甲型流感病毒DNA序列的长记忆ARFIMA模型

流感病毒分为三类:甲型(A型),乙型(B型),丙型(C型).在这三种类型中甲型(A型)流感病毒是最致命的流感病毒,对人类引起了严重疾病.本文对甲型流感病毒DNA序列建立了一种新的时间序列模型,即CGR(Chaos Game Representation)弧度序列.利用CGR坐标将甲流病毒DNA序列转换成CGR弧度序列,且引入长记忆ARFIMA模型去拟合此类序列,发现随机找来的10条H1N1序列,10条H3N2序列都具有长相关性且拟合很好,并且还发现这两种序列可以尝试用不同的ARFIMA模型去识别,其中H1 关键词： 甲型流感 时间序列模型 CGR (p')" href="#">ARFIMA(p d 模型')" href="#">q)模型     

血凝素蛋白及抗体相互作用的太赫兹光谱主成分分析

采用太赫兹时域光谱系统, 测量了7种不同浓度的血凝素蛋白及其与特异性抗体、无关抗体对照组反应的透射光谱, 采用光谱预处理及主成分分析法, 对多个太赫兹光谱参数进行分析. 结果显示, 主成分分析在数据降维的同时, 可以突出数据的主要变化趋势; 在原始变量相关性一致的条件下, 约化吸收截面与血凝素蛋白浓度之间表现出最强的相关性, 而介电损耗角正切值更适合于对血凝素蛋白-抗体复合物的聚类效果进行定性分析. 该研究表明主成分分析法对于太赫兹生物光谱的分析及进一步研究蛋白质的结构和功能具有重要的指导意义.     

Molecular basis of the structure and function of H1 hemagglutinin of influenza virus

Influenza virus hemagglutinin (HA) contains antigenic sites recognized by the host immune system, cleavage sites cleaved by host proteases, receptor binding sites attaching to sialyl receptors on the target cell, and fusion peptides mediating membrane fusion. Change in an amino acid(s) in these sites may affect the potential of virus infection and spread within and between hosts. Influenza viruses with H1 HA infect birds, pigs and humans and have caused two of the four pandemics in the past 100 years: 1918 pandemic that killed 21-50 million people and 2009 pandemic that caused more than 18,000 deaths. Understanding the relationship between antigenic structure and immune specificity, the receptor binding specificity in virus transmission, how the cleavage site controls pathogenicity, and how the fusion peptide causes membrane fusion for the entry of influenza virus into the host cell should provide information to find more effective ways to prevent and control influenza.     

Human immunodeficiency virus type 1 efficiently binds to human fetal astrocytes and induces neuroinflammatory responses independent of infection

Background  

HIV-1 infects human astrocytes in vitro and in vivo but the frequency of infected cells is low and its biological significance is unknown. In studies in vitro, recombinant gp120 alone can induce profound effects on astrocyte biology, suggesting that HIV-1 interaction with astrocytes and its functional consequences extend beyond the limited levels of infection in these cells. Here we determined the relative efficiencies of HIV-1 binding and infection in human fetal astrocytes (HFA), mainly at the single cell level, using HIV-1 tagged with green fluorescence protein (GFP)-Vpr fusion proteins, termed HIV-GFP, to detect virus binding and HIV-1 expressing Rev and NefGFP fusion proteins to detect productive infection.     

Using fluorescence measurement of zinc ions liberated from ZnS nanoparticle labels in bioassay for <Emphasis Type="Italic">Escherichia coli</Emphasis> O157:H7

In this study, an alternative approach using ZnS nanoparticle biolabels as fluorescence signal transducers is reported for the immunoassay of E. coli O157:H7 in tap water samples. Instead of measuring the fluorescence of ZnS nanoparticles in the assay, the fluorescence signal is generated through the binding of zinc ions released from nanoparticle labels with zinc-ion sensitive fluorescence indicator Fluozin-3. In the assay, ZnS nanoparticles around 50 nm in diameter were synthesized, bioconjugated, and applied for the detection of E. coli O157:H7. The assay shows a detection range over two orders of magnitude and a detection limit around 1000 colony-forming units (cfu) of E. coli O157:H7.     

