Design principles of a bacterial signalling network

Cellular biochemical networks have to function in a noisy environment using imperfect components. In particular, networks involved in gene regulation or signal transduction allow only for small output tolerances, and the underlying network structures can be expected to have undergone evolution for inherent robustness against perturbations. Here we combine theoretical and experimental analyses to investigate an optimal design for the signalling network of bacterial chemotaxis, one of the most thoroughly studied signalling networks in biology. We experimentally determine the extent of intercellular variations in the expression levels of chemotaxis proteins and use computer simulations to quantify the robustness of several hypothetical chemotaxis pathway topologies to such gene expression noise. We demonstrate that among these topologies the experimentally established chemotaxis network of Escherichia coli has the smallest sufficiently robust network structure, allowing accurate chemotactic response for almost all individuals within a population. Our results suggest that this pathway has evolved to show an optimal chemotactic performance while minimizing the cost of resources associated with high levels of protein expression. Moreover, the underlying topological design principles compensating for intercellular variations seem to be highly conserved among bacterial chemosensory systems.     

Detection in vivo of protein-DNA interactions within the lac operon of Escherichia coli

Studies of the sequence-specific binding of proteins to DNA have so far relied on in vitro experiments using cloned restriction fragments containing the relevant DNA sequences. We have applied the genomic sequencing technique of Church and Gilbert to show that the interactions observed in vitro occur in vivo. We use this approach to study the binding of regulatory proteins to the lac operon in vivo and detect changes in the reactivity (inhibition or enhancement) of guanines to methylation by dimethyl sulphate caused by the proximity of proteins to the N-7 atom of these guanines. We can detect the simultaneous binding of the catobolite gene activator protein (CAP) and the Lac repressor to their specific recognition sequences, and following induction of the lac operon we observe effects that are related to RNA polymerase binding or RNA elongation. We have successfully used oligonucleotide probes as short as 17 bases to display genomic sequence.     

乳糖诱导mIL-9蛋白高效表达研究

研究了乳糖诱导重组工程菌pET(32a+)-rmIL-9/BL21(DE3)高效表达rmIL-9融合蛋白的实验条件,探讨规模化生产rmIL-9的可行性.分别考察乳糖诱导时机、诱导浓度、诱导时间等参数对rmIL-9融合蛋白表达的影响,并通过正交实验,筛选最佳的乳糖诱导条件.结果显示,对于rmIL-9融合蛋白,乳糖作为诱导剂可达到良好的诱导效果,诱导产物的表达量可优于IPTG诱导产物.最优诱导表达条件为:当菌液OD600值为1时,添加终浓度为5g/L的乳糖,诱导9 h可以高效表达目的蛋白.实验表明,采用乳糖可以诱导rmIL-9融合蛋白基因的高效表达,此为动物实验评价rmIL-9治疗黑色素瘤提供了前期基础.     

人工酶与定向进化的前沿与挑战

 定向进化是在实验室环境中，在分子水平上模拟进化过程，得到具有期望特征的蛋白质的方法，目前已成为蛋白质设计改造的重要方法。定向进化不仅可以用于天然蛋白质的改造，也可以通过改造现有的酶，使其具有新的催化活性，从而构建人工酶。本文重点介绍工业生物催化、纳米酶设计和光催化3个方向的前沿成果，并讨论人工酶与定向进化领域存在的挑战和问题。     

Protein dispensability and rate of evolution.

If protein evolution is due in large part to slightly deleterious amino acid substitutions, then the rate of evolution should be greater in proteins that contribute less to individual fitness. The rationale for this prediction is that relatively dispensable proteins should be subject to weaker purifying selection, and should therefore accumulate mildly deleterious substitutions more rapidly. Although this argument was presented over twenty years ago, and is fundamental to many applications of evolutionary theory, the prediction has proved difficult to confirm. In fact, a recent study showed that essential mouse genes do not evolve more slowly than non-essential ones. Thus, although a variety of factors influencing the rate of protein evolution have been supported by extensive sequence analysis, the relationship between protein dispensability and evolutionary rate has remained unconfirmed. Here we use the results from a highly parallel growth assay of single gene deletions in yeast to assess protein dispensability, which we relate to evolutionary rate estimates that are based on comparisons of sequences drawn from twenty-one fully annotated genomes. Our analysis reveals a highly significant relationship between protein dispensability and evolutionary rate, and explains why this relationship is not detectable by categorical comparison of essential versus non-essential proteins. The relationship is highly conserved, so that protein dispensability in yeast is also predictive of evolutionary rate in a nematode worm.     

