motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences

Next-generation sequencing technology enables the identification of thousands of gene regulatory sequences in many cell types and organisms. We consider the problem of testing if two such sequences differ in their number of binding site motifs for a given transcription factor (TF) protein. Binding site motifs impart regulatory function by providing TFs the opportunity to bind to genomic elements and thereby affect the expression of nearby genes. Evolutionary changes to such functional DNA are hypothesized to be major contributors to phenotypic diversity within and between species; but despite the importance of TF motifs for gene expression, no method exists to test for motif loss or gain. Assuming that motif counts are Binomially distributed, and allowing for dependencies between motif instances in evolutionarily related sequences, we derive the probability mass function of the difference in motif counts between two nucleotide sequences. We provide a method to numerically estimate this distribution from genomic data and show through simulations that our estimator is accurate. Finally, we introduce the R package {\tt motifDiverge} that implements our methodology and illustrate its application to gene regulatory enhancers identified by a mouse developmental time course experiment. While this study was motivated by analysis of regulatory motifs, our results can be applied to any problem involving two correlated Bernoulli trials

Noncoding Sequences Near Duplicated Genes Evolve Rapidly

Gene expression divergence and chromosomal rearrangements have been put forward as major contributors to phenotypic differences between closely related species. It has also been established that duplicated genes show enhanced rates of positive selection in their amino acid sequences. If functional divergence is largely due to changes in gene expression, it follows that regulatory sequences in duplicated loci should also evolve rapidly. To investigate this hypothesis, we performed likelihood ratio tests (LRTs) on all noncoding loci within 5 kb of every transcript in the human genome and identified sequences with increased substitution rates in the human lineage since divergence from Old World Monkeys. The fraction of rapidly evolving loci is significantly higher nearby genes that duplicated in the common ancestor of humans and chimps compared with nonduplicated genes. We also conducted a genome-wide scan for nucleotide substitutions predicted to affect transcription factor binding. Rates of binding site divergence are elevated in noncoding sequences of duplicated loci with accelerated substitution rates. Many of the genes associated with these fast-evolving genomic elements belong to functional categories identified in previous studies of positive selection on amino acid sequences. In addition, we find enrichment for accelerated evolution nearby genes involved in establishment and maintenance of pregnancy, processes that differ significantly between humans and monkeys. Our findings support the hypothesis that adaptive evolution of the regulation of duplicated genes has played a significant role in human evolution

DBEndo: a web-based endodontic case management tool

BACKGROUND: The success of endodontic treatment depends-among many other factors-on good documentation. Paper-based records are often difficult to read or incomplete and commercially available tools focus on billing. An electronic record captures the state of treatment at all times. Databases are a common tool in everyday life. RESULTS: Here, we present a database created for the Charite-Universitatsmedizin Berlin, Germany. Through consistent digital documentation, data analytics of patients, root canal anatomies, instrumentation techniques, efficacy of chemical disinfection, root filling techniques, and corresponding recall success rates, which needed extensive research before, are now easy to perform. Tables and even graphics and data analystics are only one click away and can be exported to other programs. CONCLUSIONS: DBEndo is a database to store and visualise internally, as well as to share endodontic cases online. For academic use we provide the database including all forms and some anonymous data for free at: http://dbendo.charite.de . Through easy import and export of the data, the system is open and flexible

Two different subunits of importin cooperate to recognize nuclear localization signals and bind them to the nuclear envelope

AbstractBackground: Selective protein import into the cell nucleus occurs in two steps: binding to the nuclear envelope, followed by energy-dependent transit through the nuclear pore complex. A 60 kD protein, importin, is essential for the first nuclear import step, and the small G protein Ran/TC4 is essential for the second. We have previously purified the 60 kD importin protein (importin 60) as a single polypeptide.Results We have identified importin 90, a 90 kD second subunit that dissociates from importin 60 during affinity chromatography on nickel (II)–nitrolotriacetic acid–Sepharose, a technique that was originally used to purify importin 60. Partial amino-acid sequencing of Xenopus importin 90 allowed us to clone and sequence its human homologue; the amino-acid sequence of importin 90 is strikingly conserved between the two species. We have also identified a homologous budding yeast sequence from a database entry. Importin 90 potentiates the effects of importin 60 on nuclear protein import, indicating that the importin complex is the physiological unit responsible for import. To assess whether nuclear localization sequences are recognized by cytosolic receptor proteins, a biotin-tagged conjugate of nuclear localization signals linked to bovine serum albumin was allowed to form complexes with cytosolic proteins in Xenopus egg extracts; the complexes were then retrieved with streptavidin–agarose. The pattern of bound proteins was surprisingly simple and showed only two predominant bands: those of the importin complex. We also expressed the human homologue of importin 60, Rch1p, and found that it was able to replace its Xenopus counterpart in a functional assay. We discuss the relationship of importin 60 and importin 90 to other nuclear import factors.Conclusion Importin consists of a 60 and a 90 kD subunit. Together, they constitute a cytosolic receptor for nuclear localization signals that enables import substrates to bind to the nuclear envelope

