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.

Layer-by-layer assembly of carbon nanotubes and Prussian blue nanoparticles: A potential tool for biosensing devices

A promising method for assembling carbon nanotubes (CNTs) and poly(diallyldimethylammonium chloride) protected Prussian blue nanoparticles (P-PB) to form three-dimensional (3D) nanostructured films is proposed. The electrostatic interaction, combined with layer-by-layer self-assembly (LBL), between negatively charged CNTs and positively charged P-PB is strong enough to drive the formation of the 3D nanostructured films. Thus, prepared multilayer films were characterized by ultraviolet-visible-near-infrared spectroscopy (UV-vis-NIR), scanning electron microscopy (SEM) and cyclic voltammetry (CV).

Interaction of echinomycin with guanine: electrochemistry and spectroscopy studies

The interaction of antitumor antibiotic, echinomycin (Echi) with guanine (Gua) was thoroughly investigated by adsorptive transfer stripping cyclic voltammetry, ultraviolet and visible adsorption spectra (UV/Vis) and Fourier-transform infrared spectroscopy (FTIR). Electrochemistry provided a simple tool for verifying the occurrence of interaction between Echi and Gua. Echi could be accumulated from the solution and give well-defined electrochemical signals in 0.1 M phosphate buffer solution (pH 7.0) only when Gua was present on the surface of the electrochemically pretreated glass carbon electrode (GCE), suggesting a strong binding of Echi to Gua. All the acquired spectral data showed that a new adduct between Echi and Gua was formed, and two pairs of adjacent intermolecular hydrogen bonds between the Ala backbone atoms in Echi and Gua (Ala-NH to Gua-N3 and Gua-NH2 to Ala-CO) played a dominating role in the interaction. Electrochemistry coupled with spectroscopy techniques could provide a relatively easy way to obtain useful insights into the molecular mechanism of drug-DNA interactions, which should be important in the development of new anticancer drugs with specific base recognition.

Roles of microRNA in plant defense and virus offense interaction

MicroRNAs (miRNA) that are around 22 nucleotides long non-protein-coding RNAs, play key regulatory roles in plants. Recent research findings show that miRNAs are involved in plant defense and viral offense systems. Advances in understanding the mechanism of miRNA biogenesis and evolution are useful for elucidating the complicated roles they play in viral infection networks. In this paper a brief summary of evolution of plant anti-virus defense is given and the function of miRNAs involved in plant-virus competition is highlighted. It is believed that miRNAs have several advantages over homology-dependent and siRNA-mediated gene silencing when they are applied biotechnologically to promote plant anti-virus defense. miRNA-mediated anti-virus pathway is an ancient mechanism with a promising future. However, using miRNAs as a powerful anti-virus tool will be better realized only if miRNA genomics and functions in plant viral infection are fully understood.

花岗岩风化土微观结构及其工程地质特性研究

Saprolite is the residual soil resulted from completely weathered or highly weathered granite and with corestones of parent rock. It is widely distributed in Hong Kong. Slope instability usually happens in this layer of residual soil and thus it is very important to study the engineering geological properties of Saprolite. Due to the relic granitic texture, the deformation and strength characteristics of Saprolite are very different from normal residual soils. In order to investigate the effects of the special microstructure on soil deformation and strength, a series of physical, chemical and mechanical tests were conducted on Saprolite at Kowloon, Hong Kong. The tests include chemical analysis, particle size analysis, mineral composition analysis, mercury injection, consolidation test, direct shear test, triaxial shear test, optical analysis, SEM & TEM analysis, and triaxial shear tests under real-time CT monitoring.Based on the testing results, intensity and degree of weathering were classified, factors affecting and controlling the deformation and strength of Saprolite were identified, and the interaction between those factors were analyzed.The major parameters describing soil microstructure were introduced mainly based on optical thin section analysis results. These parameters are of importance and physical meaning to describe particle shape, particle size distribution (PSD), and for numerical modeling of soil microstructure. A few parameters to depict particle geometry were proposed or improved. These parameters can be used to regenerate the particle shape and its distribution. Fractal dimension of particle shape was proposed to describe irregularity of particle shapes and capacity of space filling quantitatively. And the effect of fractal dimension of particle shape on soil strength was analyzed. At the same time, structural coefficient - a combined parameter which can quantify the overall microstructure of rock or soil was introduced to study Saprolite and the results are very positive. The study emphasized on the fractal characteristics of PSD and pore structure by applying fractal theory and method. With the results from thin section analysis and mercury injection, it was shown that at least two fractal dimensions Dfl(DB) and Df2 (Dw), exist for both PSD and pore structure. The reasons and physical meanings behind multi-fractal dimensions were analyzed. The fractal dimensions were used to calculate the formation depth and weathering rate of granite at Kowloon. As practical applications, correlations and mathematical models for fractal dimensions and engineering properties of soil were established. The correlation between fractal dimensions and mechanical properties of soil shows that the internal friction angle is mainly governed by Dfl 9 corresponding to coarse grain components, while the cohesion depends on Df2 , corresponding to fine grain components. The correlations between the fractal dimension, friction angle and cohesion are positive linear.Fractal models of PSD and pore size distribution were derived theoretically. Fragmentation mechanism of grains was also analyzed from the viewpoint of fractal. A simple function was derived to define the theoretical relationship between the water characteristic curve (WCC) and fractal dimension, based on a number of classical WCC models. This relationship provides a new analytical tool and research method for hydraulic properties in porous media and solute transportation. It also endues fractal dimensions with new physical meanings and facilitates applications of fractal dimensions in water retention characteristics, ground water movement, and environmental engineering.Based on the conclusions from the fractal characteristics of Saprolite, size effect on strength was expressed by fractal dimension. This function is in complete agreement with classical Weibull model and a simple function was derived to represent the relationship between them.In this thesis, the phenomenon of multi-fractal dimensions was theoretically analyzed and verified with WCC and saprolite PSD results, it was then concluded that multi-fractal can describe the characteristics of one object more accurately, compared to single fractal dimension. The multi-fractal of saprolite reflects its structural heterogeneity and changeable stress environment during the evolution history.

Soil column chromatography for correlation between capacity factors and soil organic partition coefficients for eight pesticides

A soil column chromatographic method was developed to measure the capacity factors (k') of pesticides, in which soil acted as a stationary phase and methanol-water mixture as an eluent. The k' values of eight pesticides, including three insecticides (methiocarb, azinphos-methyl, fenthion), four fungicides (triadimenol, fuberidazole, tebuconazole, pencycuron), and one herbicide (atrazine), were found to be well fitted to a retention equation, ln k'=ln k(w)'-S-phi. Due to similar interactions of solutes with soil and solvent in both sorption determination and retention experiment, log k' has a good linear correlation with log K-oc for the eight pesticides from different classes, in contrast with poor correlation between log k' from C-18 column and log K-oc. So the method provides a tool for rapid estimation of K-oc from experimental k'. (C) 1999 Elsevier Science Ltd. All rights reserved.