In-situ FTIR study on adsorption and oxidation of native and thermally denatured calf thymus DNA at glassy carbon electrodes

In-situ Fourier transform infra-red (FTIR) spectra of native and thermally denatured calf thymus DNA (CT DNA) adsorbed and/or oxidized at a glassy carbon (GC) electrode surface are reported. The adsorption of native DNA occurs throughout the potential range (-0.2 similar to 1.3 V) studied, and the adsorbing state of DNA at electrode surface is changed from through the C=O band of bases and pyrimidine rings to through the C=O of cytosine and imidazole rings while the potential shifts negatively from 1.3 V to -0.2 V. An in-situ FTIR spectrum of native CT DNA adsorbed at GC electrode surface is similar to that of the dissolved DNA, indicating that the structure of CT DNA is not distorted while it is adsorbed at the GC electrode surface. In the potential range of -0.2 similar to 1.30 V, the temperature-denatured CT DNA is adsorbed at the electrode surface first, then undergoes electrochemical oxidation reaction and following that, diffuses away from the electrode surface. (C) 2001 Elsevier Science B.V. All rights reserved.

PCR-DGGE Fingerprinting Analysis of Plankton Communities and Its Relationship to Lake Trophic Status

Plankton communities in eight lakes of different trophic status near Yangtze, China were characterized by using denatured gradient gel electrophoresis (DGGE). Various water quality parameters were also measured at each collection site. Following extraction of DNA from plankton communities, 16S rRNA and 18S rRNA genes were amplified with specific primers for prokaryotes and eukaryotes, respectively; DNA profiles were developed by DGGE. The plankton community of each lake had its own distinct DNA profile. The total number of bands identified at 34 sampling stations ranged from 37 to 111. Both prokaryotes and eukaryotes displayed complex fingerprints composed of a large number of bands: 16 to 59 bands were obtained with the prokaryotic primer set; 21 to 52 bands for the eukaryotic primer set. The DGGE-patterns were analyzed in relation to water quality parameters by canonical correspondence analysis (CCA). Temperature, pH, alkalinity, and the concentration of COD, TP and TN were strongly correlated with the DGGE patterns. The parameters that demonstrated a strong correlation to the DGGE fingerprints of the plankton community differed among lakes, suggesting that differences in the DGGE fingerprints were due mainly to lake trophic status. Results of the present study suggest that PCR-DGGE fingerprinting is an effective and precise method of identifying changes to plankton community composition, and therefore could be a useful ecological tool for monitoring the response of aquatic ecosystems to environmental perturbations.

Isolation and identification of a novel WSSV nucleocapsid protein by cDNA phage display using an scFv antibody

In a previous study, a scFv phage display library against white spot syndrome virus (WSSV) was constructed and yielded a clone designated A I with conformational specificity against native but not denatured viral antigen. Although the clone A1 has been used successfully as a diagnostic antibody, its precise target antigen has not been elucidated. A different strategy was adopted involving the construction of a second T7 phage display library utilizing mRNA isolated from shrimp infected with WSSV. Following RT-PCR and T7 phage library construction, phages displaying the candidate epitope were selected with A I scFv. Since successive enrichment steps were not associated with an increased titer of the phages, enrichment after successive tests was confirmed by PCR resulting in the prefer-red selection of a specific DNA sequence encoding a novel nucleocapsid protein WSSV388. Immune electron microscopy revealed that WSSV388 is located on the nucleocapsid. This result demonstrated that unknown antigen could be identified by phage display using the epitope conformation dependent scFv. (c) 2006 Elsevier B.V. All rights reserved.

Real-Time Study of Genomic DNA Structural Changes upon Interaction with Small Molecules Using Dual-Polarization Interferometry

The structural changes of genomic DNA upon interaction with small molecules have been studied in real time using dual-polarization interferometry (DPI). Native or thermally denatured DNA was immobilized on the silicon oxynitride surface via a preadsorbed poly(ethylenimine) (PEI) layer. The mass loading was similar for both types of DNA, however, native DNA formed a looser and thicker layer due to its rigidity, unlike the more flexible denatured DNA, which mixed with PEI to form a denser and thinner layer. Ethidium bromide (EtBr), a classical intercalator, induced the large thickness decrease and density increase of native DNA (double-stranded), but a slight increase in both the thickness and density of denatured DNA (partial single-stranded).

Label free electrochemiluminescence protocol for sensitive DNA detection with a tris(2,2'-bipyridyl)ruthenium(II) modified electrode based on nucleic acid oxidation

Label free electrochemiluminescence (ECL) DNA detection based on catalytic guanine and adenine bases oxidation using tris(2,2'-bipyridyl)ruthenium(II) [Ru(bpy)(3)(2+)] modified glassy carbon (GC) electrode was demonstrated in this work. The modified GC electrode was prepared by casting carbon nanotubes (CNT)/Nafion/Ru(bpy)(3)(2+) composite film on the electrode surface. ECL signals of doublestranded DNA and their thermally denatured counterparts can be distinctly discriminated using cyclic voltammetry (CV) with a low concentration (3.04 x 10(-8) mol/L for Salmon Testes-DNA). Most importantly, sensitive single-base mismatch detection of p53 gene sequence segment was realized with 3.93 x 10(-10) mol/L employing CV stimulation (ECL signal of C/A mismatched DNA oligonucleotides was 1.5-fold higher than that of fully base-paired DNA oligonucleotides). Label free, high sensitivity and simplicity for single-base mismatch discrimination were the main advantages of the present ECL technique for DNA detection over the traditional DNA sensors.

