Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids

<p>Abstract</p> <p>Background</p> <p>Rosids are a major clade in the angiosperms containing 13 orders and about one-third of angiosperm species. Recent molecular analyses recognized two major groups (i.e., fabids with seven orders and malvids with three orders). However, phylogenetic relationships within the two groups and among fabids, malvids, and potentially basal rosids including Geraniales, Myrtales, and Crossosomatales remain to be resolved with more data and a broader taxon sampling. In this study, we obtained DNA sequences of the mitochondrial <it>matR </it>gene from 174 species representing 72 families of putative rosids and examined phylogenetic relationships and phylogenetic utility of <it>matR </it>in rosids. We also inferred phylogenetic relationships within the "rosid clade" based on a combined data set of 91 taxa and four genes including <it>matR</it>, two plastid genes (<it>rbcL</it>, <it>atpB</it>), and one nuclear gene (18S rDNA).</p> <p>Results</p> <p>Comparison of mitochondrial <it>matR </it>and two plastid genes (<it>rbcL </it>and <it>atpB</it>) showed that the synonymous substitution rate in <it>matR </it>was approximately four times slower than those of <it>rbcL </it>and <it>atpB</it>; however, the nonsynonymous substitution rate in <it>matR </it>was relatively high, close to its synonymous substitution rate, indicating that the <it>matR </it>has experienced a relaxed evolutionary history. Analyses of our <it>matR </it>sequences supported the monophyly of malvids and most orders of the rosids. However, fabids did not form a clade; instead, the COM clade of fabids (Celastrales, Oxalidales, Malpighiales, and Huaceae) was sister to malvids. Analyses of the four-gene data set suggested that Geraniales and Myrtales were successively sister to other rosids, and that Crossosomatales were sister to malvids.</p> <p>Conclusion</p> <p>Compared to plastid genes such as <it>rbcL </it>and <it>atpB</it>, slowly evolving <it>matR </it>produced less homoplasious but not less informative substitutions. Thus, <it>matR </it>appears useful in higher-level angiosperm phylogenetics. Analysis of <it>matR </it>alone identified a novel deep relationship within rosids, the grouping of the COM clade of fabids and malvids, which was not resolved by any previous molecular analyses but recently suggested by floral structural features. Our four-gene analysis supported the placements of Geraniales, Myrtales at basal nodes of the rosid clade and placed Crossosomatales as sister to malvids. We also suggest that the core part of rosids should include fabids, malvids and Crossosomatales.</p

Measuring non-Markovianity of processes with controllable system-environment interaction

Non-Markovian processes have recently become a central topic in the study of open quantum systems. We realize experimentally non-Markovian decoherence processes of single photons by combining time delay and evolution in a polarization-maintaining optical fiber. The experiment allows the identification of the process with strongest memory effects as well as the determination of a recently proposed measure for the degree of quantum non-Markovianity based on the exchange of information between the open system and its environment. Our results show that an experimental quantification of memory in quantum processes is indeed feasible which could be useful in the development of quantum memory and communication devices.Comment: 5 pages, 4 figures. V2: Minor modifications, title change

Photometric Variability in the CSTAR Field: Results From the 2008 Data Set

The Chinese Small Telescope ARray (CSTAR) is the first telescope facility built at Dome A, Antarctica. During the 2008 observing season, the installation provided long-baseline and high-cadence photometric observations in the i-band for 18,145 targets within 20 deg2 CSTAR field around the South Celestial Pole for the purpose of monitoring the astronomical observing quality of Dome A and detecting various types of photometric variability. Using sensitive and robust detection methods, we discover 274 potential variables from this data set, 83 of which are new discoveries. We characterize most of them, providing the periods, amplitudes and classes of variability. The catalog of all these variables is presented along with the discussion of their statistical properties.Comment: 38 pages, 11 figures, 4 tables; Accepted for publication in ApJ

Discovery of Stable and Selective Antibody Mimetics from Combinatorial Libraries of Polyvalent, Loop-Functionalized Peptoid Nanosheets.

The ability of antibodies to bind a wide variety of analytes with high specificity and high affinity makes them ideal candidates for therapeutic and diagnostic applications. However, the poor stability and high production cost of antibodies have prompted exploration of a variety of synthetic materials capable of specific molecular recognition. Unfortunately, it remains a fundamental challenge to create a chemically diverse population of protein-like, folded synthetic nanostructures with defined molecular conformations in water. Here we report the synthesis and screening of combinatorial libraries of sequence-defined peptoid polymers engineered to fold into ordered, supramolecular nanosheets displaying a high spatial density of diverse, conformationally constrained peptoid loops on their surface. These polyvalent, loop-functionalized nanosheets were screened using a homogeneous Förster resonance energy transfer (FRET) assay for binding to a variety of protein targets. Peptoid sequences were identified that bound to the heptameric protein, anthrax protective antigen, with high avidity and selectivity. These nanosheets were shown to be resistant to proteolytic degradation, and the binding was shown to be dependent on the loop display density. This work demonstrates that key aspects of antibody structure and function-the creation of multivalent, combinatorial chemical diversity within a well-defined folded structure-can be realized with completely synthetic materials. This approach enables the rapid discovery of biomimetic affinity reagents that combine the durability of synthetic materials with the specificity of biomolecular materials

