B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data

Summary: Bisulfite sequencing, a combination of bisulfite treatment and high-throughput sequencing, has proved to be a valuable method for measuring DNA methylation at single base resolution. Here, we present B-SOLANA, an approach for the analysis of two-base encoding (colorspace) bisulfite sequencing data on the SOLiD platform of Life Technologies. It includes the alignment of bisulfite sequences and the determination of methylation levels in CpG as well as non-CpG sequence contexts. B-SOLANA enables a fast and accurate analysis of large raw sequence datasets

Genetic polymorphisms in DPF3 associated with risk of breast cancer and lymph node metastases

BACKGROUND: Several studies have identified rare genetic variations responsible for many cases of familial breast cancer but their contribution to total breast cancer incidence is relatively small. More common genetic variations with low penetrance have been postulated to account for a higher proportion of the population risk of breast cancer. METHODS AND RESULTS: In an effort to identify genes that influence non-familial breast cancer risk, we tested over 25,000 single nucleotide polymorphisms (SNPs) located within approximately 14,000 genes in a large-scale case-control study in 254 German women with breast cancer and 268 age-matched women without malignant disease. We identified a marker on chromosome 14q24.3-q31.1 that was marginally associated with breast cancer status (OR = 1.5, P = 0.07). Genotypes for this SNP were also significantly associated with indicators of breast cancer severity, including presence of lymph node metastases (P = 0.006) and earlier age of onset (P = 0.01). The association with breast cancer status was replicated in two independent samples (OR = 1.35, P = 0.05). High-density association fine mapping showed that the association spanned about 80 kb of the zinc-finger gene DPF3 (also known as CERD4). One SNP in intron 1 was found to be more strongly associated with breast cancer status in all three sample collections (OR = 1.6, P = 0.003) as well as with increased lymph node metastases (P = 0.01) and tumor size (P = 0.01). CONCLUSION: Polymorphisms in the 5' region of DPF3 were associated with increased risk of breast cancer development, lymph node metastases, age of onset, and tumor size in women of European ancestry. This large-scale association study suggests that genetic variation in DPF3 contributes to breast cancer susceptibility and severity

Paediatric leukaemia DNA methylation profiling using MBD enrichment and SOLiD sequencing on archival bone marrow smears

BACKGROUND: Acute Lymphoblastic Leukaemia (ALL) is the most common cancer in children. Over the past four decades, research has advanced the treatment of this cancer from a less than 60% chance of survival to over 85% today. The causal molecular mechanisms remain unclear. Here, we performed sequencing-based genomic DNA methylation profiling of eight paediatric ALL patients using archived bone marrow smear microscope slides. FINDINGS: SOLiD™ sequencing data was collected from Methyl-Binding Domain (MBD) enriched fractions of genomic DNA. The primary tumour and remission bone marrow sample was analysed from eight patients. Four patients relapsed and the relapsed tumour was analysed. Input and MBD-enriched DNA from each sample was sequenced, aligned to the hg19 reference genome and analysed for enrichment peaks using MACS (Model-based Analysis for ChIP-Seq) and HOMER (Hypergeometric Optimization of Motif EnRichment). In total, 3.67 gigabases (Gb) were sequenced, 2.74 Gb were aligned to the reference genome (average 74.66% alignment efficiency). This dataset enables the interrogation of differential DNA methylation associated with paediatric ALL. Preliminary results reveal concordant regions of enrichment indicative of a DNA methylation signature. CONCLUSION: Our dataset represents one of the first SOLiD™MBD-Seq studies performed on paediatric ALL and is the first to utilise archival bone marrow smears. Differential DNA methylation between cancer and equivalent disease-free tissue can be identified and correlated with existing and published genomic studies. Given the rarity of paediatric haematopoietic malignancies, relative to adult counterparts, our demonstration of the utility of archived bone marrow smear samples to high-throughput methylation sequencing approaches offers tremendous potential to explore the role of DNA methylation in the aetiology of cancer

High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology

Methyl-CpG binding domain protein sequencing (MBD-seq) is widely used to survey DNA methylation patterns. However, the optimal experimental parameters for MBD-seq remain unclear and the data analysis remains challenging. In this study, we generated high depth MBD-seq data in MCF-7 cell and developed a bi-asymmetric-Laplace model (BALM) to perform data analysis. We found that optimal efficiency of MBD-seq experiments was achieved by sequencing ∼100 million unique mapped tags from a combination of 500 mM and 1000 mM salt concentration elution in MCF-7 cells. Clonal bisulfite sequencing results showed that the methylation status of each CpG dinucleotides in the tested regions was accurately detected with high resolution using the proposed model. These results demonstrated the combination of MBD-seq and BALM could serve as a useful tool to investigate DNA methylome due to its low cost, high specificity, efficiency and resolution

Association between a variation in the phosphodiesterase 4D gene and bone mineral density

