Rapid evolution of mammalian X-linked testis microRNAs

Background: MicroRNAs (miRNAs), which are small, non-coding RNAs approximately 21-nucleotides in length, have become a major focus of research in molecular biology. Mammalian miRNAs are proposed to regulate approximately 30% of all protein-coding genes. P

Cloning and characterization of the first amphibian bradykinin gene

More than ten bradykinin-related peptides and their cDNAs; have been identified from amphibians, but their genes are unknown. In present study, four cDNAs encoding one, two, four and six copies of bradykinin-related peptides were cloned from the frog (Odorrana grahami) skin cDNA library, respectively. Three bradykinin-related peptides (bradykinin, Thr6-bradykinin, Leu5Thr6-bradykinin) were deduced from these four cDNA sequences. Based on the cDNA sequence, the gene sequence encoding an amphibian bradykinin-related peptide from O. grahami was determined. It is composed of 7481 base pairs including two exons and two introns. The first exon codes signal peptide and the second exon codes acidic spacer peptide and Thr6-bradykinin. The promoter region of the bradykinin gene contains several putative recognition sites for nuclear factors, such as SRY, GATA-1, LYF-1, DeltaE, CDXA, NKX-2.5, MIF1 and S8. The current work may facilitate to understand the regulation and possible functions of amphibian skin bradykinin-related peptides. (C) 2009 Elsevier Masson SAS. All rights reserved.

DEVELOPMENT OF MICROSATELLITE LOCI FOR PINUS KORAIENSIS (PINACEAE)

Premise of the study: Microsatellite markers were developed for Pinus koraiensis to characterize its genetic diversity and understand its population structure. Methods and Results: Using the Fast Isolation by AFLP of Sequences COntaining (FIASCO) Repeats protocol, 20 primer sets were developed in Chinese populations of P. koraiensis. Three of the markers showed polymorphism with two alleles per locus when assessed in a sample of two populations of P. koraiensis from the Changbai Mountain in the Jilin Province of China. Five and three loci were successfully amplified in P. taiwanensis and P. massoniana, respectively. The amplification size of these loci matches those in P. koraiensis. Conclusions: These markers may be useful for further investigation of population genetics of P. koraiensis.

A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution

Nectogaline shrews are a major component of the small mammalian fauna of Europe and Asia, and are notable for their diverse ecology, including utilization of aquatic habitats. So far, molecular phylogenetic analyses including nectogaline species have been unable to infer a well-resolved, well-supported phylogeny, thus limiting the power of comparative evolutionary and ecological analyses of the group. Here, we employ Bayesian phylogenetic analyses of eight mitochondrial and three nuclear genes to infer the phylogenetic relationships of nectogaline shrews. We subsequently use this phylogeny to assess the genetic diversity within the genus Episoriculus, and determine whether adaptation to aquatic habitats evolved independently multiple times. Moreover, we both analyze the fossil record and employ Bayesian relaxed clock divergence dating analyses of DNA to assess the impact of historical global climate change on the biogeography of Nectogalini. We infer strong support for the polyphyly of the genus Episoriculus. We also find strong evidence that the ability to heavily utilize aquatic habitats evolved independently in both Neomys and Chimarrogale + Nectogale lineages. Our Bayesian molecular divergence analysis suggests that the early history of Nectogalini is characterized by a rapid radiation at the Miocene/Pliocene boundary, thus potentially explaining the lack of resolution at the base of the tree. Finally, we find evidence that nectogalines once inhabited northern latitudes, but the global cooling and desiccating events at the Miocene/Pliocene and Pliocene/Pleistocene boundaries and Pleistocene glaciation resulted in the migration of most Nectogalini lineages to their present day southern distribution. (C) 2010 Elsevier Inc. All rights reserved.

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

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.

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]

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.

Structural, electrical, and optical properties of InAsxSb1-x epitaxial films grown by liquid-phase epitaxy

The InAsxSb1-x films were grown on (100) GaSb substrates by liquid-phase epitaxy, and their structural, electrical, and optical properties were investigated. The high-resolution x-ray diffraction results reveal that the single crystalline InAsxSb1-x films with a midrange composition are epitaxially grown on the GaSb substrates. Temperature dependence of the Hall mobility was theoretically modeled by considering several predominant scattering mechanisms. The results indicate that ionized impurity and dislocation scatterings dominate at low temperatures, while polar optical phonon scattering is important at room temperature (RT). Furthermore, the InAsxSb1-x films with the higher As composition exhibit the better crystalline quality and the higher mobility. The InAs0.35Sb0.65 film exhibits a Hall mobility of 4.62x10(4) cm(2) V-1 s(-1). The cutoff wavelength of photoresponse is extended to about 12 mu m with a maximum responsivity of 0.21 V/W at RT, showing great potential for RT long-wavelength infrared detection. (C) 2008 American Institute of Physics. [DOI: 10.1063/1.2989116]