An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform

The proper identification of differentially methylated CpGs is central in most epigenetic studies. The Illumina HumanMethylation450 BeadChip is widely used to quantify DNA methylation; nevertheless, the design of an appropriate analysis pipeline faces severe challenges due to the convolution of biological and technical variability and the presence of a signal bias between Infinium I and II probe design types. Despite recent attempts to investigate how to analyze DNA methylation data with such an array design, it has not been possible to perform a comprehensive comparison between different bioinformatics pipelines due to the lack of appropriate data sets having both large sample size and sufficient number of technical replicates. Here we perform such a comparative analysis, targeting the problems of reducing the technical variability, eliminating the probe design bias and reducing the batch effect by exploiting two unpublished data sets, which included technical replicates and were profiled for DNA methylation either on peripheral blood, monocytes or muscle biopsies. We evaluated the performance of different analysis pipelines and demonstrated that: (1) it is critical to correct for the probe design type, since the amplitude of the measured methylation change depends on the underlying chemistry; (2) the effect of different normalization schemes is mixed, and the most effective method in our hands were quantile normalization and Beta Mixture Quantile dilation (BMIQ); (3) it is beneficial to correct for batch effects. In conclusion, our comparative analysis using a comprehensive data set suggests an efficient pipeline for proper identification of differentially methylated CpGs using the Illumina 450K arrays

The Nordic back pain subpopulation program: predicting outcome among chiropractic patients in Finland

<p>Abstract</p> <p>Background</p> <p>In a previous Swedish study it was shown that it is possible to predict which chiropractic patients with persistent LBP will not report definite improvement early in the course of treatment, namely those with LBP for altogether at least 30 days in the past year, who had leg pain, and who did not report definite general improvement by the second treatment. The objectives of this study were to investigate if the predictive value of this set of variables could be reproduced among chiropractic patients in Finland, and if the model could be improved by adding some new potential predictor variables.</p> <p>Methods</p> <p>The study was a multi-centre prospective outcome study with internal control groups, carried out in private chiropractic practices in Finland. Chiropractors collected data at the 1st, 2^ndand 4^thvisits using standardized questionnaires on new patients with LBP and/or radiating leg pain. Status at base-line was identified in relation to pain and disability, at the 2^ndvisit in relation to disability, and "definitely better" at the 4^thvisit in relation to a global assessment. The Swedish questionnaire was used including three new questions on general health, pain in other parts of the spine, and body mass index.</p> <p>Results</p> <p>The Swedish model was reproduced in this study sample. An alternative model including leg pain (yes/no), improvement at 2^ndvisit (yes/no) and BMI (underweight/normal/overweight or obese) was also identified with similar predictive values. Common throughout the testing of various models was that improvement at the 2^ndvisit had an odds ratio of approximately 5. Additional analyses revealed a dose-response in that 84% of those patients who fulfilled none of these (bad) criteria were classified as "definitely better" at the 4^thvisit, vs. 75%, 60% and 34% of those who fulfilled 1, 2 or all 3 of the criteria, respectively.</p> <p>Conclusion</p> <p>When treating patients with LBP, at the first visits, the treatment strategy should be different for overweight/obese patients with leg pain as it should be for all patients who fail to improve by the 2^ndvisit. The number of predictors is also important.</p

Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways

BACKGROUND: Interpreting large-scale studies from microarrays or next-generation sequencing for further experimental testing remains one of the major challenges in quantitative biology. Combining expression with physical or genetic interaction data has already been successfully applied to enhance knowledge from all types of high-throughput studies. Yet, toolboxes for navigating and understanding even small gene or protein networks are poorly developed. RESULTS: We introduce two Cytoscape plug-ins, which support the generation and interpretation of experiment-based interaction networks. The virtual pathway explorer viPEr creates so-called focus networks by joining a list of experimentally determined genes with the interactome of a specific organism. viPEr calculates all paths between two or more user-selected nodes, or explores the neighborhood of a single selected node. Numerical values from expression studies assigned to the nodes serve to score identified paths. The pathway enrichment analysis tool PEANuT annotates networks with pathway information from various sources and calculates enriched pathways between a focus and a background network. Using time series expression data of atorvastatin treated primary hepatocytes from six patients, we demonstrate the handling and applicability of viPEr and PEANuT. Based on our investigations using viPEr and PEANuT, we suggest a role of the FoxA1/A2/A3 transcriptional network in the cellular response to atorvastatin treatment. Moreover, we find an enrichment of metabolic and cancer pathways in the Fox transcriptional network and demonstrate a patient-specific reaction to the drug. CONCLUSIONS: The Cytoscape plug-in viPEr integrates –omics data with interactome data. It supports the interpretation and navigation of large-scale datasets by creating focus networks, facilitating mechanistic predictions from –omics studies. PEANuT provides an up-front method to identify underlying biological principles by calculating enriched pathways in focus networks. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-015-2017-z) contains supplementary material, which is available to authorized users

