scholarly journals Efficient RNA interference depends on global context of the target sequence: quantitative analysis of silencing efficiency using Eulerian graph representation of siRNA

2004 ◽  
Vol 32 (4) ◽  
pp. 1469-1479 ◽  
Author(s):  
P. Pancoska
Keyword(s):  
Quantitative Analysis ◽  
Rna Interference ◽  
Graph Representation ◽  
Target Sequence ◽  
Global Context ◽  
Eulerian Graph

scholarly journals Computational Design of Antiviral RNA Interference Strategies That Resist Human Immunodeficiency Virus Escape

2005 ◽  
Vol 79 (3) ◽  
pp. 1645-1654 ◽  
Author(s):  
Joshua N. Leonard ◽  
David V. Schaffer
Keyword(s):  
Human Immunodeficiency Virus ◽  
Rna Interference ◽  
Highly Active Antiretroviral Therapy ◽  
Viral Evolution ◽  
Regulation Of Gene Expression ◽  
Computational Design ◽  
Delivery Systems ◽  
Target Sequence ◽  
Therapeutic Success ◽  
Immunodeficiency Virus

ABSTRACT Recently developed antiviral strategies based upon RNA interference (RNAi), which harnesses an innate cellular system for the targeted down-regulation of gene expression, appear highly promising and offer alternative approaches to conventional highly active antiretroviral therapy or efforts to develop an AIDS vaccine. However, RNAi is faced with several challenges that must be overcome to fully realize its promise. Specifically, it degrades target RNA in a highly sequence-specific manner and is thus susceptible to viral mutational escape, and there are also challenges in delivery systems to induce RNAi. To aid in the development of anti-human immunodeficiency virus (anti-HIV) RNAi therapies, we have developed a novel stochastic computational model that simulates in molecular-level detail the propagation of an HIV infection in cells expressing RNAi. The model provides quantitative predictions on how targeting multiple locations in the HIV genome, while keeping the overall RNAi strength constant, significantly improves efficacy. Furthermore, it demonstrates that delivery systems must be highly efficient to preclude leaving reservoirs of unprotected cells where the virus can propagate, mutate, and eventually overwhelm the entire system. It also predicts how therapeutic success depends upon a relationship between RNAi strength and delivery efficiency and uniformity. Finally, targeting an essential viral element, in this case the HIV TAR region, can be highly successful if the RNAi target sequence is correctly selected. In addition to providing specific predictions for how to optimize a clinical therapy, this system may also serve as a future tool for investigating more fundamental questions of viral evolution.

scholarly journals Human Immunodeficiency Virus Type 1 Escapes from RNA Interference-Mediated Inhibition

2004 ◽  
Vol 78 (5) ◽  
pp. 2601-2605 ◽  
Author(s):  
Atze T. Das ◽  
Thijn R. Brummelkamp ◽  
Ellen M. Westerhout ◽  
Monique Vink ◽  
Mandy Madiredjo ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Rna Interference ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Antiviral Drug ◽  
Target Sequence ◽  
Small Interfering Rnas ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT Short-term assays have suggested that RNA interference (RNAi) may be a powerful new method for intracellular immunization against human immunodeficiency virus type 1 (HIV-1) infection. However, RNAi has not yet been shown to protect cells against HIV-1 in long-term virus replication assays. We stably introduced vectors expressing small interfering RNAs (siRNAs) directed against the HIV-1 genome into human T cells by retroviral transduction. We report here that an siRNA directed against the viral Nef gene (siRNA-Nef) confers resistance to HIV-1 replication. This block in replication is not absolute, and HIV-1 escape variants that were no longer inhibited by siRNA-Nef appeared after several weeks of culture. These RNAi-resistant viruses contained nucleotide substitutions or deletions in the Nef gene that modified or deleted the siRNA-Nef target sequence. These results demonstrate that efficient inhibition of HIV-1 replication through RNAi is possible in stably transduced cells. Therefore, RNAi could become a realistic gene therapy approach with which to overcome the devastating effect of HIV-1 on the immune system. However, as is known for antiviral drug therapy against HIV-1, antiviral approaches involving RNAi should be used in a combined fashion to prevent the emergence of resistant viruses.

