Prevalent positive epistasis in Escherichia coli and Saccharomyces cerevisiae metabolic networks

Epistasis refers to the interaction between genes. Although high-throughput epistasis data from model organisms are being generated and used to construct genetic networks(1-3), the extent to which genetic epistasis reflects biologically meaningful interactions remains unclear(4-6). We have addressed this question through in silico mapping of positive and negative epistatic interactions amongst biochemical reactions within the metabolic networks of Escherichia coli and Saccharomyces cerevisiae using flux balance analysis. We found that negative epistasis occurs mainly between nonessential reactions with overlapping functions, whereas positive epistasis usually involves essential reactions, is highly abundant and, unexpectedly, often occurs between reactions without overlapping functions. We offer mechanistic explanations of these findings and experimentally validate them for 61 S. cerevisiae gene pairs.

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

Understanding the dynamics of eukaryotic transcriptome is essential for studying the complexity of transcriptional regulation and its impact on phenotype. However, comprehensive studies of transcriptomes at single base resolution are rare, even for modern organisms, and lacking for rice. Here, we present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative splicing in the rice transcriptome revealed that alternative cis-splicing occurred in similar to 33% of all rice genes. This is far more than previously reported. In addition, we also identified 234 putative chimeric transcripts that seem to be produced by trans-splicing, indicating that transcript fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell. Taken together, our data provide extensive evidence that transcriptional regulation in rice is vastly more complex than previously believed.

Chemical Constituents from the Leaves and Stems of Schisandra lancifolia

A new nortriterpenoid, 20-hydroxymicrandilactone D (1) and a novel lignan glycoside, lancilignanside A (2) were isolated from leaves and stems of Schisandra lancifolia, together with three known nortriterpenoids (3-5) and nine known phenolics (6-14). The structures of new compounds 1 and 2 were determined by detailed analysis of their 1D and 2D NMR spectra, and chemical evidences. In addition, compounds 1-2, 6-7, and 9-11 showed anti-human immunodeficiency virus (HIV)-1 activities with 50% effective concentration (EC50) in the range of 3.0-99.0 mu g/ml. Compound 12 was not bioactive in this assay with EC50 more than 200 mu g/ml.

Molecular and morphological analysis of endangered species Gymnodiptychus integrigymnatus (Teleostei: Cyprinidae)

Gymnodiptychus integrigymnatus is a critically endangered species endemic to the Gaoligongshan Mountains. It was thought to be only distributed in several headwater-streams of the Longchuanjiang River (west slope of the Gaoligongshan Mountains, belonging to the Irrawaddy River drainage). In recent years, dozens of G. integrigymnatus specimens have been collected in some streams on the east slope of the Gaoligongshan Mountains (the Salween drainage). We performed a morphological and genetic analyses (based on cytochrome b and D-loop) of the newly discovered populations of G. integrigymnatus to determine whether the degree of separation of these populations warrants species status. Our analysis from the cytochrome b gene revealed that nine individuals from the Irrawaddy drainage area and seven individuals from the Salween drainage area each have only one unique haplotype. The genetic distance between the two haplotypes is 1.97%. Our phylogenetic analysis revealed that G. integrigymnatus is closely related to highly specialized schizothoracine fishes. Analysis from the mitochondrial control region revealed that G. integrigymnatus has relatively high genetic diversity (pi was 0.00891 and h was 0.8714), and individuals from different river drainages do not share the same haplotypes. The AMOVA results indicated 87.27% genetic variability between the Salween and Irrawaddy populations. Phylogenetic trees show two major geographic groups corresponding to the river systems. We recommend that G. integrigymnatus should be considered as a high priority for protected species status in the Gaoligongshan Mountains National Nature Reserve, and that the area of the Gaoligongshan Mountains National Nature Reserve should be expanded to cover the entire distribution of G. integrigymnatus. Populations of G. integrigymnatus from different river systems should be treated as evolutionarily significant units.

Threatened fishes of the world: Plesiomyzon baotingensis (Zheng & Chen, 1980) (Cypriniformes: Balitoridae)

We are grateful to all the voluntary donors of DNA samples in this study. We thank Hui Zhang and Yan-jiao Li for their technical help. We also thank Dr. Darren Curnoe for his critical reading of the manuscript. This study was supported by grants from the National 973 project of China (2007CB947701,2007CB815705), the Chinese Academy of Sciences (KSCX1YW-R-34, Westlight Doctoral Program), the National Natural Science Foundation of China (30525028, 30700445, 30630013 and 30771181), and the Natural Science Foundation of Yunnan Province of China (2007C100M, 2009CD107).

Anomalous photogalvanic effect of circularly polarized light incident on the two-dimensional electron gas in AlxGa1-xN/GaN heterostructures at room temperature

Under normal incidence of circularly polarized light at room temperature, a charge current with swirly distribution has been observed in the two-dimensional electron gas in Al0.25Ga0.75N/GaN heterostructures. We believe that this anomalous charge current is produced by a radial spin current via the reciprocal spin Hall effect. It suggests a new way to research the reciprocal spin Hall effect and spin current on the macroscopic scale and at room temperature.

