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.

Differential selection on gene translation efficiency between the filamentous fungus Ashbya gossypii and yeasts

Background: The filamentous fungus Ashbya gossypii grows into a multicellular mycelium that is distinct from the unicellular morphology of its closely related yeast species. It has been proposed that genes important for cell cycle regulation play central

A new species of genus Pseudogyrinocheilus (Teleostei: Cyprinidae) from Guangxi, China

A new species, Pseudogyrinocheilus longisulcus, was discovered from a tributary of Pearl River in Jingxi Co., Guangxi, China, The new species can be distinguished from other species of Pseudogyrinocheilus by the following combination of characteristics: prolonged post-labial grooves, and extended antero-medially close to anterior end of middle lower lip, but not meeting with its counterpart; posterior margin of lower lip free; scales of abdomen from thorax to pectoral-fin base embedded under skin; lateral-line scales 40-42; dark stripe longitudinal along lateral line on flank. The key to the species of Pseudogyrinocheilus is provided.

Characteristics of the microbial communities in the integrated vertical-flow constructed wetlands

Microorganisms play an important role in removing pollutants from constructed wetlands. We investigated the microbial characteristics in a novel integrated vertical-flow constructed wetland (IVCW), which has been in operation in Wuhan, China since 1998. We used phospholipid fatty acid (PLFA) and amoA gene to analyze the structure and diversity of the microbial community within the IVCW. PLFA results suggested that the amount of bacterial PLFA was significantly higher than that of fungal PLFA, but the total microbial biomass represented by PLFA index was low in the system. Microbial spatial distribution showed significantly higher bacterial (both G(+) and G(-)) and fungal biomass in the surface than in the subsurface layers. The ratios of monounsaturated to branched PLFA demonstrated that an anaerobic layer sandwiched by two aerobic layers existed in the IVCW, consistent with the redox potential results. Analysis of the amoA revealed the presence of Nitrosomonas-like sequences in the surface substrate of the downflow chamber and apparent diversities of ammonia-oxidizing bacteria in the system. These results suggest that microorganisms, despite their relatively low biomass, have inhabited the IVCW, and the results will offer some valuable information on microbe to system designers and managers.

Functional analysis of FP25K of Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus

The fp25k gene of Helicoverpa armigera single nucleocapsid nucleopolyhedrovirus (HearNPV) was studied. HearNPV fp25k gene transcription was found starting from about 18 h post-infection, and protein could be detected from the same time with antiserum against FP25K. To study the function of HearNPV fp25k, a recombinant HearNPV (HaBacWD11) with an enhanced green fluorescent protein (GFP) gene replacing the fp25k was constructed using HaBacHZ8, a bacmid of HearNPV that lacks the polyhedrin gene. Growth curve analysis showed that HaBacWD11 produced higher titres of budded viruses (BVs) than its wild-type counterpart HaBacHZ8-GFP. Electron microscopic analysis indicated that at the late stage of infection, the number of intranuclear enveloped nucleocapsids in HaBacWD11-infected cells was much less than that of HaBacHZ8-GFP. A rescue recombinant virus HaBacWD14 was constructed by reintroducing fp25k gene into HaBacWD11. The growth curve and electron microscopic analysis of the rescued recombinant confirmed that the increase of BV yield and the decrease of the virion production in infected cells were the result of fp25k deletion. The expression of membrane fusion protein (Ha133) and ODV-E66 were studied using the FP25K mutants HaBacWD11 and HaBacHZ8-GFP. Unlike FP25K mutants in Autographa californica multicapsid NPV (AcMNPV), which caused an increase in the expression of membrane fusion protein GP64 and a decrease of ODV-E66, no obvious changes at the expression level of Ha133 and ODV-E66 were observed in HearNPV FP25K mutant.

Qianlabeo striatus, a new genus and species of Labeoninae from Guizhou Province, China (Teleostei : Cyprinidae)

Qianlabeo striatus gen. et sp. nov. is described from a stream tributary to the Beipan Jiang of the upper Zhu Jiang (Pearl River) drainage in Matou, Anshun County, Guizhou Province, China. This monotypic genus is mainly characterized by its oromadibular morphology, namely an upper lip only present in and fully adnate to the side of the upper jaw, not covered by the pendulous rostral fold; the median portion of the upper jaw lacking an upper lip but bearing a thin, flexible and cornified cutting edge that is fully covered by the pendulous rostral fold; a postlabial groove prolonged, extended anteromedially close to the anteromost point of the midline of the lower lip but not to meet with its counterpart. The type species of this genus, Q. striatus has a longitudinal dark stripe along the side of the body.

First-principles study on the structural and electronic properties of ultrathin ZnO nanofilms

First-principles calculations; ZnO nanofilms; Electronic properties; Quantum effects； NANOBELTS; NANORINGS; WURTZITE; ENERGY Abstract: Using first-principles density-functional calculations, we have studied the structural and electronic properties Of Ultrathin ZnO {0001} nanofilms. The structural parameters, the charge densities, band structures and density of states have been investigated. The results show that there are remarkable charge transfers from Zn to O atoms in the ZOO nanofilms. All the ZOO nanofilms exhibit direct wide band gaps compared with bulk counterpart, and the gap decreases with increased thickness of the nanofilms. The decreased band gap is associated with the weaker ionic bonding within layers and the less localization of electrons in thicker films. A staircase-like density of states occurs at the bottom of conduction band, indicating the two-dimensional quantum effects in ZnO nanofilms.

