Search results for "PORES"

RabbitQC: high-speed scalable quality control for sequencing data

2019

Abstract Motivation Modern sequencing technologies continue to revolutionize many areas of biology and medicine. Since the generated datasets are error-prone, downstream applications usually require quality control methods to pre-process FASTQ files. However, existing tools for this task are currently not able to fully exploit the capabilities of computing platforms leading to slow runtimes. Results We present RabbitQC, an extremely fast integrated quality control tool for FASTQ files, which can take full advantage of modern hardware. It includes a variety of operations and supports different sequencing technologies (Illumina, Oxford Nanopore and PacBio). RabbitQC achieves speedups between …

Transition to ballistic regime for heat transport in helium II

2014

The size-dependent and flux-dependent effective thermal conductivity of narrow capillaries filled with superfluid helium is analyzed from a thermodynamic continuum perspective. The classical Landau evaluation of the effective thermal conductivity of quiescent superfluid, or the Gorter-Mellinck regime of turbulent superfluids, are extended to describe the transition to ballistic regime in narrow channels wherein the radius $R$ is comparable to (or smaller than) the phonon mean-free path $\ell$ in superfluid helium. To do so we start from an extended equation for the heat flux incorporating non-local terms, and take into consideration a heat slip flow along the walls of the tube. This leads f…

RNaseE-mediated mRNA degradation as determinant of polarity in phage f1.

2008

RNA processing and degradation are important steps in the regulation of gene expression. The genes present on the DNA of filamentous phage f1 are expressed at very different levels. A group of genes which are expressed at a very low level (genes III, VI, I and IV is located in the region IF of the phage DNA. The current model proposes that expression of the genes III. VI and I (which form an operon) is regulated by readthrough transcription at a weak terminator located at the end of gene III, while that of gene IV by a terminator located at the end of it. In contrast with this, we found that very long transcripts complementary to the entire f1 DNA are synthesized in the infected cells and t…

Arginine deficiency leads to impaired cofilin dephosphorylation in activated human T lymphocytes

2012

The amino acid arginine is fundamentally involved in the regulation of the immune response during infection, inflammatory diseases and tumor growth. Arginine deficiency (e.g. due to the myeloid cell enzyme arginase) inhibits proliferation and effector functions of activated T lymphocytes. Here, we studied intracellular mechanisms mediating this suppression of human T lymphocytes. Our proteomic analysis revealed an impaired dephosphorylation of the actin-binding protein cofilin upon T-cell activation in the absence of arginine. We show that this correlates with alteration of actin polymerization and impaired accumulation of CD2 and CD3 in the evolving immunological synapse in T cell-antigen …

Performance of industrial strains of Saccharomyces cerevisae during wine fermentation is affected by manipulation strategies based on sporulation.

2002

Genetic manipulation of industrial wine yeast strains has become an essential tool for both the study of the molecular mechanisms underlaying their physiology and the improvement of their fermentative properties. The construction of null mutants for any gene in these usually diploid strains, by using a procedure based on sporulation of a heterozygote lacking one copy of the gene of interest, has been tested as an alternative to the tedious work of sequential disruption of the complete set of copies. Our results indicate that most of the homozygotes resulting from sporulation of wine yeast strains are defective in glucose consumption under microvinification conditions in synthetic must and p…

Carbohydrate-Mediated Biomolecular Recognition and Gating of Synthetic Ion Channels

2013

Nanochannel-based biosensing devices have been proposed for selective detection of protein analyte molecules. However, the design and miniaturization of reusable channel-based biosensors is still a challenge in nanoscience and biotechnology. We present here a reusable nanofluidic biosensor based on reversible lectin-carbohydrate interactions. The nanochannels are fabricated in heavy ion tracked polymer membranes. The channel walls are functionalized with p-aminophenyl alpha-D-mannopyranoside (APMP) monolayers through carbodiimide coupling chemistry. The chemical (mannopyranoside) groups on the inner channel walls serve as binding sites and interact with specific protein molecules. The bindi…

Protein diffusion through charged nanopores with different radii at low ionic strength

2014

[EN] The diffusion of two similar molecular weight proteins, bovine serum albumin (BSA) and bovine haemoglobin (BHb), through nanoporous charged membranes with a wide range of pore radii is studied at low ionic strength. The effects of the solution pH and the membrane pore diameter on the pore permeability allow quantifying the electrostatic interaction between the chargedpore and the protein. Because of the large screening Debye length, both surface and bulk diffusion occur simultaneously. By increasing the pore diameter, the permeability tends to the bulk self-diffusion coefficient for each protein. By decreasing the pore diameter, the charges on the pore surface electrostatically hinder …

Resistance to space simulating conditions and sporicidal treatments of spores from bacilli of extreme environments origins: implication for Astrobiol…

Microorganisms able to tolerate environmental extremes, or extremophiles, are ideal candidates to extend our knowledge on the limitations for terrestrial life, including sporicidal treatments, and on their ability to survive under conditions mimicking space environments. The spore resistance of bacilli isolated from extreme environments, cold (Antarctic soils) and hot (shallow hydrothermal vents of Eolian Islands, Italy), was evaluated towards environmental stressors (wet- and dry-heat, low and high pH values), sporicidal treatments and stresses simulating space-environments (UV-C and X-rays irradiations, desiccations by low pressure, exposition to oxidizing agents and low pressure plasma),…

Field distribution ofSorosphaera viticolain commercial vineyards in Germany

2006

In the year 2000, resting spores of a previously undescribed plasmodiophorid were found in roots of Vitis spp. This plasmodiophorid was identified as a member of the genus Sorosphaera Schroeter and described as Sorosphaera viticola Kirchmair, Neuhauser, Huber. To attain information on the field distribution of Sorosphaera viticola, a selective screening was conducted in two commercial vineyards in Germany. A study to determine a correlation of Sorosphaeraviticola infection to grapevine growth was also performed.

CRYPTIC SPECIES RELATED TO DALDINIA CONCENTRICA AND D. ESCHSCHOLZII, WITH NOTES ON D. BAKERI

2004

Daldinia macaronesica (from the Canary Islands and Madeira), D. palmensis (from the Canary Islands), D. martinii and D. raimundi (from Sicily), and D. vanderguchtiae (from Jersey, Channel Islands) spp. nov., are described, based on new combinations of teleomorphic and anamorphic characters. They all resemble the pantropical D. eschscholzii and/or the European D. concentrica with regard to teleomorphic characters and secondary metabolite profiles generated by analytical HPLC. The status of the newly described taxa was established by SEM of ascospores and microscopic studies of their anamorphs in comparison with various materials of the aforementioned known species. HPLC and SEM studies on th…