BACKGROUND: Fragility fractures caused by osteoporosis are a major cause of morbidity and mortality in aging populations. Bone mineral density (BMD) is a useful surrogate marker for risk of fracture and is a highly heritable trait. The genetic variants underlying this genetic contribution are largely unknown. METHODS: We performed a large-scale association study investigating more than 25,000 single nucleotide polymorphisms (SNPs) located within 16,000 genes. Allele frequencies were estimated in contrasting DNA pools from white females selected for low (<0.87 g/cm(2), n = 319) and high (> 1.11 g/cm(2), n = 321) BMD at the lumbar spine. Significant findings were verified in two additional sample collections. RESULTS: Based on allele frequency differences between DNA pools and subsequent individual genotyping, one of the candidate loci indicated was the phosphodiesterase 4D (PDE4D) gene region on chromosome 5q12. We subsequently tested the marker SNP, rs1498608, in a second sample of 138 white females with low (<0.91 g/cm(2)) and 138 females with high (>1.04 g/cm(2)) lumbar spine BMD. Odds ratios were 1.5 (P = 0.035) in the original sample and 2.1 (P = 0.018) in the replication sample. Association fine mapping with 80 SNPs located within 50 kilobases of the marker SNP identified a 20 kilobase region of association containing exon 6 of PDE4D. In a second, family-based replication sample with a preponderance of females with low BMD, rs1498608 showed an opposite relationship with BMD at different sites (p = 0.00044-0.09). We also replicated the previously reported association of the Ser37Ala polymorphism in BMP2, known to interact biologically with PDE4D, with BMD. CONCLUSION: This study indicates that variants in the gene encoding PDE4D account for some of the genetic contribution to bone mineral density variation in humans. The contrasting results from different samples indicate that the effect may be context-dependent. PDE4 inhibitors have been shown to increase bone mass in normal and osteopenic mice, but up until now there have been no reports implicating any member of the PDE4 gene family in human osteoporosis

Welcome to Hydrogen—A New International and Interdisciplinary Open Access Journal of Growing Interest in Our Society

The 2018 Intergovernmental Panel on Climate Change (IPCC) report [...

A Gene Network Model of Resource Allocation to Growth and Reproduction

We present a model of optimal allocation of resources to reproduction and growth in a simple multicellular organism with limited lifespan, using a gene network formalism to simulate gene interactions within cells. The model is compatible with more conventional approaches to allocation problems in life history and in addition provides connections between processes at the gene and cell levels on one hand and life history strategies on the other. The model may offer an example of how a genotype orchestrating development imposes constraints on the optimal solutions that evolution can reach. Introduction How an organism uses energy and other resources extracted from the environment to promote its survival and growth, produce offspring or store for future needs is crucial for the organism&apos;s fitness. Life-history traits of an organism, that determine when and in what proportions the organism allocates resources during its lifetime, include age and size at first reproduction, number and size..

Drosophila

We have formulated a computational model of Drosophila early neurogenesis, the process by which neuroblasts and sensory organ precursor (SOP) cells differentiate from within proneural clusters of cells. The model includes intracellular gene regulatory interactions as well as lateral cell-cell signalling. It makes predictions about how the interplay of factors like proneural cluster shape and size, gene expression levels, and strength of cell-cell signalling determines the timing and position of appearance of neuroblasts and SOP cells; and about the robustness of this process and the effects of gene product level perturbations on cell differentiation. Introduction One of the very early steps in neural development is the generation of neuronal precursor cells in appropriate numbers and their precise positioning, which to a large extent determines the identity of their progeny. In Drosophila, neuroblasts and sensory organ precursor (SOP) cells differentiate from epithelia to give rise t..

H2S in Black Sea: Turning an environmental threat to an opportunity for clean H2 production via an Electrochemical Membrane Reactor. Research progress in H2S-PROTON Project

The present study aims to examine and evaluate the concept of H2S decomposition to H2 production in (H2)-conducting electrochemical reactors. In such a complex process, one of the major issues raised is the optimal selection of materials for the electrochemical cell. Specifically, the anode electrode should exhibit high catalytic activity and electronic conductivity, in order to make the process efficient. In this context, and before the electrochemical tests, a number of transition metal catalysts supported on CeO2 were prepared using the wet impregnation method and tested for their performance regarding the activity/stability of the H2S decomposition reaction, in the absence and presence of H2O. The experimental results are accompanied by the corresponding thermodynamic calculations, at various reaction conditions. The physico-chemical characteristics of the employed catalysts were determined using the BET, XRD, SEM and elemental analysis methods. The experimental results showed that the catalysts 20% wt. Co/CeO2 and 30% wt. Co/CeO2 exhibit high H2S conversions, in the absence and presence of H2O respectively, comparable to conversions indicated by thermodynamics and with remarkable stability, which is attributed to the in-situ sulfation of catalysts’ active components during their exposure at the feedstock mixture