Cutoff variation induces different topological properties: A new discovery of amino acid network within protein

An increasing attention has been dedicated to the characterization of complex networks within the protein world. Before now most investigations about protein structures were only considered where the interactive cutoff distance R_c=5 or 7 Å. It is noteworthy that the length of peptide bond is about 1.5 Å, the length of hydrogen bond is about 3 Å, the range of London-van der Waals force is about 5 Å and the range of hydrophobic effect can reach to 12 Å in protein molecule. Present work reports a study on the topological properties of the amino acid network constructed by different interactions above. The results indicate that the small-world property of amino acid network constructed by the peptide and hydrogen bond, London-van der Waals force and the hydrophobic effect is strong, very strong and relatively weak, respectively. Besides, there exists a precise exponential relation C∝k^−0.5 at R_c=12 Å. It means that the amino acid network constructed by the hydrophobic effect tend to be hierarchical. Functional modules could be the cause for hierarchical modularity architecture in protein structures. This study on amino acid interactive network for different interactions facilitates the identification of binding sites which is strongly linked with protein function, and furthermore provides reasonable understanding of the underlying laws of evolution in genomics and proteomics.     

WNK1基因不同转录本在小鼠肾脏中的表达及意义

目的研究WNK1基因长短两个转录本在小鼠肾脏组织中的表达分布特征,为进一步研究它们的生物学功能提供实验数据.方法 RT-PCR扩增两个转录本的特异性片段,Northern印迹杂交证实片段特异性后,将片段克隆入pGEM-T载体中,体外转录同位素标记的正义和反义RNA探针,在小鼠肾脏组织石蜡切片上进行原位杂交检测.结果 WNK1基因长转录本微弱广泛地表达在小鼠肾脏组织上,短转录本特异地表达在小鼠肾脏皮质部的远曲小管上.结论在肾脏,WNK1基因的短转录本是功能性转录本,其编码的蛋白质在生物学功能上可能与其它激酶不同.     

番茄转录因子基因SlWRKY6的克隆与原核表达分析

该研究基于番茄基因组数据库SGN(Sol Genomic Network)信息,利用RT PCR从栽培番茄‘M82’(Solanum lycopersicum)中成功克隆到番茄SlWRKY6基因(登录号：Solyc02g080890),通过qRT PCR方法和原核表达初步验证其生物学功能。结果表明：(1)生物信息学分析显示,番茄SlWRKY6基因ORF全长1 653 bp,编码550个氨基酸,其蛋白结构含有1个WRKYGQK保守结构域和C₂H₂锌指结构域,属于IIb类;其基因启动子上游1 500 bp含有多个激素响应元件和非生物胁迫响应元件。(2)进化树分析显示,SlWRKY6与潘那利番茄SpWRKY31 X1(NP_001352691.1)的相似性最高,且定位于细胞核内。(3)qRT PCR结果显示,SlWRKY6基因在番茄根、茎、叶中均有表达,在叶中的表达量最高,且受盐和干旱诱导表达。(4)SDS PAGE及Western blot结果显示,pET 30a SlWRKY6重组蛋白的大小约66 kDa,与预期大小一致。(5)原核表达分析显示,重组菌E. coli BL21∷pET 30a SlWRKY6在不同浓度盐(NaCl)和干旱(Mannitol)胁迫下生长速度显著低于对照菌E. coli BL21∷pET 30a,且在400 mmol/L NaCl、800 mmol/L甘露醇胁迫条件下最为显著;滴板实验初步验证SlWRKY6转录因子能提高重组菌E. coli BL21∷pET 30a SlWRKY6在ABA和pH 9(NaOH)胁迫的耐受性;在400 mmol/L NaCl、pH 5(HCl)、800 mmol/L甘露醇胁迫条件下耐受能力降低。研究表明,SlWRKY6转录因子可能通过参与ABA途径来响应非生物胁迫。     

用改良的MTT法测定rhG-CSF活性

ＭＴＴ测定法是根据线粒体脱氢酶催化ＭＴＴ形成蓝色甲■的多少来检测活细胞数和功能状态的,但原始方法中存在着一些问题,如敏感性偏低、有机溶剂产生蛋白质沉淀以及产物的溶解度偏低等。为了摸索测定 ｒｈＧ－ＣＳＦ活性的最适条件,我们以 ＮＦＳ－６０细胞为对象,比较了多种溶解缓冲液,并且对细胞数、ＭＴＴ浓度及保留时间、溶解液用量等条件进行了选择。结果表明,ＤＭＦ－２０％ＳＤＳ和 ２０％ＳＤＳ的效果最好,测定时细胞数为每孔 １０００个细胞,所加 ＭＴＴ浓度为 １ｍｇ／ｍｌ,保留时间为 ４ ｈ,溶解液的用量为每孔 １００μｌ。     

Response of osteoblasts to low fluid shear stress is time dependent

The process of mechanotransduction of bone, the conversion of a mechanical stimulus into a biochemical response, is known to occur in osteoblasts in response to fluid shear stress. In order to understand the reaction of osteoblasts to various times of flow perfusion, osteoblasts were seeded on three-dimensional scaffolds, and cultured in the following conditions: continuous flow perfusion, intermittent flow perfusion, and static condition. We collected samples on day 4, 8 and 12 for analysis. Osteoblast proliferation was demonstrated by cell proliferation and scanning electron microscopy assay. Additionally, the expression of known markers of differentiation, including alkaline phosphatase and osteocalcin, were tested by qRT-PCR and alkaline phosphatase activity assay, and the deposition of calcium was used as an indicator of mineralization demonstrated by calcium content assay. The results supported that low fluid shear stress plays an important role in the activation of osteoblasts: enhance cell proliferation, increase calcium deposition, and promote the expression of osteoblastic markers. Furthermore, the continuous flow perfusion is a more favorable environment for the initiation of osteoblast activity compared with intermittent flow perfusion. Therefore, the force and time of fluid shear stress are important parameters for osteoblast activation.