Analysis of the volatile components of five Turkish Rhododendron species by headspace solid-phase microextraction and GC-MS (HS-SPME-GC-MS)

Volatile constituents of various solvent extracts (n-hexane, CH2Cl2, H2O) of 15 different organs (leaves, flowers, fruits) of five Rhododendron species (Ericaceae) growing in Turkey were trapped with headspace solid-phase microextraction (HS-SPME) technique and analyzed by GC-MS. A total of 200 compounds were detected and identified from organic extracts, while the water extracts contained only traces of few volatiles. The CH2Cl2 extract of the R. luteum flowers was found to exhibit the most diverse composition: 34 compounds were identified, with benzyl alcohol (16.6%), limonene (14.6%) and p-cymene (8.4%) being the major compounds. The CH2Cl2-solubles of R. x sochadzeae leaves contained only phenyl ethyl alcohol. This study indicated appreciable intra-specific variations in volatile compositions within the genus. Different anatomical parts also showed altered volatile profiles. This is the first application of HS-SPME-GC-MS on the volatiles of Rhododendron species

Secondary metabolites of Phlomis viscosa and their biological activities

Further phytochemical studies on the aerial parts of Phlomis viscosa (Lamiaceae) led to the isolation of 24 compounds: 3 iridoid glycosides, 10 phenylethanoid glycosides, a megastigmane glycoside and a hydroquinone glycoside, as well as 2 lignan glucosides and 7 neolignan glucosides, 1 of which is new (17b). Compound 17b was obtained as a minor component of an inseparable mixture (2:1) of 2 neolignan glucosides (17a/b), and characterized as 3',4-O-dimethylcedrusin 9-O-b -glucopyranoside. Full NMR data of the known 8-O-4' neolignan glucoside, erythro-1-(4-O-b-glucopyranosyl-3-methoxyphenyl)- 2-{2-methoxyl-4-[1-(E)-propene-3-ol]-phenoxyl}-propane-1,3-diol (18) are also reported. All isolated compounds were screened for cell growth inhibition versus 3 tumor cell lines (MCF7, NCI-H460, and SF-268) and several phenylethanoid glycosides were found to possess weak antitumoral activity. The phenylethanoid glycosides were also evaluated for their free radical (DPPH) scavenging, antibacterial and antifungal activities. The free radical (DPPH) scavenging activities of verbascoside (4), isoacteoside (5), forsythoside B (10), myricoside (13) and samioside (14) were found to be comparable to that of dl-a -tocopherol. Compounds 4, 5, 10 and 14 (MIC: 500 m g/mL) as well as Leucosceptoside A (8) and 13 (MIC:1000 m g/mL) showed very weak activity against Gram (+) bacteria

Spectropolarimetric investigation of the propagation of magnetoacoustic waves and shock formation in sunspot atmospheres

Velocity oscillations in sunspot umbrae have been measured simultaneously in two spectral lines: the photospheric Silicon I 10827 A line and the chromospheric Helium I 10830 A multiplet. From the full Stokes inversion of temporal series of spectropolarimetric observations we retrieved, among other parameters, the line of sight velocity temporal variations at photospheric and chromospheric heights. Chromospheric velocity oscillations show a three minute period with a clear sawtooth shape typical of propagating shock wave fronts. Photospheric velocity oscillations have basically a five minute period, although the power spectrum also shows a secondary peak in the three minute band which has proven to be predecessor for its chromospheric counterpart. The derived phase spectra yield a value of the atmospheric cut-off frequency around 4 mHz and give evidence for the upward propagation of higher frequency oscillation modes. The phase spectrum has been reproduced with a simple model of linear vertical propagation of slow magneto-acoustic waves in a stratified magnetized atmosphere that accounts for radiative losses through Newton's cooling law. The model explains the main features in the phase spectrum, and allows us to compute the theoretical time delay between the photospheric and chromospheric signals, which happens to have a strong dependence on frequency. We find a very good agreement between this and the time delay obtained directly from the cross-correlation of photospheric and chromospheric velocity maps filtered around the 6 mHz band. This allows us to infer that the 3-minute power observed at chromospheric heights comes directly from the photosphere by means of linear wave propagation, rather than from non-linear interaction of 5-minute (and/or higher frequency) modes.Comment: aastex preprint, 32 pages, 12 figure

