基于贝叶斯网络的DNA序列剪接位点预测

采用基于贝叶斯网络的建模方法,预测真核生物DNA序列中的剪接位点．分别建立了供体位点和受体位点模型,并根据两种位点的生物学特性,对模型的拓扑结构和上下游节点的选择进行了优化．通过贝叶斯网络的最大似然学习算法求出模型参数后,利用10分组交互验证方法对测试数据进行剪接位点预测。结果显示,受体位点的平均预测准确率为92．5％,伪受体位点的平均预测准确率为94．0％,供体位点的平均预测准确率为92．3％,伪供体位点的平均预测准确率为93．5％,整体效果要好于基于使用独立和条件概率矩阵、以及隐Markov模型的预测方法．表明利用贝叶斯网络对剪接位点建模是预测剪接位点的一种有效手段．     

双向凝胶电泳分析小鼠子宫内膜胚泡着床点和着床旁组织蛋白质组

目的 :研究小鼠子宫内膜胚泡着床点和着床旁蛋白质表达图谱及其差异。方法 :用固相pH梯度双向凝胶电泳分离 5d .p .c .(dayspostcoitum)小鼠子宫内膜胚泡着床点和着床旁总蛋白 ,同时分离同龄未交配小鼠子宫内膜总蛋白 ,银染显色 ,PDQuest 2DE软件分析。结果 :图像分析测得三块胶的匹配率达 74 5 %以上 ,在等电点pI 3～ 1 0、分子量 1 4 4～ 75 4kDa范围内分离得未交配小鼠子宫内膜蛋白点大约 81 0个 ,受孕小鼠子宫内膜胚泡着床旁和着床点蛋白质点分别大约为 95 0个和 1 0 4 0个 ,其中至少 90个蛋白点在三种不同的生理状态间有 2倍以上的量变。结论 :在“着床窗口期” ,小鼠子宫内膜特别是着床位点内膜合成更多的蛋白质 ,以适宜胚泡成功地植入。     

Interaction of Divalent Metal Ions with Zn2+-Glycerophosphocholine Cholinephosphodiesterase from Ox Brain

The effect of divalent metal ions on the activity of glycerophosphocholine cholinephosphodiesterse from ox brain was examined. Zn²⁺- and Co²⁺-glycerophosphocholine cholinephosphodiesterases were prepared from the exposure of apoenzyme to Zn²⁺ and Co²⁺, respectively, and the properties of two metallo-phosphodiesterases were compared to those of native phosphodiesterase. Although two metallo-enzymes were similar in expressing Km value, optimum pH or sensitivity to Cu²⁺, they differed in the susceptibility to the inhibition by thiocholine or tellurite; while Co²⁺-phosphodiesterase was more sensitive to tellurites, Zn²⁺-phosphodiesterase was more susceptible to inhibition by thiocholine. In addition, Zn²⁺-phosphodiesterase was more thermo-stable than Co²⁺ enzyme. Separately, when properties of native phosphodiesterase were compared to those of each metallo-phosphodiesterase, native phosphodiesterase was found to be quite similar to Zn²⁺-phosphodiesterase in many respects. Even in thermo-stability, native enzyme resembled Zn²⁺-phosphodiesterase rather than Co²⁺-enzyme. Consistent with this, the stability of native phosphodiesterase was maintained in the presence of Zn²⁺, but not Co²⁺. Mn²⁺ was also as effective as Zn²⁺ in the stabilization of the enzyme. Noteworthy, the native enzyme was found to be inhibited competitively by Cu²⁺ with a Ki value of 20 M, and its inhibitory action was antagonized effectively by Zn²⁺ or Co²⁺. Also, choline, another competitive inhibitor of the enzyme, appeared to antagonize the inhibitory action of Cu²⁺. Taken together, it is suggested that there may be multiple binding sites for divalent metal ions in the molecule of glycerophosphocholine cholinephosphodiesterase.     

