Zebrafish peptidoglycan recognition protein SC (zfPGRP-SC) mediates multiple intracellular signaling pathways

Insect PGRPs can function as bacterial recognition molecules triggering proteolytic and/or signal transduction pathways, with the resultant production of antimicrobial peptides. To explore if zebrafish peptidoglycan recognition protein SC (zfPGRP-SC) has such effects, RNA interference (siRNA) and high-density oligonucleotide microarray analysis were used to identify differentially expressed genes regulated by zfPGRP-SC. The mRNA levels for a set of genes involved in Toll-like receptor signaling pathway, such as TLRs, SARM, MyD88, TRAF6 and nuclear factor (NF)-kappa B2 (p100/p52), were examined by quantitative RT-PCR (QT-PCR). The results from the arrays and QT-PCR showed that the expression of 133 genes was involved in signal transduction pathways, which included Toll-like receptor signaling, Wnt signaling, BMP signaling, insulin receptor signaling, TGF-beta signaling, GPCR signaling, small GTPase signaling, second-messenger-mediated signaling, MAPK signaling, JAK/STAT signaling, apoptosis and anti-apoptosis signaling and other signaling cascades. These signaling pathways may connect with each other to form a complex network to regulate not just immune responses but also other processes such as development and apoptosis. When transiently over-expressed in HEK293T cells, zfPGRP-SC inhibited NF-kappa B activity with and without lipopolysacharide (LPS) stimulation. (C) 2008 Elsevier Ltd. All rights reserved.

The acute effects of microcystin LR on the transcription of nine glutathione S-transferase genes in common carp Cyprinus carpio L.

The glutathione S-transferases play important roles in the detoxification of microcystin. In this experiment, nine glutathione S-transferase genes including cytosolic GSTs (rho, mu, theta, alpha and pi), mitochondrial GST (kappa) and microsomal GSTs (mGST1, mGST2 and mGST3) were cloned from common carp Cyprinus carpio. The mRNA abundance of each carp GST isoform in liver was analyzed by real time PCR. The relative changes after stimulation with microcystin LR were also analyzed: increased levels of transcription of GST alpha, rho and mGST3 isoforms were detected at 6 h post stimulation; the transcription of mu, theta and mGST2 isoforms were relatively stable; and all the GST isoforms except GST kappa and rho recovered to original levels compared with controls at 72 h. It is suggested that MC-LR showed different effects on the transcription of nine carp GST isoforms. (c) 2006 Elsevier B.V. All rights reserved.

Cloning and analysis of 16 Rab genes from macronuclear DNA of Euplotes octocarinatus

Rab proteins belong to the largest family of the Ras superfamily of small GTPase that play an important role in intracellular vesicular traffic. So far, almost 60 members of Rab family have been identified in mammalian cells. To further study the diversity and function of Rab protein in evolution, unicellular protozoa ciliates, Euplotes octocarinatus, were used in this study, Rab genes were screened by PCR method from macronuclear DNA of E. octocarinatus. Sixteen Rab genes were obtained. They share 87.6 - 99.5% identities. Highly conserved GTP-binding domains were found. There are some hot regions that diverse sharply in these genes as well.

Growth-Parameter Spaces and Optical Properties of Cubic Boron Nitride Films on Si(001)

Cubic boron nitride (c-BN) films were deposited on Si(001) substrates in an ion beam assisted deposition (IBAD) system under various conditions, and the growth parameter spaces and optical properties of c-BN films have been investigated systematically. The results indicate that suitable ion bombardment is necessary for the growth of c-BN films, and a well defined parameter space can be established by using the P/a-parameter. The refractive index of BN films keeps a constant of 1.8 for the c-BN content lower than 50%, while for c-BN films with higher cubic phase the refractive index increases with the c-BN content from 1.8 at chi(c) = 50% to 2.1 at chi(c) = 90%. Furthermore, the relationship between n and rho for BN films can be described by the Anderson-Schreiber equation, and the overlap field parameter gamma is determined to be 2.05.

Noiseless method for checking the Peres separability criterion by local operations and classical communication

We present a method for checking the Peres separability criterion in an arbitrary bipartite quantum state rho(AB) within local operations and classical communication scenario. The method does not require noise operation which is needed in making the partial transposition map physically implementable. The main task for the two observers, Alice and Bob, is to measure some specific functions of the partial transposed matrix. With these functions, they can determine the eigenvalues of rho(T)(AB)(B), among which the minimum serves as an entanglement witness.