Structural, elastic, and electronic properties of cubic perovskite BaHfO3 obtained from first principles

We investigated the structural, elastic, and electronic properties of the cubic perovskite-type BaHfO3 using a first-principles method based on the plane-wave basis set. Analysis of the band structure shows that perovskite-type BaHfO3 is a wide gap indirect semiconductor. The band-gap is predicted to be 3.94 eV within the screened exchange local density approximation (sX-LDA). The calculated equilibrium lattice constant of this compound is in good agreement with the available experimental and theoretical data reported in the literatures. The independent elastic constants (C-11, C-12, and C-44), bulk modules B and its pressure derivatives B', compressibility beta, shear modulus G, Young's modulus Y, Poisson's ratio nu, and Lame constants (mu, lambda) are obtained and analyzed in comparison with the available theoretical and experimental data for both the singlecrystalline and polycrystalline BaHfO3. The bonding-charge density calculation make it clear that the covalent bonds exist between the Hf and 0 atoms and the ionic bonds exist between the Ba atoms and HfO3 ionic groups in BaHfO3. (C) 2009 Elsevier B.V. All rights reserved.

Spin relaxation and dephasing mechanism in (Ga,Mn)As studied by time-resolved Kerr rotation

Spin dynamics in (Ga,Mn)As films grown on GaAs(001) was investigated by Time-resolved magneto-optical Kerr effect. The Kerr signal decay time of (Ga,Mn)As without external magnetic field applied was found to be several hundreds picoseconds, which suggested that photogenerated polarized holes and magnetic ions are coupled as a ferromagnetic system. Nonmonotonic temperature dependence of relaxation and dephasing (R&D) time and Larmor frequency manifests that Bir-Aronov-Pikus mechanism dominates the spin R&D time at low temperature, while D'yakonov-Perel mechanism dominates the spin R&D time at high temperature, and the crossover between the two regimes is Curie temperature.

An investigation of the mode characteristics of SOI submicron rib waveguides using the film mode matching method

The mode characteristics of SOI (silicon-on-insulator) submicron rib waveguides are very different from those of micrometer-sized ones. Using the full-vector film mode matching method, we propose a simple criterion to determine whether a waveguide mode is guided or not. The single-mode condition for deep-etched waveguides is obtained using this criterion. We also obtain the inherent TM mode leakage and sharp cancelation effects due to TE-TM mode coupling in shallow-etched rib waveguides from numerical simulations, which agree well with the analytical results based on total internal reflection and interference theories.

A new p-n structure ultraviolet photodetector with p(-)-GaN active region

A new ultraviolet photodetector of employing p menus type GaN (p(-)-GaN) as the active layer is proposed. It is easy to obtain the p(-)-GaN layer with low carrier concentration. As a result, the depletion region can be increased and the quantum efficiency can be improved. The influence of some structure parameters on the performance of the new device is investigated. Through the simulation calculation, it is found that the quantum efficiency increases with the decrease of the barrier height between the metal electrode and the p(-)-GaN layer, and it is also found that the quantum efficiency can be improved by reducing the thickness of the p(-)-GaN layer. To fabricate the new photodetector with high performance, we should employ thin p(-)-GaN layer as the active layer and reduce the Schottky barrier height.

森林流域单元水文模型的构建与应用

目前全球缺水、水污染、洪涝灾害以及水土流失仍然非常严重，尤其在我国北方地区。流域水文模型可用来进行不同需水管理的情景分析，为解决我国水问题提供科学依据。分布式水文模型是流域水文模型的发展方向，具有显著特点：1）应用前景广泛，不仅可以模拟流域水文过程，还可以协助模拟泥沙或污染物的运移过程，为水利工程设计、水土保持、环境保护等领域提供技术支持；2）能够预测流域土地利用或气候变化下的流域水文响应过程变化，为管理部门提供决策支持；3）模型所需要的参数全部具有物理意义，可通过实际测量确定，适合模拟实测系列较短或是无观测流域的水文过程；4）对于目前国际水文界的前沿问题—水文尺度转换提供了一种有效的解决途径。 然而分布式水文模型还不完善，如1)真实性问题。对一些水文过程和边界条件还不确定。2)尺度转换问题。目前很少考虑尺度对参数有效性的影响。3)检验问题。还无法判断对有些难以测量的水文状态变量的模拟正确与否。4)计算时间和数据存储的问题。有些分布式水文模型虽然具有很强的水文物理基础和完善的模型结构，但是计算时间过长和(或)数据存储过大，难以应用。上述问题的核心就是对分布式水文模型的核心—单元水文模型的研究不够，需要为进一步完善单元水文模型进行研究。 本文采用饱和入渗理论、Saint-Venant方程、Richards方程、Penman-Monteith方程等等构建了以有限差分法求解的适用于森林流域的单元水文模型，并通过实验室模拟试验和坡地径流场资料进行了验证，主要结论为： 通过不同坡度和不同雨强下的室内坡面产汇流实验模拟，表明：该模型模拟的坡面流和壤中流过程与实测过程基本一致，峰现时间、径流历时、峰值流量、出流总量模拟值与实测值的相对误差均较小，基本小于10%。模型的模拟精度较高，实用性较强，为深入研究壤中流机制和改进流域降雨-径流模型提供了理论依据。 通过坡地径流观测场实测资料的验证，表明：该模型模拟的坡面流过程精度较高，累计流量的精度更高于小时过程的精度，离差系数、效率系数、确定系数均较理想，具有应用价值，有助于改善分布式水文模型在森林流域的模拟效果。

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.

Theoretical foundation of Zisman's empirical equation for wetting of liquids on solid surfaces

Theories of wetting of liquids on solid surfaces under the condition that van der Waals force is dominant are briefly reviewed. We show theoretically that Zisman's empirical equation for wetting of liquids on solid surfaces is a linear approximation of the Young-van der Waals equation in the wetting region, and we express the two parameters in Zisman's empirical equation in terms of the dielectric polarizabilities of the solid and liquids. The materials contained in this paper are suitable for physics teaching of wetting phenomena for undergraduate, graduate, general physicist, etc.