PILER-CR: Fast and accurate identification of CRISPR repeats

BACKGROUND: Sequencing of prokaryotic genomes has recently revealed the presence of CRISPR elements: short, highly conserved repeats separated by unique sequences of similar length. The distinctive sequence signature of CRISPR repeats can be found using general-purpose repeat- or pattern-finding software tools. However, the output of such tools is not always ideal for studying these repeats, and significant effort is sometimes needed to build additional tools and perform manual analysis of the output. RESULTS: We present PILER-CR, a program specifically designed for the identification and analysis of CRISPR repeats. The program executes rapidly, completing a 5 Mb genome in around 5 seconds on a current desktop computer. We validate the algorithm by manual curation and by comparison with published surveys of these repeats, finding that PILER-CR has both high sensitivity and high specificity. We also present a catalogue of putative CRISPR repeats identified in a comprehensive analysis of 346 prokaryotic genomes. CONCLUSION: PILER-CR is a useful tool for rapid identification and classification of CRISPR repeats. The software is donated to the public domain. Source code and a Linux binary are freely available at

Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'

We combined large-scale mRNA expression analysis and gene mapping to identify genes and loci that control hematopoietic stem cell (HSC) function. We measured mRNA expression levels in purified HSCs isolated from a panel of densely genotyped recombinant inbred mouse strains. We mapped quantitative trait loci (QTLs) associated with variation in expression of thousands of transcripts. By comparing the physical transcript position with the location of the controlling QTL, we identified polymorphic cis-acting stem cell genes. We also identified multiple trans-acting control loci that modify expression of large numbers of genes. These groups of coregulated transcripts identify pathways that specify variation in stem cells. We illustrate this concept with the identification of candidate genes involved with HSC turnover. We compared expression QTLs in HSCs and brain from the same mice and identified both shared and tissue-specific QTLs. Our data are accessible through WebQTL, a web-based interface that allows custom genetic linkage analysis and identification of coregulated transcripts.

Complex nature of SNP genotype effects on gene expression in primary human leucocytes.

This is a freely-available open access publication. Please cite the published version which is available via the DOI link in this record.BACKGROUND: Genome wide association studies have been hugely successful in identifying disease risk variants, yet most variants do not lead to coding changes and how variants influence biological function is usually unknown. METHODS: We correlated gene expression and genetic variation in untouched primary leucocytes (n = 110) from individuals with celiac disease - a common condition with multiple risk variants identified. We compared our observations with an EBV-transformed HapMap B cell line dataset (n = 90), and performed a meta-analysis to increase power to detect non-tissue specific effects. RESULTS: In celiac peripheral blood, 2,315 SNP variants influenced gene expression at 765 different transcripts (< 250 kb from SNP, at FDR = 0.05, cis expression quantitative trait loci, eQTLs). 135 of the detected SNP-probe effects (reflecting 51 unique probes) were also detected in a HapMap B cell line published dataset, all with effects in the same allelic direction. Overall gene expression differences within the two datasets predominantly explain the limited overlap in observed cis-eQTLs. Celiac associated risk variants from two regions, containing genes IL18RAP and CCR3, showed significant cis genotype-expression correlations in the peripheral blood but not in the B cell line datasets. We identified 14 genes where a SNP affected the expression of different probes within the same gene, but in opposite allelic directions. By incorporating genetic variation in co-expression analyses, functional relationships between genes can be more significantly detected. CONCLUSION: In conclusion, the complex nature of genotypic effects in human populations makes the use of a relevant tissue, large datasets, and analysis of different exons essential to enable the identification of the function for many genetic risk variants in common diseases.Coeliac UKNetherlands Organization for Scientific ResearchCeliac Disease Consortium (an innovative cluster approved by the Netherlands Genomics Initiative and partly funded by the Dutch government)Netherlands Genomics InitiativeWellcome Trus

Primordial magnetic fields at preheating

Using lattice techniques we investigate the generation of long range cosmological magnetic fields during a cold electroweak transition. We will show how magnetic fields arise, during bubble collisions, in the form of magnetic strings. We conjecture that these magnetic strings originate from the alignment of magnetic dipoles associated with EW sphaleron-like configurations. We also discuss the early thermalisation of photons and the turbulent behaviour of the scalar fields after tachyonic preheating.Comment: 7 pages. Talk presented at Lattice200

Strain-controlled criticality governs the nonlinear mechanics of fibre networks

Disordered fibrous networks are ubiquitous in nature as major structural components of living cells and tissues. The mechanical stability of networks generally depends on the degree of connectivity: only when the average number of connections between nodes exceeds the isostatic threshold are networks stable (Maxwell, J. C., Philosophical Magazine 27, 294 (1864)). Upon increasing the connectivity through this point, such networks undergo a mechanical phase transition from a floppy to a rigid phase. However, even sub-isostatic networks become rigid when subjected to sufficiently large deformations. To study this strain-controlled transition, we perform a combination of computational modeling of fibre networks and experiments on networks of type I collagen fibers, which are crucial for the integrity of biological tissues. We show theoretically that the development of rigidity is characterized by a strain-controlled continuous phase transition with signatures of criticality. Our experiments demonstrate mechanical properties consistent with our model, including the predicted critical exponents. We show that the nonlinear mechanics of collagen networks can be quantitatively captured by the predictions of scaling theory for the strain-controlled critical behavior over a wide range of network concentrations and strains up to failure of the material

