Friction and diffusion of matter-wave bright solitons

We consider the motion of a matter-wave bright soliton under the influence of a cloud of thermal particles. In the ideal one-dimensional system, the scattering process of the quasiparticles with the soliton is reflectionless, however, the quasiparticles acquire a phase shift. In the realistic system of a Bose-Einstein condensate confined in a tight waveguide trap, the transverse degrees of freedom generate an extra but small nonlinearity in the system which gives rise to finite reflection and leads to dissipative motion of the soliton. We calculate the velocity and temperature-dependent frictional force and diffusion coefficient of a matter wave bright soliton immersed in a thermal cloud

Stoichiometry of a regulatory splicing complex revealed by single-molecule analyses

Splicing is regulated by complex interactions of numerous RNA-binding proteins. The molecular mechanisms involved remain elusive, in large part because of ignorance regarding the numbers of proteins in regulatory complexes. Polypyrimidine tract-binding protein (PTB), which regulates tissue-specific splicing, represses exon 3 of α-tropomyosin through distant pyrimidine-rich tracts in the flanking introns. Current models for repression involve either PTB-mediated looping or the propagation of complexes between tracts. To test these models, we used single-molecule approaches to count the number of bound PTB molecules both by counting the number of bleaching steps of GFP molecules linked to PTB within complexes and by analysing their total emissions. Both approaches showed that five or six PTB molecules assemble. Given the domain structures, this suggests that the molecules occupy primarily multiple overlapping potential sites in the polypyrimidine tracts, excluding propagation models. As an alternative to direct looping, we propose that repression involves a multistep process in which PTB binding forms small local loops, creating a platform for recruitment of other proteins that bring these loops into close proximity

Recombination-dependent repair of DNA double-strand breaks with purified proteins from Escherichia coli

International audienc

Double-stranded DNA Stimulates the Fibrillation of α-Synuclein in vitro and is Associated with the Mature Fibrils: An Electron Microscopy Study

Filamentous aggregates formed by α-synuclein are a prominent and presumably key etiological factor in Parkinson's and other neurodegenerative diseases characterized by motor disorders. Numerous studies have demonstrated that various environmental and intracellular factors affect the fibrillation properties of α-synuclein, e.g. by accelerating the process of assembly. Histones, the major component and constituent of chromatin, interact specifically with α-synuclein and enhance its fibrillation significantly. Here, we report that another component of chromatin, double-stranded DNA (dsDNA), either linear or supercoiled, also interacts with wild-type α-synuclein, leading to a significant stimulation of α-synuclein assembly into mature fibrils characterized by a reduced lag phase. In general, the morphology of the fibrils remains unchanged in the presence of linear dsDNA. Electron microscopy reveals that DNA forms various types of complexes upon association with the fibrils at their surface without distortion of the double-helical structure. The existence of these complexes was confirmed by the electrophoresis, which also demonstrated that a fraction of the associated DNA was resistant to digestion by restriction endonucleases. Fibrils assembled from the α-synuclein mutants A30P and A53T and the C-terminally truncated variants (encoding amino acid residues 1–108 or 1–124) also form complexes with linear dsDNA. Possible mechanisms and implications of dsDNA–α-synuclein interactions are discussed

"Votre enfant a de la fièvre" participation des pharmaciens à l'élaboration et l'évaluation d'un message de santé au sein du réseau COURLYGONES (enquête de faisabilité auprès de 55 parents, dans 10 officines de l'agglomération lyonnaise et étude des ventes de paracétamol et d'ibuprofène de l'OCP Vaulx en Velin)

LYON1-BU Santé (693882101) / SudocSudocFranceF

Static Curvature and Flexibility Measurements of DNA with Microscopy. A Simple Renormalization Method, its Assessment by Experiment and Simulation

International audienc

Identification, cloning and characterization of a new DNA-binding protein from the hyperthermophilic methanogen Methanopyrus kandleri

Three novel DNA-binding proteins with apparent molecular masses of 7, 10 and 30 kDa have been isolated from the hyperthermophilic methanogen Methanopyrus kandleri. The proteins were identified using a blot overlay assay that was modified to emulate the high ionic strength intracellular environment of M.kandleri proteins. A 7 kDa protein, named 7kMk, was cloned and expressed in Escherichia coli. As indicated by CD spectroscopy and computer-assisted structure prediction methods, 7kMk is a substantially α-helical protein possibly containing a short N-terminal β-strand. According to analytical gel filtration chromatography and chemical crosslinking, 7kMk exists as a stable dimer, susceptible to further oligomerization. Electron microscopy showed that 7kMk bends DNA and also leads to the formation of loop-like structures of ∼43.5 ± 3.5 nm (136 ± 11 bp for B-form DNA) circumference. A topoisomerase relaxation assay demonstrated that looped DNA is negatively supercoiled under physiologically relevant conditions (high salt and temperature). A BLAST search did not yield 7kMk homologs at the amino acid sequence level, but based on a multiple alignment with ribbon–helix–helix (RHH) transcriptional regulators, fold features and self-association properties of 7kMk we hypothesize that it could be related to RHH proteins

The transition in spliceosome assembly from complex E to complex A purges surplus U1 snRNPs from alternative splice sites.

Spliceosomes are assembled in stages. The first stage forms complex E, which is characterized by the presence of U1 snRNPs base-paired to the 5' splice site, components recognizing the 3' splice site and proteins thought to connect them. The splice sites are held in close proximity and the pre-mRNA is committed to splicing. Despite this, the sites for splicing appear not to be fixed until the next complex (A) forms. We have investigated the reasons why 5' splice sites are not fixed in complex E, using single molecule methods to determine the stoichiometry of U1 snRNPs bound to pre-mRNA with one or two strong 5' splice sites. In complex E most transcripts with two alternative 5' splice sites were bound by two U1 snRNPs. However, the surplus U1 snRNPs were displaced during complex A formation in an ATP-dependent process requiring an intact 3' splice site. This process leaves only one U1 snRNP per complex A, regardless of the number of potential sites. We propose a mechanism for selection of the 5' splice site. Our results show that constitutive splicing components need not be present in a fixed stoichiometry in a splicing complex

Sound ontology for the paper “An approach for structuring sound sample libraries using ontology”

<p>This is a supplementary material for a paper titled “An approach for structuring sound sample libraries using ontology” submitted to the Knowledge Engineering and Semantic Web conference (2016). http://2016.kesw.ru/</p