工业企业材料订货优化决策支持系统研究

在工业企业的产品成本中,材料成本占据着相当大的比重。如何根据生产需要对材料的订货批量、订货批次及订货周期进行决策,将影响到企业的产品成本和经济效益。这里对运用计算机的特有功能,结合材料存储优化决策原理和模型建立的订货优化决策支持系统的原理和应用进行了阐述。     

苜蓿银纹夜蛾核型多角体病毒Gp64蛋白的优化表达

研究培养基成份、pH值、接种量、诱导温度、诱导时间及诱导剂浓度等条件对苜蓿银纹夜蛾核型多角体病毒Gp64蛋白在大肠杆菌BL21(DE3)中表达水平的影响.SDS-PAGE电泳分析结果表明:在37℃的LB培养基中培养3h,用终浓度为0.3mmoL/L的IPTG于30℃诱导5h时表达水平最高.苜蓿银纹夜蛾核型多角体病毒Gp64重组蛋白在大肠杆菌中的优化表达为深度解析其在病毒感染过程中的功能奠定了基础.     

近红外光谱技术对液态奶制品中乳糖、脂肪及蛋白质的定量检测

用InfraXact多功能近红外分析仪和正交实验设计,研究了不同预处理和校正方法对建模效果的影响,建立了液态奶制嘉中脂肪、乳糖和蛋白质质量含量的定标模型。利用目标函数法对模型进行评定,并对选出的最优模型的适用性进行验证．结果表明,最优模型对糖、脂肪和蛋白质的相对标准偏差分别为4．12％,7．04％,9．61％,相对误差分别为2．82,6．28,2．72．正交实验方法能综合考虑不同预处理方法和校正方法对模型建立的影响．近红外光谱分析法能够实现对牛奶中脂肪、乳糖和蛋白质质量含量进行快速、无损的定量检测．     

A combined algorithm for genome-wide prediction of protein function

The availability of over 20 fully sequenced genomes has driven the development of new methods to find protein function and interactions. Here we group proteins by correlated evolution, correlated messenger RNA expression patterns and patterns of domain fusion to determine functional relationships among the 6,217 proteins of the yeast Saccharomyces cerevisiae. Using these methods, we discover over 93,000 pairwise links between functionally related yeast proteins. Links between characterized and uncharacterized proteins allow a general function to be assigned to more than half of the 2,557 previously uncharacterized yeast proteins. Examples of functional links are given for a protein family of previously unknown function, a protein whose human homologues are implicated in colon cancer and the yeast prion Sup35.     

Neutron scattering studies of lac repressor

The lac repressor, a tetrameric protein of identical subunits [molecular weight (MW) 4 x 38,500], interacts specifically with the lac operator, preventing the expression of the structural genes of the lac operon. The presence of an inducer (such as isopropyl-beta-D-thiogalactoside; IPTG) which binds to the repressor, prevents operator binding by lowering the association constant by a factor of 10(3) (ref. 3). Genetic and biochemical analysis have shown that the major part--if not all--of the binding site for the lac operator is located in the 60 N-terminal residues of the protein. In certain conditions, limited trypsinolysis of the protein yields four N-terminal 'headpieces' each containing 51 or 59 residues, and a tetrameric core with full inducer binding activity. It was shown recently that this headpiece is able to bind nucleic acids, and interacts with the lac operator, giving the same pattern of sensitivity with respect to the methylation of the bases as does the intact repressor. We are studying the interaction of lac repressor with DNA by neutron scattering using contrast variation and discuss here measurements on the protein, its tryptic core and their complexes with IPTG. Our results demonstrate that the headpieces are located far (67 +/- 10 A) from the centre of mass of a somewhat elongated core, and that the inducer does not significantly change the radius of gyration of the protein.     

Sequence homology between Lac and Gal repressors and three sugar-binding periplasmic proteins

Many proteins consist of several independent folding units or domains, each specifying a different function. Repressor proteins such as Lac or lambda cI carry small N-terminal domains which recognize DNA sequences and larger C-terminal domains which are required for effector recognition and/or oligomerization. The native periplasmic metabolite-binding proteins consist of short membrane-recognizing signal sequences and larger C-terminal metabolite-binding domains which also recognize membrane-bound proteins involved in transport and chemotaxis. The DNA-recognizing domains of many repressors are homologous, as are the sugar-recognizing periplasmic proteins. Here I demonstrate that the sugar-binding domains of the Lac and Gal repressors are homologous with the sugar-binding domains of three periplasmic proteins.     

