Balance of Power in Host-Virus Arms Races

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SiRNA and shRNA screens advance key understanding of host factors required for HIV-1 replication

A recent RNAi screen used a genome-wide shRNA library to search for cellular factors required for HIV-1 replication. This work complements three other siRNA-based screening studies and potentially opens the door to the discovery of factors that are important for HIV-1 replication in physiological host cells such as T lymphocytes. shRNA screens can be further improved, and they could promise to unravel new pathways and new facets of virus-cell interactions. © 2009 Kok et al; licensee BioMed Central Ltd.published_or_final_versio

'One Health' for the people of Hong Kong and the world

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An EBV microRNA targets DICE1 tumor suppressor gene

Poster Session 2: Host-Cell Interactions – Non-Coding RNA, Exosomes, and Epigenetics: no. 13.19MicroRNAs (miRNAs) play a critical role in post-transcriptional regulation of gene expression. Several herpesviruses have been shown to express viral miRNAs. Identification of the targets of these miRNAs might derive mechanistic insight into viral pathogenesis. We have previously demonstrated that Epstein-Barr virus (EBV)-encoded miR-BART5 targets p53-upregulated modulator of apoptosis (PUMA) in nasopharyngeal carcinoma (NPC) and this regulation is important for the EBV persistence and survival of EBV-infected cell survivals. In addition to the anti-apoptotic role of miR-BART5, other oncogenic activities of EBV miRNAs may also contribute to the development of lymphocytic or epithelial malignancies. In this study, we screened for potential targets of EBV miRNAs and found that EBV miR-BART3-5p potently suppressed the expression of DICE1 tumor suppressor in cultured cells. DICE1 is known …postprin

Insights into recovery of multi-component shale gas by CO2 injection: A molecular perspective

Understanding the mechanism behind shale gas recovery is of great importance for achieving optimum shale gas productivity. In this work, we use Grand Canonical Monte Carlo (GCMC) simulations to investigate the adsorption and recovery mechanisms of ternary hydrocarbon mixtures comprising methane, ethane and propane in kerogen nanopores. For the adsorption of hydrocarbon mixtures in kerogen slit pores, density distributions of each component are analyzed and the results indicate that densities of methane and ethane in the first adsorption layer increase as pressure increases, while an opposite trend is observed for propane. A stronger confinement effect is observed on the heavier hydrocarbon components, increasing the difficulty of recovery. For the recovery of the multi-component shale gas, we propose a reference recovery route with pressure drawdown and CO2 injection combined and the recovery efficiency is compared to the condition with only pressure drawdown applied. Significant enhancement in recovery ratio for all three components is observed with the CO2 injection and a better performance is shown on heavier components and smaller pores. An increase of 60% and 40% in propane recovery ratio is achieved in the 2-nm and 4-nm kerogen slit pores, respectively. Recovery mechanisms of pressure drawdown and CO2 injection are investigated in detail. The pressure drawdown method recovers methane from the first adsorption layer and middle of slit pore simultaneously, while extracting ethane and propane mainly from the middle of slit pore; the recovery due to CO2 injection mainly takes place in the adsorption layers. Pressure drawdown tends to extract the lighter components and CO2 injection is efficient in the recovery of heavier hydrocarbons. As pore width increases, the recovery ratio of pressure drawdown increases, while that of CO2 injection decreases. Besides, the CO2 sequestration ratio is higher in smaller kerogen slit pores

Human TRBP and PACT directly interact with each other and associate with dicer to facilitate the production of small interfering RNA

Mammalian Dicer interacts with double-stranded RNA-binding protein TRBP or PACT to mediate RNA interference and micro-RNA processing. TRBP and PACT are structurally related but exert opposite regulatory activities on PKR. It is not understood whether TRBP and PACT are simultaneously required for Dicer. Here we show that TRBP directly interacts with PACT in vitro and in mammalian cells. TRBP and PACT form a triple complex with Dicer and facilitate the production of small interfering RNA (siRNA) by Dicer. Knockdown of both TRBP and PACT in cultured cells leads to significant inhibition of gene silencing mediated by short hairpin RNA but not by siRNA, suggesting that TRBP and PACT function primarily at the step of siRNA production. Taken together, these findings indicate that human TRBP and PACT directly interact with each other and associate with Dicer to stimulate the cleavage of double-stranded or short hairpin RNA to siRNA. Our work significantly alters the current model for the assembly and function of the Dicer-containing complex that generates siRNA and micro-RNA in human. © 2007 by The American Society for Biochemistry and Molecular Biology, Inc.postprin

