Construction and control of plasmid DNA network

The influences of different cations on plasmid DNA network structures on a mica substrate were investigated by atomic force microscopy (AFM). Interactions between the DNA strands and mica substrate, and between the DNA strands themselves were more strongly influenced by the complex cations (Fe(phen)(3)(2+), Ni(phen)(3)(2+), and Co(phen)(3)(3+)) than by the simple cations (Mg2+, Mn2+, Ni2+, Ca2+, Co3+). The mesh height of the plasmid DNA network was higher when the complex cations were added to DNA samples. The mesh size decreased with increasing DNA concentration and increased with decreasing DNA concentration in the same cation solution sample. Hence, plasmid DNA network height can be controlled by selecting different cations, and the mesh size can be controlled by adjusting plasmid DNA concentration.

Construction and characterization of a fosmid library for pathogenic bacterium Vibrio anguillarum

Vibrio anguillarum is a common bacterial pathogen in fish. However, little is known about its pathogenic mechanism, in part, because the entire genome has not been completely sequenced. We constructed a fosmid library for V. anguillarum containing 960 clones with an average insert size of 37.7 kb and 8.6-fold genome coverage. We characterized the library by end-sequencing 50 randomly selected clones. This generated 93 sequences with a total length of 57 485 by covering 1.4% of the whole genome. Of these sequences, 58 (62.4%) were homologous to known genes, 30 (32.3%) were genes with hypothetical functions, and the remaining 5 (5.3%) were unknown genes. We demonstrated the utility of this library by PCR screening of 10 genes. This resulted in an average of 6.2 fosmid clones per screening. This fosmid library offers a new tool for gene screening and cloning of V. anguillarum, and for comparative genomic studies among Vibrio species.

Construction and characterization of a bacterial artificial chromosome library of marine macroalga Porphyra yezoensis (Rhodophyta)

A large-DNA-fragment library is necessary for research into the Porphyra genome. In this study, a bacterial artificial chromosome (BAC) library of Porphyra yezoensis was constructed and characterized. The library contains 54,144 BAC clones with an average insert size of about 65 kb and fewer than 0.7% of clones without large inserts. Therefore, its capacity is more than 6.6 P. yezoensis genome equivalents, and the probability of recovering any nuclear DNA sequence from the library is higher than 99%. The library shows good fidelity and stability. A putative trehalose-6-phosphate synthase (TPS) gene was successfully screened out from the library. The above results show that the library is useful for gene cloning and genomic research in P. yezoensis.

Construction and characterization of a live, attenuated esrB mutant of Edwardsiella tarda and its potential as a vaccine against the haemorrhagic septicaemia in turbot, Scophthamus maximus (L.)

The esrB gene of Edwardsiella tarda, which encodes a regulator protein of the type III secretion system, was mutated by the unmarked deletion method and reintroduced by allelic exchange into the chromosome of E. tarda LSE40 by means of the suicide vector pRE 112. The LSE40 esrB mutant was highly attenuated when inoculated intraperitoneally into turbot Scophthamus maximus L., showing a 50% lethal dose of 10(8.1) cfu/fish. The esrB mutants were not recoverable from the internal organs at 14 days post-inoculation. Vaccination with a single dose of 10(5)-10(7) cfu/fish of the esrB mutant elicited significant protection against the wildtype strain of E. tarda LSE40 (relative percentage survival > 50%). The protection correlated well with the antibody titres in the serum of vaccinated fish. (c) 2006 Elsevier Ltd. All rights reserved.

Construction and characterization of two bacterial artificial chromosome libraries of Zhikong scallop, Chlamys farreri Jones et Preston, and identification of BAC clones containing the genes involved in its innate immune system

Large-insert bacterial artificial chromosome (BAC) libraries are necessary for advanced genetics and genomics research. To facilitate gene cloning and characterization, genome analysis, and physical mapping of scallop, two BAC libraries were constructed from nuclear DNA of Zhikong scallop, Chlamys farreri Jones et Preston. The libraries were constructed in the BamHI and MboI sites of the vector pECBAC1, respectively. The BamHI library consists of 73,728 clones, and approximately 99% of the clones contain scallop nuclear DNA inserts with an average size of 110 kb, covering 8.0x haploid genome equivalents. Similarly, the MboI library consists of 7680 clones, with an average insert of 145 kb and no insert-empty clones, thus providing a genome coverage of 1.1x. The combined libraries collectively contain a total of 81,408 BAC clones arrayed in 212 384-well microtiter plates, representing 9.1x haploid genome equivalents and having a probability of greater than 99% of discovering at least one positive clone with a single-copy sequence. High-density clone filters prepared from a subset of the two libraries were screened with nine pairs of Overgos designed from the cDNA or DNA sequences of six genes involved in the innate immune system of mollusks. Positive clones were identified for every gene, with an average of 5.3 BAC clones per gene probe. These results suggest that the two scallop BAC libraries provide useful tools for gene cloning, genome physical mapping, and large-scale sequencing in the species.