城市建筑工程造价效益分配优化控制技术

传统工程造价效益分配控制技术忽略了工程造价与质量、效率的关系,只考虑工程造价效益分配,不能满足建筑质量与施工效率要求。为此,提出一种新的城市建筑工程造价效益分配优化控制技术。分析了工程造价效益分配控制原理。根据Kalman方程生成质量量化状态方程,实现质量量化调度。按照自回归理论对工程造价效益主要变量进行统计,获取效率测度模型回归结果。依据城市建筑工程造价效益分配控制变量,完成保证高质量情况下工程造价成本建模;将材料费与人工费看作经济性指标,对效益型指标与经济性指标进行关联性分解,获取工程质量-效率-造价效益分配控制模型。将工程造价效益对偶收益看作线性博弈过程,对其进行联合求解,获取最优决策函数,联合求解选用遗传算法。实验结果表明,所提技术贴合度与成熟度高,在保证质量与效率的情况下,工程造价效益分配控制结果较好。     

φ10启动子控制下大肠杆菌中rhNTA表达的乳糖诱导

采用乳糖作为诱导物,对φ启动子控制下重组蛋白rhNTA（a new thrombolytic agent）在大肠杆菌中的表达进行研究,结果为培养12h（诱导6h）后湿菌体重量86．0－100．2g/L、目标蛋白占细胞总蛋白的40％－50％。研究了关键基质组分、乳糖诱导等对表达的作用。结果表明,基础料和补充氮源中酵母膏的比例、诱导时机和乳糖流加方式等对表达量的提高有明显的影响。实验显示,采用乳糖诱导时重组蛋白的可溶性部分占有较大的比例。     

Functional profiling of the Saccharomyces cerevisiae genome

Determining the effect of gene deletion is a fundamental approach to understanding gene function. Conventional genetic screens exhibit biases, and genes contributing to a phenotype are often missed. We systematically constructed a nearly complete collection of gene-deletion mutants (96% of annotated open reading frames, or ORFs) of the yeast Saccharomyces cerevisiae. DNA sequences dubbed 'molecular bar codes' uniquely identify each strain, enabling their growth to be analysed in parallel and the fitness contribution of each gene to be quantitatively assessed by hybridization to high-density oligonucleotide arrays. We show that previously known and new genes are necessary for optimal growth under six well-studied conditions: high salt, sorbitol, galactose, pH 8, minimal medium and nystatin treatment. Less than 7% of genes that exhibit a significant increase in messenger RNA expression are also required for optimal growth in four of the tested conditions. Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics.     

Growth regulation of a cellular tumour antigen, p53, in nontransformed cells

Many transformed cells in culture have been found to express elevated levels of a cellular tumour antigen, termed p53. This protein has also been implicated in the regulation of cellular growth. For these reasons experiments were designed to examine the expression of p53 as quiescent cultures of nontransformed 3T3 fibroblasts were stimulated to reenter the cell cycle. Synchronous populations of cells were obtained by releasing a culture from density-dependent inhibition of growth with the addition of fresh serum. Steady-state levels of p53 protein and mRNA were measured as a function of time after addition of serum to quiescent cultures and the rate of synthesis of p53 protein was analysed at a number of time points. The results, reported here, demonstrate an increase in the synthesis and steady-state levels of p53 protein and mRNA prior to DNA synthesis in late G1, and suggest a role for p53 in the progression of cells from a growth-arrested state to an actively dividing state.     

基于PSO的多级反馈放大器的设计与仿真

采用粒子群优化算法,在高电压增益、低输出电阻的要求下,选择电压增益与输出电阻的比作为适应度函数,对两级直接耦合负反馈放大电路电阻的参数进行优化设计.对结果的电阻值经EWB软件仿真,闭环电压增益与优化理论计算的平均误差为1.65%,说明理论的正确性.优化结果显示,输出电阻总是趋于设定值的底限,以使适应度函数为最大,符合算法的要求.同时根据对放大器指标的不同需求,可以改变适应度函数,找到的最好效果.