Electrochemiluminescence-based DNA detection using guanine oxidation at electrostatic self-assembly of Ru(bpy)(3)(2+)-doped silica nanoparticles on indium tin oxide electrode

A Ru(bpy)(3)(2+)-doped silica nanoparticle-[Ru@Silica] modified indium tin oxide electrode was prepared by simple electrostatic self-assembly technique, and one-electron catalytic oxidation of guanine bases in double-strand and denatured DNA was realized using the electrochemiluminescence detection means.

Co-electrospun poly(lactide-co-glycolide), gelatin, and elastin blends for tissue engineering scaffolds

In this study, we describe composite scaffolds composed of synthetic and natural materials with physicochemical properties suitable for tissue engineering applications. Fibrous scaffolds were co-electrospun from a blend of a synthetic biodegradable polymer (poly(lactic-co-glycolic acid), PLGA, 10% solution) and two natural proteins, gelatin (denatured collagen, 8% solution) and (x-elastin (20% solution) at ratios of 3:1:2 and 2:2:2 (v/v/v). The resulting PLGA-gelatin-elastin (PGE) fibers were homogeneous in appearance with an average diameter of 380 80 mn, which was considerably smaller than fibers made under identical conditions from the starting materials (PLGA, 780 +/- 200 nm; gelatin, 447 +/- 1.23 nm; elastin, 1060 170 nm). Upon hydration, PGE fibers swelled to an average fiber diameter of 963 +/- 132 nm, but did not disintegrate. Importantly, PGE scaffolds were stable in an aqueous environment without crosslinking, and were more elastic than those made of pure elastin fibers. To investigate the cytocompatibility of PGE, we cultured H9c2 rat cardiac myoblasts and rat bone marrow stromal cells (BMSCs) on fibrous PGE scaffolds. We found that myoblasts grew equally as well or slightly better on the scaffolds than on tissue-culture plastic. Microscopic evaluation confirmed that myoblasts reached confluence on the scaffold surfaces while simultaneously growing into the scaffolds.

Direct electron transfer between hemoglobin and a glassy carbon electrode facilitated by lipid-protected gold nanoparticles

We synthesized a kind of gold nanoparticle protected by a synthetic lipid (didodecyidimethylammonium bromide, DDAB). With the help of these gold nanoparticles, hemoglobin can exhibit a direct electron transfer (DET) reaction. The formal potential locates at -169 mV vs. Ag/AgCl. Spectral data indicated the hemoglobin on the electrode was not denatured. The lipid-protected gold nanoparticles were very stable (for at least 8 months). Their average diameter is 6.42 nm. It is the first time to use monolayer-protected nanoparticles to realize the direct electrochemistry of protein.

Study on adsorption and oxidation of calf thymus DNA at glassy carbon electrode

The oxidation and adsorption of the temperature-denatured DNA at GC electrode are studied by differential pulse voltammetry and in situ FTIR spectroelectrochemistry. The temperature-denatured DNA is adsorbed and formed a DNA multilayer at electrode surface. The temperature-denatured DNA showing partly reversible process was first observed based on the reduction peaks appearing at negative scans and the reversible spectral change. The oxidation product of the temperature-denatured DNA can not diffuse away from the electrode surface easily due to the impediment of the DNA multilayer, so it can be partly reduced.

Scanning tunnelling microscopy observation of cytochrome-c denaturation induced by bromopyrogal red on highly oriented pyrolytic graphite

The denaturation of cytochrome-e (cyt-c) induced by bromopyrogal red (BPR) was studied by scanning tunnelling microscopy (STM) on the electrochemically pretreated highly oriented pyrolytic graphite (HOPG) surface. STM images reveal that denatured cyt-c molecules exist in variable states including aggregates, globular compact, partially unfolded and combined with BPR molecule. The apparently low image contrast of denatured cyt-c observed in this experiment comparing to that of native cyt-c molecules, and the relative low image contrast of the unfolded part comparing with the compact globular part, are ascribed to the unfavourable tunnelling paths for the conformational variations of denatured cyt-c molecules. (C) 1997 Elsevier Science B.V.

