Modeling the spontaneous initiation of the polymerization of methyl methacrylate

The mechanism of the spontaneous initiation of the polymerization of methyl methacrylate (MMA) was investigated theoretically. The six minimum energy paths (MEP) of the possible reactions were calculated using the density functional theory (DFT) in conjunction with the B3LYP functional and 6-31G* basis set. The Diels-Alder initiation mechanism (path (I) and path (II)) with remarkably high energy barriers is not applicable to MMA. Four favorable paths were found (path (III), path (IV), path (V) and path (VI)), which are supporting the Flory mechanism. Path (V) has the lowest active energy. Therefore this path is considered as the main path for the spontaneous polymerization of MMA. Figure The mechanism of the spontaneous initiation of the polymerization of methyl methacrylate (MMA) was investigated theoretically. The six minimum energy paths (MEP) of the possible reactions were calculated using the density functional theory (DFT) in conjunction with the B3LYP functional and 6-31G* basis set.     

Simulation, construction and characterization of a multi-functional thrombolytic agent with anti-thrombosis activity

Prourokinase (scu-PA), a thrombolytic agent, was inserted between Gly118 and Ile119 with foreign antithrombosis functional motif (Lys-Gly-Asp-Trp-motif) to construct a multi-functional chimeric molecule. The molecular model of a chimera was simulated and predicted. The recombinant chimeric protein was expressed by the baculovirus-insect cell expression system and purified by affinity chromatography. The physico-chemical characteristics of the chimeric molecule were assayed. The thrombolytic activity was determined to be 90000 IU/mg of fibrinolytic special activity by the fibrin-plate method. The anti-thrombosis activities were also assayed with IC₅₀ of 9.6 μM by an inhibition test of ADP-induced platelet aggregation.     

Dispersal failure contributes to plant losses in NW Europe

The ongoing decline of many plant species in Northwest Europe indicates that traditional conservation measures to improve the habitat quality, although useful, are not enough to halt diversity losses. Using recent databases, we show for the first time that differences between species in adaptations to various dispersal vectors, in combination with changes in the availability of these vectors, contribute significantly to explaining losses in plant diversity in Northwest Europe in the 20th century. Species with water- or fur-assisted dispersal are over-represented among declining species, while others (wind- or bird-assisted dispersal) are under-represented. Our analysis indicates that the 'colonization deficit' due to a degraded dispersal infrastructure is no less important in explaining plant diversity losses than the more commonly accepted effect of eutrophication and associated niche-based processes. Our findings call for measures that aim to restore the dispersal infrastructure across entire regions and that go beyond current conservation practices.     

Identification of C4 responsive genes in the facultative C4 plant Hydrilla verticillata

The aquatic monocot Hydrilla verticillata (L.f.) Royle is a well-documented facultative C₄ NADP-malic enzyme species in which the C₄ and Calvin cycles operate in the same cell with the specific carboxylases confined to the cytosol and chloroplast, respectively. Several key components had already been characterized at the molecular level, thus the purpose of this study was to begin to identify other, less obvious, elements that may be necessary for a functional single-cell C₄ system. Using differential display, mRNA populations from C₃ and C₄ H. verticillata leaves were screened and expression profiles compared. From this study, 65 clones were isolated and subjected to a customized macroarray analysis; 25 clones were found to be upregulated in C₄ leaves. Northern and semi-quantitative RT-PCR analyses were used for confirmation. From these screenings, 13 C₄ upregulated genes were identified. Among these one encoded a previously recognized C₄ phosphoenolpyruvate carboxylase, and two encoded distinct pyruvate orthophosphate dikinase isoforms, new findings for H. verticillata. Genes that encode a transporter, an aminotransferase and two chaperonins were also upregulated. Twelve false positives, mostly housekeeping genes, were determined from the Northern/semi-quantitative RT-PCR analyses. Sequence data obtained in this study are listed in the dbEST database (DV216698 to DV216767). As a single-cell C₄ system that lacks Kranz anatomy, a better understanding of how H. verticillata operates may facilitate the design of a transgenic C₄ system in a C₃ crop species.Srinath K. Rao and Hiroshi Fukayama contributed equally to this study.     