Influenza virus pathogenicity regulated by host cellular proteases,cytokines and metabolites,and its therapeutic options

Influenza A virus (IAV) causes significant morbidity and mortality. The knowledge gained within the last decade on the pandemic IAV(H1N1)2009 improved our understanding not only of the viral pathogenicity but also the host cellular factors involved in the pathogenicity of multiorgan failure (MOF), such as cellular trypsin-type hemagglutinin (HA₀) processing proteases for viral multiplication, cytokine storm, metabolic disorders and energy crisis. The HA processing proteases in the airway and organs for all IAV known to date have been identified. Recently, a new concept on the pathogenicity of MOF, the “influenza virus–cytokine–trypsin” cycle, has been proposed involving up-regulation of trypsin through pro-inflammatory cytokines, and potentiation of viral multiplication in various organs. Furthermore, the relationship between causative factors has been summarized as the “influenza virus–cytokine–trypsin” cycle interconnected with the “metabolic disorders–cytokine” cycle. These cycles provide new treatment concepts for ATP crisis and MOF. This review discusses IAV pathogenicity on cellular proteases, cytokines, metabolites and therapeutic options.     

分子模拟在生物化学中的应用实例

分子模拟是一种描述和模拟分子和分子体系运动状态和性质的方法.随着电子计算机技术的飞速发展,分子模拟进入了一个前所未有的新时代.在此之前,人们只能通过机械模型和纸笔计算进行简单的分子模拟,现在通过利用电子计算机人们可以做更为复杂、更为全面的分子模拟.本文通过两个实例来简单阐述了分子模拟在生物化学中的应用.一则是通过模拟膦酰基氧化腈和丙乙腈的1,3偶极环加成反应过程,用密度泛函理论方法在B3LYP/6-31G(d,p)水平上解释了得到2∶1的加成产物的现象,来解释1,3偶极环加成反应得到2:1加成产物的现象.一则是通过结构生物信息学的方法建立H5N1高致病性禽流感病毒蛋白的三维结构,模拟其与一些药物分子的相互作用,研究H5N1的活性中心.     

Characterization of self-assembled monolayers (SAMs) on silicon substrate comparative with polymer substrate for Escherichia coli O157:H7 detection

This article presents the characterization of two substrates, silicon and polymer coated with gold, that are functionalized by mixed self-assembled monolayers (SAMs) in order to efficiently immobilize the anti-Escherichia coli O157:H7 polyclonal purified antibody.A biosurface functionalized by SAMs (self-assembled monolayers) technique has been developed. Immobilization of goat anti-E. coli O157:H7 antibody was performed by covalently bonding of thiolate mixed self-assembled monolayers (SAMs) realized on two substrates: polymer coated with gold and silicon coated with gold. The F(ab′)₂ fragments of the antibodies have been used for eliminating nonspecific bindings between the Fc portions of antibodies and the Fc receptor on cells. The properties of the monolayers and the biofilm formatted with attached antibody molecules were analyzed at each step using infrared spectroscopy (FTIR-ATR), atomic force microscopy (AFM), scanning electron microscopy (SEM) and cyclic voltammetry (CV). In our study the gold-coated silicon substrates approach yielded the best results.These experimental results revealed the necessity to investigate each stage of the immobilization process taking into account in the same time the factors that influence the chemistry of the surface and the further interactions as well and also provide a solid basis for further studies aiming at elaborating sensitive and specific immunosensor or a microarray for the detection of E. coli O157:H7.     

可用于现场快速检测的小型化多通道光谱测量系统

现有商用光谱仪虽然能够以极高的光谱分辨率对目标物进行测量与分析,但是存在系统复杂、体积庞大和价格昂贵等缺点,难以满足现场检测等应用需求.为了解决该问题,提出了可用于现场快速检测的小型化多通道光谱测量系统.相较于传统光谱仪,提出的小型化多通道光谱测量系统不仅结构紧凑而且光谱分辨率高;另外,多通道设计可以用于同时检测多个样...     

iHADAMAC: a complementary tool for sequential resonance assignment of globular and highly disordered proteins

An experiment, iHADAMAC, is presented that yields information on the amino-acid type of individual residues in a protein by editing the (1)H-(15)N correlations into seven different 2D spectra, each corresponding to a different class of amino-acid types. Amino-acid type discrimination is realized via a Hadamard encoding scheme based on four different spin manipulations as recently introduced in the context of the sequential HADAMAC experiment. Both sequential and intra-residue HADAMAC experiments yield highly complementary information that greatly facilitate resonance assignment of proteins with high frequency degeneracy, as demonstrated here for a 188-residue intrinsically disordered protein fragment of the hepatitis C virus protein NS5A.     

