1,336 research outputs found
RSAT 2011: regulatory sequence analysis tools
RSAT (Regulatory Sequence Analysis Tools) comprises a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. Thirteen new programs have been added to the 30 described in the 2008 NAR Web Software Issue, including an automated sequence retrieval from EnsEMBL (retrieve-ensembl-seq), two novel motif discovery algorithms (oligo-diff and info-gibbs), a 100-times faster version of matrix-scan enabling the scanning of genome-scale sequence sets, and a series of facilities for random model generation and statistical evaluation (random-genome-fragments, random-motifs, random-sites, implant-sites, sequence-probability, permute-matrix). Our most recent work also focused on motif comparison (compare-matrices) and evaluation of motif quality (matrix-quality) by combining theoretical and empirical measures to assess the predictive capability of position-specific scoring matrices. To process large collections of peak sequences obtained from ChIP-seq or related technologies, RSAT provides a new program (peak-motifs) that combines several efficient motif discovery algorithms to predict transcription factor binding motifs, match them against motif databases and predict their binding sites. Availability (web site, stand-alone programs and SOAP/WSDL (Simple Object Access Protocol/Web Services Description Language) web services): http://rsat.ulb.ac.be/rsat/
Thermodynamics of a Colloidal Particle in a Time-Dependent Non-Harmonic Potential
We study the motion of an overdamped colloidal particle in a time-dependent
non-harmonic potential. We demonstrate the first law-like balance between
applied work, exchanged heat, and internal energy on the level of a single
trajectory. The observed distribution of applied work is distinctly
non-Gaussian in good agreement with numerical calculations. Both the Jarzynski
relation and a detailed fluctuation theorem are verified with good accuracy
The structure and energetics of He and He nanodroplets doped with alkaline earth atoms
We present systematic results, based on density functional calculations, for
the structure and energetics of He and He nanodroplets doped with
alkaline earth atoms. We predict that alkaline earth atoms from Mg to Ba go to
the center of He drops, whereas Ca, Sr, and Ba reside in a deep dimple at
the surface of He drops, and Mg is at their center. For Ca and Sr, the
structure of the dimples is shown to be very sensitive to the He-alkaline earth
pair potentials used in the calculations. The transition
of strontium atoms attached to helium nanodroplets of either isotope has been
probed in absorption experiments. The spectra show that strontium is solvated
inside He nanodroplets, supporting the calculations. In the light of our
findings, we emphasize the relevance of the heavier alkaline earth atoms for
analyzing mixed He-He nanodroplets, and in particular, we suggest their
use to experimentally probe the He-He interface.Comment: Typeset using Revtex, 20 pages and 8 Postscript file
Tunability of Critical Casimir Interactions by Boundary Conditions
We experimentally demonstrate that critical Casimir forces in colloidal
systems can be continuously tuned by the choice of boundary conditions. The
interaction potential of a colloidal particle in a mixture of water and
2,6-lutidine has been measured above a substrate with a gradient in its
preferential adsorption properties for the mixture's components. We find that
the interaction potentials at constant temperature but different positions
relative to the gradient continuously change from attraction to repulsion. This
demonstrates that critical Casimir forces respond not only to minute
temperature changes but also to small changes in the surface properties.Comment: 4 figures;
http://www.iop.org/EJ/article/0295-5075/88/2/26001/epl_88_2_26001.htm
Photodissociation of Conformer-Selected Ubiquitin Ions Reveals Site-Specific Cis/Trans Isomerization of Proline Peptide Bonds
Ultraviolet photodissociation (UVPD) of gas-phase proteins has attracted increased attention in recent years. This growing interest is largely based on the fact that, in contrast to slow heating techniques such as collision induced dissociation (CID), the cleavage propensity after absorption of UV light is distributed over the entire protein sequence, which can lead to a very high sequence coverage as required in typical top-down proteomics applications. However, in the gas phase, proteins can adopt a multitude of distinct and sometimes coexisting conformations, and it is not clear how this three-dimensional structure affects the UVPD fragmentation behavior. Using ion mobilityâUVPDâmass spectrometry in conjunction with molecular dynamics simulations, we provide the first experimental evidence that UVPD is sensitive to the higher order structure of gas-phase proteins. Distinct UVPD spectra were obtained for different extended conformations of 11+ ubiquitin ions. Assignment of the fragments showed that the majority of differences arise from cis/trans isomerization of one particular proline peptide bond. Seen from a broader perspective, these data highlight the potential of UVPD to be used for the structural analysis of proteins in the gas phas
Remote participation during glycosylation reactions of galactose building blocks: Direct evidence from cryogenic vibrational spectroscopy