The Evolution of Compact Binary Star Systems

We review the formation and evolution of compact binary stars consisting of white dwarfs (WDs), neutron stars (NSs), and black holes (BHs). Binary NSs and BHs are thought to be the primary astrophysical sources of gravitational waves (GWs) within the frequency band of ground-based detectors, while compact binaries of WDs are important sources of GWs at lower frequencies to be covered by space interferometers (LISA). Major uncertainties in the current understanding of properties of NSs and BHs most relevant to the GW studies are discussed, including the treatment of the natal kicks which compact stellar remnants acquire during the core collapse of massive stars and the common envelope phase of binary evolution. We discuss the coalescence rates of binary NSs and BHs and prospects for their detections, the formation and evolution of binary WDs and their observational manifestations. Special attention is given to AM CVn-stars -- compact binaries in which the Roche lobe is filled by another WD or a low-mass partially degenerate helium-star, as these stars are thought to be the best LISA verification binary GW sources.Comment: 105 pages, 18 figure

Natural hazards in Australia: heatwaves

As part of a special issue on natural hazards, this paper reviews the current state of scientific knowledge of Australian heatwaves. Over recent years, progress has been made in understanding both the causes of and changes to heatwaves. Relationships between atmospheric heatwaves and large-scale and synoptic variability have been identified, with increasing trends in heatwave intensity, frequency and duration projected to continue throughout the 21st century. However, more research is required to further our understanding of the dynamical interactions of atmospheric heatwaves, particularly with the land surface. Research into marine heatwaves is still in its infancy, with little known about driving mechanisms, and observed and future changes. In order to address these knowledge gaps, recommendations include: focusing on a comprehensive assessment of atmospheric heatwave dynamics; understanding links with droughts; working towards a unified measurement framework; and investigating observed and future trends in marine heatwaves. Such work requires comprehensive and long-term collaboration activities. However, benefits will extend to the international community, thus addressing global grand challenges surrounding these extreme events

RNA delivery by extracellular vesicles in mammalian cells and its applications.

The term 'extracellular vesicles' refers to a heterogeneous population of vesicular bodies of cellular origin that derive either from the endosomal compartment (exosomes) or as a result of shedding from the plasma membrane (microvesicles, oncosomes and apoptotic bodies). Extracellular vesicles carry a variety of cargo, including RNAs, proteins, lipids and DNA, which can be taken up by other cells, both in the direct vicinity of the source cell and at distant sites in the body via biofluids, and elicit a variety of phenotypic responses. Owing to their unique biology and roles in cell-cell communication, extracellular vesicles have attracted strong interest, which is further enhanced by their potential clinical utility. Because extracellular vesicles derive their cargo from the contents of the cells that produce them, they are attractive sources of biomarkers for a variety of diseases. Furthermore, studies demonstrating phenotypic effects of specific extracellular vesicle-associated cargo on target cells have stoked interest in extracellular vesicles as therapeutic vehicles. There is particularly strong evidence that the RNA cargo of extracellular vesicles can alter recipient cell gene expression and function. During the past decade, extracellular vesicles and their RNA cargo have become better defined, but many aspects of extracellular vesicle biology remain to be elucidated. These include selective cargo loading resulting in substantial differences between the composition of extracellular vesicles and source cells; heterogeneity in extracellular vesicle size and composition; and undefined mechanisms for the uptake of extracellular vesicles into recipient cells and the fates of their cargo. Further progress in unravelling the basic mechanisms of extracellular vesicle biogenesis, transport, and cargo delivery and function is needed for successful clinical implementation. This Review focuses on the current state of knowledge pertaining to packaging, transport and function of RNAs in extracellular vesicles and outlines the progress made thus far towards their clinical applications