Search results for "alignment"
showing 10 items of 627 documents
Characterization of PAMP/PRR interactions in European eel (Anguilla anguilla) macrophage-like primary cell cultures
2013
The eel (Anguilla anguilla) has been identified as a vulnerable species with stocks dramatically declining over the past decade. In an effort to support the species from overfishing of wild stocks increased interest in eel aquaculture has been notable. In order to expand the scarce knowledge concerning the biology of this species significant research efforts are required in several fields of biology. The development of cell culture systems to study the immune response is a key step towards an increased understanding of the immune response and to develop resources to support further study in this threatened species. Macrophages are one of the most important effector cells of the innate immun…
Modular Breath Analyzer (MBA): Introduction of a Breath Analyzer Platform Based on an Innovative and Unique, Modular eNose Concept for Breath Diagnos…
2021
Exhaled breath analysis for early disease detection may provide a convenient method for painless and non-invasive diagnosis. In this work, a novel, compact and easy-to-use breath analyzer platform with a modular sensing chamber and direct breath sampling unit is presented. The developed analyzer system comprises a compact, low volume, temperature-controlled sensing chamber in three modules that can host any type of resistive gas sensor arrays. Furthermore, in this study three modular breath analyzers are explicitly tested for reproducibility in a real-life breath analysis experiment with several calibration transfer (CT) techniques using transfer samples from the experiment. The experiment …
The crystal structure of bacteriophage Qβ at 3.5 å resolution
1996
Abstract Background: The capsid protein subunits of small RNA bacteriophages form a T=3 particle upon assembly and RNA encapsidation. Dimers of the capsid protein repress translation of the replicase gene product by binding to the ribosome binding site and this interaction is believed to initiate RNA encapsidation. We have determined the crystal structure of phage Qβ with the aim of clarifying which factors are the most important for particle assembly and RNA interaction in the small phages. Results The crystal structure of bacteriophage Qβ determined at 3.5 a resolution shows that the capsid is stabilized by disulfide bonds on each side of the flexible loops that are situated around the fi…
Novel Glutamate–Putrescine Ligase Activity in Haloferax mediterranei: A New Function for glnA-2 Gene
2021
This article belongs to the Section Cellular Biochemistry.
Immunoaffinity purification and characterization of mitochondrial membrane-bound D-3-hydroxybutyrate dehydrogenase from Jaculus orientalis.
2008
Abstract Background The interconversion of two important energy metabolites, 3-hydroxybutyrate and acetoacetate (the major ketone bodies), is catalyzed by D-3-hydroxybutyrate dehydrogenase (BDH1: EC 1.1.1.30), a NAD+-dependent enzyme. The eukaryotic enzyme is bound to the mitochondrial inner membrane and harbors a unique lecithin-dependent activity. Here, we report an advanced purification method of the mammalian BDH applied to the liver enzyme from jerboa (Jaculus orientalis), a hibernating rodent adapted to extreme diet and environmental conditions. Results Purifying BDH from jerboa liver overcomes its low specific activity in mitochondria for further biochemical characterization of the e…
Cloning and expression of genes involved in conidiation and surface properties of Penicillium camemberti grown in liquid and solid cultures.
2008
International audience; Based on bioinformatic data on model fungi, the rodA and wetA genes encoding, respectively, a RodA hydrophobin protein and the WetA protein involved in conidiation mechanisms, were PCR-cloned and characterized for the first time in Penicillium camemberti. These results, completed by a sequence of the brlA gene (available in GenBank), which encodes a major transcriptional regulator also involved in the conidiation mechanism, were used to compare, by qRT-PCR, the expression of the three genes in liquid and solid cultures in a synthetic medium. While expression of the brlA and wetA genes increased dramatically in both culture conditions after 4 days of growth, expressio…
One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.
2020
Mapping of high-throughput sequencing (HTS) reads to a single arbitrary reference genome is a frequently used approach in microbial genomics. However, the choice of a reference may represent a source of errors that may affect subsequent analyses such as the detection of single nucleotide polymorphisms (SNPs) and phylogenetic inference. In this work, we evaluated the effect of reference choice on short-read sequence data from five clinically and epidemiologically relevant bacteria (Klebsiella pneumoniae, Legionella pneumophila, Neisseria gonorrhoeae, Pseudomonas aeruginosa and Serratia marcescens). Publicly available whole-genome assemblies encompassing the genomic diversity of these species…
Zero axial irradiance by annular screens with angular variation
1992
For optical alignment, it may be convenient to use a three-dimensional diffraction pattern with zero irradiance along the optical axis. This pattern is created here by using annular screens in the form of a phase daisy, a daisy flower, or a pie, with an even number of slices of an equal central angle and with every other slice with a phase retardation of 180 degrees . We recognize this form of angular variation as a particular solution of a wider set of functions that are able to produce zero axial irradiance.
Field-free molecular alignment of asymmetric top molecules using elliptically polarized laser pulses
2008
International audience; We show theoretically that a short specific elliptically polarized laser pulse driving an asymmetric top molecule can induce postpulse revivals of three-dimensional (3-D) alignment. By choosing the field ellipticity resulting in the best compromise between the alignment of two molecular axes, we demonstrate that efficient 3-D alignment can be achieved at low temperature. In the experiment, the field-free alignment of moderately cool ethylene molecules is probed by using a technique based on the optical Kerr effect. Control of 3-D field-free alignment opens the door to a large range of applications in chemistry as well as in molecular optics.
Avoided motifs: short amino acid strings missing from protein datasets.
2020
Abstract According to the amino acid composition of natural proteins, it could be expected that all possible sequences of three or four amino acids will occur at least once in large protein datasets purely by chance. However, in some species or cellular context, specific short amino acid motifs are missing due to unknown reasons. We describe these as Avoided Motifs, short amino acid combinations missing from biological sequences. Here we identify 209 human and 154 bacterial Avoided Motifs of length four amino acids, and discuss their possible functionality according to their presence in other species. Furthermore, we determine two Avoided Motifs of length three amino acids in human proteins…