The topological configuration and conformational analysis of mRNA in translation

The theoretical model construction of mRNA hairpin structure and single-stranded structure as well as the simulation studies on RNA structure determined by the X-ray crystal diffraction and nuclear magnetic resonance revealed that in translation, after mRNA being unfolded into single-stranded structure, its topological configuration was closely correlative with the original hairpin structure. The conformational features of single-stranded mRNA appeared as helical regions alternating with curly regions to different extents, which might exert the influence on the folding of nascent polypeptide by various regulating effects including different translational rates.

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.

Classical two-site fidelity and quantum phase transitions in the Ising model and the extended Hubbard model

In this Letter, the classical two-site-ground-state fidelity (CTGF) is exploited to identify quantum phase transitions (QPTs) for the transverse field Ising model (TFIM) and the one-dimensional extended Hubbard model (EHM). Our results show that the CTGF exhibits an abrupt change around the regions of criticality and can be used to identify QPTs in spin and fermionic systems. The method is especially convenient when it is connected with the density-matrix renormalization group (DMRG) algorithm. (C) 2008 Elsevier B.V. All rights reserved.

automatic construction of finite algebras

This paper deals withmodel generation for equational theories, i.e., automatically generating (finite) models of a given set of (logical) equations. Our method of finite model generation and a tool for automatic construction of finite algebras is described. Some examples are given to show the applications of our program. We argue that, the combination of model generators and theorem provers enables us to get a better understanding of logical theories. A brief comparison between our tool and other similar tools is also presented.

Entanglement dynamics and chaos in the Dicke model

We study dynamical properties of quantum entanglement in the Dicke model with and without the rotating-wave approximation. Specifically, we investigate the maximal entanglement and mean entanglement which reflect the underlying chaos in the system, and a good classical-quantum correspondence is found. We also show that the maximal linear entropy can be more sensitive to chaos than the mean linear entropy.

悬索桥隧道式锚碇与围岩系统的破坏模式研究

The anchorages are unparalleled structures only in a suspension bridge, and as main bearing facilities, play an important role in connecting the superstructures and the ground. The tunnel anchorage, as one alternative type of the anchorages, has more advantages over its counterpart, the gravity anchorage. With the tunnel anchorages adopted, not only can surface excavation be reduced to protect the environment, and natural condition of the rock be utilized and potential bearing capacity of surrounding rock be mobilized to save engineering cost, but also the technological predominance of auxiliary engineering measures, such as prestressed concrete, anchoring piles, rock anchors and collar beam between the two separated anchorages, can be easily cooperated to work together harmoniously under the circumstances of poor rock quality. There are plentiful high mountains and deep canyons in west part of China, and long-span bridge construction is inevitably encountered in order to realize leapfrogging development of the transportation infrastructure. Western mountainous areas usually possess the conditions for constructing tunnel anchorages, and therefore, the tunnel anchorages, which are conformed to the conception of resource conservative and sustainable society, extremely have application and popularization value in western underdeveloped region. The scientific and technological problem about the design, construction and operation of tunnel anchorages should be further investigated. Combining the engineering of western tunnel anchorages for the Balinghe Suspension Bridge, this paper probed into the survey method and in-situ test method for tunnel anchorages, scientific rock quality evaluation of surrounding rock to provide reasonable physical and mechanical parameters for design, construction and operation of tunnel anchorages, bearing capacity estimation for tunnel anchorage, deformation prediction of the anchorage-rockmass system, tunnel-anchorage slope stability analysis and the evaluation of excavation stability and degree of safety of the anchorage tunnel. The following outcomes were obtained: 1. Materials of tunnel anchorages of suspension bridge built (and in progress) at home and abroad were systematically sorted out, with the engineering geological condition and geomechanical property of surrounding rock around the anchorage tunnel, the design size of anchorages and the construction method of anchorage tunnel paid more emphasis on, to unveil the internal relationship between the engineering geological conditions of surrounding rock and the design size and axis angle of anchorages and provide references for future design, construction and study of tunnel anchorages. 2. Physical and mechanical parameters were recommended based on three domestic and foreign methods of rock quality evaluation. 3. In-situ tests, adopting the back-thrust method, of two kinds of reduced scale model, 1/30 and 1/20, for the tunnel anchorages were conducted in the declining exploration drift with rock mass at the test depth being the same as surrounding rock around real anchorages, and reliable field rockmass displacement data were acquired. Attenuation relation between the increment of distance from the anchorage and the decrement of rockmass displacement under maximum test load, and influential scope suffered by anchorage load were obtained. 4. Using similarity theory, the magnitude of real anchorage and rockmass displacement under design load and degree of safety of the anchorage system were deduced. Furthermore, inversion analysis to deformation modulus of slightly weathered dolomite rock, the surrounding rock of anchorage tunnel, was performed by the means of numerical simulation. 5. The influential law of the geometrical size to the limit bearing capacity of tunnel anchorage was studied. 6. Based on engineering geological survey data, accounting for the combination of strata layer and adverse discontinuities, the failure patterns of tunnel anchorage slope were divided into three modes: sliding of splay saddle pier slope, superficial-layer slippage, and deep-layer slippage. Using virtual work principle and taking anchorage load in account, the stability of the three kinds of failure patterns were analyzed in detail. 7. The step-by-step excavation of anchorage tunnel, the numerical overload and the staged decrement of rock strength parameters were numerically simulated to evaluate the excavation stability of surrounding rock around anchorage tunnel, the overload performance of tunnel anchorage, and the safety margin of strength parameters of the surrounding rock.