Direct observation of excitonic polaron in InAs/GaAs quantum dots

We report a direct observation of excitonic polaron in InAs/GaAs quantum dots using the photoluminescence (PL) spectroscopy. We observe that a new peak s' emerges below the s-shell which has anomalous temperature dependence emission energy. The peak s' anticrosses with s at a certain temperature, with a large anticrossing gap up to 31 meV. The behavior of the new peak, which cannot be interpreted using Huang-Rhys model, provides a direct evidence for strong coupling between exciton and LO phonons, and the formation of the excitonic polaron. The strong coupling between exciton and phonons opens a way to coherently control the polaron states.

Structure and magnetic property of (Ga,Cr)As films with different Cr contents

We report variations in structure and magnetic property of (Ga,Cr) As films with increasing Cr content x. Due to phase segregation, a tendency towards inhomogeneous distribution with increasing x is confirmed. Barkhausen-like magnetization and large remanent magnetic moment were also clearly observed in the samples with x<5.3%. However, spin-glass-like behaviors were observed in both dc and ac magnetic measurements, which might originate from the competition between magnetic nucleation and frustration of long ferromagnetic order in this inhomogeneous system. All the samples exhibit characteristics of variable-range hopping conductivity at temperature below 150 K. Typical magnetic circular dichroism structure was observed in the sample with x=7.9%.

Proposal of an Ultracompact Triplexer Using Photonic Crystal Waveguide with an Air Holes Array

We propose an ultracompact triplexer based on a shift of the cutoff frequency of the fundamental mode in a planar photonic crystal waveguide (PCW) with a triangular lattice of air holes. The shift is realized by modifying the radii of the border holes adjacent to the PCW core. Some defect holes are introduced to control the beam propagation. The numerical results obtained by the finite-difference time-domain method show that the presented triplexer can separate three specific wavelengths, i.e. 1310, 1490 and 1550 nm with the extinction ratios higher than - 18 dB. The designed device with a size as compact as 12 mu m x 6.5 mu m is feasible for the practical application, and can be utilized in the system of fiber to the home.

Dislocation scattering in AlxGa1-xN/GaN heterostructures

The theoretical electron mobility limited by dislocation scattering of a two-dimensional electron gas confined near the interface of AlxGa1-xN/GaN heterostructures was calculated. Based on the model of treating dislocation as a charged line, an exponentially varied potential was adopted to calculate the mobility. The estimated mobility suggests that such a choice can simplify the calculation without introducing significant deviation from experimental data, and we obtained a good fitting between the calculated and experimental results. It was found that the measured mobility is dominated by interface roughness and dislocation scattering at low temperatures if dislocation density is relatively high (>10(9) cm(-2)), and accounts for the nearly flattening-out behavior with increasing temperature.

The formation and electronic structures of 3d transition-metal atoms doped in silicon nanowires

Using first-principles methods, we systematically study the mechanism of defect formation and electronic structures for 3d transition-metal impurities (V, Cr, Mn, Fe, and Co) doped in silicon nanowires. We find that the formation energies of 3d transition-metal impurities with electrons or holes at the defect levels always increase as the diameters of silicon nanowires decrease, which suggests that self-purification, i.e., the difficulty of doping in silicon nanowires, should be an intrinsic effect. The calculated results show that the defect formation energies of Mn and Fe impurities are lower than those of V, Cr, and Co impurities in silicon nanowires. It indicates that Mn and Fe can easily occupy substitutional site in the interior of silicon nanowires. Moreover, they have larger localized moments, which means that they are good candidates for Si-based dilute magnetic semiconductor nanowires. The doping of Mn and Fe atom in silicon nanowires introduces a pair of energy levels with t(2) symmetry. One of which is dominated by 3d electrons of Mn or Fe, and the other by neighboring dangling bonds of Si vacancies. In addition, a set of nonbonding states localized on the transition-metal atom with e symmetry is also introduced. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.3000445]

Epitaxial Semiconductor Quantum Wires

The investigation on the direct epitaxial quantum wires (QWR) using MBE or MOCVD has been persuited for more than two decades, more lengthy in history as compared with its quantum dot counterpart. Up to now, QWRs with various structural configurations have been produced with different growth methods. This is a reviewing article consisting mainly of two parts. The first part discusses QWRs of various configurations, together with laser devices based on them, in terms of the two growth mechanisms, self-ordering and self-assembling. The second part gives a brief review of the electrical and optical properties of QWRs.

Influence of Si doping on magnetic properties of (Ga,Mn)As

We have systematically investigated the magnetic properties of Si-doped (Ga,Mn)As films. When the Si content is low, both Curie temperature (T-C) and carrier density (p) decrease compared with undoped (Ga,Mn)As, whereas a monotonic increase of T-C and p is observed with further increase in the doping content of Si. We discuss the possible mechanism for the changes obtained by different Si doping contents and attribute the results to a competition between the existence of Si-Ga (Si substitutes for Ga site) that acts as a donor and Si-I (Si interstitials) which is in favor of the improvement of ferromagnetism. (C) 2008 Elsevier B.V. All rights reserved.

Characterization of ZnMgO hexagonal-nanotowers/films on m-plane sapphire synthesized by metal organic chemical vapour deposition

ZnMgO hexagonal-nanotowers/films grown on m-plane sapphire substrates were successfully synthesized using a vertical low-pressure metal organic chemical vapour deposition system. The structural and optical properties of the as-obtained products were characterized using various techniques. They were grown along the non-polar [1 0 (1) over bar 0] direction and possessed wurtzite structure. The ZnMgO hexagonal-nanotowers were about 200 nm in diameter at the bottom and 120 nm in length. Photoluminescence and Raman spectra show that the products have good crystal quality with few oxygen vacancies. With Mg incorporation, multiple-phonon scattering becomes weak and broad, and the intensities of all observed vibrational modes decrease. The ultraviolet near band edge emission shows a clear blueshift (as much as 100 meV) and broadening compared with that of pure ZnO products.