Mutagenesis and genome engineering of Epstein-Barr virus in cultured human cells by CRISPR/Cas9

The clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein 9 nuclease (Cas9) system is a powerful genome-editing tool for both chromosomal and extrachromosomal DNA. DNA viruses such as Epstein–Barr virus (EBV), which undergoes episomal replication in human cells, can be effectively edited by CRISPR/Cas9. We have demonstrated targeted editing of the EBV genome by CRISPR/Cas9 in several lines of EBV-infected cells. CRISPR/Cas9-based mutagenesis and genome engineering of EBV provides a new method for genetic analysis, which has some advantages over bacterial artificial chromosome-based recombineering. This approach might also prove useful in the cure of EBV infection. In this chapter, we use the knockout of the BART promoter as an example to detail the experimental procedures for construction of recombinant EBV in human cells.postprin

Adenoviral delivery of RNA decoys restores cellular proapoptotic protein PUMA expression by silencing Epstein-Barr virus-encoded miR-BART5 in nasopharyngeal carcinoma cells

Poster Session 1 - Vaccines and Anti-Viral Therapeutics: no. 3.17Epstein-Barr virus (EBV) encodes 48 mature microRNAs that play important roles in viral maintenance and promote host cell survival by regulating viral transcripts expression, inhibiting apoptosis or facilitating to evade cell immune surveillance. We have previously shown that EBV-encoded miR-BART5 targets and downregulates cellular pro-apoptotic protein p53-upregulated modulator of apoptosis (PUMA) to promote cellular survival of EBV-infected nasopharyngeal carcinoma (NPC) cells. Since compromising miR-BART5 might induce apoptosis of EBV-infected NPC cell, in this study we have established an adenoviral expression system to deliver anti-miR-BART5 decoys to NPC cells. The anti-miR-BART5 decoys comprised 6 tandem repeats of miR-BART5 binding sites and their expression was driven by EBVEBER2 promoter. They were designed to serve as a competitive inhibitor of miR-BART5 to reverse miR-BART5's inhibitory effects on PUMA in EBV-infected NPC cells. The RNA polymerase III-dependent EBER2 promoter is particularly strong in ...postprin

CRTC1 transcriptional coactivator is required for hepatitis B virus gene expression and replication

This journal suppl. entitled: Metabolism, Diet and Disease 2014: Cancer and metabolismConference Theme: Cancer and metabolismPoster Presentation: P31BACKGROUND: Chronic hepatitis B virus (HBV) infection occurs in over 400 million people worldwide, 15-40% of whom will terminally develop severe liver diseases including hepatocellular carcinoma. Although development of HCC is a multi-step process, high HBV DNA level is a major risk factor for disease progression. Transcription of HBV from the cccDNA template is essential for its replication and requires CREB transcription factor, a master regulator of cell metabolism. However, transcriptional coactivators that facilitate CREB-dependent activation of HBV transcription remain to be identified and characterized …published_or_final_versio

Mechanisms for kerogen wettability transition from water-wet to CO2-wet: Implications for CO2 sequestration

Geological CO2 sequestration (GCS) is an essential building block of the global strategy to alleviate greenhouse gas emissions and mitigate the climate change. Injecting CO2 into the shale formations can not only reduce carbon emissions but also enhance oil recovery (EOR). Rock wettability is of great importance to CO2 storage as it determines the efficiency of structural and residual trapping of CO2 and plays a crucial role in CO2-EOR. In this work, molecular dynamics (MD) simulations are adopted to investigate the CO2-H2O-kerogen systems under various CO2 pressures. In a vacuum or under low CO2 pressures, kerogen surface is weakly water-wet thanks to the hydrogen bonding between H2O and kerogen. As CO2 pressure increases, kerogen wettability shifts from water-wet to CO2-wet, because more CO2 molecules accumulate at the H2O-kerogen interface and a distinct CO2 thin film emerges. Density functional theory (DFT) calculations reveal that the O-containing functional groups preferably adsorb H2O molecules over CO2 through hydrogen bonding, which is responsible for the weakly water-wet tendency at low CO2 pressures. In contrast, the carbon skeleton of kerogen exhibits a stronger affinity to CO2, leading to the formation of CO2 thin film on the kerogen surface. The CO2 crowding close to the kerogen surface at high CO2 pressures gives rise to the CO2-wet state. This study provides, for the first time, the fundamental mechanism for the kerogen wettability transition from water-wet to CO2-wet. The work also indicates that wettability of the mature kerogen is more likely to be CO2-wet during GCS, which is unfavorable for capillary trapping of CO2, but is favorable for CO2-EOR