (1.5%) behaved being entirely in plateau zone. An application of the time-temperature superposition (TTS) allowed the construction of master curve and an Arrhenius-type TTS principle was used to yield the activation energy of 161.4 kJ mol(-1).     

Cell-based immobilization strategy for sensitive piezoelectric immunoassay of total prostate specific antigen

A novel yeast cell-based strategy for the immobilization of antibodies using an amine-terminated self-assembly film has been proposed. A quartz crystal microbalance sensor was according fabricated by coupling with anti-prostate specific antigen (anti-PSA) for PSA immunoassay. The crystal was modified with cysteamine to deposit yeast cells, on which anti-PSA antibodies were immobilized. The surface topologies of the as-prepared crystals were characterized by use of scanning electron microscopy. In contrast to the traditional glutaraldehyde (GLU) approach, the yeast cells could allow antibody molecules bound with higher bioactivity and achieve better immunoreaction capability. Results indicate that immunoassay prepared using the developed yeast cell-binding procedure exhibits increased analytical performance compared with that produced using the GLU cross-linking procedure. A PSA serum concentration in the range of 5.0-604.0ngml(-1) can be determined by this new system.     

Evaluation of the hormonal function and histological features of heterotopic isogenic ovarian transplantation in rats

The purpose of the study was to determine the feasibility of preserving ovarian function after heterotopic transplantation by means of microvascular anastomosis of the transplanted vascular pedicles to a set of preselected vessels. Six groups of 10 Sprague-Dawley inbred rats were used in this study. Group I underwent bilateral ovariectomy operation and served as the ovariectomy control. Group II underwent bilateral ovariectomy followed by heterotopic isogenic ovarian implantation. Group III underwent bilateral ovariectomy and isogenic heterotopic ovarian transplantation by means of microvascular anastomosis. Group IV served as the laparotomy sham-operated control. Group V served as the ovarian donor for group II. Group VI served as the donor of the ovarian-kidney vascular pedicle complex for group III. Postoperative ovarian estradiol levels were measured, and histological characteristics were elucidated in groups I, II, III, and IV. The results demonstrated that the estradiol level of the transplantation group was comparable to that of the sham operation group and was significantly higher than that of the implantation group. Histologically normal ovarian architecture was observed in the sham group (IV) and also in the transplantation group (III). Altered architecture was observed in the implantation group (II). These findings indicate that extraabdominal heterotopic ovarian transplantation with microvascular anastomosis led to normal ovarian hormonal function and was effective in preserving oocyte production capacity.     

CASA: a server for the critical assessment of protein sequence alignment accuracy

SUMMARY: A public server for evaluating the accuracy of protein sequence alignment methods is presented. CASA is an implementation of the alignment accuracy benchmark presented by Sauder et al. (Proteins, 40, 6-22, 2000). The benchmark currently contains 39321 pairwise protein structure alignments produced with the CE program from SCOP domain definitions. The server produces graphical and tabular comparisons of the accuracy of a user's input sequence alignments with other commonly used programs, such as BLAST, PSI-BLAST, Clustal W, and SAM-T99. AVAILABILITY: The server is located at http://capb.dbi.udel.edu/casa.