Site-directed gene integration in transgenic zebrafish mediated by cre recombinase using a combination of mutant Lox sites

With current gene-transfer techniques in fish, insertion of DNA into the genome occurs randomly and in many instances at multiple sites. Associated position effects, copy number differences, and multiple gene interactions make gene expression experiments difficult to interpret and fish phenotype less predictable. To meet different fish engineering needs, we describe here a gene targeting model in zebrafish. At first, four target zebrafish lines, each harboring a single genomic lox71 target site, were generated by zebrafish transgenesis. The zygotes of transgenic zebrafish lines were coinjected with capped Cre mRNA and a knockin vector pZklox66RFP. Site-specific integration event happened from one target zebrafish line. In this line two integrant zebrafish were obtained from more than 80,000 targeted embryos (integrating efficiency about 10(-4) to 10(-5)) and confirmed to have a sole copy of the integrating DNA at the target genome site. Genomic polymerase chain reaction analysis and DNA sequencing verified the correct gene target events where lox71 and lox66 have accurately recombined into double mutant lox72 and wild-type loxP. Each integrant zebrafish chosen for analysis harbored the transgene rfp at the designated egfp concatenates. Although the Cre-mediated recombination is site specific, it is dependent on a randomly placed target site. That is, a genomic target cannot be preselected for integration based solely on its sequence. Conclusively, an rfp reporter gene was successfully inserted into the egfp target locus of zebrafish genome by Cre-lox-mediated recombination. This site-directed knockin system using the lox71/lox66 combination should be a promising gene-targeting platform serving various purposes in fish genetic engineering.

反假频重建理论及其在储层预测中的应用

To extend the cross-hole seismic 2D data to outside 3D seismic data, reconstructing the low frequency data to high frequency data is necessary. Blind deconvolution method is a key technology. In this paper, an implementation of Blind deconvolution is introduced. And optimized precondition conjugate gradient method is used to improve the stability of the algorithm and reduce the computation. Then high-frequency retrieved Seismic data and the cross-hole seismic data is combined for constraint inversion. Real data processing proved the method is effective. To solve the problem that the seismic data resolution can’t meet the request of reservoir prediction in the river face thin-layers in Chinese eastern oil fields, a high frequency data reconstruction method is proposed. The extrema of the seismic data are used to get the modulation function which operated with the original seismic data to get the high frequency part of the reconstruction data to rebuild the wide band data. This method greatly saves the computation, and easy to adjust the parameters. In the output profile, the original features of the seismic events are kept, the common feint that breaking the events and adding new zeros to produce alias is avoided. And the interbeded details are enhanced compared to the original profiles. The effective band of seismic data is expended and the method is approved by the processing of the field data. Aim to the problem in the exploration and development of Chinese eastern oil field that the high frequency log data and the relative low frequency seismic data can’t be merged, a workflow of log data extrapolation constrained by time-phase model based on local wave decomposition is raised. The seismic instantaneous phase is resolved by local wave decomposition to build time-phase model, the layers beside the well is matched to build the relation of log and seismic data, multiple log info is extrapolated constrained by seismic equiphase map, high precision attributes inverse sections are produced. In the course of resolve the instantaneous phase, a new method of local wave decomposition --Hilbert transform mean mode decomposition(HMMD) is raised to improve the computation speed and noise immunity. The method is applied in the high resolution reservoir prediction in Mao2 survey of Daqing oil field, Multiple attributes profiles of wave impedance, gamma-ray, electrical resistivity, sand membership degree are produced, of which the resolution is high and the horizontal continuous is good. It’s proved to be a effective method for reservoir prediction and estimation.

