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Mapping RNA Sequences that Contact Viral Capsid Proteins in Virions

Featured protocol,  Authors: C. Cheng Kao
C. Cheng KaoAffiliation: Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
For correspondence: ckao@indiana.edu
Bio-protocol author page: a4851
Ella Chuang
Ella ChuangAffiliation: Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
Bio-protocol author page: a4852
James Ford
James FordAffiliation: The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
Bio-protocol author page: a4853
Jie Huang
Jie HuangAffiliation: The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
Bio-protocol author page: a4854
Ram Podicheti
Ram PodichetiAffiliation: The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
Bio-protocol author page: a4855
 and Doug B. Rusch
Doug B. RuschAffiliation: The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
Bio-protocol author page: a4856
date: 7/20/2017, 11 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2398.

Brief version appeared in J Virol, Aug 2016
We have adapted the methodology of CLIP-seq (Crosslinking-Immunoprecipitation and DNA Sequencing) to map the segments of encapsidated RNAs that contact the protein shells of virions. Results from the protocol report on the RNA sequences that contact the viral capsid.

Vaginal HSV-2 Infection and Tissue Analysis

Featured protocol,  Authors: Marie Beck Iversen
Marie Beck IversenAffiliation: Department of Biomedicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
Bio-protocol author page: a4818
Søren Riis Paludan
Søren Riis PaludanAffiliation: Department of Biomedicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
Bio-protocol author page: a4819
 and Christian Kanstrup Holm
Christian Kanstrup HolmAffiliation: Department of Biomedicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
For correspondence: holm@biomed.au.dk
Bio-protocol author page: a4820
date: 7/5/2017, 188 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2383.

Brief version appeared in Nat Immunol, Feb 2016
The vaginal murine HSV-2 infection model is very useful in studying mucosal immunity against HSV-2 (Overall et al., 1975; Renis et al., 1976; Parr and Parr, 2003). Histologically, the vagina of Depo-Provera-treated mice is lined by a single layer of mucus secreting columnar epithelial cells overlying two to three layers of proliferative cells. Even though this is morphologically different from the human vagina, it closely resembles the endocervical epithelium, which is thought to be the primary site of HSV-2 infection in women (Parr et al., 1994; Kaushic et al., 2011). In the protocol presented here, mice are pre-treated with Depo-Provera before intra-vaginal inoculation with HSV-2. The virus replicates in the mucosal epithelium from where it spreads to and replicates in the CNS including the spinal cord, brain stem, cerebrum and cerebellum. Cytokine responses can be detected in vaginal washings using ELISA or in vaginal tissues using qPCR. Further, the recruitment of leukocytes to the vagina can be determined by flow cytometry. The model is suitable for research of both innate and adaptive immunity to HSV-2 infection.

Mapping RNA Sequences that Contact Viral Capsid Proteins in Virions

Authors: C. Cheng Kao
C. Cheng KaoAffiliation: Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
For correspondence: ckao@indiana.edu
Bio-protocol author page: a4851
Ella Chuang
Ella ChuangAffiliation: Department of Molecular & Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
Bio-protocol author page: a4852
James Ford
James FordAffiliation: The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
Bio-protocol author page: a4853
Jie Huang
Jie HuangAffiliation: The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
Bio-protocol author page: a4854
Ram Podicheti
Ram PodichetiAffiliation: The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
Bio-protocol author page: a4855
 and Doug B. Rusch
Doug B. RuschAffiliation: The Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
Bio-protocol author page: a4856
date: 7/20/2017, 11 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2398.

[Abstract] We have adapted the methodology of CLIP-seq (Crosslinking-Immunoprecipitation and DNA Sequencing) to map the segments of encapsidated RNAs that contact the protein shells of virions. Results from the protocol report on the RNA sequences that contact the viral capsid....

Vaginal HSV-2 Infection and Tissue Analysis

Authors: Marie Beck Iversen
Marie Beck IversenAffiliation: Department of Biomedicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
Bio-protocol author page: a4818
Søren Riis Paludan
Søren Riis PaludanAffiliation: Department of Biomedicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
Bio-protocol author page: a4819
 and Christian Kanstrup Holm
Christian Kanstrup HolmAffiliation: Department of Biomedicine, Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
For correspondence: holm@biomed.au.dk
Bio-protocol author page: a4820
date: 7/5/2017, 188 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2383.

[Abstract] The vaginal murine HSV-2 infection model is very useful in studying mucosal immunity against HSV-2 (Overall et al., 1975; Renis et al., 1976; Parr and Parr, 2003). Histologically, the vagina of Depo-Provera-treated mice is lined by a single layer of mucus secreting columnar epithelial cells overlying ...

Single Genome Sequencing of Expressed and Proviral HIV-1 Envelope Glycoprotein 120 (gp120) and nef Genes

Authors: David J. Nolan
David J. NolanAffiliation 1: Bioinfoexperts, LLC, Thibodaux, Louisiana, USA
Affiliation 2: Department of Pathology, Immunology and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
Bio-protocol author page: a4654
Susanna L. Lamers
Susanna L. LamersAffiliation: Bioinfoexperts, LLC, Thibodaux, Louisiana, USA
Bio-protocol author page: a4655
Rebecca Rose
Rebecca RoseAffiliation: Bioinfoexperts, LLC, Thibodaux, Louisiana, USA
Bio-protocol author page: a4656
James J. Dollar
James J. DollarAffiliation 1: Bioinfoexperts, LLC, Thibodaux, Louisiana, USA
Affiliation 2: Department of Pathology, Immunology and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
Bio-protocol author page: a4657
Marco Salemi
Marco SalemiAffiliation: Department of Pathology, Immunology and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
Bio-protocol author page: a4658
 and Michael S. McGrath
Michael S. McGrathAffiliation 1: Departments of Laboratory Medicine, Pathology, and Medicine, University of California at San Francisco, San Francisco, California, USA
Affiliation 2: The AIDS and Cancer Specimen Resource, University of California at San Francisco, San Francisco, California, USA
For correspondence: MMcGrath@php.ucsf.edu
Bio-protocol author page: a4659
date: 6/20/2017, 215 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2334.

