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Isolation and Expansion of HIV from Cells and Body Fluids by Coculture

HIV can be recovered from infected patients at all stages of the disease spectrum. Typically, the quantity of biologically active virus, or viral protein, in body tissues is below the level of direct detection by either antigen capture or reverse transcriptase assays. Consequently, the virus ...

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Detection of Nucleic Acids in Cells and Tissues by In Situ Polymerase Chain Reaction

The solution-based polymerase chain reaction (PCR) method for amplification of defined gene sequences has proved a valuable tool not only for basic researchers but also for clinical scientists. Using even a minute amount of DNA or RNA and choosing a thermostable enzyme from a large variety of s ...

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Studying the HPV Life Cycle in 3A Trophoblasts and Resulting Pathophysiology

Human papillomavirus (HPV) productive infection has been long considered to be restricted to the squamous epithelium. However, we have demonstrated that both HPV type 16 (HPV-16) and type 31b (HPV-31b) productively replicate in a trophoblast cell line, 3A. Trophoblasts are an important c ...

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The Cottontail Rabbit Papillomavirus Model of High-Risk HPV-Induced Disease

Animal models are essential to study the pathogenesis of papillomavirus infection and develop strategies for treatment and prevention. This review details use of the cottontail rabbit papillomavirus (CRPV)-laboratory rabbit model. The protocols describe how to infect rabbits ...

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The HPV Xenograft Severe Combined Immunodeficiency Mouse Model

The permissive propagation of papillomaviruses outside their natural hosts has not been possible, which is an important restriction to the study of human papillomavirus (HPV) infections and associated diseases. Since the mid-1980s, several models have been described that rely on the ...

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Codon Optimization of Papillomavirus Genes

Early and late genes of human and animal papillomaviruses show a codon composition seemingly unfavorable for expression in mammalian cells. It remains unclear how the viruses manage to achieve high levels of late gene expression during the viral life cycle. One possible solution could be th ...

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Measuring the Induction or Inhibition of Apoptosis by HPV Proteins

Many viral proteins influence the cellular pathways that control cell proliferation and cell death. Some viral proteins trigger apoptotic cell death, and this may be important in host defense and viral spread. In other cases, viral proteins inhibit apoptosis. In this chapter, we will descri ...

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Identification of HPV Variants

The vast majority of anogenital carcinomas are caused by high-risk human papillomaviruses (HPVs), and among Western nations HPV-16 is usually the most predominant cancer-associated type. As a DNA virus, HPV type 16 has a relatively stable genome that is believed to have co-evolved with its host ...

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In Vitro Assays of Substrate Degradation Induced by High-Risk HPV E6 Oncoproteins

The high-risk mucosal human papillomavirus E6 proteins were the first viral proteins that were shown to use the ubiquitin proteasome pathway for the inactivation of their cellular target proteins. The first substrate to be identified was the p53 tumor suppressor protein, and since then ma ...

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Analysis of Adeno-Associated Virus and HPV Interaction

It is slowly becoming accepted that adeno-associated virus (AAV) is another significant factor involved in cervical carcinogenesis. However, unlike human papillomavirus (HPV), which is positively associated with cervical cancer, AAV is negatively associated with this cancer. ...

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Transformation Assays for HPV Oncoproteins

A cornerstone of human papillomavirus (HPV) research was the demonstration that those HPV types associated with the development of cervical cancer encode two potent oncoproteins, while those HPV types associated with only benign lesions do not. Thus both HPV-16 E6 and E7 will transform est ...

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Analysis of E7/Rb Associations

The product of the early gene E7 is one of the major transforming proteins of human papillomaviruses (HPVs). It exerts its activity by associating with and altering the biological functions of several cellular proteins involved in the control of fundamental events, such as cell proliferat ...

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Preparation of Recombinant HIV-1 Gag Protein and Assembly of Virus-Like Particles In Vitro

The mechanism of assembly of retroviruses is not fully understood. Purification of retroviral Gag protein and studying its solution state and assembly properties might provide insights into retroviral assembly mechanisms. Here we describe a rapid method for the purification of Gag a ...

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Methods for the Analysis of HIV-1 Nucleocapsid Protein Interactions with Oligonucleotides

HIV-1 Nucleocapsid protein (NC) is a small basic protein that contains two retroviral zinc fingers. It is a highly effective nucleic acid chaperone that plays a critical role in viral replication acting as a cofactor in reverse transcription as well as other aspects of the viral lifecycle. We have u ...

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Methods for Analysis of Incorporation and Annealing Methods for Analysis of tRNALys in HIV-1

In HIV-1, tRNALys3 serves as the primer for reverse transcription of minus strand strong stop cDNA. During viral assembly, the tRNALys isoacceptors, tRNALys1,2 and tRNALys3, are selectively packaged into the virion. The selectively packaging of tRNALys3 facilitates the annealing of t ...

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Real-Time PCR Analysis of HIV-1 Replication Post-entry Events

The reverse transcriptase enzyme plays an essential role in the HIV-1 life cycle by converting a single-stranded viral RNA genome into a double-stranded viral DNA through a complex process known as reverse transcription. The resulting double-stranded DNA is integrated into the host chr ...

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Cell-Free Assays for HIV-1 Uncoating

Uncoating is an essential step in the retrovirus life cycle about which little is known. Uncoating is defined as the specific dissociation of the capsid shell from the viral core in the host cell cytoplasm. In this chapter, biochemical assays for studying HIV-1 uncoating in vitro are described. Th ...

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Analysis of 2-LTR Circle Junctions of Viral DNA in Infected Cells

The unintegrated viral DNA synthesized during human immunodeficiency virus type 1 infection includes linear and circular forms. Circular forms of viral DNA are surrogate markers for nuclear import of viral DNA during virus replication as well as events surrounding the completion of r ...

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HIV-1 Recombination: An Experimental Assay and a Phylogenetic Approach

The generation of genetic diversity is a fundamental characteristic of HIV-1 replication, allowing the virus to successfully evade the immune response and antiviral therapies. Although mutations are the first step towards diversity, mixing of the mutations through the process of re ...

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Methods of Preparation and Analysis of Intracellular Reverse Transcription Complexes

Shortly after penetration into the cell, HIV-1 must reverse transcribe its genome into a double-stranded DNA molecule and must gain access to the nucleus of nondividing cells for productive infection. There is limited knowledge of these early events in HIV-1 life cycle. We have developed meth ...

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