AVO分析与地震资料叠前储层预测技术

In this paper we base on the anisotropic theory and Zoeppritz function of the transmission theory and the law of amplitude versus offset simplify seismic reflection coefficient of different media, analyze the characteristic of the gas or oil saturated stratum or the VTI and HTI models. Discuss the P wave reflection relationship and the meanings of the different parameters. We use measured parameters of a reservoir to simulate the characteristic of the reservoir, study the different effects of stratum saturated with gas or oil and analyze the characteristic of the seismic response of different models which change with different incident angles and different azimuths. Using the field data of logs ,analyze the rock property parameters, build the relationship of logs and parameters by Gassmann theory or empirical function. Calculate the density and the shear modulus and bulk modulus, reconstruct the log curves, calculate shear wave logs and correlate the logs affected by mud and other environmental factors. Finally perform the relationship of the seismic data log of saturated stratum and enhance the ability and reliability in reservoir prediction. Our aim is by the prestack seismic processing to get high solution and amplitude preserved seismic data. Because in incident angle gathers or azimuthal gathers, the low signal to noise ratio and low different covers affect the result of the prestack reservoir prediction. We apply prestack noise erase, cell regularization process and relatively amplitude preservation in the high solution seismic process routine to preserve the characteristic of stratum response, and erase the effects of the noise. In this paper we finished prestack invertion in the BYT survey and fractured reservoir depiction in MB survey. By the invertion and multiple attributes crossplot. we can get the stratum profiles and oil indicator profiles which can predict the distribution of the reservoir and oil. In the MB survey, we get orientation and density of fractured reservoir by the azimuthal seismic amplitude and depict the potential oil and gas reservoir. Prestak invertion works better in distinguishing oil and reservoir.

Effective elastic moduli of two-dimensional solids with multiple cracks

An accurate method which directly accounts for the interactions between different microcracks is used for analyzing the elastic problem of multiple cracks solids. The effective elastic moduli for randomly oriented cracks and parallel cracks are evaluated for the representative volume element (RVE) with microcracks in infinite media. The numerical results are compared with those from various micromechanics models and experimental data. These results show that the present method is simple and provides a direct and efficient approach to dealing with elastic solids containing multiple cracks.

Interactions of Penny-Shaped Cracks in Three-Dimensional Solids

The interaction of arbitrarily distributed penny-shaped cracks in three-dimensional solids is analyzed in this paper. Using oblate spheroidal coordinates and displacement functions, an analytic method is developed in which the opening and the sliding displacements on each crack surface are taken as the basic unknown functions. The basic unknown functions can be expanded in series of Legendre polynomials with unknown coefficients. Based on superposition technique, a set of governing equations for the unknown coefficients are formulated from the traction free conditions on each crack surface. The boundary collocation procedure and the average method for crack-surface tractions are used for solving the governing equations. The solution can be obtained for quite closely located cracks. Numerical examples are given for several crack problems. By comparing the present results with other existing results, one can conclude that the present method provides a direct and efficient approach to deal with three-dimensional solids containing multiple cracks.

A scheme for multiple sequences alignment optimization-an improvement based on family representative mechanics features

As a basic tool of modern biology, sequence alignment can provide us useful information in fold, function, and active site of protein. For many cases, the increased quality of sequence alignment means a better performance. The motivation of present work is to increase ability of the existing scoring scheme/algorithm by considering residue–residue correlations better. Based on a coarse-grained approach, the hydrophobic force between each pair of residues is written out from protein sequence. It results in the construction of an intramolecular hydrophobic force network that describes the whole residue–residue interactions of each protein molecule, and characterizes protein's biological properties in the hydrophobic aspect. A former work has suggested that such network can characterize the top weighted feature regarding hydrophobicity. Moreover, for each homologous protein of a family, the corresponding network shares some common and representative family characters that eventually govern the conservation of biological properties during protein evolution. In present work, we score such family representative characters of a protein by the deviation of its intramolecular hydrophobic force network from that of background. Such score can assist the existing scoring schemes/algorithms, and boost up the ability of multiple sequences alignment, e.g. achieving a prominent increase (50%) in searching the structurally alike residue segments at a low identity level. As the theoretical basis is different, the present scheme can assist most existing algorithms, and improve their efficiency remarkably.

Self-induced transmission on intersubband resonance in multiple quantum wells

We investigate the nonlinear propagation of ultrashort pulses on resonant intersubband transitions in multiple semiconductor quantum wells. It is shown that the nonlinearity rooted from electron-electron interactions destroys the condition giving rise to self-induced transparency. However, by adjusting the area of input pulse, we find the signatures of self-induced transmission due to a full Rabi flopping of the electron density, and this phenomenon can be approximately interpreted by the traditional standard area theorem via defining the effective area of input pulse.

Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals

An analysis of the nuclear beta-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed clement (SINE) insertion events. Mammalian-wide interspersed repeats (MIRs) are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage-specific SINE sequences are also found to have independently inserted into this intron in Carnivora, Artiodactyla and Lagomorpha. In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR clement is a hot spot for successive insertions of other SINEs. The unexpected MIR excision as a result of a random deletion in the rat intron locus and the non-random site targeting detected by this study indicate that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. Implications for SINE sequence evolution upon and following integration, as well as the fascinating interactions between retroposons and the host genomes are discussed.

Origin of the blueshift in the infrared absorbance of intersubband transitions in AlxGa1-x/GaN multiple quantum wells

A self-consistent calculation of the subband energy levels of n-doped quantum wells is studied. A comparison is made between theoretical results and experimental data. In order to account for the deviations between them, the ground-state electron-electron exchange interactions, the ground-state direct Coulomb interactions, the depolarization effect, and the exciton-like effect are considered in the simulations. The agreement between theory and experiment is greatly improved when all these aspects are taken into account. The ground-to-excited-state energy difference increases by 8 meV from its self-consistent value if one considers the depolarization effect and the exciton-like effect only. It appears that the electron-electron exchange interactions account for most of the observed residual blueshift for the infrared intersubband absorbance in AlxGa1-xN/GaN multiple quantum wells. It seems that electrons on the surface of the k-space Fermi gas make the main contribution to the electron-electron exchange interactions, while for electrons further inside the Fermi gas it is difficult to exchange their positions. (C) 2004 Elsevier B.V. All rights reserved.

Optimization of multiple filamentation of femtosecond laser pulses in air using a pinhole

The robustness and prolongation of multiple filamentation (MF) for femtosecond laser propagation in air are investigated experimentally and numerically. It is shown that the number, pattern, propagation distance, and spatial stability of MF can be controlled by a variable-aperture on-axis pinhole. The random MF pattern can be optimized to a deterministic pattern. In our numerical simulations, we configured double filaments to principlly simulate the experimental MF interactions. It is experimentally and numerically demonstrated that the pinhole can reduce the modulational instability of MF and is favorable for a more stable MF evolution. (c) 2007 Optical Society of America.

Resonant magnetopolaron effects due to interface phonons in GaAs/AlGaAs multiple quantum well structures

Polaron cyclotron resonance (CR) has been studied in three modulation-doped GaAs/Al0.3Ga0.7As multiple quantum well structures in magnetic field up to 30 T. Large avoided-level-crossing splittings of the CR near the GaAs reststrahlen region, and smaller splittings in the region of the AlAs-like optical phonons of th AlGaAs barriers, are observed. Based on a comparison with a detailed theoretical calculation, the high frequency splitting, the magnitude of which increases with decreasing well width, is assigned to resonant polaron interactions with AlAs-like interface phonons.

Solitary magnon excitations in a one-dimensional antiferromagnet with Dzyaloshinsky-Moriya interactions

We investigate solitary excitations in a model of a one-dimensional antiferromagnet including a single-ion anisotropy and a Dzyaloshinsky-Moriya antisymmetric exchange interaction term. We employ the Holstein-Primakoff transformation, the coherent state ansatz and the time variational principle. We obtain two partial differential equations of motion by using the method of multiple scales and applying perturbation theory. By so doing, we show that the motion of the coherent amplitude must satisfy the nonlinear Schrodinger equation. We give the single-soliton solution.

Uncovering the rules for protein-protein interactions from yeast genomic data

Identifying protein-protein interactions is crucial for understanding cellular functions. Genomic data provides opportunities and challenges in identifying these interactions. We uncover the rules for predicting protein-protein interactions using a frequent pattern tree (FPT) approach modified to generate a minimum set of rules (mFPT), with rule attributes constructed from the interaction features of the yeast genomic data. The mFPT prediction accuracy is benchmarked against other commonly used methods such as Bayesian networks and logistic regressions under various statistical measures. Our study indicates that mFPT outranks other methods in predicting the protein-protein interactions for the database used. We predict a new protein-protein interaction complex whose biological function is related to premRNA splicing and new protein-protein interactions within existing complexes based on the rules generated.