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Concept: Separation

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BACKGROUND: The metagenomics approach allows the simultaneous sequencing of all genomes in an environmental sample. This results in high complexity datasets, where in addition to repeats and sequencing errors, the number of genomes and their abundance ratios are unknown. Recently developed next-generation sequencing (NGS) technologies significantly improve the sequencing efficiency and cost. On the other hand, they result in shorter reads, which makes the separation of reads from different species harder. Among the existing computational tools for metagenomic analysis, there are similarity-based methods that use reference databases to align reads and composition-based methods that use composition patterns (i.e., frequencies of short words or l-mers) to cluster reads. Similarity-based methods are unable to classify reads from unknown species without close references (which constitute the majority of reads). Since composition patterns are preserved only in significantly large fragments, composition-based tools cannot be used for very short reads, which becomes a significant limitation with the development of NGS. A recently proposed algorithm, AbundanceBin, introduced another method that bins reads based on predicted abundances of the genomes sequenced. However, it does not separate reads from genomes of similar abundance levels. RESULTS: In this work, we present a two-phase heuristic algorithm for separating short paired-end reads from different genomes in a metagenomic dataset. We use the observation that most of the l-mers belong to unique genomes when l is sufficiently large. The first phase of the algorithm results in clusters of l-mers each of which belongs to one genome. During the second phase, clusters are merged based on l-mer repeat information. These final clusters are used to assign reads. The algorithm could handle very short reads and sequencing errors. It is initially designed for genomes with similar abundance levels and then extended to handle arbitrary abundance ratios. The software can be download for free at http://www.cs.ucr.edu/~tanaseio/toss.htm. CONCLUSIONS: Our tests on a large number of simulated metagenomic datasets concerning species at various phylogenetic distances demonstrate that genomes can be separated if the number of common repeats is smaller than the number of genome-specific repeats. For such genomes, our method can separate NGS reads with a high precision and sensitivity.

Concepts: Genomics, Species, Metagenomics, Separation, Legal separation, Heuristic, Jane Arden, Jack Bond

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The mammalian need for social proximity, attachment and belonging may have an adaptive and evolutionary value in terms of survival and reproductive success. Consequently, ostracism may induce strong negative feelings of social exclusion. Recent studies suggest that slow, affective touch, which is mediated by a separate, specific C tactile neurophysiological system than faster, neutral touch, modulates the perception of physical pain. However, it remains unknown whether slow, affective touch, can also reduce feelings of social exclusion, a form of social pain. Here, we employed a social exclusion paradigm, namely the Cyberball task (N = 84), to examine whether the administration of slow, affective touch may reduce the negative feelings of ostracism induced by the social exclusion manipulations of the Cyberball task. As predicted, the provision of slow-affective, as compared to fast-neutral, touch led to a specific decrease in feelings of social exclusion, beyond general mood effects. These findings point to the soothing function of slow, affective touch, particularly in the context of social separation or rejection, and suggest a specific relation between affective touch and social bonding.

Concepts: Sociology, Neuroscience, Pain, Sensory system, Sense, Somatosensory system, Emotion, Separation

28

Preparative high-speed counter-current chromatography (HSCCC) was successfully applied to the isolation and purification of two macrolactin antibiotics from marine bacterium Bacillus amyloliquefaciens for the first time using stepwise elution with a pair of two-phase solvent systems composed of n-hexane-ethyl acetate-methanol-water at (1:4:1:4, v/v) and (3:4:3:4, v/v). The preparative HSCCC separation was performed on 300mg of crude sample yielding macrolactin B (22.7mg) and macrolactin A (40.4mg) in a one-step separation, with purities over 95% as determined by HPLC. The structures of these compounds were identified by MS, (1)H NMR and (13)C NMR. Our results demonstrated that HSCCC was an efficient technique to separate marine antibiotics, which provide an approach to solve the problem of their sample availability for drug development.

Concepts: Bacteria, Chromatography, High performance liquid chromatography, Analytical chemistry, Gas chromatography, Bacillus, Bacillus amyloliquefaciens, Separation

28

Use of elevated electric fields and helium-rich gases has recently enabled differential ion mobility spectrometry (IMS) with a resolving power up to R ∼ 300. Here we applied that technique to a protein (ubiquitin), achieving R up to ∼80 and separating previously unresolved conformers. While still limited by conformational multiplicity, this resolution is some 4 times greater than that previously reported using either conventional (drift-tube or traveling-wave) or differential IMS. The capability for fine resolution of protein conformers may open new avenues for proteoform separations in top-down and intact-protein proteomics.

Concepts: Electric charge, Mass spectrometry, Proteomics, Display resolution, Resolution, Separation, Ion mobility spectrometry

28

Previous investigators reported the impairment of foveal visual acuity by nearby flanking targets (contour interaction) is reduced or eliminated when acuity is measured using low contrast targets. Unlike earlier studies, we compared contour interaction for high and low contrast acuity targets using flankers at fixed angular separations, rather than at specific multiples of the acuity target’s stroke width. Percent correct letter identification was determined in 4 adult observers for computer generated, high and low contrast dark Sloan letters surrounded by 4 equal contrast flanking bars. Two low contrast targets were selected to reduce each observer’s visual acuity by 0.2 and 0.4 logMAR. The contour interaction functions measured for high and low contrast letters are very similar when percent correct letter identification is plotted against the flanker separation in min arc. These results indicate that contour interaction of foveal acuity targets occurs within a fixed angular zone of a few min arc, regardless of the size or contrast of the acuity target.