腐植酸增值尿素的多谱学分子结构表征

尿素生产过程中加入腐植酸生产腐植酸增值尿素,可以有效延缓尿素水解,提高作物产量与氮肥利用效率,然而在此过程中腐植酸(HA)与尿素(U)主要发生什么反应还未见报道。利用风化煤源HA生产含腐植酸5%, 10%及20%的腐植酸增值尿素(HAU5, HAU10及HAU20),采集并分析了HAU5, HAU10, HAU20及U的红外谱图及其二阶导数谱图,用XPS与O(1s)NEXAFS分别对HAU20, HA及U进行表征;通过无水乙醇溶解HAU20的方式去除了HAU20中的尿素,并利用FTIR与XPS对醇不溶物(UHA)进行表征。结果表明：(1)FTIR原谱图及二阶导数谱图表明,腐植酸增值尿素伯胺C—N振动强度低于普通尿素,且振动强度随着HA添加量的提高而降低,XPS N(1s)与O(1s)NEXAFS检测到HAU20中分别存在较多仲胺氮与非羰基氧,且FTIR发现UHA酰胺特征明显,表明腐植酸增值尿素制备过程中HA与U发生了反应。(2)XPS C(1s)表明,HAU20与UHA羧基碳比例少于HA, FTIR结果表明,UHA中不存在HA中检测到的羧酸C—O—H面内弯曲振动,羧基CO伸缩振动位置发...     

Spectroscopy properties of the amide group in valpromide and some derivatives with antiepileptic activity

Infrared spectra at 300 and 77 K and Raman spectra at 300 K of the valpromide (Vpd), N‐substituted derivatives, N‐ethylvalpromide (Etvpd), N‐isopropylvalpromide (Ipvpd) and the N,N‐disubstituted derivative, N,N‐dimethylvalpromide (Dmvpd) with antiepileptic activity, have been measured and analyzed with results derived from computational chemistry calculation. In agreement with theoretical predictions, experimental data indicate that while in Etvpd, Dmvpd and Ipvpd there are four different conformational co‐existing components (Etvpd: TTCG⁺, TCCG⁻, TTTC, G⁺G⁺C G⁺; Dmvpd: TTCC, G⁻TTA⁺, G⁺A⁻TC, G⁺A⁻C A⁺; Ipvpd: TTCT, TCCT, TCCC, G⁻ TTT) in the Vpd there are only three distinct stable conformations of C₁ symmetry group: TTC, TCT, G⁺G⁺T. Based on the accuracy of the B3LYP calculation, with the 6‐31 + G** basis set estimated by comparison between the predicted values of the vibrational modes and the available experimental data, we performed a structural and vibrational study of the amide group in the Vpd and their derivatives. We found that small nonplanarity deviations of C(O)N backbone induce significant changes on the structural and spectroscopic properties. These are not compatible with the decreasing of the resonance effect as it is produced when the twisting around the C(O) N increases. From the Natural Bond Orbital (NBO) analysis the existence of stabilizing electrostatic interactions of type C H···O/N and C H···H N/C, which induce significant structural changes and a complex electronic redistribution of charge on the π‐system in those structures becomes evident. We view this as a consequence of the filled electron density change Lewis‐type NBOs type lp_{O1, 2}, lp_N1, σ_{(C H)N acyl} and empty non‐Lewis NBOs type σ*_{(C H)N acyl}, σ*_{N H}. Copyright © 2009 John Wiley & Sons, Ltd.     

Biological interface study of HA/ZrO2 graded composite in a dog lumbar vertebra bone defect model

This study compared bony fusion in autologous bone grafting with HA/ZrO₂ graded composite in terms of mineral depositions, histological characteristics, and biomechanical properties of bonding interface. Twenty-four beagle dogs were established four places of bone defect in two adjacent lumbar vertebral bodies (L4 and L5) and were successively implanted with HA/ZrO₂ graded composite (group A), HA/ZrO₂ unilayer composite (group B), pure ZrO₂ (group C), and pure HA (group D). After operation, lumbar vertebral specimens were respectively harvested per time at week 6, 12, and 16. Then, the bony fusion interface was evaluated by fluorescence microscope and computer image analysis system to measure mineral apposition rates (MAR). Histological analysis of specimen was used to determine bone bonding rates (BBR) and possible foreign body reactions associated with each groups. And interface bonding force between implant and autogenous bone was quantified with biomechanical push-out test. Compared with other groups, group A led to significantly higher MAR from week 6 to 12 (p < 0.05). Histologically, new bony tissue and hyaline cartilage were seen around the HA/ZrO₂ graded composite, accompanied by mild chronic inflammation. And the BBR of HA/ZrO₂ graded composite were the highest (p < 0.05), while reaching (90.3 ± 3.8) % at week 16. Moreover, the biomechanical push-out tests revealed that the maximum interface shear strength of group A was respectively (2.64 ± 0.16) MPa, (2.95 ± 0.19) MPa, and (3.45 ± 0.23) MPa at week 6, 12, and 16, which all possessed significantly statistical differences with other three groups (p < 0.05).     