Method for measuring two-qubit entanglement of formation by local operations and classical communication

We present a parametrically efficient method for measuring the entanglement of formation E-f in an arbitrarily given unknown two-qubit state rho(AB) by local operations and classical communication. The two observers, Alice and Bob, first perform some local operations on their composite systems separately, by which the desired global quantum states can be prepared. Then they estimate seven functions via two modified local quantum networks supplemented a classical communication. After obtaining these functions, Alice and Bob can determine the concurrence C and the entanglement of formation E-f.

Back-to-back Schottky diode adopted for the measurement of GaN films and its Schottky contacts

A new measurement method for GaN films and their Schottky contacts is reported in this paper. Instead of the fabrication of Ohmic contacts, this measurement is based on a special back-to-back Schottky diode that has a rectifying character. A mathematical model indicates that the electronic parameters of the materials can be deduced from the device's I-V data. In the experiment of an unintentionally doped n-type GaN layer with a residual carrier density 7 x 10(16) cm(-3), the analysis by the new method gives the layer's sheet resistance rho(s) = 497 Omega, the electron mobility mu(n) =, 613 cm(2) V-1 s(-1) and the ideality factor of the Ni/Au-GaN Schottky contacts n = 2.5, which are close to the data obtained by the traditional measurements: rho(s) = 505 Omega, mu(n) = 585 cm(2) V-1 s(-1) and n = 3.0. The method reported can be adopted not only for GaN films but also for other semiconductor materials, especially in the cases where Ohmic contacts of high quality are hard to make or their fabricating process affects the film's character.

Method for detecting concurrence without the structural physical approximation by local operations and classical communication

We present a modified method for detecting the concurrence in an arbitrary two-qubit quantum state rho(AB) with local operations and classical communication. In this method, it is not necessary for the two observers to prepare the quantum state rho(AB) by the structural physical approximation. Their main task is to measure four specific functions via two local quantum networks. With these functions they can determine the concurrence and then the entanglement of formation.

Fabrication and properties of Sb-doped ZnO thin films grown by radio frequency (RF) magnetron sputtering

Sb-doped and undoped ZnO thin films were deposited on Si (100) substrates by radio frequency (RF) magnetron sputtering. X-ray diffraction (XRD) and scanning electron microscopy (SEM) analyses revealed that all the films had polycrystalline wurtzite structure and c-axis preferred orientation. Room temperature Hall measurements showed that the as-grown films were n-type and conducting (rho similar to 1-10 Omega cm). Annealing in a nitrogen ambient at 400 degrees C for 1 h made both samples highly resistive (rho > 10(3) Omega cm). Increasing the annealing temperature up to 800 C, the resistivity of the ttndoped ZnO film decreased gradually, but it increased for the Sb-doped ZnO film. In the end, the Sb-doped ZnO film annealed at 800 C became semi-insulating with a resistivity of 10(4)Omega cm. In addition, the effects of annealing treatment and Sb-doping on the structural and electrical properties are discussed. (c) 2006 Elsevier B.V. All rights reserved.

Magneto-transport characteristics of two-dimensional electron gas for Si delta-doped InAlAs/InGaAs single quantum well

Magneto-transport measurements have been carried out on a Si heavily delta-doped In0.52Al0.48As/In(0.53)G(0.47)As single quantum well in the temperature range between 1.5 and 60 K under magnetic field up to 10 T. We studied the Shubnikov-de Haas(SdH) effect and the Hall effect for the In0.52Al0.48As/In(0.53)G(0.47)As single quantum well occupied by two subbands, and have obtained the electron concentration, mobility, effective mass and energy levels respectively. The electron concentrations of the two subbands derived from mobility spectrum combined with multi-carrier fitting analysis are well consistent with the result from the SdH oscillation. From fast Fourier transform analysis for d(2)rho/dB(2)-1/B, it is observed that there is a frequency of f(1)-f(2) insensitive to the temperature, besides the frequencies f(1), f(2) for the two subbands and the frequency doubling 2f(1), both dependent on the temperature. This is because That the electrons occupying the two different subbands almost have the same effective mass in the quantum well and the magneto-intersubband scattering between the two subbands is strong.

