Analysis of specific gene by integration of isothermal amplification and electrophoresis on poly(methyl methacrylate) microchips

We have successfully achieved the integration of isothermal amplification and the subsequent analysis of specific gene fragments on poly(methyl methacrylate) microchips. In our experiments, loop-mediated isothermal amplification, which can offer higher specificity and efficiency than PCR, has been performed at a constant temperature (65 degreesC). After amplification, products could be either examined by the integrated microchip-based electrophoresis or directly observed by naked eye with SYBR Green I added into the reaction solution. By such an integrated microsystem, the amplification and the subsequent analysis of prostate-specific antigen gene with template concentration at 23 fg/muL could be finished within 15 min, which demonstrates its advantages of high specificity, good reproducibility, and fast speed in gene detection.

Profiling of Complex Microbial Populations by Denaturing Gradient Gel Electrophoresis Analysis of Polymerase Chain Reaction-Amplified Genes Coding for 16S rRNA

We describe a new molecular approach to analyzing the genetic diversity of complex microbial populations. This technique is based on the separation of polymerase chain reaction-amplified fragments of genes coding for 16S rRNA, all the same length, by denaturing gradient gel electrophoresis (DGGE). DGGE analysis of different microbial communities demonstrated the presence of up to 10 distinguishable bands in the separation pattern, which were most likely derived from as many different species constituting these populations, and thereby generated a DGGE profile of the populations. We showed that it is possible to identify constituents which represent only 1% of the total population. With an oligonucleotide probe specific for the V3 region of 16S rRNA of sulfate-reducing bacteria, particular DNA fragments from some of the microbial populations could be identified by hybridization analysis. Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. The results we obtained demonstrate that this technique will contribute to our understanding of the genetic diversity of uncharacterized microbial populations.

Soil microbial community analysis using terminal restriction fragment length polymorphisms

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a polymerase chain reaction (PCR)-fingerprinting method that is commonly used for comparative microbial community analysis. The method can be used to analyze communities of bacteria, archaea, fungi, other phylogenetic groups or subgroups, as well as functional genes. The method is rapid, highly reproducible, and often yields a higher number of operational taxonomic units than other, commonly used PCR-fingerprinting methods. Sizing of terminal restriction fragments (T-RFs) can now be done using capillary sequencing technology allowing samples contained in 96- or 384-well plates to be sized in an overnight run. Many multivariate statistical approaches have been used to interpret and compare T-RFLP fingerprints derived from different communities. Detrended correspondence analysis and the additive main effects with multiplicative interaction model are particularly useful for revealing trends in T-RFLP data. Due to biases inherent in the method, linking the size of T-RFs derived from complex communities to existing sequence databases to infer their taxonomic position is not very robust. This approach has been used successfully, however, to identify and follow the dynamics of members within very simple or model communities. The T-RFLP approach has been used successfully to analyze the composition of microbial communities in soil, water, marine, and lacustrine sediments, biofilms, feces, in and on plant tissues, and in the digestive tracts of insects and mammals. The T-RFLP method is a user-friendly molecular approach to microbial community analysis that is adding significant information to studies of microbial populations in many environments.

Degradation of aquatic humic material by ultraviolet light

Natural humic water was treated with ultraviolet (UV) light and UV + hydrogen peroxide . The effects on the dissolved organic carbon content (DOC), the UV-absorbance at 254 nm (UV-abs.), the molecular size distribution, pH, and mutagenic activity were monitored, and the identity and concentrations of the most abundant gas chromatographable organic degradation products were determined. The DOC content and the UV-abs. of the water decreased substantially during treatment with. The decreases were dependent on the time of irradiation (UV dose) as well as on the H2O2 dose applied. The humus macromolecules were degraded to smaller fragments during irradiation. At higher UV doses, however, part of the dissolved organic matter (DOM) was found to precipitate, probably as a result of polymerization. Oxalic acid, acetic acid, malonic acid, and n-butanoic acid were the most abundant degradation products detected. These acids were found to account for up to 20% and 80% of the DOM in UV- and waters, respectively. No mutagenic activity was generated by the UV irradiation or the treatment. It is further concluded that the substantial mutagenic activity formed during chlorination of humic waters cannot be decreased by using UV irradiation as a pretreatment step.