Electron microprobe analysis of elemental distribution in excavated human femurs

Elemental distributions have been determined for femur cross sections of eight individuals from the Gibson and Ledders Woodland sites. The analyses were obtained by x-ray fluorescence with a scanning electron microscope. Movement of an element from soil to bone should give rise to inhomogeneous distributions within the bone. We found that the distributions of zinc, strontium, and lead are homogeneous throughout the femur. In contrast, iron, aluminum, potassium, and manganese show clear buildup along the outer surface of the femur and sometimes along the inner (endosteal) surface, as the result of postmortem enrichment. The buildup penetrates 10-400 micron into the femur. The major elements calcium and sodium show homogeneous distributions, but considerable material could be lost by leaching (10-15%) without causing a palpable effect on the electron maps. Magnesium shows buildup on the outer edge of some samples. These results suggest that diagenetic contamination may exclude Fe, Al, K, Mn, and probably Mg from use as indicators of ancient data. The homogeneous distributions of Zn, Sr, and Pb suggest that these elements are not altered appreciably and may serve as useful dietary indicators.     

分支位点在真核基因受体位点识别中的作用

真核基因受体位点识别是剪接位点识别的一部分,也是基因识别中的重要环节,一直受到研究人员的关注。已有的研究结果显示受体位点的识别与分支位点有关,然而关于分支位点和受体位点识别的关系问题,目前还无人将其作为专门的问题予以深入研究。从受体位点识别出发,选取不同的受体位点序列长度,以神经网络为识别工具,对分支位点在受体位点识别中的作用做了深入研究和分析。实验结果表明,受体位点序列的特征信息集中在分支位点一例,因此分支位点在受体位点识别中具有重要作用。研究结果为受体位点识别问题中序列特征提取提供了依据。     

Implication by site-directed mutagenesis of Arg314 and Tyr316 in the coenzyme site of pig mitochondrial NADP-dependent isocitrate dehydrogenase

Sequence alignment of pig mitochondrial NADP-dependent isocitrate dehydrogenase with eukaryotic (human, rat, and yeast) and Escherichia coli isocitrate dehydrogenases reveals that Tyr316 is completely conserved and is equivalent to the E. coli Tyr345, which interacts with the 2'-phosphate of NADP in the crystal structure [Hurley et al., Biochemistry 30 (1991) 8671-8678]. Lys321 is also completely conserved in the five isocitrate dehydrogenases. Either an arginine or lysine residue is found among the enzymes from other species at the position corresponding to the pig enzyme Arg314. While Arg323 is not conserved among all species, its proximity to the coenzyme site makes it a good candidate for investigation. The importance of these four amino acids to the function of pig mitochondrial NADP-isocitrate dehydrogenase was studied by site-directed mutagenesis. Mutants (R314Q, Y316F, Y316L, K321Q, and R323Q) were generated by a megaprimer polymerase chain reaction method. Wild-type and mutant enzymes were expressed in E. coli and purified to homogeneity. All mutant and wild-type enzymes exhibited comparable molecular weights indicative of the dimeric enzyme. Mutations do not cause an appreciable change in enzyme secondary structure as revealed by circular dichroism measurements. The kinetic parameters (V(max) and K(M) values) of K321Q and R323Q are similar to those of wild-type, indicating that Lys321 and Arg323 are not involved in enzyme function. R314Q exhibits a 10-fold increase in K(M) for NADP as compared to that of wild-type, while they have comparable V(max) values. These results suggest that Arg314 contributes to the affinity between the enzyme and NADP. The hydroxyl group of Tyr316 is not required for enzyme function since Y316F exhibits similar kinetic parameters to those of wild-type. Y316L shows a 4-fold increase in K(M) for NADP and a decrease in V(max) as compared to wild-type, suggesting that the aromatic ring of the Tyr of isocitrate dehydrogenase contributes to the affinity for coenzyme, as well as to catalysis. The K(i) for NAD of R314Q, Y316F, and Y316L is comparable to that of wild-type, indicating that the Arg314 and Tyr316 may be located near the 2'-phosphate of enzyme-bound NADP.     

The universal mechanism for iron translocation to the ferroxidase site in ferritin, which is mediated by the well conserved transit site

Ferritins are ubiquitous iron storage proteins. Recently, we identified a novel metal-binding site, transit site, in the crystal structure of phytoferritin. To elucidate the function of the transit site in ferritin from other species, we prepared transit-site-deficient mutants of human H ferritin, E140A and E140Q, and their iron oxidation kinetics was analyzed. The initial velocities of iron oxidization were reduced in the variants, especially in E140Q. The crystal structure of E140Q showed that the side chain of the mutated Gln140 was fixed by a hydrogen bond, whereas that of native Glu140 was flexible. These results suggest that the conserved transit site also has a function to assist with the metal ion sequestration to the ferroxidase site in ferritins from vertebrates.     