Magnetotransport in two-dimensional electron gas: The interplay between spin-orbit interaction and Zeeman splitting

We investigate theoretically the interplay between Zeeman splitting, Rashba spin-orbit interaction (RSOI), and Dresselhaus spin-orbit interaction (DSOI) and its influence on the magnetotransport property of two-dimensional electron gas (2DEG) at low temperature. Our theoretical results show that the nodes of the beating patterns of the magnetoresistivity rho(xx) for 2DEG with RSOI or DSOI alone depend sensitively on the total spin splitting induced by these three spin splitting mechanisms. It is interesting to find that the eigenstates in the presence of RSOI alone are connected with those in the presence of DSOI alone but with opposite Zeeman splitting by a time-reversal transformation. Consequently, the magnetoresistivities exhibit exactly the same oscillation patterns for these two cases. For strong RSOI or DSOI alone, the magneto-oscillation of rho(xx) shows two distinct periods. For 2DEG with both RSOI and DSOI, the beating patterns vanish for equal RSOI and DSOI strengths and vanishing Zeeman splitting. They will appear again, however, when Zeeman splitting or the difference between RSOI and DSOI strengths increases.

Ras 超家族蛋白的起源演化研究

Ras 超家族蛋白是真核生物中普遍存在的一类小分子GTP 结合蛋白。它们 具有高度保守的GTP 结合结构域，根据序列结构和细胞功能被分为七个家族： Sar1、Arf、SRβ、Ran、Rab、Rho 和Ras。这些蛋白分别行使着真核生物特有的 细胞功能，诸如运输小泡的形成和转运（Sar1、Arf、Rab），胞质骨架的建成（Rho）， 细胞核-胞质运输及核膜重建（Ran）等，其起源演化和真核细胞的起源密切相关。 本文利用生物信息学手段和分子生物学实验调查研究了原核生物和原生生物中 Ras 超家族蛋白同源物的存在情况，并进行了分子系统分析，对Ras 超家族蛋白 的起源演化问题进行了较为深入、系统的探讨。获得了以下结果和结论： 1）通过原核生物基因组的搜索和序列结构分析，在一些真细菌中首次鉴定 出了高度相似于真核生物Ras 超家族蛋白的原核生物同源物，且实验证明它们的 基因具有表达活性；在原细菌中的产甲烷菌和热原体中也发现有序列分歧较大的 同源物。并在更多的真细菌种类中鉴定出了更多的前人已报道的另一种小分子 GTP 结合蛋白—MglA。序列比对分析表明MglA 蛋白具有自己独特的序列特征， 与真核生物的Ras 超家族蛋白序列差异较大。进一步的分子系统分析显示：真核 生物Ras 超家族蛋白的七个家族中，Ran、Rab、Rho 和Ras 等四个家族聚在一 起，上述我们所鉴定的真细菌的Ras 超家族蛋白同源物则紧聚在其外围；真核生 物的另三个家族（Sar1、Arf、SRβ）聚成另一枝，并接着与产甲烷原细菌的的同 源物及真细菌的MglA 蛋白聚在一起。这些结果表明：Ras 超家族蛋白不是前人 所认为的为真核生物所特有，实际上在一些原核生物中就已产生；真核生物Ras 超家族蛋白的祖先也不太可能是前人所认为的为真细菌的MglA；真核生物Ras 超家族蛋白的七个家族可能有两种不同的起源：Ran、Rab、Rho 和Ras 等可能 来源于蓝细菌或蛋白菌，或二者的共同祖先，而Sar1、Arf 和SRβ 可能来源于产 甲烷原细菌，这也可能反映了真核细胞“融合起源”的历史。 2）通过搜索一些较为低等的单细胞真核生物——原生生物基因组中Ras 超 家族蛋白，并结合一系列其他处在不同进化地位真核生物的Ras 超家族蛋白进行 分析，发现Sar1、Arf、Rab 和Ran 家族的蛋白在真核生物中普遍存在，而SRβ、 Rho 和Ras 家族蛋白在有些真核生物中未找到。根据各家族蛋白在真核生物中的分布情况推测在真核生物的最近共同祖先中存在的Ras 超家族蛋白可能有下列 两种情况：（1）最近的共同祖先已经具有了所有七个家族的蛋白，并且至少有 11 个成员：1 个Sar1、1 个SRβ、3 个Arf（Arf1、Arl1、Arl2）、3 个Rab（Rab1、 Rab6、Rab11）、1 个Ran、1 个Rho（Rac）和1 个Ras（RheB）。因而，部分真 核生物中缺少SRβ、Rho 和Ras 家族蛋白很可能是因基因丢失所致。植物中Ras 家族蛋白的缺少应该是由于在进化早期，其祖先绿藻丢失了单个Ras 家族蛋白基 因所致；（2）根据Cavalier-Smith 的真核生物划分为单鞭毛（变形虫类、真菌和 后生动物）和双鞭毛（藻类、植物和除变形虫外的原生动物）两大类的分类观点， 真核生物最近的共同祖先可能只具有除Ras 家族而外的六个家族的成员，而Ras 家族蛋白则是在此两大类群分化以后在单鞭毛类生物中才产生的，多数双鞭毛类 生物如原生动物、绿藻和植物中没有Ras 的情况应该是一种祖征，而个别双鞭毛 类生物如红藻具有的Ras 家族蛋白则很可能是从单鞭毛类生物那里水平基因转 移而来的。至于SRβ 和Rho 家族蛋白在部分物种中的缺少，则还是可能因为基 因丢失所致。此外，变形虫类生物中大量的Ras 超家族蛋白提示基因组的大小或 进化地位的高低并不是Ras 超家族蛋白成员多少的决定性因素，而细胞相应生理 活动的需求才是家族成员增多的关键。

