用DREAM技术纠正人工合成基因中的突变

目的：介绍一种简便、有效的定点突变技术。方法：根据突变位点附近的DNA序列推导出氨基酸序列,再以此氨基酸序列进行逆翻译,这样在不改变氨基酸序列的前提下可以得到数目巨大的隐性突变体（silent mutants）,这些突变体中包含大量的限制性内切酶位点,选择合适的酶切位点设计引物用PCR技术扩增两侧DNA片段,然后以相应酶切融合这两个片段即可完成定点突变。结果：用该方法成功地在人工合成的含有缺失的可溶性组织因子基因的472位插入C,T两个碱基,校正了阅读框架,获得了预期的目的基因。结论：该方法简便、有效, 避免了多轮PCR和合成长引物导致突变的可能性,这种改进的PCR 定点诱变技术我们称之为“设计限制酶辅助突变”（Designed Restriction Enzyme Assisted Mutagenesis, DREAM）。此技术简单方便, 诱变的成功率高, 适于实验室常规应用。     

促进植物高效遗传转化的发育调节因子及其在玉米中的应用进展*

高效遗传转化技术体系的建立对植物功能基因组学研究和作物新品种的培育均具有促进作用,目前,再生效率低下是限制许多植物高效遗传转化体系建立的主要技术屏障之一。随着对植物分生组织和体细胞胚形成过程研究的深入,鉴定到了一些关键调控基因,统称为发育调节因子。发育调节因子应用于植物遗传转化后,可以有效改善植物分生组织诱导和再生能力,为提高遗传转化效率提供了重要机遇。综述了7类发育调节因子在提高植物遗传转化效率中的研究进展,重点介绍了其中3类在促进玉米遗传转化中的应用,最后展望了建立植物高效遗传转化体系的发展方向。     

Autophagy and senescence: A new insight in selected human diseases

Senescence and autophagy play important roles in homeostasis. Cellular senescence and autophagy commonly cause several degenerative processes, including oxidative stress, DNA damage, telomere shortening, and oncogenic stress; hence, both events are known to be interrelated. Autophagy is well known for its disruptive effect on human diseases, and it is currently proposed to have a direct effect on triggering senescence and quiescence. However, it is yet to be proven whether autophagy has a positive or negative impact on senescence. It is known that elevated levels of autophagy induce cell death, whereas inadequate autophagy can trigger cellular senescence. Both have important roles in human diseases such as aging, renal degeneration, neurodegenerative disorders, and cancer. Therefore, this review aims to highlight the relevance of senescence and autophagy in selected human ailments through a summary of recent findings on the connection and effects of autophagy and senescence in these diseases.     

活性污泥微生物胞外多聚物生物合成途径与菌胶团形成的调控机制

活性污泥法是借助活性污泥微生物菌胶团形成来实现泥水重力分离和部分污泥回用,辅以曝气供氧,在曝气池中高密度的微生物细胞可将溶解性有机污染物迅速降解、转化后为己所用,外排的剩余污泥带走大量有机质和氮磷,水质得以净化。活性污泥微生物所合成的胶质状胞外多聚物(Extracellular polymeric substances,EPS)是污泥菌胶团形成必不可少的"黏合剂",吸水性极高,这也造成剩余污泥难以处置和利用。我们初步总结了活性污泥微生物宏基因组研究概况,利用分子遗传学和基因组学手段,对活性污泥优势种动胶菌(Zoogloea)和其他菌胶团形成菌的EPS生物合成途径和菌胶团形成与调控机制加以研究,鉴定出一个约40 kb的胞外多糖生物合成大型基因簇和一个由7个基因组成的小型基因簇,该基因簇中除胞外多糖合成相关基因外,还编码组氨酸激酶Prs K和反应调节蛋白Prs R双组分系统,可激活RpoNσ因子共同调控一类称之为PEP-CTERM的新型胞外蛋白质的表达,参与菌胶团的形成。PEP-CTERM富含天冬酰胺(缩写为Asn或者N)残基,可能与胞外多糖通过N-连锁的糖基化形成复合物,包裹微生物细胞群体来介导菌胶团的形成。类似的PEP-CTERM基因和胞外多糖合成基因簇在许多重要的活性污泥细菌如聚磷菌和全程氨氧化菌中存在,说明这些细菌也是菌胶团形成菌,可通过污泥沉淀和回用在活性污泥中得以富集。这些研究结果可供活性污泥膨胀控制、污泥减量和剩余污泥资源和能源回收利用参考。     

