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 denaturing gradient gel electrophoresis

The most biological diversity on this planet is probably harbored in soils. Understanding the diversity and function of the microbiological component of soil poses great challenges that are being overcome by the application of molecular biological approaches. This review covers one of many approaches being used: separation of polymerase chain reaction (PCR) amplicons using denaturing gradient gel electrophoresis (DGGE). Extraction of nucleic acids directly from soils allows the examination of a community without the limitation posed by cultivation. Polymerase chain reaction provides a means to increase the numbers of a target for its detection on gels. Using the rRNA genes as a target for PCR provides phylogenetic information on populations comprising communities. Fingerprints produced by this method have allowed spatial and temporal comparisons of soil communities within and between locations or among treatments. Numerous samples can be compared because of the rapid high throughput nature of this method. Scientists now have the means to begin addressing complex ecological questions about the spatial, temporal, and nutritional interactions faced by microbes in the soil environment.

algorithms for computing weak bisimulation equivalence

IEEE Comp Soc, IFIP, Tianjin Normal Univ

A Review of Active Appearance Models

Active appearance model (AAM) is a powerful generative method for modeling deformable objects. The model decouples the shape and the texture variations of objects, which is followed by an efficient gradient-based model fitting method. Due to the flexible and simple framework, AAM has been widely applied in the fields of computer vision. However, difficulties are met when it is applied to various practical issues, which lead to a lot of prominent improvements to the model. Nevertheless, these difficulties and improvements have not been studied systematically. This motivates us to review the recent advances of AAM. This paper focuses on the improvements in the literature in turns of the problems suffered by AAM in practical applications. Therefore, these algorithms are summarized from three aspects, i.e., efficiency, discrimination, and robustness. Additionally, some applications and implementations of AAM are also enumerated. The main purpose of this paper is to serve as a guide for further research.

A topography/chemical composition gradient polystyrene surface: Toward the investigation of the relationship between surface wettability and surface structure and chemical composition

In this paper, we have prepared of a topography/chemical composition gradient polystyrene (PS) surface, i.e., an orthogonal gradient surface, to investigate the relationship between surface wettability and surface structure and chemical composition. The prepared surface shows a one-dimensional gradient in wettability in the x, y, and diagonal directions, including hydrophobic to hydrophilic, superhydrophobic to hydrophobic, superhydrophobic to superhydrophilic gradients, and so forth.

"Dual-Parallel-Channel" Shape-Gradient Surfaces: Toward Oriented and Reversible Movement of Water Droplets

In this paper, we prepared "dual-parallel-channel" shape-gradient surfaces, on which water droplets can reversibly and orientedly move between two adjacent pools under the guidance of an external voltage. Furthermore, it is found that the motion speed is governed by several parameters, including bath condition, gradient angle, and the working voltage. In this self-transportation process of water droplets, the external voltage works like a traffic light, which can give "moving", "stopping", "turning" and "straight-going" signals to the Water droplets.

Shape-gradient composite surfaces: Water droplets move uphill

The approach of water droplets self-running horizontally and uphill without any other forces was proposed by patterning the shape-gradient hydrophilic material (i.e., mica) to the hydrophobic matrix (i.e., wax or low-density polyethylene (LDPE)). The shape-gradient composite surface is the best one to drive water droplet self-running both at the high velocity and the maximal distance among four different geometrical mica/wax composite surfaces. The driving force for the water droplets self-running includes: (1) the great difference in wettability of surface materials, (2) the low contact angle hysteresis of surface materials, and (3) the space limitation of the shape-gradient transportation area. Furthermore, the average velocity and the maximal distance of the self-running were mainly determined by the gradient angle (alpha), the droplet volume, and the difference of the contact angle hysteresis. Theoretical analysis is in agreement with the experimental results.

Pattern formation in a confined polymer film induced by a temperature gradient

We have studied a morphological instability of a double layer comprising the polymer film and air gap confined between the two plates set to different temperatures. The temperature gradient across the double layer causes the breakup of the polymer film into well-defined columnar, striped or spiral structures spanning the two plates. The pattern formation mechanisms have been discussed. The formed patterns can be transferred to produce PDMS stamp, a key element of soft lithography for future microfabrication.

Optical intensity gradient by colloidal photonic crystals with a graded thickness distribution

Gradient colloidal crystals with a thickness gradient were prepared by the vertical deposition technique with vertically graded concentration suspensions. The thickness of the gradient colloidal crystal gradually changes at different positions along the specific gradient direction of the crystal. The thickness gradient was determined by the concentration gradient, depending on the initial colloidal concentration and the settling time. The optical transmission intensity at the dip wavelength can be tuned by changing the thickness of the colloidal crystals. The gradient colloidal crystals lead to a gradient of optical intensity at the dip in transmission light. The gradient of optical intensity at the dip increases as the thickness gradient of the colloidal crystal increases.

THE CHARGE-DISTRIBUTION AND THE ELECTRIC-FIELD GRADIENT IN THE HIGH-TEMPERATURE SUPERCONDUCTOR TLBA2CAN-1CUNO2N+3 (N = 1 TO 3)

The net charges at atoms in the high-temperature superconductor TlBa2Can-1CunO2n+3 (n = 1 to 3) are calculated by means of the tight-binding approximation based on the EHMO method. The results indicate that the charge distribution in this kind of compounds possesses a specially layered arrangement. An insulating Ba-Ba layer is inserted between the Cu-O layer and the Tl-O layer. There may exist a weak coupling between the Cu-O layer and the Tl-O layer through the interaction of the same O(2) atom with both the Cu atom and the Tl atom. The existence of the Ca in the compounds can cause the valence fluctuation at the Cu atom. The calculated electric field gradients at atoms implies that the conducting electron or hole may move in the Cu-O layer, which is closest to the Tl-O layer, along the a-b plane.

The statistic inversion algorithms of water constituents for the Huanghai Sea and the East China Sea

A group of statistical algorithms are proposed for the inversion of the three major components of Case-H waters in the coastal area of the Huanghai Sea and the East China Sea. The algorithms are based on the in situ data collected in the spring of 2003 with strict quality assurance according to NASA ocean bio-optic protocols. These algorithms are the first ones with quantitative confidence that can be applied for the area. The average relative error of the inversed and in situ measured components' concentrations are: Chl-a about 37%, total suspended matter (TSM) about 25%, respectively. This preliminary result is quite satisfactory for Case-H waters, although some aspects in the model need further study. The sensitivity of the input error of 5% to remote sensing reflectance (Rrs) is also analyzed and it shows the algorithms are quite stable. The algorithms show a large difference with Tassan's local SeaWiFS algorithms for different waters, except for the Chl-a algorithm.