Concepts: Visual acuity, Target Corporation, Binary relation, Separation, Specific Identification, Observer, Snellen chart

27

Mining activities may contribute significant amounts of metals to surrounding soils. Assessing the potential effects and extent of metal contamination requires the differentiation between geogenic and additional anthropogenic sources. This study compares the use of conventional probability plots with two forms of fractal analysis (number-size and concentration-area) to separate geochemical populations of ore-related elements in agricultural area soils adjacent to Pb-Zn mining operations in the Irankuh Mountains, central Iran. The two general approaches deliver similar spatial groupings of univariate geochemical populations, but the fractal methods provide more distinct separation between populations and require less data manipulation and modeling than the probability plots. The concentration-area fractal approach was more effective than the number-size fractal and probability plotting methods at separating sub-populations within the samples affected by contamination from the mining operations. There is a general lack of association between major elements and ore-related metals in the soils. The background populations display higher relative variation in the major elements than the ore-related metals whereas near the mining operations there is far greater relative variation in the ore-related metals. The extent of the transport of contaminants away from the mine site is partly a function of the greater dispersion of Zn compared with Pb and As, however, the patterns indicate dispersion of contaminants from the mine site is via dust and not surface/groundwater. A combination of geochemical and graphical assessment, with different methods of threshold determination, is shown to be effective in separating geogenic and anthropogenic geochemical patterns.

Concepts: Mathematics, Effect, Zinc, Geology, Heavy metal music, Separation, Jane Arden, Jack Bond

27

A reversed phase chromatographic system, composed of a stationary phase of C silica gel (ODS, 20μm) and a mobile phase of ethanol/water, was used to separate liquiritin and liquiritigenin in the raw material of flavonoids. The linear adsorption isotherm and the equilibrium-dispersive model were adopted to approximatively describe the chromatographic separation behaviors of liquiritin and liquiritigenin in the raw material under different column temperatures, ethanol contents and flow rates of the mobile phase, sample concentrations and feeding times. Combined with orthogonal design, the ED model was used to optimize the chromatographic separating conditions, the corresponding experimental result with a good agreement was obtained and the overload separation was realized.

Concepts: Chromatography, Analytical chemistry, Gas chromatography, Thin layer chromatography, Separation, Silica gel, Jane Arden, Jack Bond

27

To study the preparation and separation of Konjac oligosaccharides, Konjac Glucomannan was degraded by the combination of γ-irradiation and β-mannanase, and then the degradation product was separated by ultrafiltration. To our interest, for most of Konjac oligosaccharides obtained by this method, the molecular mass was lower than 2200Da. In addition, the 1000Da molecular weight cut off membrane could effectively separate the Konjac oligosaccharides. In conclusion, the combination of γ-irradiation and β-mannanase was an efficient method to obtain Konjac oligosaccharides, and the oligosaccharides of molecular mass lower than 1000Da could be effectively separated by ultrafiltration.

Concepts: Molecule, Mass, Atomic mass unit, Molecular mass, Separation, Glucomannan, Konjac, Shirataki noodles

27

Capillary electrophoresis-mass spectrometry (CE-MS) is a powerful analytical tool, especially in the case of chiral separations, due to the fact that it combines the high efficiency, short analysis time, and versatility of the CE with the sensitivity, selectivity, and the capacity for the identification of unknown chiral compounds offered by MS detection. This chapter describes three methodologies enabling the chiral separation of cationic and anionic compounds using different strategies, illustrating the most employed approaches used in chiral CE-MS. The first methodology uses the partial filling technique for the enantioseparation of a cationic compound using a neutral cyclodextrin. Secondly, the enantioseparation of a cationic compound using low concentrations of a neutral cyclodextrin under acidic conditions is described. Finally, a methodology for the chiral separation of an anionic compound employing low concentrations of a native cyclodextrin under basic conditions is illustrated.

Concepts: Scientific method, Amino acid, Amine, Epistemology, Analytical chemistry, Chirality, Methodology, Separation

24

A novel silica-based stationary phase with branched octadecyl groups was prepared by the sequential employment of the Michael addition reaction and photoinduced thiol-yne click chemistry with 3-aminopropyl-functionalized silica microspheres as the initial material. The resulting stationary phase denoted as SiO2 -N(C18)4 was characterized by elemental analysis, FTIR spectroscopy and Raman spectroscopy, demonstrating the existence of branched octadecyl groups in silica microspheres. The separations of benzene homologous compounds, acid compounds and amine analogues were conducted, demonstrating mixed-mode separation mechanism on SiO2 -N(C18)4 . Baseline separation of basic drugs mixture was acquired with the mobile phase of ACN/H2 O (5%, v/v). The SiO2 -N(C18)4 was further applied to separate Corydalis yanhusuo Wang water extracts, and more baseline separation peaks were obtained for SiO2 -N(C18)4 than those on Atlantis dC18 column. It can be expected that this new silica-based stationary phase will exhibit great potential in the analysis of basic compounds. This article is protected by copyright. All rights reserved.

Concepts: Chromatography, Analytical chemistry, Raman spectroscopy, Organic chemistry, All rights reserved, Separation, Copyright, Corydalis