ArlR反应调节蛋白在表皮葡萄球菌不同生长期表达的检测

表皮葡萄球菌(Staphylococcus epidermidis,SE)是寄居在人体和黏膜表面的条件致病菌,因可在医疗植入材料表面形成生物膜(biofilm)而具有致病性。细菌双组分信号转导系统可调控生物膜形成,但其调控机制在SE中研究甚少。本课题对arlRS双组分信号转导系统的反应蛋白ArlR在细菌不同生长期的表达情况进行初步研究。首先构建ArlR原核表达质粒,用纯化重组ArlR免疫小鼠,获得多克隆抗-ArlR抗体,免疫Dot方法检测结果显示小鼠抗-ArlR血清效价>1∶100000。进一步采用蛋白免疫印迹法检测ArlR在SE1457野生株不同生长期中的表达水平,结果显示,ArlR在2h表达量较低,到4h达高峰,6～10h表达量较4h降低。利用反转录实时荧光定量聚合酶链反应检测arlR基因在不同生长期的转录水平,结果显示相应时间点ArlR蛋白表达水平与arlR基因转录水平一致。本研究结果为后期研究双组分信号转导系统arlRS对SE生物膜形成的影响奠定基础。     

Biocontrol of Listeria monocytogenes on Fresh-Cut Produce by Treatment with Lytic Bacteriophages and a Bacteriocin

The fresh-cut produce industry has been the fastest-growing portion of the food retail market during the past 10 years, providing consumers with convenient and nutritious food. However, fresh-cut fruits and vegetables raise food safety concerns, because exposed tissue may be colonized more easily by pathogenic bacteria than intact produce. This is due to the higher availability of nutrients on cut surfaces and the greater potential for contamination because of the increased amount of handling. We found that applied Listeria monocytogenes populations survived and increased only slightly on fresh-cut Red Delicious apples stored at 10°C but increased significantly on fresh-cut honeydew melons stored at 10°C over 7 days. In addition, we examined the effect of lytic, L. monocytogenes-specific phages via two phage application methods, spraying and pipetting, on L. monocytogenes populations in artificially contaminated fresh-cut melons and apples. The phage mixture reduced L. monocytogenes populations by 2.0 to 4.6 log units over the control on honeydew melons. On apples, the reduction was below 0.4 log units. In combination with nisin (a bacteriocin), the phage mixture reduced L. monocytogenes populations by up to 5.7 log units on honeydew melon slices and by up to 2.3 log units on apple slices compared to the control. Nisin alone reduced L. monocytogenes populations by up to 3.2 log units on honeydew melon slices and by up to 2.0 log units on apple slices compared to the control. The phage titer was stable on melon slices, but declined rapidly on apple slices. The spray application of the phage and phage plus nisin reduced the bacterial numbers at least as much as the pipette application. The effectiveness of the phage treatment also depended on the initial concentration of L. monocytogenes.     

Engineering mouse apolipoprotein A-I into a monomeric, active protein useful for structural determination

Apolipoprotein AI (apoAI), the major protein component of HDL, is one of the best predictors of coronary artery disease (CAD), with high apoAI and HDL levels being correlated with low occurrences of CAD. The primary function of apoAI is to recruit phospholipid and cholesterol for assembly of HDL particles. Like other exchangeable apolipoproteins, lipid-free apoAI forms a mixture of different oligomers even at 1.0 mg/mL. This self-association property of the exchangeable apolipoproteins is closely associated with the lipoprotein-binding activity of this protein family. It is unclear if the self-association property of apolipoprotein is required for its lipoprotein-binding activity. We developed a novel method for engineering an oligomeric protein to a monomeric, biologically active protein. Using this method, we generated a monomeric mouse apoAI mutant that is active. This mutant contains the first 216 residues of mouse apoAI and replaces six hydrophobic residues with either polar or smaller hydrophobic residues at the defined positions (V118A/A119S/L121Q/T191S/T195S/T199S). Cross-linking results show that this mutant is greater than 90% monomeric at 8 mg/mL. CD, DSC, and NMR results indicate that the mutant maintains an identical secondary, tertiary structure and stability as those of the wild-type mouse apoAI. Lipid-binding assays suggest that the mutant shares an equal lipoprotein-binding activity as that of the wild-type apoAI. In addition, both the monomeric mutant and the wild-type protein make nearly identical rHDL particles. With this monomeric mouse apoAI, high-quality NMR data has been collected, allowing for the NMR structural determination of lipid-free apoAI. On the basis of these results, we conclude that this apoAI mutant is a monomeric, active apoAI useful for structural determination.     

