Identifying Phage Sequences From Metagenomic Data Using Deep Neural Network With Word Embedding and Attention Mechanism.

Phages are the functional viruses that infect bacteria and they play important roles in microbial communities and ecosystems. Phage research has attracted great attention due to the wide applications of phage therapy in treating bacterial infection in recent years. Metagenomics sequencing technique can sequence microbial communities directly from an environmental sample. Identifying phage sequences from metagenomic data is a vital step in the downstream of phage analysis. However, the existing methods for phage identification suffer from some limitations in the utilization of the phage feature for prediction, and therefore their prediction performance still need to be improved further. In this article, we propose a novel deep neural network (called MetaPhaPred) for identifying phages from metagenomic data. In MetaPhaPred, we first use a word embedding technique to encode the metagenomic sequences into word vectors, extracting the latent feature vectors of DNA words. Then, we design a deep neural network with a convolutional neural network (CNN) to capture the feature maps in sequences, and with a bi-directional long short-term memory network (Bi-LSTM) to capture the long-term dependencies between features from both forward and backward directions. The feature map consists of a set of feature patterns, each of which is the weighted feature extracted by a convolution filter with convolution kernels in the CNN slide along the input feature vectors. Next, an attention mechanism is used to enhance contributions of important features. Experimental results on both simulated and real metagenomic data with different lengths demonstrate the superiority of the proposed MetaPhaPred over the state-of-the-art methods in identifying phage sequences.

Molecular Dynamics Simulation Study on the Interactions of Mixed Cationic/Anionic Collectors on Muscovite (001) Surface in Aqueous Solution.

In this study, the adsorption mechanisms of dodecylamine hydrochloride(DDAHC), sodium dodecyl sulfate (SDS), sodium dodecyl benzene sulfonate(SDBS), and their mixed anionic/cationic collectors at ten different molar ratios on a muscovite (Mcv) surface in neutral aqueous solution were assessed by molecular dynamics simulations (MDS). According to the snapshot, interaction energy, radial distribution function (RDF), and density profile between the Mcv surface and collector molecules, the individual DDAHC collector was an effective collector for the flotation of Mcv. The molar ratio of anionic/cationic collectors was determined to be an essential factor in the flotation recovery of Mcv. The DDAHC collector was involved in the adsorption of the mixed anionic/cationic collectors on the Mcv (001) surface, whereas SDS and SDBS collectors were co-adsorbed with DDAHC. The mixed cationic/anionic collector showed the best adsorption on the Mcv surface in a molar ratio of 2. Additionally, SDBS, which has one more benzene ring than SDS, was more likely to form spherical micelles with DDAHC, thus resulting in better adsorption on the Mcv surface. The results of micro-flotation experiments indicated that the DDAHC collector could improve the flotation recovery of Mcv in neutral aqueous solution, which was in agreement with MDS-derived findings. In conclusion, DDAHC alone is the optimum collector for Mcv flotation under the neutral aqueous conditions, while the mixture of DDAHC and SDBS collectors (molar ratio = 2:1) exhibits the similar flotation performance.

Combination of small interfering RNA and lamivudine on inhibition of human B virus replication in HepG2.2.15 cells.

AIM: To observe the inhibition of hepatitis B virus (HBV) replication and expression by combination of siRNA and lamivudine in HepG2.2.15 cells. METHODS: Recombinant plasmid psil-HBV was constructed and transfected into HepG2.2.15 cells. The transfected cells were cultured in lamivudine-containing medium (0.05 micromol/L) and harvested at 48, 72 and 96 h. The concentration of HBeAg and HBsAg was determined using ELISA. HBV DNA replication was examined by real-time PCR and the level of HBV mRNA was measured by RT-PCR. RESULTS: In HepG2.2.15 cells treated with combination of siRNA and lamivudine, the secretion of HBeAg and HBsAg into the supernatant was found to be inhibited by 91.80% and 82.40% (2.89+/-0.48 vs 11.73+/-0.38, P<0.05; 4.59+/-0.57 vs 16.25+/-0.48, P<0.05) at 96 h, respectively; the number of HBV DNA copies within culture medium was also significantly decreased at 96 h (1.04+/-0.26 vs 8.35+/-0.33, P<0.05). Moreover, mRNA concentration in HepG2.2.15 cells treated with combination of siRNA and lamivudine was obviously lower compared to those treated either with siRNA or lamivudine (19.44+/-0.17 vs 33.27+/-0.21 or 79.9+/-0.13, P<0.05). CONCLUSION: Combination of siRNA and lamivudine is more effective in inhibiting HBV replication as compared to the single use of siRNA or lamivudine in HepG2.2.15 cells.