F-Seq: a feature density estimator for high-throughput sequence tags

Summary: Tag sequencing using high-throughput sequencing technologies are now regularly employed to identify specific sequence features, such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq). To intuitively summarize and display individual sequence data as an accurate and interpretable signal, we developed F-Seq, a software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser

Comparison and validation of 2 analytical methods for the determination of free fatty acids in dairy products by gas chromatography with flame ionization detection

peer-reviewedAccurate quantification of free fatty acids (FFA) in dairy products is important for quality control, nutritional, antimicrobial, authenticity, legislative, and flavor purposes. In this study, the performance of 2 widely used gas chromatographic flame ionization detection methods for determination of FFA in dairy products differing in lipid content and degree of lipolysis were evaluated. We used a direct on-column approach where the isolated FFA extract was injected directly and a derivatization approach where the FFA were esterified in the injector to methyl esters using tetramethylammonium hydroxide as a catalyst. A comprehensive validation was undertaken to establish method linearity, limits of detection, limits of quantification, accuracy, and precision. Linear calibrations of 3 to 700mg/L (R2>0.999) and 20 to 700mg/L (R2>0.997), and limits of detection and limits of quantification of 0.7 and 3mg/L and 5 and 20mg/L were obtained for the direct injection on-column and the derivatization method, respectively. Intraday precision of 1.5 to 7.2% was obtained for both methods. The direct injection on-column method had the lower levels of limits of detection and quantification, because FFA are directly injected onto the GC as opposed to the split injection used in the derivatization method. However, the direct injection on-column method experienced accumulative column phase deterioration and irreversible FFA absorption because of the acidic nature of the injection extract, which adversely affected method robustness and the quantification of some longer chain FFA. The derivatization method experienced issues with quantification of butyric acid at low concentrations because of coelution with the injection solvent peak, loss of polyunsaturated FFA due to degradation by tetramethylammonium hydroxide, and the periodic emergence of by-product peaks of the tetramethylammonium hydroxide reaction that interfered with the quantification of some short-chain FFA. The derivatization method is more robust, and because the derivatization step can be automated, it is more suitable for routine analysis of FFA in dairy products. However, considerable scope exists to develop an alternative gas chromatography with flame ionization detection method to quantify FFA in dairy products without any limitations that is robust and accurate

DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types

DNase-seq is primarily used to identify nucleosome-depleted DNase I hypersensitive (DHS) sites genome-wide that correspond to active regulatory elements. However, ∼40 yr ago it was demonstrated that DNase I also digests with a ∼10-bp periodicity around nucleosomes matching the exposure of the DNA minor groove as it wraps around histones. Here, we use DNase-seq data from 49 samples representing diverse cell types to reveal this digestion pattern at individual loci and predict genomic locations where nucleosome rotational positioning, the orientation of DNA with respect to the histone surface, is stably maintained. We call these regions DNase I annotated regions of nucleosome stability (DARNS). Compared to MNase-seq experiments, we show DARNS correspond well to annotated nucleosomes. Interestingly, many DARNS are positioned over only one side of annotated nucleosomes, suggesting that the periodic digestion pattern attenuates over the nucleosome dyad. DARNS reproduce the arrangement of nucleosomes around transcription start sites and are depleted at ubiquitous DHS sites. We also generated DARNS from multiple lymphoblast cell line (LCL) samples. We found that LCL DARNS were enriched at DHS sites present in most of the original 49 samples but absent in LCLs, while multi-cell-type DARNS were enriched at LCL-specific DHS sites. This indicates that variably open DHS sites are often occupied by rotationally stable nucleosomes in cell types where the DHS site is closed. DARNS provide additional information about precise DNA orientation within individual nucleosomes not available from other nucleosome positioning assays and contribute to understanding the role of chromatin in gene regulation

Development and validation of a quantitative confirmatory method for 30 β-lactam antibiotics in bovine muscle using liquid chromatography coupled to tandem mass spectrometry

peer-reviewedA method was developed for the confirmatory and quantitative analysis of 30 β-lactam antibiotic residues in bovine muscle. The method includes 12 penicillins (amoxicillin, ampicillin, cloxacillin, dicloxacillin, mecillinam, methicillin, nafcillin, oxacillin, penicillin G, penicillin V, piperacillin, ticarcillin), 12 cephalosporins (cefacetrile, cefadroxil, cephalexin, cefalonium, cefazolin, cefoperazone, cefotaxime, cefquinome, cefuroxime, desacetyl cephapirin, desfuroylceftiofur cysteine disulfide, desfuroylceftiofur dimer), five carbapenems (biapenem, doripenem, ertapenem, imipenem, meropenem) and faropenem. Samples were extracted using a simple solvent extraction with acetonitrile:water (80:20, v/v) and C18 dispersive solid-phase extraction (d-SPE) clean-up, followed by ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC–MS/MS) detection. Chromatography was performed on a reversed phase CSH C18 column, using a binary gradient separation comprising of 0.01% formic acid and 0.2 mM ammonium acetate in water (mobile phase A) and 0.01% formic acid in acetonitrile (mobile phase B). The mass spectrometer was operated in the positive electrospray ionisation mode (ESI(+)). Validation was performed following the 2002/657/EC guidelines. Trueness ranged between 69% and 143% and precision ranged between 2.0% and 29.9% under within-laboratory reproducibility conditions. The developed method uses minimal sample preparation and 30 test samples can be analysed by a single analyst in a single day. To the best of our knowledge, this is the first method for carbapenems in foodstuff that does not require derivatisation.FIRM programm