Theoretical study on the influence of different NˆN ligands on the electronic structures and optoelectronic properties of heteroleptic Iridium(III) complexes

DFT/TDDFT calculations were carried out to investigate the electronic structures, absorption and phosphorescence properties of a series of heteroleptic Ir(III) complexes consisting of two N-heterocyclic carbene ligands and a conjugated bicyclic N,N′-heteroaromatic (N?N) ligand. On the basis of the results reported herein, we attempt to explain the experimental observations according to which complex (mpmi)₂Ir(pybi) (1) [Hmpmi = 1-(4-tolyl)-3-methyl-imidazole; Hpybi = 2-(pyridin-2-yl)-1H-benzo[d]imidazole] emits green light with an extremely high-quantum phosphorescence efficiency (Φ _PL ) of 79.3%, while a relatively lower Φ _PL (only 11%) was measured for (fpmi)₂Ir(tfpypz) (2) [fpmi = 1-(4-fluorophenyl)-3-methylimdazolin-2-ylidene-C, C^2′; tfpypz = 2-(3-(trifluoromethyl)-1H-pyrazol-5-yl)pyridinato] emitting blue light by tuning the N?N ligands. Besides, we also designed (fpmi)₂Ir(pyN3) (3) [pyN3H = 2-(5-(trifluoromethyl)-2H-1,2,4-triazol-3-yl)pyridine] and (fpmi)₂Ir(pyN4) (4) [pyN4H = 2-(1H-tetrazol-5-yl)pyridine] to explore the influence of electron-withdrawing substituents on N?N ligands on the electronic and optical properties of these Ir(III) complexes. The results revealed that electron-withdrawing substituents can stabilise both HOMOs and LUMOs and induce HOMO–LUMO energy gap change. Moreover, the emission properties can be significantly tuned by introducing different N?N ligands. While new insights were gained on structural and electronic properties, the extremely high Φ _PL of 1 was found to be not inherent to spin-orbital coupling effects, but determined by its large transition dipole moment (μ_{S 1}) upon S ₀–S ₁ transition compared with that of 2. On the basis of these results, the designed complexes 3 and 4 are considered to be the promising candidates for blue-emitting phosphorescence materials with higher Φ _PL than the complex 2.     

FTIR investigation of the effects of ultra-strong static magnetic field on the secondary structures of protein in bacteria

Secondary structures of protein in Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) exposed to the ultra-strong static magnetic field (SMF) were investigated by Fourier transformation infrared spectroscopy (FTIR). Difference index D value of amide I (1600–1700 cm⁻¹) showed that the ultra-strong magnetic field had little impact on S. aureus, but had strong impact on E. coli. The results indicated that 3.46–9.92% of the disorder coils in the secondary structures of protein in E. coli were turned into α-helices under SMF while applying deconvolution and curve fitting to amide I. At the same time, intermolecular β-sheets transforming into intramolecular ones suggested that cohesion among protein molecules had been destroyed and intramolecular hydrogen bonds strengthened. All the differences among the compositions of protein’s secondary structures in E. coli were mostly due to the varying degrees of various proteins affected by the magnetic field. The results may provide new insights into the structural changes of proteins induced by the SMF.     

