Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved

Transcriptomic and proteomic analyses of rhabdomyosarcoma cells reveal differential cellular gene expression in response to enterovirus 71 infection

10.1111/j.1462-5822.2005.00644.xCellular Microbiology84565-58

Succession of fungi on wood of Avicennia alba and A. lanata in Singapore

Canadian Journal of Botany6792686-269

Lignicolous marine fungi of Singapore

Canadian Journal of Botany66112167-217

Optimization of processing parameters for the preparation of phytosterol microemulsions by the solvent displacement method

The purpose of this study was to optimize the parameters involved in the production of water-soluble phytosterol microemulsions for use in the food industry. In this study, response surface methodology (RSM) was employed to model and optimize four of the processing parameters, namely, the number of cycles of high-pressure homogenization (1-9 cycles), the pressure used for high-pressure homogenization (100-500 bar), the evaporation temperature (30-70 °C), and the concentration ratio of microemulsions (1-5). All responses-particle size (PS), polydispersity index (PDI), and percent ethanol residual (ER)-were well fit by a reduced cubic model obtained by multiple regression after manual elimination. The coefficient of determination (R 2) and absolute average deviation (AAD) value for PS, PDI, and ER were 0.9628 and 0.5398, 0.9953 and 0.7077, and 0.9989 and 1.0457, respectively. The optimized processing parameters were 4.88 (approximately 5) homogenization cycles, homogenization pressure of 400 bar, evaporation temperature of 44.5 0C, and concentration ratio of microemulsions of 2.34 cycles (approximately 2 cycles) of high-pressure homogenization. The corresponding responses for the optimized preparation condition were a minimal particle size of 328 nm, minimal polydispersity index of 0.159, and <0.1 of ethanol residual. The chi-square test verified the model, whereby the experimental values of PS, PDI, and ER agreed with the predicted values at a 0.05 level of significance

Relation between morbidity and current treatment in patients who present with acute asthma to polyclinics

Singapore Medical Journal416259-263SIMJ

Induction of apoptosis in melanoma A375 cells by a chloroform fraction of Centratherum anthelminticum (L.) seeds involves NF-kappaB, p53 and Bcl-2-controlled mitochondrial signaling pathways

Background: Centratherum anthelminticum (L.) Kuntze (scientific synonyms: Vernonia anthelmintica; black cumin) is one of the ingredients of an Ayurvedic preparation, called Kayakalpâ, commonly applied to treat skin disorders in India and Southeast Asia. Despite its well known anti-inflammatory property on skin diseases, the anti-cancer effect of C. anthelminticum seeds on skin cancer is less documented. The present study aims to investigate the anti-cancer effect of Centratherum anthelminticum (L.) seeds chloroform fraction (CACF) on human melanoma cells and to elucidate the molecular mechanism involved. Methods: A chloroform fraction was extracted from C. anthelminticum (CACF). Bioactive compounds of the CACF were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Human melanoma cell line A375 was treated with CACF in vitro. Effects of CACF on growth inhibition, morphology, stress and survival of the cell were examined with MTT, high content screening (HSC) array scan and flow cytometry analyses. Involvement of intrinsic or extrinsic pathways in the CACF-induced A375 cell death mechanism was examined using a caspase luminescence assay. The results were further verified with different caspase inhibitors. In addition, Western blot analysis was performed to elucidate the changes in apoptosis-associated molecules. Finally, the effect of CACF on the NF-κB nuclear translocation ability was assayed. Results: The MTT assay showed that CACF dose-dependently inhibited cell growth of A375, while exerted less cytotoxic effect on normal primary epithelial melanocytes. We demonstrated that CACF induced cell growth inhibition through apoptosis, as evidenced by cell shrinkage, increased annexin V staining and formation of membrane blebs. CACF treatment also resulted in higher reactive oxygen species (ROS) production and lower Bcl-2 expression, leading to decrease mitochondrial membrane potential (MMP). Disruption of the MMP facilitated the release of mitochondrial cytochrome c, which activates caspase-9 and downstream caspase-3/7, resulting in DNA fragmentation and up-regulation of p53 in melanoma cells. Moreover, CACF prevented TNF-α-induced NF-κB nuclear translocation, which further committed A375 cells toward apoptosis. Conclusions: Together, our findings suggest CACF as a potential therapeutic agent against human melanoma malignancy