Complex organization of the Streptomyces avermitilis genes encoding the avermectin polyketide synthase

The avermectin (Av) polyketide synthase (PKS) and erythromycin (Er) PKS are encoded by modular repeats of DNA, but the genetic organization of the modules encoding Av PKS is more complex than Er PKS. Sequencing of several related DNA fragments from Streptomyces avermitilis that are part of the Av biosynthetic gene cluster, revealed that they encode parts of large multifunctional PKS proteins. The Av PKS proteins show strong similarity to each other, as well as similarity to Er PKS proteins [Donadio et al., Science 252 (1991) 675–679] and fatty acid synthases. Partial DNA sequencing of the 65-kb region containing all the related sequence elements in the avr genes provides evidence for twelve modular repeats encoding FAS-like domains. The genes encoding the Av PKS are organized as two sets of six modular repeats which are convergently transcribed.

不同碎石含量及直径对土壤水分入渗过程的影响

Cumulative infiltration; Wetting front; Content of rock fragments; Size of rock fragments; 【摘要】 由于成土原因或人类活动,一些土壤中含有不同含量及大小的碎石。碎石的存在改变了土壤的某些物理特性,入渗过程也因此受到影响。本研究采用定水头入渗试验装置,对7种不同碎石含量(0%,10%,20%,30%,40%,50%,60%)及4种不同碎石直径(0.2~0.5cm,0.5~1.0 cm,1.0~3.0 cm,3.0~4.0 cm)的土壤水分入渗过程进行室内研究,旨在分析碎石含量及直径对土壤入渗过程的影响及其原因,为土石混合介质的研究提供一些理论基础。

Oligoaniline-Functionalized terpyridine ligands and their ruthenium(II) complexes: synthesis, spectroscopic property and redox behaviors

A series of oligoaniline-functionalized mono- and bis-topic terpyridine ligands, i.e. C6H5[N(R)C6H4](n)TPY (R = H, butyl, tert-butyloxycarbonyl; n = 1-4; TPY = 2,2':6',2"-terpyridyl) and TPYC6H4[N(R)C6H4](m)TPY (R = H, tert-butyloxycarbonyl; m = 2, 4), and the corresponding monoand bis-nuclear ruthenium(II) complexes have been synthesized and verified. The spectroscopic results indicate that two kinds of pi-pi* transitions from TPY and oligoaniline fragments of ligands strongly shift to lower energy, and the metal-to-ligand charge-transfer transition ((MLCT)-M-1) bands of all obtained complexes are considerably red-shifted (Delta lambda(max) = 22-64 nm) and their intensities become much more intense (approximately 4-6 times), compared with those of the reported complex [Ru(TPY)(2)](2+). Moreover, the spectroscopic properties of the ligands and complexes with longer oligoaniline units (n = 3, 4) are markedly influenced by the external stimulus, such as the oxidation and proton acid doping.

Characterization of linear epitope of the beta(2)-microglobulin via combination of MALDI-TOF-MS with immunoaffinity

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry(MALDI-TOF-MS), in combination with immunoaffinity provided a powerful tool for determining epitope (antigenic determinant) in protein. The linear epitope of the beta(2)-microglobulin was characterized in the paper. The method as follows: at first beta(2)-microglobulin was digested by a proteolytic enzyme to produce an appropriate set of peptide fragments, then peptide fragments containing the linear epitope were selected and separated from the pool of peptide fragments by immunoprecipitation with the monoclonal antibody. The agarose beads were collected carefully after the reaction. Unbound peptides would be washed away, while the peptides containing the epitope would remain bound to the immobilized antibody after. the beads were washed several times with appropriate buffer. At last the masses of the bound peptides were identified directly by MALDI-TOF MS. Using Endoproteinase Glu-C Endoproteinase Lys-C and Trypsin in the experiment, the linear epitope of beta(2)-microglobulin was located within peptide fragment 59-69, that is, DWSFYLLYYTE.