RNA interference by small hairpin RNAs synthesised under control of the human 7S K RNA promoter

2004 ◽  
Vol 385 (9) ◽  
pp. 791-794 ◽  
Author(s):  
Dorota Koper-Emde ◽  
Lutz Herrmann ◽  
Björn Sandrock ◽  
Bernd-Joachim Benecke
Keyword(s):  
Rna Interference ◽  
Gene Promoter ◽  
Target Sequence ◽  
Small Nuclear Rna ◽  
Small Interfering Rnas ◽  
Rna Duplexes ◽  
Inhibit Gene Expression ◽  
Short Hairpin Rnas ◽  
Rna Promoter

AbstractSmall interfering RNAs (siRNAs) represent RNA duplexes of 21 nucleotides in length that inhibit gene expression. We have used the human gene-external 7S K RNA promoter for synthesis of short hairpin RNAs (shRNAs) which efficiently target human lamin mRNA via RNA interference (RNAi). Here we demonstrate that orientation of the target sequence within the shRNA construct is important for interference. Furthermore, effective interference also depends on the length and/or structure of the shRNA. Evidence is presented that the human 7S K promoter is more activein vivothan other gene-external promoters, such as the human U6 small nuclear RNA (snRNA) gene promoter.

scholarly journals Human Immunodeficiency Virus Type 1 Escape Is Restricted When Conserved Genome Sequences Are Targeted by RNA Interference

2007 ◽  
Vol 82 (6) ◽  
pp. 2895-2903 ◽  
Author(s):  
Karin Jasmijn von Eije ◽  
Olivier ter Brake ◽  
Ben Berkhout
Keyword(s):  
Human Immunodeficiency Virus ◽  
Rna Interference ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Viral Escape ◽  
Specific Gene ◽  
Target Sequence ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT RNA interference (RNAi) is a cellular mechanism in which small interfering RNAs (siRNAs) mediate sequence-specific gene silencing by cleaving the targeted mRNA. RNAi can be used as an antiviral approach to silence the human immunodeficiency virus type 1 (HIV-1) through stable expression of short-hairpin RNAs (shRNAs). We previously reported efficient HIV-1 inhibition by an shRNA against the nonessential nef gene but also described viral escape by mutation or deletion of the nef target sequence. The objective of this study was to obtain insight in the viral escape routes when essential and highly conserved sequences are targeted in the Gag, protease, integrase, and Tat-Rev regions of HIV-1. Target sequences were analyzed of more than 500 escape viruses that were selected in T cells expressing individual shRNAs. Viruses acquired single point mutations, occasionally secondary mutations, but—in contrast to what is observed with nef—no deletions were detected. Mutations occurred predominantly at target positions 6, 8, 9, 14, and 15, whereas none were selected at positions 1, 2, 5, 18, and 19. We also analyzed the type of mismatch in the siRNA-target RNA duplex, and G-U base pairs were frequently selected. These results provide insight into the sequence requirements for optimal RNAi inhibition. This knowledge on RNAi escape may guide the design and selection of shRNAs for the development of an effective RNAi therapy for HIV-1 infections.

scholarly journals Hepatitis C Virus Replicons Escape RNA Interference Induced by a Short Interfering RNA Directed against the NS5b Coding Region

2005 ◽  
Vol 79 (11) ◽  
pp. 7050-7058 ◽  
Author(s):  
Joyce A. Wilson ◽  
Christopher D. Richardson
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Rna Interference ◽  
Point Mutations ◽  
Subsequent Treatment ◽  
Escape Mutant ◽  
Target Sequence ◽  
Short Interfering Rna ◽  
Coding Region ◽  
Interfering Rna

ABSTRACT RNA interference represents an exciting new technology that could have therapeutic applications for the treatment of viral infections. Hepatitis C virus (HCV) is a major cause of chronic liver disease and affects over 270 million individuals worldwide. The HCV genome is a single-stranded RNA that functions as both an mRNA and a replication template, making it an attractive target for therapeutic approaches using short interfering RNA (siRNA). We have shown previously that double-stranded siRNA molecules designed to target the HCV genome block gene expression and RNA synthesis from hepatitis C replicons propagated in human liver cells. However, we now show that this block is not complete. After several treatments with a highly effective siRNA, we have shown growth of replicon RNAs that are resistant to subsequent treatment with the same siRNA. However, these replicon RNAs were not resistant to siRNA targeting another part of the genome. Sequence analysis of the siRNA-resistant replicons showed the generation of point mutations within the siRNA target sequence. In addition, the use of a combination of two siRNAs together severely limited escape mutant evolution. This suggests that RNA interference activity could be used as a treatment to reduce the devastating effects of HCV replication on the liver and the use of multiple siRNAs could prevent the emergence of resistant viruses.