Correlation of Microstructure and Properties of Cold Gas Sprayed INCONEL 718 Coatings

In the cold gas spray process, deposition of particles takes place through intensive plastic deformation upon impact in a solid state at temperatures well below their melting point. The high particle impact velocities and corresponding peening effects can lead to high compressive residual stresses in cold spray coatings. This can be advantageous with regard to mechanical properties as fatigue life and hence, cold spray is an ideal process for repair applications. In this study, INCONEL 718 particles were cold sprayed by using nitrogen as propellant gas. The deposited coatings with different thicknesses were characterized using electron microscopy techniques to study grain refinement and precipitates in the coating. In addition, depth-resolved residual stress measurements have been performed by the incremental hole drilling method. The residual stress depth profiles in the coatings indicate compressive residual stresses of several hundred MPa which are hardly influenced by the coating thickness. In addition, large compressive stress levels are found in surface- near regions of the substrate due to the grit blasting process. Furthermore, a post-heat treatment analysis was performed to investigate its influence on residual stresses and bonding strength. These findings are used to develop a consistent explanation of the dependence of strength values on thickness

Deformation-Induced Martensite: A New Paradigm for Exceptional Steels

Atom-probe tomography (APT) and synchrotron X-ray diffraction (XRD) were combined to study the carbon supersaturation of ferrite for two pearlitic steel-wire compositions, eutectoid and hypereutectoid. The samples were cold-drawn at different strains up to true drawing strains for the eutectoid steel and the hypereutectoid steel, respectively. The wire diameters range from 1.7 mm down to 0.058 mm for the eutectoid steel and from 0.54 mm down to 0.02 mm for the hypereutectoid steel. The findings reveal that cold-drawing of pearlitic steel wires leads to a carbon-supersaturated ferrite causing a spontaneous tetragonal distortion of the ferrite unit cell through a strain-induced deformation driven martensitic transformation. We fi nd that the drawing process induced a significant increase in the carbon content inside the originally nearcarbon-free ferrite until a steady state is approached at drawing strains larger than ca. 4 for the wires. The change of carbon concentration in the ferrite grains during the drawing process is closely related to the tetragonal distortion of the ferrite unit cell

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes

GC-biased gene conversion (gBGC) is a recombination-associated process that favors the fixation of G/C alleles over A/T alleles. In mammals, gBGC is hypothesized to contribute to variation in GC content, rapidly evolving sequences, and the fixation of deleterious mutations, but its prevalence and general functional consequences remain poorly understood. gBGC is difficult to incorporate into models of molecular evolution and so far has primarily been studied using summary statistics from genomic comparisons. Here, we introduce a new probabilistic model that captures the joint effects of natural selection and gBGC on nucleotide substitution patterns, while allowing for correlations along the genome in these effects. We implemented our model in a computer program, called phastBias, that can accurately detect gBGC tracts about 1 kilobase or longer in simulated sequence alignments. When applied to real primate genome sequences, phastBias predicts gBGC tracts that cover roughly 0.3% of the human and chimpanzee genomes and account for 1.2% of human-chimpanzee nucleotide differences. These tracts fall in clusters, particularly in subtelomeric regions; they are enriched for recombination hotspots and fast-evolving sequences; and they display an ongoing fixation preference for G and C alleles. They are also significantly enriched for disease-associated polymorphisms, suggesting that they contribute to the fixation of deleterious alleles. The gBGC tracts provide a unique window into historical recombination processes along the human and chimpanzee lineages. They supply additional evidence of long-term conservation of megabase-scale recombination rates accompanied by rapid turnover of hotspots. Together, these findings shed new light on the evolutionary, functional, and disease implications of gBGC. The phastBias program and our predicted tracts are freely available. © 2013 Capra et al

Generation of x-ray radiation in a storage ring by a superconductive cold-bore invacuum undulator

The first beam measurements with a cold-bore superconducting in-vacuum undulator in a storage ring are reported. Undulators are x-ray generators in light sources. The physical limitations of these devices limit the intensity and the brilliance of the x-ray beam. At present the undulators are made from permanent magnets. It was shown in earlier papers that at low electron beam intensities superconductive wires in the vacuum beam pipe can overcome the limitations inherent to permanent magnet undulators. It was argued that the use of these novel devices in light sources with high beam currents may be limited by the extreme anomalous skin effect regime in Cu at 4.2 K, which has so far undergone very little investigation, and the power deposited by the infrared part of the synchrotron radiation. The purpose of this paper is to present measurements of these effects at the synchrotron light source ANKA with stored currents up to 200 mA