A study of isomeric diglycosyl flavonoids by SORI CID of Fourier transform ion cyclotron mass Spectrometry in negative ion mode

High-resolution Sustained off resonance irradiation (SORI) CID was employed to distinguish four pairs of isomeric diglycosyl flavonoids in the negative mode using the electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FTICR MS). All of these isomers can be distinguished via MS/MS data. For these diglycosyl flavones and flavanones, the deprotonated alpha 1-->6 linkage diglycosyl flavonoids produce fewer fragments than the alpha 1-->2 linkage type compounds and the Retro-Diels-Alder (RDA) reaction in MS/MS only takes place when the aglycone is a flavanone and glycosylated with an alpha 1-->2 intersaccharide linkage disaccharide. The deprotonation sites after collisional activation are discussed according to the high mass accuracy and high-resolution data of tandem spectrometry. Some of these high-resolution SORI CID product ions from alpha 1-->2 linkage diglycosyl flavonoids involve multibond cleavages; the possible mechanism is discussed based on the computer modeling using Gaussian 03 program package at the B3LYP/6-31G level of theory. Unambiguous elementary composition data provides fragmentation information that has not been reported previously.

New carbazole-based copolymers as amorphous hole-transporting materials for multilayer light-emitting diodes

New carbazole-based copolymers, which contain various concentrations of 9-alkyl-3, 6-carbazole fragments in the main chain connected via alkylene spacers, have been synthesized by Ni(0)-catalyzed Yamamoto-type aryl-aryl coupling reactions. Full characterization of the copolymer structure by NMR spectroscopy and elemental analysis is presented. These compounds represent amorphous materials of high thermal stability with glass transition temperatures of 151-162 degrees C and thermal decomposition starting at temperatures > 390 degrees C. UV-Vis absorption and photoluminescence emission of the copolymers confirmed that the effectively conjugated segment in the 3,6-linked carbazole-type copolymers is limited to dyads (dimeric units). However, copolymers with varying concentrations of the oligocarbazole chromophores demonstrate different charge injection and transport properties in multilayer light-emitting diodes with the copolymers as the hole transport and Alq(3) as the electroluminescent/electron transport layer. The device based on a copolymer composed of oligocarbazole blocks with an average length of around four carbazoles exhibited the best overall performance with a turn-on voltage of 3.5 V, a maximal photometric efficiency of 4.1 cd center dot A(-1) and maximum brightness of about 4 200 cd center dot m(-2).

High-dimensional assembly depending on polyoxoanion templates, metal ion coordination geometries, and a flexible bis(imidazole) ligand

By introducing the flexible 1,1'-(1,4-butanediyl)bis(imidazole) (bbi) ligand into the polyoxovanadate system, five novel polyoxoanion-templated architectures based on [As8V14O42](4-) and [V16O38Cl](6-) building blocks were obtained: [M(bbi)(2)](2)[As8V14O42(H2O)] [M = Co (1), Ni (2), and Zn (3)], [Cu(bbi)](4)[As8V14O42(H2O)] (4), and [Cu(bbi)](6)[V16O38Cl] (5). Compounds 1-3 are isostructural, and they exhibit a binodal (4,6)-connected 2D structure with Schlafli symbol (3(4)center dot 4(2))(3(4)center dot 4(4)center dot 5(4)center dot 6(3))(2), in which the polyoxoanion induces a closed four-membered circuit of M-4(bbi)(4). Compound 4 exhibits an interesting 3D framework constructed from tetradentate [As8V14O42](4-) cluster anions and cationic ladderlike double chains. There exists a bigger M-8(bbi)(6)O-2 circuit in 4. The 3D extended structure of 5 is composed of heptadentate [V16O38Cl](6-) anions and flexural cationic chains; the latter consists of six Cu(bbi) segments arranged alternately. It presents the largest 24-membered circuit of M-24(bbi)(24) so far observed made of bbi molecules and transition-metal cations. Investigation of their structural relations shows the important template role of the polyoxoanions and the synergetic interactions among the polyoxoanions, transition-metal ions, and flexible ligand in the assembly process.