Charge Deficiency, Charge Transport and Comparison of Dimensions

We study the relative index of two orthogonal infinite dimensional projections which, in the finite dimensional case, is the difference in their dimensions. We relate the relative index to the Fredholm index of appropriate operators, discuss its basic properties, and obtain various formulas for it. We apply the relative index to counting the change in the number of electrons below the Fermi energy of certain quantum systems and interpret it as the charge deficiency. We study the relation of the charge deficiency with the notion of adiabatic charge transport that arises from the consideration of the adiabatic curvature. It is shown that, under a certain covariance, (homogeneity), condition the two are related. The relative index is related to Bellissard's theory of the Integer Hall effect. For Landau Hamiltonians the relative index is computed explicitly for all Landau levels.Comment: 23 pages, no figure

Integrated Operational Taxonomic Units (IOTUs) in Echolocating Bats: A Bridge between Molecular and Traditional Taxonomy

Background: Nowadays, molecular techniques are widespread tools for the identification of biological entities. However, until very few years ago, their application to taxonomy provoked intense debates between traditional and molecular taxonomists. To prevent every kind of disagreement, it is essential to standardize taxonomic definitions. Along these lines, we introduced the concept of Integrated Operational Taxonomic Unit (IOTU). IOTUs come from the concept of Operational Taxonomic Unit (OTU) and paralleled the Molecular Operational Taxonomic Unit (MOTU). The latter is largely used as a standard in many molecular-based works (even if not always explicitly formalized). However, while MOTUs are assigned solely on molecular variation criteria, IOTUs are identified from patterns of molecular variation that are supported by at least one more taxonomic characteristic. Methodology/Principal Findings: We tested the use of IOTUs on the widest DNA barcoding dataset of Italian echolocating bats species ever assembled (i.e. 31 species, 209 samples). We identified 31 molecular entities, 26 of which corresponded to the morphologically assigned species, two MOTUs and three IOTUs. Interestingly, we found three IOTUs in Myotis nattereri, one of which is a newly described lineage found only in central and southern Italy. In addition, we found a level of molecular variability within four vespertilionid species deserving further analyses. According to our scheme two of them (i.e. M. bechsteinii and Plecotus auritus) should be ranked as unconfirmed candidate species (UCS). Conclusions/Significance: From a systematic point of view, IOTUs are more informative than the general concept of OTUs and the more recent MOTUs. According to information content, IOTUs are closer to species, although it is important to underline that IOTUs are not species. Overall, the use of a more precise panel of taxonomic entities increases the clarity in the systematic field and has the potential to fill the gaps between modern and traditional taxonomy

Detection of magnetic dipole lines of Fe XII in the ultraviolet spectrum of the dwarf star Epsilon Eri

We report observations of the dwarf star Epsilon Eri (K2 V) made with the Space Telescope Imaging Spectrograph (STIS) on the Hubble Space Telescope (HST). The high sensitivity of the STIS instrument has allowed us to detect the magnetic dipole transitions of Fe XII at 1242.00A and 1349.38A for the first time in a star other than the Sun. The width of the stronger line at 1242.00A has also been measured; such measurements are not possible for the permitted lines of Fe XII in the extreme ultraviolet. To within the accurcy of the measurements, the N V and the Fe XII lines occur at their rest wavelengths. Electron densities and line widths have been measured from other transition region lines. Together, these can be used to investigate the non-thermal energy flux in the lower and upper transition region, which is useful in constraining possible heating processes. The Fe XII lines are also present in archival STIS spectra of other G/K-type dwarfs.Comment: 12 pages, 4 figures, submitted to MNRAS letters (11 Jan 2001

Myotis rufoniger genome sequence and analyses: M-rufoniger's genomic feature and the decreasing effective population size of Myotis bats

