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

Winterteelt komkommers, 1961-1962

<p><b>Copyright information:</b></p><p>Taken from "Mitochondrial sequences help to resolve deep phylogenetic relationships in rosids"</p><p>http://www.biomedcentral.com/1471-2148/7/217</p><p>BMC Evolutionary Biology 2007;7():217-217.</p><p>Published online 10 Nov 2007</p><p>PMCID:PMC2222252.</p><p></p>rcentages >50. For nodes where ML and MP analyses differ in topology, only the ML BS percentages are shown; asterisks denote contradictory resolutions between ML tree and MP strict consensus of all shortest trees

Trace the Accretion Geometry of H 1743--322 with Type C Quasi-periodic Oscillations in Multiple Outbursts

We present a systematic analysis of type C quasi-periodic oscillation (QPO) observations of H 1743--322 throughout the Rossi X-ray Timing Explorer (RXTE) era. We find that, while different outbursts have significant flux differences, they show consistent positive correlations between the QPO fractional root-mean-square (rms) amplitude and non-thermal fraction of the emission, which indicate an independence of the intrinsic QPO rms on individual outburst brightness in H 1743--322. However, the dependence of the QPO rms on frequency is different between the outburst rise and decay phases, where QPO fractional rms of the decay phase is significantly lower than that of the rise phase at low frequencies. The spectral analysis also reveals different ranges of coronal temperature between the two outburst stages. A semi-quantitative analysis shows that the Lense-Thirring precession model could be responsible for the QPO rms differences, requiring a variable coronal geometric shape. However, the variable-Comptonization model could also account for the findings. The fact that the rms differences and the hysteresis traces in the hardness-intensity diagram (HID) accompany each other indicates a connection between the two phenomena. By correlating the findings with QPO phase lags and the quasi-simultaneous radio flux previously published, we propose there could be corona-jet transitions in H 1743--322 similar to those that have been recently reported in GRS 1915+105.Comment: 21 pages, 12 figure

The LAMOST Complete Spectroscopic Survey of Pointing Area (LaCoSSPAr) in the Southern Galactic Cap I. The Spectroscopic Redshift Catalog

We present a spectroscopic redshift catalog from the LAMOST Complete Spectroscopic Survey of Pointing Area (LaCoSSPAr) in the Southern Galactic Cap (SGC), which is designed to observe all sources (Galactic and extra-galactic) by using repeating observations with a limiting magnitude of $r=18.1~mag$ in two $20~deg^2$ fields. The project is mainly focusing on the completeness of LAMOST ExtraGAlactic Surveys (LEGAS) in the SGC, the deficiencies of source selection methods and the basic performance parameters of LAMOST telescope. In both fields, more than 95% of galaxies have been observed. A post-processing has been applied to LAMOST 1D spectrum to remove the majority of remaining sky background residuals. More than 10,000 spectra have been visually inspected to measure the redshift by using combinations of different emission/absorption features with uncertainty of $\sigma_{z}/(1+z)<0.001$. In total, there are 1528 redshifts (623 absorption and 905 emission line galaxies) in Field A and 1570 redshifts (569 absorption and 1001 emission line galaxies) in Field B have been measured. The results show that it is possible to derive redshift from low SNR galaxies with our post-processing and visual inspection. Our analysis also indicates that up to 1/4 of the input targets for a typical extra-galactic spectroscopic survey might be unreliable. The multi-wavelength data analysis shows that the majority of mid-infrared-detected absorption (91.3%) and emission line galaxies (93.3%) can be well separated by an empirical criterion of $W2-W3=2.4$. Meanwhile, a fainter sequence paralleled to the main population of galaxies has been witnessed both in $M_r$/$W2-W3$ and $M_*$/$W2-W3$ diagrams, which could be the population of luminous dwarf galaxies but contaminated by the edge-on/highly inclined galaxies ($\sim30\%$).Comment: 19 pages, 14 figures, 2 MRT, accepted by ApJ

IVSPlat 1.0: an integrated virtual screening platform with a molecular graphical interface