Active sites of ligands and their receptors are made of common peptides that are also found elsewhere

The simultaneous emergence in evolution of a ligand and its receptor might have entailed their active sites being drawn from the pool of common oligopeptides. This was tested on the principal components of cell-matrix interaction: the RGD (Arg-Gly-Asp) site of matrix proteins and the EKKD (Gly-Lys-Lys-Asp) site of integrin cell-surface receptor. In the 32 diverse proteins scrutinized, which totalled 14,806 residues, there were 104 Arg-Gly dipeptides. Most common of the tripeptides beginning with Arg-Gly were Arg-Gly-Leu, Arg-Gly-Gly, and Arg-Gly-Asp; each was found in ten copies. RGD tripeptide was one of the commonest; the fortuitous presence of an RGD site was noted in two enzymes, fibrinogen, a pituitary hormone precursor, and a viral structural protein. The 32 proteins also contained 121 Lys-Lys dipeptides. Of the tetrapeptides centered by Lys-Lys, the commonest was Lys-Lys-Lys-Lys, in four copies. Second most common were Gly-Lys-Lys-Lys, Val-Lys-Lys-Leu, and Glu-Lys-Lys-Asp; each occurred in three copies. The fortuitous presence of an EKKD site was noted in three proteins—an intracellular transport protein, a pituitary hormone precursor and a protein of the cerebrospinal fluid. In most instances, protein-protein interaction between the fortuitously present active sites appears to bring about deleterious consequences. Occasionally, however, the fortuitous active site appears to confer a new function to a protein bearing it.     

Quadruplexes of human telomere dG3(TTAG3)3 sequences containing guanine abasic sites

This study was performed to evaluate how the loss of a guanine base affects the structure and stability of the three-tetrad G-quadruplex of 5′-dG₃(TTAG₃)₃, the basic quadruplex-forming unit of the human telomere DNA. None of the 12 possible abasic sites hindered the formation of quadruplexes, but all reduced the thermodynamic stability of the parent quadruplex in both NaCl and KCl. The base loss did not change the Na⁺-stabilized intramolecular antiparallel architecture, based on CD spectra, but held up the conformational change induced in dG₃(TTAG₃)₃ in physiological concentration of KCl. The reduced stability and the inhibited conformational transitions observed here in vitro for the first time may predict that unrepaired abasic sites in G-quadruplexes could lead to changes in the chromosome’s terminal protection in vivo.     

通过食谱分析探讨田螺山与梁王城遗址先民对渔业资源的利用

对渔业食用资源的利用是人类生业经济的重要方面,然而至今尚无专文介绍如何定量分析渔业食物资源在先民食物结构中所占的比例。本文采用利用同位素传递信号重建食谱(FRUITS)模型,以田螺山遗址与梁王城遗址已发表的先民和动植物稳定同位素数据为例,对先民食物结构中的多种食物资源比重进行分析。结果显示,梁王城遗址渔业资源在食谱中占5%~22%;田螺山遗址淡水渔业资源在食谱中占5%~20%,而海洋渔业资源在10%以下。     

Prediction of protein-mannose binding sites using random forest

Mannose is an abundant cell surface monosaccharide and has an important role in many biochemical processes. It binds to a great diversity of receptor proteins. In this study we have employed Random Forest for prediction of mannose binding sites. Mannosebinding site is taken to be a sphere around the centroid of the ligand and the sphere is subdivided into different layers and atom wise and residue wise features were extracted for each layer. The method achieves 95.59 % of accuracy using Random Forest with 10 fold cross validation. Prediction of mannose binding site analysis will be quite useful in drug design.     