Myotis rufoniger is a vesper bat in the genus Myotis. Here we report the whole genome sequence and analyses of the M. rufoniger. We generated 124 Gb of short-read DNA sequences with an estimated genome size of 1.88 Gb at a sequencing depth of 66x fold. The sequences were aligned to M. brandtii bat reference genome at a mapping rate of 96.50% covering 95.71% coding sequence region at 10x coverage. The divergence time of Myotis bat family is estimated to be 11.5 million years, and the divergence time between M. rufoniger and its closest species M. davidii is estimated to be 10.4 million years. We found 1,239 function-altering M. rufoniger specific amino acid sequences from 929 genes compared to other Myotis bat and mammalian genomes. The functional enrichment test of the 929 genes detected amino acid changes in melanin associated DCT, SLC45A2, TYRP1, and OCA2 genes possibly responsible for the M. rufoniger's red fur color and a general coloration in Myotis. N6AMT1 gene, associated with arsenic resistance, showed a high degree of function alteration in M. rufoniger. We further confirmed that the M. rufoniger also has batspecific sequences within FSHB, GHR, IGF1R, TP53, MDM2, SLC45A2, RGS7BP, RHO, OPN1SW, and CNGB3 genes that have already been published to be related to bat's reproduction, lifespan, flight, low vision, and echolocation. Additionally, our demographic history analysis found that the effective population size of Myotis clade has been consistently decreasing since similar to 30k years ago. M. rufoniger's effective population size was the lowest in Myotis bats, confirming its relatively low genetic diversity

How many human proteoforms are there?

Despite decades of accumulated knowledge about proteins and their post-translational modifications (PTMs), numerous questions remain regarding their molecular composition and biological function. One of the most fundamental queries is the extent to which the combinations of DNA-, RNA- and PTM-level variations explode the complexity of the human proteome. Here, we outline what we know from current databases and measurement strategies including mass spectrometry-based proteomics. In doing so, we examine prevailing notions about the number of modifications displayed on human proteins and how they combine to generate the protein diversity underlying health and disease. We frame central issues regarding determination of protein-level variation and PTMs, including some paradoxes present in the field today. We use this framework to assess existing data and to ask the question, "How many distinct primary structures of proteins (proteoforms) are created from the 20,300 human genes?" We also explore prospects for improving measurements to better regularize protein-level biology and efficiently associate PTMs to function and phenotype

An Estimation of Erinaceidae Phylogeny: A Combined Analysis Approach

BACKGROUND: Erinaceidae is a family of small mammals that include the spiny hedgehogs (Erinaceinae) and the silky-furred moonrats and gymnures (Galericinae). These animals are widely distributed across Eurasia and Africa, from the tundra to the tropics and the deserts to damp forests. The importance of these animals lies in the fact that they are the oldest known living placental mammals, which are well represented in the fossil record, a rarity fact given their size and vulnerability to destruction during fossilization. Although the Family has been well studied, their phylogenetic relationships remain controversial. To test previous phylogenetic hypotheses, we combined molecular and morphological data sets, including representatives of all the genera. METHODOLOGY AND PRINCIPAL FINDINGS: We included in the analyses 3,218 bp mitochondrial genes, one hundred and thirty-five morphological characters, twenty-two extant erinaceid taxa, and five outgroup taxa. Phylogenetic relationships were reconstructed using both partitioned and combined data sets. As in previous analyses, our results strongly support the monophyly of both subfamilies (Galericinae and Erinaceinae), the Hylomys group (to include Neotetracus and Neohylomys), and a sister-relationship of Atelerix and Erinaceus. As well, we verified that the extremely long branch lengths within the Galericinae are consistent with their fossil records. Not surprisingly, we found significant incongruence between the phylogenetic signals of the genes and the morphological characters, specifically in the case of Hylomys parvus, Mesechinus, and relationships between Hemiechinus and Paraechinus. CONCLUSIONS: Although we discovered new clues to understanding the evolutionary relationships within the Erinaceidae, our results nonetheless, strongly suggest that more robust analyses employing more complete taxon sampling (to include fossils) and multiple unlinked genes would greatly enhance our understanding of the Erinaceidae. Until then, we have left the nomenclature of the taxa unchanged; hence it does not yet precisely reflect their phylogenetic relationships or the depth of their genetic diversity