Electroblotting onto activated glass. High efficiency preparation of proteins from analytical sodium dodecyl sulfate-polyacrylamide gels for direct sequence analysis

We have developed a new method for the isolation of proteins for microsequencing. It consists of electrophoretic transfer (electroblotting) of proteins or their cleavage fragments onto activated glass filter paper sheets immediately after separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The proteins are immobilized on the glass fiber sheets by ionic interactions or by covalent attachment. A wide range of proteins can be prepared in this fashion with no apparent restriction due to solubility, size, charge, or other intrinsic properties of the proteins. As little as 50 ng of the transferred proteins can be detected using Coomassie Blue or fluorescent dye staining procedures and even smaller amounts of radiolabeled proteins by autoradiography. After detection, the protein- containing bands or spots are cut out and inserted directly into a gas- phase sequenator. The piece of glass fiber sheet acts as a support for the protein during the sequencing. Amounts of protein in the 5- to 150- pmol range can be sequenced, and extended runs can be obtained from the blotted samples because of improved stepwise yields and lower backgrounds. The method has been successfully applied to the sequencing of a variety of proteins and peptides isolated from one-dimensional and two-dimensional polyacrylamide gels

The influence of coronal EUV irradiance on the emission in the He I 10830 A and D3 multiplets

Two of the most attractive spectral windows for spectropolarimetric investigations of the physical properties of the plasma structures in the solar chromosphere and corona are the ones provided by the spectral lines of the He I 10830 A and 5876 A (or D3) multiplets, whose polarization signals are sensitive to the Hanle and Zeeman effects. However, in order to be able to carry out reliable diagnostics, it is crucial to have a good physical understanding of the sensitivity of the observed spectral line radiation to the various competing driving mechanisms. Here we report a series of off-the-limb non-LTE calculations of the He I D3 and 10830 A emission profiles, focusing our investigation on their sensitivity to the EUV coronal irradiation and the model atmosphere used in the calculations. We show in particular that the intensity ratio of the blue to the red components in the emission profiles of the He I 10830 A multiplet turns out to be a good candidate as a diagnostic tool for the coronal irradiance. Measurements of this observable as a function of the distance to the limb and its confrontation with radiative transfer modeling might give us valuable information on the physical properties of the solar atmosphere and on the amount of EUV radiation at relevant wavelengths penetrating the chromosphere from above.Comment: 19 pages, 11 figures (pre-print format). Accepted for publication in Ap

Bounds for the adiabatic approximation with applications to quantum computation

We present straightforward proofs of estimates used in the adiabatic approximation. The gap dependence is analyzed explicitly. We apply the result to interpolating Hamiltonians of interest in quantum computing.Comment: 15 pages, one figure. Two comments added in Secs. 2 and

Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis.

Deciphering physiological changes that mediate transition of Mycobacterium tuberculosis between replicating and nonreplicating states is essential to understanding how the pathogen can persist in an individual host for decades. We have combined RNA sequencing (RNA-seq) of 5' triphosphate-enriched libraries with regular RNA-seq to characterize the architecture and expression of M. tuberculosis promoters. We identified over 4,000 transcriptional start sites (TSSs). Strikingly, for 26% of the genes with a primary TSS, the site of transcriptional initiation overlapped with the annotated start codon, generating leaderless transcripts lacking a 5' UTR and, hence, the Shine-Dalgarno sequence commonly used to initiate ribosomal engagement in eubacteria. Genes encoding proteins with active growth functions were markedly depleted from the leaderless transcriptome, and there was a significant increase in the overall representation of leaderless mRNAs in a starvation model of growth arrest. The high percentage of leaderless genes may have particular importance in the physiology of nonreplicating M. tuberculosis

Molecular Systematics of the Fishing Bat Myotis (Pizonyx) vivesi

Phylogenetic reconstructions based on molecular data have shown recurrent morphological convergence during evolution of the species-rich genus Myotis. Species or groups of species with similar feeding strategies have evolved independently several times to produce remarkable similarities in external morphology. In this context, we investigated the contentious phylogenetic position of 1 of the 2 piscivorous bat species, Myotis vivesi, which was not included in previous molecular studies. This bat, endemic to the coasts and islands of the Gulf of California, Mexico, was long classified in its own genus, Pizonyx, because of its distinctive morphology. To reconstruct its phylogenetic origins relative to other Myotis, we sequenced the mitochondrial cytochrome-b gene of 2 M. vivesi and related vespertilionids. These outgroups included Pipistrellus subflavus, a member of the subgenus Perimyotis, sometimes classified within the genus Myotis. Unexpectedly, all reconstructions placed M. vivesi within a strongly supported clade including all other typical neotropical and Nearctic Myotis. This molecular phylogeny supports an endemic radiation of New World Myotis. Other Myotis species with similar adaptations to gaffing prey from the water surface present no close phylogenetic relationships with M. vivesi, indicating that such adaptations are convergences. On the other hand, P. subflavus is genetically as distant from the genus Myotis as from other Pipistrellus species, suggesting that generic rank to Perimyotis is warrante

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

Phosphorylation-based signaling networks mediate the effect of ligand affinity of the activation of naive primary T-cells

Comunicaciones a congreso

Delayed effects of transcriptional responses in Mycobacterium tuberculosis exposed to nitric oxide suggest other mechanisms involved in survival.

Mycobacterium tuberculosis has succeeded as a human pathogen for tens of thousands of years thanks to its ability to resist and adapt to the adverse conditions it encounters upon infection. Bacterial adaptation to stress is commonly viewed in the context of transcriptional regulation, with the implicit expectation that an initial transcriptomic response is tightly coupled to an ensuing proteomic response. However, after challenging M. tuberculosis with nitric oxide we found that the rapid transcriptional responses, detectable within minutes of nitric oxide exposure, typically took several hours to manifest on the protein level. Furthermore, early proteomic responses were dominated by the degradation of a set of proteins, specifically those containing damaged iron-sulphur clusters. Overall, our findings are consistent with transcriptional responses participating mostly in late-stage recovery rather than in generating an immediate resistance to nitric oxide stress, suggesting that survival of M. tuberculosis under acute stress is contingent on mechanisms other than transcriptional regulation. These findings provide a revised molecular understanding of an important human pathogen

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