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis

BACKGROUND: RNA sequencing has become a ubiquitous technology used throughout life sciences as an effective method of measuring RNA abundance quantitatively in tissues and cells. The increase in use of RNA-seq technology has led to the continuous development of new tools for every step of analysis from alignment to downstream pathway analysis. However, effectively using these analysis tools in a scalable and reproducible way can be challenging, especially for non-experts. RESULTS: Using the workflow management system Snakemake we have developed a user friendly, fast, efficient, and comprehensive pipeline for RNA-seq analysis. VIPER (Visualization Pipeline for RNA-seq analysis) is an analysis workflow that combines some of the most popular tools to take RNA-seq analysis from raw sequencing data, through alignment and quality control, into downstream differential expression and pathway analysis. VIPER has been created in a modular fashion to allow for the rapid incorporation of new tools to expand the capabilities. This capacity has already been exploited to include very recently developed tools that explore immune infiltrate and T-cell CDR (Complementarity-Determining Regions) reconstruction abilities. The pipeline has been conveniently packaged such that minimal computational skills are required to download and install the dozens of software packages that VIPER uses. CONCLUSIONS: VIPER is a comprehensive solution that performs most standard RNA-seq analyses quickly and effectively with a built-in capacity for customization and expansion

The Sloan Digital Sky Survey Quasar Catalog IV. Fifth Data Release

We present the fourth edition of the Sloan Digital Sky Survey (SDSS) Quasar Catalog. The catalog contains 77,429 objects; this is an increase of over 30,000 entries since the previous edition. The catalog consists of the objects in the SDSS Fifth Data Release that have luminosities larger than M_i = -22.0 (in a cosmology with H_0 = 70 km/s/Mpc, Omega_M = 0.3, and Omega_Lambda = 0.7) have at least one emission line with FWHM larger than 1000 km/s, or have interesting/complex absorption features, are fainter than i=15.0, and have highly reliable redshifts. The area covered by the catalog is 5740 sq. deg. The quasar redshifts range from 0.08 to 5.41, with a median value of 1.48; the catalog includes 891 quasars at redshifts greater than four, of which 36 are at redshifts greater than five. Approximately half of the catalog quasars have i < 19; nearly all have i < 21. For each object the catalog presents positions accurate to better than 0.2 arcsec. rms per coordinate, five-band (ugriz) CCD-based photometry with typical accuracy of 0.03 mag, and information on the morphology and selection method. The catalog also contains basic radio, near-infrared, and X-ray emission properties of the quasars, when available, from other large-area surveys. The calibrated digital spectra cover the wavelength region 3800--9200A at a spectral resolution of ~2000. The spectra can be retrieved from the public database using the information provided in the catalog. The average SDSS colors of quasars as a function of redshift, derived from the catalog entries, are presented in tabular form. Approximately 96% of the objects in the catalog were discovered by the SDSS.Comment: 37 pages, Accepted for publication in A

Competitions of magnetism and superconductivity in FeAs-based materials

Using the numerical unrestricted Hartree-Fock approach, we study the ground state of a two-orbital model describing newly discovered FeAs-based superconductors. We observe the competition of a $(0, \pi)$ mode spin-density wave and the superconductivity as the doping concentration changes. There might be a small region in the electron-doping side where the magnetism and superconductivity coexist. The superconducting pairing is found to be spin singlet, orbital even, and mixed s$_{xy}$ + d$_{x^{2}-y^{2}}$ wave (even parity).Comment: 5 pages, 3 figure

A Catalog of Luminous Infrared Galaxies in the IRAS Survey and the Second Data Release of the SDSS

We select the Luminous Infrared Galaxies by cross-correlating the Faint Source Catalogue (FSC) and Point Source Catalogue (PSC) of the IRAS Survey with the Second Data Release of the SDSS for studying their infrared and optical properties. The total number of our sample is 1267 for FSC and 427 for PSC by using 2$\sigma$ significance level cross-section. The "likelihood ratio" method is used to estimate the sample's reliability and for a more reliable subsample (908 for FSC and 356 for PSC) selection. Then a Catalog with both the infrared, optical and radio informations is presented and will be used in further works. Some statistical results show that the Luminous Infrared Galaxies are quite different from the Ultra-Luminous Infrared Galaxies. The AGN fractions of galaxies with different infrared luminosities and the radio to infrared correlations are consist with previous studies.Comment: 15 pages, 11 figures. Accepted by ChJAA. Reference adde

Subjective evaluation of the environmental quality in China's industrial corridors.

Based on 270 questionnaire surveys in 8 cities of 5 industrial corridors in China, this study aims to examine the effects of industry construction on the evaluation of environmental pollution, natural environment, built environment, personal perception and development and policy. The results show that the evaluations on environmental pollution and landscape design are both below the medium level, but the evaluations of the living comfort and safety are both above the medium level. Further analysis, females usually give lower evaluation scores than males, and age and health situations are negatively related to the evaluation results; People indicate a great desire to reduce the environmental pollution and protect the natural environment. Moreover, the landscape was analysed using colour extraction techniques based on video recording, there are significant correlations between industrial pixel ratio and evaluation results of air quality, vegetation pixel ratio and evaluation results of river water quality, and public facilities pixel ratio and evaluation results of comfort levels