Characterization of the rutin-metal complex by electrospray ionization tandem mass spectrometry

According to the strong application background of bioflavonoid and metal-flavonoid complexes, novel electrospray ionization tandem mass spectrometry (ESI-MSn) was applied to investigate the structure and fragmentation mechanism of transition metal-rutin complexes. In the full-scan mass spectra, different stoichiometric ratios of rutin-metal complexes were found. In the reaction between rutin and Cu, four kinds of complexes with four different stoichiometric ratios were produced. In the reaction between rutin and Zn, Mn(II), and Fe(II), only two kind of complexes with stoichiometric ratios of 1:1 and 1:2 occured. In further tandem mass spectrometric experiments of different rutin-metal complexes, product fragments, came from the neutral loss of the external rhamnose and the internal glucose unit, oligosaccharide chain, aglycone, and small organic molecules. According to the MSn data, we proposed a mechanism for all fragments of the rutin-Cu complex A and the structure of two rutin-Cu complexes, C and D.

Structural analysis of selected characteristic flavones by electrospray tandem mass spectrometry

Seven structure analogical flavonoid aglycones have been analyzed using electrospray ionization tandem mass spectrometry (ESI-MSn) in the negative-ion mode. The spectra obtained ESI-MSn allowed us to propose plausible schemes for their fragmentation mechanism. By analyzing the product ions spectra of deprotonated molecule ions [M-H](-), some neutral diagnostic losses and specific retro Diels-Alder fragments were obtained. By using all of these characteristic fragment ions we can specially differentiate the flavone isomer.

Studies on the flavones using liquid chromatography-electrospray ionization tandem mass spectrometry

Fragmentation pathways of nine flavone compounds have been studied by using electrospray ionization multi-stage tandem mass spectrometry (ESI-MSn). Analyzing the product ion spectra of flavonoids and aglycones, we observed some diagnostic neutral losses, such as *CH3, H2O, residue of glucose and gluconic acid, which are very useful for the identification of the functional groups in the structures. Furthermore, specific retro Diels-Alder (RDA) fragments for flavones with different hydroxyl substitution have also been discussed. The information is helpful for the rapid identification of the location site of hydroxyl substitution on flavones. Fragmentation pathways of C-glycosidic flavonoid have also been discussed using ESI-MSn, demonstrating ions [M-H-60](-), [M-H-90](-), [M-H-120](-) are characteristic ions of C-glycosidic flavonoid. According to the fragmentation mechanism of mass spectrometry and HPLC-MS data, the structures of seven flavones in Scutellaria baicalensis Georgi have been identified on-line without time-consuming isolation. The HPLC-ESI-MSn method for analyzing constituents in the Scutellaria baicalensis Georgi has been established.

Synthesis and characterization of new carbazole/fluorene-based derivatives for blue-light-emitting devices

2,7-Bis(9-ethylcarbazol-3-yl)-9,9-di(2-ethylhexyl)fluorene and a segmented copolymer composed of the same chromophores alternated with hexamethylene fragments were synthesized. The obtained materials possess good solubility in common organic solvents, high thermal stability with 1% weight loss temperature of 350-370 degrees C, and suitable glass transition temperatures. Both derivatives show blue fluorescence in dilute solutions as well as in solid state, demonstrating that excimers are not formed in the thin films. The fluorescence spectra of the materials do not show any peaks in the long-wavelength region even after annealing at 200 degrees C in air. An organic LED with the configuration of ITO/copolymer/Al generates blue electroluminescence with the maximum peak at 416 nm, rather low turn-on voltage (4.0 V), and brightness of about 400 cd/m(2). The heterostructure device based on model derivative emitted stable blue light with low operation voltage (100 cd/m(2) at similar to 11 V) and demonstrated luminescence efficiency of 0.8 cd/A.