In situ Raman imaging of osteoblastic mineralization

Hydroxyapatite (HA) is synthesized at early stages of bone formation by osteoblasts. Nondestructive observation of early stages of osteoblastic mineralization provides crucial information for biological mechanism of bone formation. Raman microscopy serves as an ideal tool to observe the osteoblastic mineralization process because it shows the chemical information of the sample at a minimally invasive level. In addition, HA is a marker for osteoblastic mineralization, and HA Raman signal is strong enough to identify mineralized spots in osteoblasts. In this research, we visualized the distribution of HA in cultured mouse osteoblasts by Raman imaging and observed the location of the mineralized spots in the culture. We monitored HA Raman signal from osteoblast culture for 3 days after administrating the osteogenic differentiation medium and observed Raman signal associated with HA. We identified mineralized spots of KUSA‐A1 by Raman imaging constructed from the distribution of HA Raman signal. We successfully visualized the distribution of the mineralized spots in the culture of KUSA‐A1. We compared our Raman images with Alizarin red S staining assay, which was a conventional method to evaluate the mineralization process. Raman imaging of the KUSA‐A1 culture visualized the mineralized spots more accurately than Alizarin red S staining assay. Raman imaging of HA serves as a powerful tool to identify the mineralized spots in an in vitro culture of osteogenic lineage cells. Copyright © 2014 John Wiley & Sons, Ltd.     

Evaluation of cross-correlation effects and measurement of one-bond couplings in proteins with short transverse relaxation times

Various strategies are described and compared for measurement of one-bond J(NH) and J(NC') splittings in larger proteins. In order to evaluate the inherent resolution obtainable in the various experiments, relaxation rates of (15)N-(1)H(N) coupled and heteronuclear decoupled resonances were measured at 600- and 800-MHz field strengths for both perdeuterated and protonated proteins. A comparison of decay rates for the two (15)N-?H(N)? doublet components shows average ratios of 4.8 and 3.5 at 800- and 600-MHz (1)H frequency, respectively, in the perdeuterated proteins. For the protonated proteins these ratios are 3.2 (800 MHz) and 2.4 (600 MHz). Relative to the regular HSQC experiment, the enhancement in TROSY (15)N resolution is 2.6 (perdeuterated; 800 MHz), 2.0 (perdeuterated; 600 MHz), 2.1 (protonated; 800 MHz), and 1.7 (protonated; 600 MHz). For the (1)H dimension, the upfield (1)H(N)-?(15)N? component on average relaxes slower than the downfield (1)H(N)-?(15)N? component by a factor of 1.8 (perdeuterated; 800 MHz) and 1.6 (perdeuterated; 600 MHz). The poor resolution for the upfield (15)N-?(1)H? doublet component in slowly tumbling proteins makes it advantageous to derive the J(NH) splitting from the difference in frequency between the narrow downfield (15)N doublet component and either the (1)H-decoupled (15)N resonance or the peak position in an experiment which J-scales the frequency of the upfield doublet component but maintains some of the advantages of the TROSY experiment.     

Ion-molecule reactions at thermal energies

Ion-molecule reactions is a generic word for reactions involving ions (both positive and negative), radicals and stable neutrals. In this presentation, use of the flowing afterglow technique to study ion-molecule reactions at thermal energies is demonstrated using the examples of positive ion-negative ion mutual neutralization of molecular nitrogen ion (N ₂ ⁺ ) with F⁻ and the reaction of atomic nitrogen with SF _n (n=1 to 5) to form NF.     

Fetuin and osteocalcin interact with calcospherite formation during the calcification process of poly(2‐hydroxyethylmethacrylate) in vitro: a Raman microspectroscopic monitoring

Calcification is a complex process implying numerous proteins acting as nucleators, ion transporters and crystal growth regulators. Several proteins impair mineralization, such as fetuin and osteocalcin [(bone Gla protein), BGP]. We have evaluated their effets on the biomimetic calcification of carboxymethylated poly(2‐hydroxyethyl methacrylate). Polymer pellets were incubated in synthetic body fluid for 4 days at 37 °C to induce nucleation. They were transferred for 11 days in a fresh medium containing fetuin (5 mg/ml) or BGP (1 mg/ml) or a combination of boths. Pellets were examined by scanning and transmission electron microscopy. Detection of proteins was done by immunogold and Raman microspectroscopy. Calcospherites were dissolved, Ca and P were dosed. BGP did not modify the amount of Ca P or the Ca/P ratio, but the mean size of calcospherites was two times larger than controls. Fetuin reduced the number of calcospherites and the amount of Ca P but increased the Ca/P ratio. Ca P deposition was reduced on pellets incubated with both proteins, and calcospherites appeared considerably smaller. Immunogold and Raman spectroscopy identified both proteins adsorbed on hydroxyapatite (HA) tablets. Noncollagenous proteins control HA crystal growth in a different manner. The interaction between fetuin and BGP reduced the amount of calcified material deposited but also affected the morphology of the calcospherites. Copyright © 2009 John Wiley & Sons, Ltd.