Recessive Inheritance of Congenital Hydrocephalus With Other Structural Brain Abnormalities Caused by Compound Heterozygous Mutations in ATP1A3

Background: ATP1A3 encodes the α3 subunit of the Na+/K+ ATPase, a fundamental ion-transporting enzyme. Primarily expressed in neurons, ATP1A3 is mutated in several autosomal dominant neurological diseases. To our knowledge, damaging recessive genotypes in ATP1A3 have never been associated with any human disease. Atp1a3 deficiency in zebrafish results in hydrocephalus; however, no known association exists between ATP1A3 and human congenital hydrocephalus (CH). / Methods: We utilized whole-exome sequencing (WES), bioinformatics, and computational modeling to identify and characterize novel ATP1A3 mutations in a patient with CH. We performed immunohistochemical studies using mouse embryonic brain tissues to characterize Atp1a3 expression during brain development. / Results: We identified two germline mutations in ATP1A3 (p. Arg19Cys and p.Arg463Cys), each of which was inherited from one of the patient’s unaffected parents, in a single patient with severe obstructive CH due to aqueductal stenosis, along with open schizencephaly, type 1 Chiari malformation, and dysgenesis of the corpus callosum. Both mutations are predicted to be highly deleterious and impair protein stability. Immunohistochemical studies demonstrate robust Atp1a3 expression in neural stem cells (NSCs), differentiated neurons, and choroid plexus of the mouse embryonic brain. / Conclusion: These data provide the first evidence of a recessive human phenotype associated with mutations in ATP1A3, and implicate impaired Na+/K+ ATPase function in the pathogenesis of CH

CompaGB: An open framework for genome browsers comparison

<p>Abstract</p> <p>Background</p> <p>Tools to visualize and explore genomes hold a central place in genomics and the diversity of genome browsers has increased dramatically over the last few years. It often turns out to be a daunting task to compare and choose a well-adapted genome browser, as multidisciplinary knowledge is required to carry out this task and the number of tools, functionalities and features are overwhelming.</p> <p>Findings</p> <p>To assist in this task, we propose a community-based framework based on two cornerstones: (i) the implementation of industry promoted software qualification method (QSOS) adapted for genome browser evaluations, and (ii) a web resource providing numerous facilities either for visualizing comparisons or performing new evaluations. We formulated 60 criteria specifically for genome browsers, and incorporated another 65 directly from QSOS's generic section. Those criteria aim to answer versatile needs, ranging from a biologist whose interest primarily lies into user-friendly and informative functionalities, a bioinformatician who wants to integrate the genome browser into a wider framework, or a computer scientist who might choose a software according to more technical features. We developed a dedicated web application to enrich the existing QSOS functionalities (weighting of criteria, user profile) with features of interest to a community-based framework: easy management of evolving data, user comments...</p> <p>Conclusions</p> <p>The framework is available at <url>http://genome.jouy.inra.fr/CompaGB</url>. It is open to anyone who wishes to participate in the evaluations. It helps the scientific community to (1) choose a genome browser that would better fit their particular project, (2) visualize features comparatively with easily accessible formats, such as tables or radar plots and (3) perform their own evaluation against the defined criteria. To illustrate the CompaGB functionalities, we have evaluated seven genome browsers according to the implemented methodology. A summary of the features of the compared genome browsers is presented and discussed.</p

Notes on wormhole existence in scalar-tensor and F(R) gravity

Some recent papers have claimed the existence of static, spherically symmetric wormhole solutions to gravitational field equations in the absence of ghost (or phantom) degrees of freedom. We show that in some such cases the solutions in question are actually not of wormhole nature while in cases where a wormhole is obtained, the effective gravitational constant G_eff is negative in some region of space, i.e., the graviton becomes a ghost. In particular, it is confirmed that there are no vacuum wormhole solutions of the Brans-Dicke theory with zero potential and the coupling constant \omega > -3/2, except for the case \omega = 0; in the latter case, G_eff < 0 in the region beyond the throat. The same is true for wormhole solutions of F(R) gravity: special wormhole solutions are only possible if F(R) contains an extremum at which G_eff changes its sign.Comment: 7 two-column pages, no figures, to appear in Grav. Cosmol. A misprint corrected, references update

Aberrant miR-29 is a predictive feature of severe phenotypes in pediatric Crohn’s disease

Publisher PD

The radial arrangement of the human chromosome 7 in the lymphocyte cell nucleus is associated with chromosomal band gene density

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ Springer-Verlag 2008.In the nuclei of human lymphocytes, chromosome territories are distributed according to the average gene density of each chromosome. However, chromosomes are very heterogeneous in size and base composition, and can contain both very gene-dense and very gene-poor regions. Thus, a precise analysis of chromosome organisation in the nuclei should consider also the distribution of DNA belonging to the chromosomal bands in each chromosome. To improve our understanding of the chromatin organisation, we localised chromosome 7 DNA regions, endowed with different gene densities, in the nuclei of human lymphocytes. Our results showed that this chromosome in cell nuclei is arranged radially with the gene-dense/GC-richest regions exposed towards the nuclear interior and the gene-poorest/GC-poorest ones located at the nuclear periphery. Moreover, we found that chromatin fibres from the 7p22.3 and the 7q22.1 bands are not confined to the territory of the bulk of this chromosome, protruding towards the inner part of the nucleus. Overall, our work demonstrates the radial arrangement of the territory of chromosome 7 in the lymphocyte nucleus and confirms that human genes occupy specific radial positions, presumably to enhance intra- and inter-chromosomal interaction among loci displaying a similar expression pattern, and/or similar replication timing