The stereoselective formation of 1,2âcisâglycosidic bonds is challenging. However, 1,2âcisâselectivity can be induced by remote participation of C4 or C6 ester groups. Reactions involving remote participation are believed to proceed via a key ionic intermediate, the glycosyl cation. Although mechanistic pathways were postulated many years ago, the structure of the reaction intermediates remained elusive owing to their shortâlived nature. Herein, we unravel the structure of glycosyl cations involved in remote participation reactions via cryogenic vibrational spectroscopy and first principles theory. Acetyl groups at C4 ensure αâselective galactosylations by forming a covalent bond to the anomeric carbon in dioxoleniumâtype ions. Unexpectedly, also benzyl ether protecting groups can engage in remote participation and promote the stereoselective formation of 1,2âcisâglycosidic bonds
Cryogenic infrared spectroscopy provides mechanistic insight into the fragmentation of phospholipid silver adducts
Tandem mass spectrometry is arguably the most important analytical tool for structure elucidation of lipids and other metabolites. By fragmenting intact lipid ions, valuable structural information such as the lipid class and fatty acyl composition are readily obtainable. The information content of a fragment spectrum can often be increased by the addition of metal cations. In particular, the use of silver ions is deeply rooted in the history of lipidomics due to their propensity to coordinate both electron-rich heteroatoms and Câ=âC bonds in aliphatic chains. Not surprisingly, coordination of silver ions was found to enable the distinction of sn-isomers in glycerolipids by inducing reproducible intensity differences in the fragment spectra, which could, however, not be rationalized. Here, we investigate the fragmentation behaviors of silver-adducted sn- and double bond glycerophospholipid isomers by probing fragment structures using cryogenic gas-phase infrared (IR) spectroscopy. Our results confirm that neutral headgroup loss from silver-adducted glycerophospholipids leads to dioxolane-type fragments generated by intramolecular cyclization. By combining high-resolution IR spectroscopy and computational modelling of silver-adducted fragments, we offer qualitative explanations for different fragmentation behaviors of glycerophospholipid isomers. Overall, the results demonstrate that gas-phase IR spectroscopy of fragment ions can significantly contribute to our understanding of lipid dissociation mechanisms and the influence of coordinating cations
The Influence of the Electron Density in Acyl Protecting Groups on the Selectivity of Galactose Formation
The stereoselective formation of 1,2-cis-glycosidic bonds is a major bottleneck in the synthesis of carbohydrates. We here investigate how the electron density in acyl protecting groups influences the stereoselectivity by fine-tuning the efficiency of remote participation. Electron-rich C4-pivaloylated galactose building blocks show an unprecedented α-selectivity. The trifluoroacetylated counterpart with electron-withdrawing groups, on the other hand, exhibits a lower selectivity. Cryogenic infrared spectroscopy in helium nanodroplets and density functional theory calculations revealed the existence of dioxolenium-type intermediates for this reaction, which suggests that remote participation of the pivaloyl protecting group is the origin of the high α-selectivity of the pivaloylated building blocks. According to these findings, an α-selective galactose building block for glycosynthesis is developed based on rational considerations and is subsequently employed in automated glycan assembly exhibiting complete stereoselectivity. Based on the obtained selectivities in the glycosylation reactions and the results from infrared spectroscopy and density functional theory, we suggest a mechanism by which these reactions could proceed
gyrA mutations and phenotypic susceptibility levels to ofloxacin and moxifloxacin in clinical isolates of Mycobacterium tuberculosis
Objectives To compare mutations in the quinolone resistance-determining region of the gyrA gene and flanking sequences with the MICs of ofloxacin and moxifloxacin for Mycobacterium tuberculosis. Methods The presence of mutations in 177 drug-resistant M. tuberculosis isolates was determined by DNA sequencing and the MICs quantified by MGIT 960. Results Single nucleotide polymorphisms were detected at codons 94 (nâ=â30), 90 (nâ=â12), 91 (nâ=â3), 89 (nâ=â1), 88 (nâ=â1) and 80 (nâ=â1). Four isolates with double mutations D94G plus A90V (nâ=â2) and D94G plus D94N (nâ=â2) reflect mixed populations. Agreement between genotypic and phenotypic susceptibility was high (â„97%) for both drugs. Mutant isolates had an MIC50 of 8.0 mg/L and an MIC90 of >10 mg/L for ofloxacin compared with an MIC50 and MIC90 of 2.0 mg/L for moxifloxacin. Codons 94 and 88 were linked to higher levels of fluoroquinolone resistance compared with codons 90, 91 and 89. The MIC distributions for the wild-type isolates ranged from â€0.5 to 2.0 mg/L for ofloxacin and from â€0.125 to 0.25 mg/L for moxifloxacin. However, 96% of the isolates with genetic alterations had MICs â€2.0 mg/L for moxifloxacin, which is within its achievable serum levels. Conclusions This study provides quantitative evidence that the addition of moxifloxacin to extensively drug-resistant tuberculosis (XDR-TB) regimens based on a clinical breakpoint of 2.0 mg/L has merit. The use of moxifloxacin in the treatment of multidrug-resistant tuberculosis may prevent the acquisition of additional mutations and development of XDR-T
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