基于结构分析地震资料去噪方法研究

With the development of oil and gas exploration, the exploration of the continental oil and gas turns into the exploration of the subtle oil and gas reservoirs from the structural oil and gas reservoirs in China. The reserves of the found subtle oil and gas reservoirs account for more than 60 percent of the in the discovered oil and gas reserves. Exploration of the subtle oil and gas reservoirs is becoming more and more important and can be taken as the main orientation for the increase of the oil and gas reserves. The characteristics of the continental sedimentary facies determine the complexities of the lithological exploration. Most of the continental rift basins in East China have entered exploration stages of medium and high maturity. Although the quality of the seismic data is relatively good, this areas have the characteristics of the thin sand thickness, small faults, small range of the stratum. It requests that the seismic data have high resolution. It is a important task how to improve the signal/noise ratio of the high frequency of seismic data. In West China, there are the complex landforms, the deep embedding the targets of the prospecting, the complex geological constructs, many ruptures, small range of the traps, the low rock properties, many high pressure stratums and difficulties of boring well. Those represent low signal/noise ratio and complex kinds of noise in the seismic records. This needs to develop the method and technique of the noise attenuation in the data acquisition and processing. So that, oil and gas explorations need the high resolution technique of the geophysics in order to solve the implementation of the oil resources strategy for keep oil production and reserves stable in Ease China and developing the crude production and reserves in West China. High signal/noise ratio of seismic data is the basis. It is impossible to realize for the high resolution and high fidelity without the high signal/noise ratio. We play emphasis on many researches based on the structure analysis for improving signal/noise ratio of the complex areas. Several methods are put forward for noise attenuation to truly reflect the geological features. Those can reflect the geological structures, keep the edges of geological construction and improve the identifications of the oil and gas traps. The ideas of emphasize the foundation, give prominence to innovate, and pay attention to application runs through the paper. The dip-scanning method as the center of the scanned point inevitably blurs the edges of geological features, such as fault and fractures. We develop the new dip scanning method in the shap of end with two sides scanning to solve this problem. We bring forward the methods of signal estimation with the coherence, seismic wave characteristc with coherence, the most homogeneous dip-sanning for the noise attenuation using the new dip-scanning method. They can keep the geological characters, suppress the random noise and improve the s/n ratio and resolution. The rutine dip-scanning is in the time-space domain. Anew method of dip-scanning in the frequency-wavenumber domain for the noise attenuation is put forward. It use the quality of distinguishing between different dip events of the reflection in f-k domain. It can reduce the noise and gain the dip information. We describe a methodology for studying and developing filtering methods based on differential equations. It transforms the filtering equations in the frequency domain or the f-k domain into time or time-space domains, and uses a finite-difference algorithm to solve these equations. This method does not require that seismic data be stationary, so their parameters can vary at every temporal and spatial point. That enhances the adaptability of the filter. It is computationally efficient. We put forward a method of matching pursuits for the noise suppression. This method decomposes any signal into a linear expansion of waveforms that are selected from a redundant dictionary of functions. These waveforms are chosen in order to best match the signal structures. It can extract the effective signal from the noisy signal and reduce the noise. We introduce the beamforming filtering method for the noise elimination. Real seismic data processing shows that it is effective in attenuating multiples and internal multiples. The s/n ratio and resolution are improved. The effective signals have the high fidelity. Through calculating in the theoretic model and applying it to the real seismic data processing, it is proved that the methods in this paper can effectively suppress the random noise, eliminate the cohence noise, and improve the resolution of the seismic data. Their practicability is very better. And the effect is very obvious.