RNA interference against hepatitis B virus with endoribonuclease-prepared siRNA despite of the target sequence variations

2007 ◽  
Vol 126 (1-2) ◽  
pp. 172-178 ◽  
Author(s):  
Chang Tan ◽  
Baoqin Xuan ◽  
Jie Hong ◽  
Zhaoyun Dai ◽  
Ruixin Hao ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Rna Interference ◽  
Hepatitis B ◽  
Target Sequence ◽  
Sequence Variations ◽  
B Virus

scholarly journals Learning Cross-Modal Context Graph for Visual Grounding

2020 ◽  
Vol 34 (07) ◽  
pp. 11645-11652
Author(s):  
Yongfei Liu ◽  
Bo Wan ◽  
Xiaodan Zhu ◽  
Xuming He
Keyword(s):  
Neural Network ◽  
Graph Matching ◽  
Graph Representation ◽  
Context Aware ◽  
Linguistic Features ◽  
Global Context ◽  
The Arts ◽  
Object Proposals ◽  
Matching Strategy ◽  
Message Propagation

Visual grounding is a ubiquitous building block in many vision-language tasks and yet remains challenging due to large variations in visual and linguistic features of grounding entities, strong context effect and the resulting semantic ambiguities. Prior works typically focus on learning representations of individual phrases with limited context information. To address their limitations, this paper proposes a language-guided graph representation to capture the global context of grounding entities and their relations, and develop a cross-modal graph matching strategy for the multiple-phrase visual grounding task. In particular, we introduce a modular graph neural network to compute context-aware representations of phrases and object proposals respectively via message propagation, followed by a graph-based matching module to generate globally consistent localization of grounding phrases. We train the entire graph neural network jointly in a two-stage strategy and evaluate it on the Flickr30K Entities benchmark. Extensive experiments show that our method outperforms the prior state of the arts by a sizable margin, evidencing the efficacy of our grounding framework. Code is available at https://github.com/youngfly11/LCMCG-PyTorch.

scholarly journals Poliovirus Escape from RNA Interference: Short Interfering RNA-Target Recognition and Implications for Therapeutic Approaches

2005 ◽  
Vol 79 (2) ◽  
pp. 1027-1035 ◽  
Author(s):  
Leonid Gitlin ◽  
Jeffrey K. Stone ◽  
Raul Andino
Keyword(s):  
Rna Interference ◽  
Target Recognition ◽  
Point Mutations ◽  
Viral Escape ◽  
Target Sequence ◽  
Rnai Machinery ◽  
Antiviral Therapies ◽  
Effective Sirnas ◽  
Escape Mutants ◽  
Interfering Rna

ABSTRACT Short interfering RNAs (siRNAs) directed against poliovirus and other viruses effectively inhibit viral replication. Although RNA interference (RNAi) may provide the basis for specific antiviral therapies, the limitations of RNAi antiviral strategies are ill defined. Here, we show that poliovirus readily escapes highly effective siRNAs through unique point mutations within the targeted regions. Competitive analysis of the escape mutants provides insights into the basis of siRNA recognition. The RNAi machinery can tolerate mismatches but is exquisitely sensitive to mutations within the central region and the 3′ end of the target sequence. Indeed, specific mutations in the target sequence resulting in G:U mismatches are sufficient for the virus to escape siRNA inhibition. However, using a pool of siRNAs to simultaneously target multiple sites in the viral genome prevents the emergence of resistant viruses. Our study uncovers the elegant precision of target recognition by the RNAi machinery and provides the basis for the development of effective RNAi-based therapies that prevent viral escape.

An Improved Quantitative Image Analyser

1977 ◽  
Vol 35 ◽  
pp. 226-227
Author(s):  
J.P. Fallon ◽  
P.J. Gregory ◽  
C.J. Taylor
Keyword(s):  
Feature Extraction ◽  
Quantitative Analysis ◽  
Frequency Content ◽  
General Sense ◽  
Physical Measurements ◽  
Quantitative Image ◽  
Image Analyser ◽  
Automatic Methods ◽  
Quantitative Results

Quantitative image analysis systems have been used for several years in research and quality control applications in various fields including metallurgy and medicine. The technique has been applied as an extension of subjective microscopy to problems requiring quantitative results and which are amenable to automatic methods of interpretation.Feature extraction. In the most general sense, a feature can be defined as a portion of the image which differs in some consistent way from the background. A feature may be characterized by the density difference between itself and the background, by an edge gradient, or by the spatial frequency content (texture) within its boundaries. The task of feature extraction includes recognition of features and encoding of the associated information for quantitative analysis.Quantitative Analysis. Quantitative analysis is the determination of one or more physical measurements of each feature. These measurements may be straightforward ones such as area, length, or perimeter, or more complex stereological measurements such as convex perimeter or Feret's diameter.

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