棉铃虫的取食营养特点与棉花抗虫素分布的关系

通过研究棉花8个部位对棉铃虫Helicoverpa armzgera的营养效果和其所含次生物质类萜烯和单宁的浓度及在组织中的分布,揭示了棉铃虫取食营养特点与棉花次生化学的关系。棉铃虫取食顶尖、转移蛀食蕾铃的习性,与有关器官或组织对幼虫的营养效果密切相关,而营养效果主要取决于类萜烯和单宁的含量。棉花顶尖嫩叶中单宁浓度随着棉花的生长发育呈升高的趋势;类萜烯浓度在第四真叶期、第六真叶期和现蕾初期之间出现一个明显的底谷,而此期幼虫主要为害顶尖。蕾铃外层的苞叶、花萼、花瓣和铃皮,因次生物质含量高,不利于幼虫生长,相反内部的花粉、子房和铃心,次生物质含量低,营养效果好,顶尖嫩叶则介于其间。类萜烯存在于组织的色素腺内,分布集中;单宁则散布于组织中,偏多分布于组织外层。结果证实,昆虫在寄主植物上的取食方式是昆虫对寄主体内变动的次生化学的一种适应,它使昆虫付出尽少代价获得最适营养效果。     

Language Differences in the Brain Network for Reading in Naturalistic Story Reading and Lexical Decision

Differences in how writing systems represent language raise important questions about whether there could be a universal functional architecture for reading across languages. In order to study potential language differences in the neural networks that support reading skill, we collected fMRI data from readers of alphabetic (English) and morpho-syllabic (Chinese) writing systems during two reading tasks. In one, participants read short stories under conditions that approximate natural reading, and in the other, participants decided whether individual stimuli were real words or not. Prior work comparing these two writing systems has overwhelmingly used meta-linguistic tasks, generally supporting the conclusion that the reading system is organized differently for skilled readers of Chinese and English. We observed that language differences in the reading network were greatly dependent on task. In lexical decision, a pattern consistent with prior research was observed in which the Middle Frontal Gyrus (MFG) and right Fusiform Gyrus (rFFG) were more active for Chinese than for English, whereas the posterior temporal sulcus was more active for English than for Chinese. We found a very different pattern of language effects in a naturalistic reading paradigm, during which significant differences were only observed in visual regions not typically considered specific to the reading network, and the middle temporal gyrus, which is thought to be important for direct mapping of orthography to semantics. Indeed, in areas that are often discussed as supporting distinct cognitive or linguistic functions between the two languages, we observed interaction. Specifically, language differences were most pronounced in MFG and rFFG during the lexical decision task, whereas no language differences were observed in these areas during silent reading of text for comprehension.     

High frequency of plant regeneration from hypocotyl explants of Brassica carinata A. Br.

An efficient tissue culture system for high frequency of plant regeneration from hypocotyl explants of Brassica carinata was developed via manipulation of culture medium and selection of explants. Explants grown on medium containing combinations of 2 mg l^-1 BA and 0.01 mg l^-1 NAA or 4 mg l^-1 kinetin and 0.01 mg l^-1 2,4-D regenerated shoots at 100% frequency. High frequency shoot regeneration occurred only from explants originating from 6 to 7-day-old but not younger or older seedlings. Explants showed higher regeneration capacity at the distal end than the proximal end, and the upper segment was more regenerative than the lower segment of hypocotyl. Regenerants were rooted on half-strength growth regulator-free medium, acclimatized and developed into normal, fertile plants.Abbreviations BA benzyladenine - 2-4-D 2,4-dichlorophenoxyacetic acid - NAA naphthaleneacetic acid - MS Murashige & Skoog     

Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes

Growing evidence supports the view that enzymatic activity results from a subtle interplay between chemical kinetics and molecular motions. A systematic analysis is performed here to delineate the type and level of coupling between catalysis and conformational mechanics. The dynamics of a set of 98 enzymes representative of different EC classes are analyzed with the Gaussian network model (GNM) and compared with experimental data. In more than 70% of the examined enzymes, the global hinge centers predicted by the GNM are found to be colocalized with the catalytic sites experimentally identified. Low translational mobility (< 7%) is observed for the catalytic residues, consistent with the fine-tuned design of enzymes to achieve precise mechanochemical activities. Ligand binding sites, while closely neighboring catalytic sites, enjoy a moderate flexibility to accommodate the ligand binding. These findings could serve as additional criteria for assessing drug binding residues and could lessen the computational burden of substrate docking searches.     

玉米转录因子zmCBF1的凝胶阻滞分析

凝胶阻滞试验是分析核酸与蛋白质相互作用的有效方法,在转录因子的功能分析中得到了广泛应用。以玉米转录因子zmCBF1与顺式元件CRT的结合为例,建立了用于转录因子分析的GRA/EMSA实验体系,并对其在应用中可能出现的问题进行了分析。     

EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences

Background  

Understanding gene regulatory networks has become one of the central research problems in bioinformatics. More than thirty algorithms have been proposed to identify DNA regulatory sites during the past thirty years. However, the prediction accuracy of these algorithms is still quite low. Ensemble algorithms have emerged as an effective strategy in bioinformatics for improving the prediction accuracy by exploiting the synergetic prediction capability of multiple algorithms.