俄罗斯马特盖奇克遗址、卡缅内洛卡遗址试掘简报

2017年8~9月,重庆市文化遗产研究院同俄罗斯科学院西伯利亚分院考古学与民族学研究所组成联合考古队,对西伯利亚两处旧石器时代遗址进行考古调查与试掘。通过调查与试掘,在叶尼塞河支流—阿巴坎河流域确认了一处旧石器时代晚期遗址—马特盖奇克遗址,该遗址石制品主要包括石核、石片和石器,原料主要是火山岩、燧石和石英岩。通过阶地比对,初步认为该遗址时代为旧石器时代晚期。另外,对库尔塔克卡缅内洛卡遗址的再次发掘出土了44件石制品,包含石核、石片和石器,原料主要是燧石、石英岩和火山岩。此次发掘进一步充实了该遗址的考古材料,也有利于进一步完善该遗址的考古年代学序列。     

Effect of calcium on sulfate uptake by barley roots

Abstract Sulfate uptake by excised roots of barley (Hordeum vulgare L.) was maximal in the presence of about 3x10^-3M CaCl₂. Kinetic studies contraindicate a stoichiometric binding of calcium to the carrier for sulfate, in contrast to findings of Cuppoletti and Segel (Biochemistry 14: 471–4718, 1975) for the filamentous fungus Penicillium notatum. In barley, calcium affects the K_m but not the V_max for sulfate uptake, presumably by altering the conformation and, thereby, the affinity of the carrier. Calcium also affects the transition site for sulfate uptake.     

血管生成素的结构与功能的研究进展

血管生成素(angiogenin,ANG)是一种有效的血管生成因子,是RNase超家族中惟一具有促血管生成能力的成员,也是目前已知的所有血管生成因子中独具核糖核酸酶活性的因子。ANG具有3个功能元件,即RNase活性中心、细胞表面结合位点及核定位序列。ANG参与血管生成的各个阶段,是其他血管生成因子诱导新血管生成的枢纽,其作用受到受体调节。在肿瘤的发生、发展及恶化过程中,ANG也具有非常重要的作用。通过对ANG促血管生成及细胞增殖机制的研究,为治疗肿瘤提供了多种靶点和途径。     

Identification of Catalytic and Substrate-binding Site Residues in Bacillus cereus ATCC7064 Oligo-1,6-glucosidase

Three active site residues (Asp199, Glu255, Asp329) and two substrate-binding site residues (His103, His328) of oligo-1,6-glucosidase (EC 3.2.1.10) from Bacillus cereus ATCC7064 were identified by site-directed mutagenesis. These residues were deduced from the X-ray crystallographic analysis and the comparison of the primary structure of the oligo-1,6-glucosidase with those of Saccharomyces carlsbergensis α-glucosidase, Aspergillus oryzae α-amylase and pig pancreatic α-amylase which act on α-1,4-glucosidic linkages. The distances between these putative residues of B. cereus oligo-1,6-glucosidase calculated from the X-ray analysis data closely resemble those of A. oryzae α-amylase and pig pancreatic α-amylase. A single mutation of Asp199→Asn, Glu255→Gln, or Asp329→Asn resulted in drastic reduction in activity, confirming that three residues are crucial for the reaction process of α-1,6-glucosidic bond cleavage. Thus, it is identified that the basic mechanism of oligo-1,6-glucosidase for the hydrolysis of α-1,6-glucosidic linkage is essentially the same as those of other amylolytic enzymes belonging to Family 13 (α-amylase family). On the other hand, mutations of histidine residues His103 and His328 resulted in pronounced dissimilarity in catalytic function. The mutation His328→Asn caused the essential loss in activity, while the mutation His103→Asn yielded a mutant enzyme that retained 59% of the κ₀/K_m of that for the wild-type enzyme. Since mutants of other α-amylases acting on α-1,4-glucosidic bond linkage lost most of their activity by the site-directed mutagenesis at their equivalent residues to His103 and His328, the retaining of activity by Hisl03→Asn mutation in B. cereus oligo-1,6-glucosidase revealed the distinguished role of His103 for the hydrolysis of α-1,6-glucosidic bond linkage.     