<p>Abstract</p> <p>Background</p> <p>The virtual screening (VS) of lead compounds using molecular docking and pharmacophore detection is now an important tool in drug discovery. VS tasks typically require a combination of several software tools and a molecular graphics system. Thus, the integration of all the requisite tools in a single operating environment could reduce the complexity of running VS experiments. However, only a few freely available integrated software platforms have been developed.</p> <p>Results</p> <p>A free open-source platform, IVSPlat 1.0, was developed in this study for the management and automation of VS tasks. We integrated several VS-related programs into a molecular graphics system to provide a comprehensive platform for the solution of VS tasks based on molecular docking, pharmacophore detection, and a combination of both methods. This tool can be used to visualize intermediate and final results of the VS execution, while also providing a clustering tool for the analysis of VS results. A case study was conducted to demonstrate the applicability of this platform.</p> <p>Conclusions</p> <p>IVSPlat 1.0 provides a plug-in-based solution for the management, automation, and visualization of VS tasks. IVSPlat 1.0 is an open framework that allows the integration of extra software to extend its functionality and modified versions can be freely distributed. The open source code and documentation are available at <url>http://kyc.nenu.edu.cn/IVSPlat/.</url></p

Amygdala Atrophy and Its Functional Disconnection with the Cortico-Striatal-Pallidal-Thalamic Circuit in Major Depressive Disorder in Females

Background Major depressive disorder (MDD) is approximately twice as common in females than males. Furthermore, female patients with MDD tend to manifest comorbid anxiety. Few studies have explored the potential anatomical and functional brain changes associated with MDD in females. Therefore, the purpose of the present study was to investigate the anatomical and functional changes underlying MDD in females, especially within the context of comorbid anxiety. Methods In this study, we recruited antidepressant-free females with MDD (N = 35) and healthy female controls (HC; N = 23). The severity of depression and anxiety were evaluated by the Hamilton Depression Rating Scale (HAM-D) and the Hamilton Anxiety Rating Scale (HAM-A), respectively. Structural and resting-state functional images were acquired on a Siemens 3.0 Tesla scanner. We compared the structural volumetric differences between patients and HC with voxel-based morphometry (VBM) analyses. Seed-based voxel-wise correlative analyses were used to identify abnormal functional connectivity. Regions with structural deficits showed a significant correlation between gray matter (GM) volume and clinical variables that were selected as seeds. Furthermore, voxel-wise functional connectivity analyses were applied to identify the abnormal connectivity relevant to seed in the MDD group. Results Decreased GM volume in patients was observed in the insula, putamen, amygdala, lingual gyrus, and cerebellum. The right amygdala was selected as a seed to perform connectivity analyses, since its GM volume exhibited a significant correlation with the clinical anxiety scores. We detected regions with disrupted connectivity relevant to seed primarily within the cortico-striatal-pallidal-thalamic circuit. Conclusions Amygdaloid atrophy, as well as decreased functional connectivity between the amygdala and the cortico-striatal-pallidal-thalamic circuit, appears to play a role in female MDD, especially in relation to comorbid anxiety

Label-Free Optical Single-Molecule Micro- and Nanosensors

This is the author accepted manuscript. The final version is available from Wiley via the DOI in this recordLabel-free optical sensor systems have emerged that exhibit extraordinary sensitivity for detecting physical, chemical, and biological entities at the micro/nanoscale. Particularly exciting is the detection and analysis of molecules, on miniature optical devices that have many possible applications in health, environment, and security. These micro- and nanosensors have now reached a sensitivity level that allows for the detection and analysis of even single molecules. Their small size enables an exceedingly high sensitivity, and the application of quantum optical measurement techniques can allow the classical limits of detection to be approached or surpassed. The new class of label-free micro- and nanosensors allows dynamic processes at the single-molecule level to be observed directly with light. By virtue of their small interaction length, these micro- and nanosensors probe light–matter interactions over a dynamic range often inaccessible by other optical techniques. For researchers entering this rapidly advancing field of single-molecule micro- and nanosensors, there is an urgent need for a timely review that covers the most recent developments and that identifies the most exciting opportunities. The focus here is to provide a summary of the recent techniques that have either demonstrated label-free single-molecule detection or claim single-molecule sensitivity.Living Systems Institute, University of Exete