A new structure of In-based ohmic contacts to n-type GaAs

Electrical, structural and reaction characteristics of In-based ohmic contacts to n-GaAs were studied. Attempts were made to form a low-band-gap interfacial phase of InGaAs to reduce the barrier height at the metal/semiconductor junction, thus yielding low-resistance, highly reliable contacts. The contacts were fabricated by e-beam sputtering Ni, NiIn and Ge targets on VPE-grown n(+)-GaAs film (approximate to 1 mu m, 2 x 10(18) cm(-3)) in ultrahigh vacuum as the structure of Ni(200 Angstrom)/NiIn(100 Angstrom)/Ge(40 Angstrom)/n(+)-GaAs/SI-GaAs, followed by rapid thermal annealing at various temperatures (500-900 degrees C). In this structure, a very thin layer of Ge was employed to play the role of heavily doping donors and diffusion limiters between In and the GaAs substrate. Indium was deposited by sputtering NiIn alloy instead of pure In in order to ensure In atoms to be distributed uniformly in the substrate; nickel was chosen to consume the excess indium and form a high-temperature alloy of Ni3In. The lowest specific contact resistivity (rho(c)) of (1.5 +/- 0.5)x 10(-6) cm(2) measured by the Transmission Line Method (TLM) was obtained after annealing at 700 degrees C for 10 s. Auger sputtering depth profile and Transmission Electron Microscopy (TEM) were used to analyze the interfacial microstructure. By correlating the interfacial microstructure to the electronical properties, InxGa1-xAs phases with a large fractional area grown epitaxially on GaAs were found to be essential for reduction of the contact resistance.

Numerical simulation of a bubble rising in shear-thinning fluids

The motion of a single bubble rising freely in quiescent non-Newtonian viscous fluids was investigated experimentally and computationally. The non-Newtonian effects in the flow of viscous inelastic fluids are modeled by the Carreau theological model. An improved level set approach for computing the incompressible two-phase flow with deformable free interface is used. The control volume formulation with the SIMPLEC algorithm incorporated is used to solve the governing equations on a staggered Eulerian grid. The simulation results demonstrate that the algorithm is robust for shear-thinning liquids with large density (rho(1)/rho(g) up to 10(3)) and high viscosity (eta(1)/eta(g) up to 10(4)). The comparison of the experimental measurements of terminal bubble shape and velocity with the computational results is satisfactory. It is shown that the local change in viscosity around a bubble greatly depends on the bubble shape and the zero-shear viscosity of non-Newtonian shear-thinning liquids. The shear-rate distribution and velocity fields are used to elucidate the formation of a region of large viscosity at the rear of a bubble as a result of the rather stagnant flow behind the bubble. The numerical results provide the basis for further investigations, such as the numerical simulation of viscoelastic fluids. (C) 2010 Elsevier B.V. All rights reserved.

Circumstantial Evidence for a Soft Nuclear Symmetry Energy at Suprasaturation Densities

Within an isospin- and momentum-dependent hadronic transport model, it is shown that the recent FOPI data on the pi(-)/pi(+) ratio in central heavy-ion collisions at SIS/GSI energies [Willy Reisdorf , Nucl. Phys. A 781, 459 (2007)] provide circumstantial evidence suggesting a rather soft nuclear symmetry energy E-sym(rho) at rho >= 2 rho(0) compared to the Akmal-Pandharipande-Ravenhall prediction. Some astrophysical implications and the need for further experimental confirmations are discussed.