Discovery of receptor-ligand interfaces in the immunoglobulin superfamily

Cell-surface-anchored immunoglobulin superfamily (IgSF) proteins are widespread throughout the human proteome, forming crucial components of diverse biological processes including immunity, cell-cell adhesion, and carcinogenesis. IgSF proteins generally function through protein-protein interactions carried out between extracellular, membrane-bound proteins on adjacent cells, known as trans-binding interfaces. These protein-protein interactions constitute a class of pharmaceutical targets important in the treatment of autoimmune diseases, chronic infections, and cancer. A molecular-level understanding of IgSF protein-protein interactions would greatly benefit further drug development. A critical step toward this goal is the reliable identification of IgSF trans-binding interfaces. We propose a novel combination of structure and sequence information to identify trans-binding interfaces in IgSF proteins. We developed a structure-based binding interface prediction approach that can identify broad regions of the protein surface that encompass the binding interfaces and suggests that IgSF proteins possess binding supersites. These interfaces could theoretically be pinpointed using sequence-based conservation analysis, with performance approaching the theoretical upper limit of binding interface prediction accuracy, but achieving this in practice is limited by the current ability to identify an appropriate multiple sequence alignment for conservation analysis. However, an important contribution of combining the two orthogonal methods is that agreement between these approaches can estimate the reliability of the predictions. This approach was benchmarked on the set of 22 IgSF proteins with experimentally solved structures in complex with their ligands. Additionally, we provide structure-based predictions and reliability scores for the 62 IgSF proteins with known structure but yet uncharacterized binding interfaces.     

结直肠癌原发与配对转移肿瘤遗传异质性研究进展

结直肠癌(colorectal cancer, CRC)是我国常见的致死性肿瘤类型之一。根据体细胞突变谱预测抗EGFR单抗治疗疗效已成为转移性结直肠癌(metastatic colorectal cancer, mCRC)治疗的标准步骤。由于临床上转移样本难以获得,只能采用原发肿瘤替代进行检测。原发和配对转移肿瘤间的遗传异质性会导致原发灶取样无法代表转移灶突变谱。目前CRC原发和配对转移肿瘤间遗传异质性程度仍存在争议。本文就CRC原发和配对转移基因组谱的对比研究进行了综述,并讨论了原发与配对转移肿瘤遗传异质性形成的原因及应对策略。     

Two new species of Drosophila (Diptera,Drosophilidae) associated with inflorescences of Goeppertia monophylla (Marantaceae) in the city of São Paulo,state of São Paulo,Brazil

Two new Brazilian species of Drosophila (subgenus Drosophila) are described and illustrated: Drosophila asymmetrica sp. nov. and Drosophila peixotoi sp. nov. Both species were collected, and emerged, from inflorescences of Goeppertia monophylla (Marantaceae) in the urban Forest Reserve of the Instituto de Biociências da Universidade de São Paulo and their types will be deposited in the Museu de Zoologia da USP. The former species, which could not be assigned to any known group, has a conspicuously asymmetric aedeagus and a narrow oviscapt valve. The latter species belongs to the guarani group and is closely related to D. guaru, D. ornatifrons and D. subbadia, from which it can be distinguished by the presence of just one conspicuous large black spine at inner lower tip of cercus instead of two spines.     

Relationships Between the Catechol Substrate Binding Site and Amphetamine, Cocaine, and Mazindol Binding Sites in a Kinetic Model of the Striatal Transporter of Dopamine In Vitro

Abstract: Experiments were conducted to determine how (−)-cocaine and S (+)-amphetamine binding sites relate to each other and to the catechol substrate site on the striatal dopamine transporter (sDAT). In controls, m -tyramine and S (+)-amphetamine caused release of dopamine from intracellular stores at concentrations ≥12-fold those observed to inhibit inwardly directed sDAT activity for dopamine. In preparations from animals pretreated with reserpine, m -tyramine and S (+)-amphetamine caused release of preloaded dopamine at concentrations similar to those that inhibit inwardly directed sDAT activity. S (+)-Amphetamine and m -tyramine inhibited sDAT activity for dopamine by competing for a common binding site with dopamine and each other, suggesting that phenethylamines are substrate analogues at the plasmalemmal sDAT. (−)-Cocaine inhibited sDAT at a site separate from that for substrate analogues. This site is mutually interactive with the substrate site ( K _int = 583 n M ). Mazindol competitively inhibited sDAT at the substrate analogue binding site. The results with (−)-cocaine suggest that the (−)-cocaine binding site on sDAT is distinct from that of hydroxyphenethylamine substrates, reinforcing the notion that an antagonist for (−)-cocaine binding may be developed to block (−)-cocaine binding with minimal effects on dopamine transporter activity. However, a strategy of how to antagonize drugs of abuse acting as substrate analogues is still elusive.