芜菁类黄酮3′-羟化酶基因的功能鉴定及启动子初步分析

类黄酮3′-羟化酶（Flavonoid 3′-hydroxylase,F3′H）是细胞色素P450单加氧酶,在花青素合成途径中催化二氢山奈酚生成二氢槲皮素,进而形成矢车菊色素。利用津田芜菁BrF3′H1和赤丸芜菁BrF3′H2基因构建过量表达载体后遗传转化烟草,转基因植株的花色加深。通过染色体步移法克隆了BrF3′H1和BrF3′H2基因上游846和851 bp的启动子序列。生物信息学分析表明,BrF3′H1P和BrF3′H2P均包含TATA box、CAAT box、光调控元件、MRE、ABRE、ATGCAAAT-motif、ERE、O2-site、RY-element、LTR等多个顺式作用元件;二者的核苷酸序列在7个位点存在差异。利用BrF3′H1P和BrF3′H2P序列替换pCAMBIA1301植物表达载体的35S启动子后遗传转化烟草。GUS组织化学染色结果表明,BrF3′H1P和BrF3′H2P序列均能驱动GUS基因表达。通过PCR方法获得了BrF3′H1P和BrF3′H2P的一系列缺失片段,融合GUS基因后转化烟草。染色结果显示,BrF3′H1P和BrF3′H2P系列缺失片段均具有起始GUS基因表达的活性。BrF3′H1和BrF3′H2基因的功能鉴定及启动子的初步分析将为揭示津田芜菁和赤丸芜菁F3′H基因的光诱导表达调控机理奠定研究基础。     

淮南采煤塌陷湖泊浮游植物功能群的季节演替及其驱动因子

在淮南矿区设置潘谢潘集站(PXPJ)、潘谢顾桥站(PXGQ)和潘谢谢桥站(PXXQ)等3个塌陷湖泊站点,分别代表3种典型矿区湖泊水文生态条件,于2013—2014年分4个季度采样并分析了3个湖泊浮游植物功能群组成、季节演替规律及其与环境和生物因子的关系。结果显示,3个湖泊的浮游植物种类可归入16个功能群,其主要优势功能群反映了小型富营养化湖泊水体的生境特征。PXPJ春季S1、X2和Y为主要优势功能群,分别以伪鱼腥藻(Pseudanabaena sp.)、具尾蓝隐藻(Chroomonas caudata Geitler)和卵形隐藻(Cryptomonas ovata Ehr.)为代表种属,随后3个季节C为第1优势功能群,以链形小环藻(Cyclotella catenata)为代表物种。PXGQ春夏秋3个季节中均以伪鱼腥藻为代表的S1功能群占绝对优势地位,冬季向C(以链形小环藻为代表)和D(以尖针杆藻为代表)为主的功能群演替。PXXQ春季X2和Y为主要优势功能群,分别以具尾蓝隐藻和卵形隐藻为代表,夏秋季以伪鱼腥藻为代表的S1功能群占据优势地位,冬季向C(链形小环藻为代表)和E(长锥形锥囊藻为代表)功能群为主的群落结构演替。水温和光照条件是驱动淮南采煤塌陷湖泊浮游植物功能群季节演替的关键环境因子,而营养盐和生物因素是导致3个湖泊功能群组成差异的重要原因。     

Enhanced performance in prediction of protein active sites with THEMATICS and support vector machines

Theoretical microscopic titration curves (THEMATICS) is a computational method for the identification of active sites in proteins through deviations in computed titration behavior of ionizable residues. While the sensitivity to catalytic sites is high, the previously reported sensitivity to catalytic residues was not as high, about 50%. Here THEMATICS is combined with support vector machines (SVM) to improve sensitivity for catalytic residue prediction from protein 3D structure alone. For a test set of 64 proteins taken from the Catalytic Site Atlas (CSA), the average recall rate for annotated catalytic residues is 61%; good precision is maintained selecting only 4% of all residues. The average false positive rate, using the CSA annotations is only 3.2%, far lower than other 3D-structure-based methods. THEMATICS-SVM returns higher precision, lower false positive rate, and better overall performance, compared with other 3D-structure-based methods. Comparison is also made with the latest machine learning methods that are based on both sequence alignments and 3D structures. For annotated sets of well-characterized enzymes, THEMATICS-SVM performance compares very favorably with methods that utilize sequence homology. However, since THEMATICS depends only on the 3D structure of the query protein, no decline in performance is expected when applied to novel folds, proteins with few sequence homologues, or even orphan sequences. An extension of the method to predict non-ionizable catalytic residues is also presented. THEMATICS-SVM predicts a local network of ionizable residues with strong interactions between protonation events; this appears to be a special feature of enzyme active sites.