In situ electrochemical scanning tunnelling microscopy investigation of structure for horseradish peroxidase and its electrocatalytic property

Immobilization of protein molecules is a fundamental problem for scanning tunnelling microscopy (STM) measurements with high resolution. In this paper, an electrochemical method has been proved to be an effective way to fix native horseradish peroxidase (HRP) as well as inactivated HRP from electrolyte onto a highly oriented pyrolytic graphite (HOPG) surface. This preparation is suitable for both ex situ and in situ electrochemical STM (ECSTM) measurements. In situ STM has been successfully employed to observe totally different structures of HRP in three typical cases: (1) in situ ECSTM reveals an oval-shaped pattern for a single molecule in neutral buffer solution, which is in good agreement with the dimension determined as 6.2 x 4.3 x 1.2. nm(3) by ex situ STM for native HRP; (2) in situ ECSTM shows that the adsorbed HRP molecules on HOPG in a denatured environment exhibit swelling globes at the beginning and then change into a V-shaped pattern after 30 min; (3) in situ ECSTM reveals a black hole in every ellipsoidal sphere for inactivated HRP in strong alkali solution. The cyclic voltammetry results indicate that the adsorbed native HRP can directly catalyse the reduction of hydrogen peroxide, demonstrating that a direct electron transfer reduction occurred between the enzyme and HOPG electrode, whereas the corresponding cyclic voltammograms for denatured HRP and inactivated HRP adsorbed on HOPG electrodes indicate a lack of ability to catalyse H2O2 reduction, which confirms that the HRP molecules lost their biological activity. Obviously, electrochemical results powerfully support in situ STM observations.

The direct electrochemistry of cryo-hydrogel immobilized myoglobin at a glassy carbon electrode

A cryo-hydrogel membrane (CHM) immobilized at a glassy carbon (GC) electrode is reported for the direct electron transfer of redox proteins. The most attractive characteristics of this CHM were its hydrophilic micro-environment for incorporated proteins to retain their activities, its high ability for protection against interference of denatured and adsorbed proteins at the electrode, its potential applications for various proteins or enzymes, as well as its high mechanical strength and thermal stability. A clear well developed and stable redox wave was obtained for commercially available horse heart myoglobin without further purification, giving a peak to peak separation Delta E(p) = 93 mV at 5 mV s(-1) and the formal electrode potential E(0)' = -0.158 V (vs. Ag/AgCl). The formal heterogeneous electron transfer rate constant was calculated as k(0)' = 5.7 X 10(-4) cm s(-1) at pH 6.5, showing rapid electron transfer was achieved. The pH controlled conformational equilibria, acid state --> natural state --> basic I state --> basic II state, of myoglobin at the CHM GC electrode in the pH range 0-13.8 were also observed and are discussed in detail.

Factors that effect antioxidant activity of C-phycocyanins from Spirulina platensis

Currently, antioxidants are added in the human diet to prevent free radical-induced cell damage, and there has been an explosive interest in the use of antioxidant nutritional supplements. The effects of different factors on the antioxidant activity of phycocyanins (PCs) were studied. The results showed that PCs generated hydroxyl radicals in the light, while scavenging them in the dark. When PCs were denatured by sodium dodecyl sulfate, urea and in alkaline condition, their ability to generate hydroxyl radicals disappeared and that of scavenging them greatly increased. This showed that the phycobilin moiety is the main part of PC involved in scavenging hydroxyl radicals. Trypsin hydrolysis of PCs showed that the apoprotein portion of the molecule also made a significant contribution to the antioxidant activity.

栉孔扇贝大规模死亡病原学研究

用平板画线法从患病栉孔扇贝（Chlamys farreri）体内分离到了一种原核生物（简称QDP）。QDP可以在改进的液体培养基MEM（含2.2%NaCl，5%小牛血清）和脑心浸液（含2.2% NaCl）中生长；菌落在显微镜下（150×）为无色、透明的小点状；革兰氏染色阴性；菌体为圆形或近似圆形。QDP在发育过程中有两种状态，一种为未成熟阶段，直径小于100nm；另一种为成熟阶段，直径变化很大，最小约60nm，最大可达4µm以上。较小的个体有拟核、核糖体和新月状的空泡，未见细胞壁；较大的个体有细胞壁，胞内大部分被空泡充满，未见拟核和核糖体。栉孔扇贝组织超簿切片电镜观查证实QDP的存在。QDP的密度随着生长发育时间的不同而有所变化，繁殖高峰期密度较大。 建立了密度梯度离心结合滤膜过滤分离技术，优化人工培养条件。最适生长温度为23℃，最适生长pH值为7.4，最适生长盐度相当于细胞培养液所需的盐浓度（0.85%NaCl）。 提取的QDP核酸能被RNase A 降解，且没有检测到DNA。以PCR、RT-PCR扩增其16SrRNA基因序列片段，PCR反应没有扩增出扩增子，而RT-PCR则扩增出了16S rRNA基因序列片段，经测定其序列全长度为1430bp，经与GENEBANK中的16S rRNA片段比较分析，与6种不同科的微生物的同源率最高的为95%-95.47%。 采用温度梯度和病原浓度梯度回归感染实验方法，较为系统地研究了QDP的致病性。研究结果表明：QDP对栉孔扇贝有强烈的致病作用，高温（23℃以上）是其致病的必要条件，证实DQP是栉孔扇贝大规模死亡的病原体之一。