MotifHub: Detection of trans-acting DNA motif group with probabilistic modeling algorithm.

BACKGROUND: Trans-acting factors are of special importance in transcription regulation, which is a group of proteins that can directly or indirectly recognize or bind to the 8-12 bp core sequence of cis-acting elements and regulate the transcription efficiency of target genes. The progressive development in high-throughput chromatin capture technology (e.g., Hi-C) enables the identification of chromatin-interacting sequence groups where trans-acting DNA motif groups can be discovered. The problem difficulty lies in the combinatorial nature of DNA sequence pattern matching and its underlying sequence pattern search space. METHOD: Here, we propose to develop MotifHub for trans-acting DNA motif group discovery on grouped sequences. Specifically, the main approach is to develop probabilistic modeling for accommodating the stochastic nature of DNA motif patterns. RESULTS: Based on the modeling, we develop global sampling techniques based on EM and Gibbs sampling to address the global optimization challenge for model fitting with latent variables. The results reflect that our proposed approaches demonstrate promising performance with linear time complexities. CONCLUSION: MotifHub is a novel algorithm considering the identification of both DNA co-binding motif groups and trans-acting TFs. Our study paves the way for identifying hub TFs of stem cell development (OCT4 and SOX2) and determining potential therapeutic targets of prostate cancer (FOXA1 and MYC). To ensure scientific reproducibility and long-term impact, its matrix-algebra-optimized source code is released at http://bioinfo.cs.cityu.edu.hk/MotifHub.

Bacteriophage MS-2 removal by submerged membrane bioreactor.

A membrane bioreactor (MBR) may serve as a pre-disinfection or disinfection unit, in addition to its solid/liquid separation and biological conversion functions, to produce sewage effluent of high quality. This bench-scale pilot study focuses on investigating the performance of a submerged MBR in pathogen removal and the factors affecting the removal, using a 0.4-microm hollow-fiber membrane module submerged in an aeration tank and bacteriophage MS-2 as the indicator organism. Removal of the MS-2 phage was found to be contributed by physical filtration by the membrane itself, biomass activity in the aeration tank and bio-filtration achieved by the biofilm developed on the membrane surface. The membrane alone gave poor virus removal (0.4+/-0.1 log) but the overall removal increased substantially with the presence of biomass and the membrane-surface-attached biofilm. The contributions of the suspended biomass and attached biofilm to the phage removal are dependent on the inter-related parameters including the concentration of mixed liquor suspended solids (MLSS), the sludge retention time (SRT) and the food to mass (F/M) ratio. The correlations between effluent flux/trans-membrane pressure and virus removal give evidence that phage removal in the MBR is most likely susceptible to both biological and physical factors including the quantity and property of the biomass and the biofilm and the membrane pore size reduction.