Hypoglycemic activity of inorganic constitutents in Eugenia jambolana seed on streptozotocin-induced diabetes in rats

Medicinal herbs used in indigenous medicines for the management of diabetes mellitus contain both organic and inorganic constituents. Some of these inorganic trace elements possess antidiabetic properties, which accounts for the activity of medicinal herbs. The aim of this study was to analyze the inorganic trace elements present in Eugenia jambolana seeds and to evaluate the hypoglycemic activity of the inorganic part of E. jambolana seeds on streptozotocin-induced diabetes. The seeds of E. jambolana seeds were reduced to ash and the inorganic elements present were assayed. The hypoglycemic efficacy of the inorganic part was tested by the glucose tolerance test on streptozotocin-induced diabetes. Elements such as zinc, chromium, vanadium, potassium, and sodium, possessing hypoglycemic activity, were present in the seed. The E. jambolana seed ashtreated diabetic rats exhibited normoglycemia and better glucose tolerance. The conclusion that the inorganic constituents might play a important role in the antidiabetic nature E. jambolana seeds was reached.     

Computational approaches for modeling regulatory cellular networks

Cellular components interact with each other to form networks that process information and evoke biological responses. A deep understanding of the behavior of these networks requires the development and analysis of mathematical models. In this article, different types of mathematical representations for modeling signaling networks are described, and the advantages and disadvantages of each type are discussed. Two experimentally well-studied signaling networks are then used as examples to illustrate the insight that could be gained through modeling. Finally, the modeling approach is expanded to describe how signaling networks might regulate cellular machines and evoke phenotypic behaviors.     

CADB: Conformation Angles DataBase of proteins

Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and 90% sequence identity between any two proteins, available in the Protein Data Bank. In addition, the database contains the necessary crystallographic parameters. The package has several flexible options and display facilities to visualize the main-chain and side-chain conformation angles for a particular amino acid residue. The package can also be used to study the interrelationship between the main-chain and side-chain conformation angles. A web based JAVA graphics interface has been deployed to display the user interested information on the client machine. The database is being updated at regular intervals and can be accessed over the World Wide Web interface at the following URL: http://144.16.71.148/cadb/.     

Structure of Mycobacterium tuberculosis single-stranded DNA-binding protein. Variability in quaternary structure and its implications

Single-stranded DNA-binding protein (SSB) is an essential protein necessary for the functioning of the DNA replication, repair and recombination machineries. Here we report the structure of the DNA-binding domain of Mycobacterium tuberculosis SSB (MtuSSB) in four different crystals distributed in two forms. The structure of one of the forms was solved by a combination of isomorphous replacement and anomalous scattering. This structure was used to determine the structure of the other form by molecular replacement. The polypeptide chain in the structure exhibits the oligonucleotide binding fold. The globular core of the molecule in different subunits in the two forms and those in Escherichia coli SSB (EcoSSB) and human mitochondrial SSB (HMtSSB) have similar structure, although the three loops exhibit considerable structural variation. However, the tetrameric MtuSSB has an as yet unobserved quaternary association. This quaternary structure with a unique dimeric interface lends the oligomeric protein greater stability, which may be of significance to the functioning of the protein under conditions of stress. Also, as a result of the variation in the quaternary structure the path adopted by the DNA to wrap around MtuSSB is expected to be different from that of EcoSSB.     

Fluorescence resonance energy transfer (FRET) microscopy imaging of live cell protein localizations

The current advances in fluorescence microscopy, coupled with the development of new fluorescent probes, make fluorescence resonance energy transfer (FRET) a powerful technique for studying molecular interactions inside living cells with improved spatial (angstrom) and temporal (nanosecond) resolution, distance range, and sensitivity and a broader range of biological applications.     

The crystal structure of 1,2,3,4,6-penta-O-benzoyl-alpha-D-mannopyranose: observation of C-H...pi interaction as a surrogate to O-H...O interaction of a free sugar

The crystal structure of the title compound was determined by X-ray crystallography. The compound crystallized in the orthorhombic space group P2(1)2(1)2(1) with four molecules in the unit cell with a=9.170(2), b=9.873 (2), c=38.831(8) A. The structure was refined to a R index of 0.041 for 7907 independent reflections. The mannopyranose unit adopts a distorted 4C1 conformation. The structure depicts unique network of C-H...pi interactions, very closely resembling the pattern of O-H...O interactions in free sugars. This intriguing and rare observation points to a notion that the supramolecular organization pertaining to a sugar is in-built in the pyranose ring itself.