Trans-eQTLs Reveal That Independent Genetic Variants Associated with a Complex Phenotype Converge on Intermediate Genes, with a Major Role for the HLA

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Expression quantitative trait loci are highly sensitive to cellular differentiation state

Blood cell development from multipotent hematopoietic stem cells to specialized blood cells is accompanied by drastic changes in gene expression for which the triggers remain mostly unknown. Genetical genomics is an approach linking natural genetic variation to gene expression variation, thereby allowing the identification of genomic loci containing gene expression modulators (eQTLs). In this paper, we used a genetical genomics approach to analyze gene expression across four developmentally close blood cell types collected from a large number of genetically different but related mouse strains. We found that, while a significant number of eQTLs (365) had a consistent “static” regulatory effect on gene expression, an even larger number were found to be very sensitive to cell stage. As many as 1,283 eQTLs exhibited a “dynamic” behavior across cell types. By looking more closely at these dynamic eQTLs, we show that the sensitivity of eQTLs to cell stage is largely associated with gene expression changes in target genes. These results stress the importance of studying gene expression variation in well-defined cell populations. Only such studies will be able to reveal the important differences in gene regulation between different ce

Codominant scoring of AFLP in association panels

A study on the codominant scoring of AFLP markers in association panels without prior knowledge on genotype probabilities is described. Bands are scored codominantly by fitting normal mixture models to band intensities, illustrating and optimizing existing methodology, which employs the EM-algorithm. We study features that improve the performance of the algorithm, and the unmixing in general, like parameter initialization, restrictions on parameters, data transformation, and outlier removal. Parameter restrictions include equal component variances, equal or nearly equal distances between component means, and mixing probabilities according to Hardy–Weinberg Equilibrium. Histogram visualization of band intensities with superimposed normal densities, and optional classification scores and other grouping information, assists further in the codominant scoring. We find empirical evidence favoring the square root transformation of the band intensity, as was found in segregating populations. Our approach provides posterior genotype probabilities for marker loci. These probabilities can form the basis for association mapping and are more useful than the standard scoring categories A, H, B, C, D. They can also be used to calculate predictors for additive and dominance effects. Diagnostics for data quality of AFLP markers are described: preference for three-component mixture model, good separation between component means, and lack of singletons for the component with highest mean. Software has been developed in R, containing the models for normal mixtures with facilitating features, and visualizations. The methods are applied to an association panel in tomato, comprising 1,175 polymorphic markers on 94 tomato hybrids, as part of a larger study within the Dutch Centre for BioSystems Genomics

Predictability of the spontaneous lumbar curve correction after selective thoracic fusion in idiopathic scoliosis

In this study we tried to achieve a better understanding of the biodynamic mechanism of balance in the scoliotic spine. Therefore we focused on the pre- and postoperative spine of patients with idiopathic scoliosis with a primary thoracic curve and a secondary lumbar curve. Several studies showed that the lumbar curve spontaneously corrects and improves after selective thoracic fusion. We try to understand and describe this spontaneous compensatory lumbar curve correction after selective thoracic correction and fusion. We performed a retrospective examination of pre- and postoperative radiographs of the spine of 38 patients with idiopathic scoliosis King type II and III. Frontal Cobb angles of the thoracic and lumbar curves were assessed on pre- and postoperative antero-posterior and side bending radiographs. We determined the postoperative corrections of the thoracic and lumbar curves. Relative (%) corrections and correlations of the postoperative corrections were calculated. The group was divided in three subgroups, depending on lumbar curve modifier, according to Lenkes classification system. The calculations were done for the whole group as for each subgroup. As expected, significant correlations were present between the relative correction of the main thoracic and the lumbar curve (mean R = 0.590; P = 0.001). The relation between relative thoracic and lumbar correction decreased with the lumbar modifier type. This study shows a highly significant correlation between the relative corrections of the main thoracic curve and the lumbar curve after selective thoracic fusion in idiopathic scoliosis. This correlation depends on lumbar curve modifier type. This new classification system seems to be of great predictable value for the spontaneous correction of the lumbar curve. Depending on the curve-type, a different technique for predicting the outcome should be used. The lumbar curve correction does not occur throughout the whole lumbar curve. Most correction is achieved in the upper part of the curve. The distal lumbar curve seems to be more rigid and less important in the spontaneous curve correction

The Atlantic Ocean at the last glacial maximum: 1. Objective mapping of the GLAMAP sea-surface conditions

Recent efforts of the German paleoceanographic community have resulted in a unique data set of reconstructed sea-surface temperature for the Atlantic Ocean during the Last Glacial Maximum, plus estimates for the extents of glacial sea ice. Unlike prior attempts, the contributing research groups based their data on a common definition of the Last Glacial Maximum chronozone and used the same modern reference data for calibrating the different transfer techniques. Furthermore, the number of processed sediment cores was vastly increased. Thus the new data is a significant advance not only with respect to quality, but also to quantity. We integrate these new data and provide monthly data sets of global sea-surface temperature and ice cover, objectively interpolated onto a regular 1°x1° grid, suitable for forcing or validating numerical ocean and atmosphere models. This set is compared to an existing subjective interpolation of the same base data, in part by employing an ocean circulation model. For the latter purpose, we reconstruct sea surface salinity from the new temperature data and the available oxygen isotope measurements