[Abstract] The current study provides detailed protocols utilized to amplify the complete HIV-1 gp120 and nef genes from single copies of expressed or integrated HIV present in fresh-frozen autopsy tissues of patients who died while on combined antiretroviral therapy (cART) with no detectable plasma viral load ...

Flow Cytometric Analysis of HIV-1 Transcriptional Activity in Response to shRNA Knockdown in A2 and A72 J-Lat Cell Lines

Authors: Daniela Boehm
Daniela BoehmAffiliation: Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
Bio-protocol author page: a4533
 and Melanie Ott
Melanie OttAffiliation 1: Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
Affiliation 2: Department of Medicine, University of California, San Francisco, CA, USA
For correspondence: mott@gladstone.ucsf.edu
Bio-protocol author page: a2100
date: 6/5/2017, 361 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2314.

[Abstract] The main obstacle to eradicating HIV-1 from patients is post-integration latency (Finzi et al., 1999). Antiretroviral treatments target only actively replicating virus, while latent infections that have low or no transcriptional activity remain untreated (Sedaghat et al., 2007). To eliminate viral reservoirs, ...

Flow Cytometric Analysis of Drug-induced HIV-1 Transcriptional Activity in A2 and A72 J-Lat Cell Lines

Authors: Daniela Boehm
Daniela BoehmAffiliation: Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
Bio-protocol author page: a4533
 and Melanie Ott
Melanie OttAffiliation 1: Gladstone Institute of Virology and Immunology, San Francisco, CA, USA
Affiliation 2: Department of Medicine, University of California, San Francisco, CA, USA
For correspondence: mott@gladstone.ucsf.edu
Bio-protocol author page: a2100
date: 5/20/2017, 543 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2290.

[Abstract] The main obstacle to eradicating HIV-1 from patients is post-integration latency (Finzi et al., 1999). Antiretroviral treatments target only actively replicating virus, while latent infections that have low or no transcriptional activity remain untreated (Sedaghat et al., 2007). A combination of antiretroviral ...

Ultradeep Pyrosequencing of Hepatitis C Virus to Define Evolutionary Phenotypes

Authors: Brendan A. Palmer
Brendan A. PalmerAffiliation: Molecular Virology Diagnostic & Research Laboratory, Department of Medicine, University College Cork, Cork, Ireland
Bio-protocol author page: a4519
Zoya Dimitrova
Zoya DimitrovaAffiliation: Division of Viral Hepatitis, Centers of Disease Control and Prevention, Atlanta, Georgia, USA
Bio-protocol author page: a4520
Pavel Skums
Pavel SkumsAffiliation: Division of Viral Hepatitis, Centers of Disease Control and Prevention, Atlanta, Georgia, USA
Bio-protocol author page: a4521
Orla Crosbie
Orla CrosbieAffiliation: Department of Gastroenterology, Cork University Hospital, Cork, Ireland
Bio-protocol author page: a4522
Elizabeth Kenny-Walsh
Elizabeth Kenny-WalshAffiliation: Department of Gastroenterology, Cork University Hospital, Cork, Ireland
Bio-protocol author page: a4523
 and Liam J. Fanning
Liam J. FanningAffiliation: Molecular Virology Diagnostic & Research Laboratory, Department of Medicine, University College Cork, Cork, Ireland
For correspondence: l.fanning@ucc.ie
Bio-protocol author page: a4524
date: 5/20/2017, 364 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2284.

[Abstract] Analysis of hypervariable regions (HVR) using pyrosequencing techniques is hampered by the ability of error correction algorithms to account for the heterogeneity of the variants present. Analysis of between-sample fluctuations to virome sub-populations, and detection of low frequency variants, are ...

Analysis of Replicative Intermediates of Adeno-associated Virus through Hirt Extraction and Southern Blotting

Authors: Martino Bardelli
Martino BardelliAffiliation: Department of Infectious Diseases, King's College London, London, United Kingdom
Present address: Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
Bio-protocol author page: a4283
Francisco Zarate-Perez
Francisco Zarate-PerezAffiliation: Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond VA, USA
Bio-protocol author page: a4284
Leticia Agundez
Leticia AgundezAffiliation: Department of Infectious Diseases, King's College London, London, United Kingdom
Present address: Department of Genetics, University College London Institute of Ophthalmology, London, United Kingdom
Bio-protocol author page: a4285
Nelly Jolinon
Nelly JolinonAffiliation: Department of Infectious Diseases, King’s College London, London, United Kingdom
Bio-protocol author page: a4486
R. Michael Linden
R. Michael LindenAffiliation: Department of Infectious Diseases, King's College London, London, United Kingdom
Present address: Genetic Medicine Institute, Pfizer Inc., London, United Kingdom
Bio-protocol author page: a4487
Carlos R. Escalante
Carlos R. EscalanteAffiliation: Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
Bio-protocol author page: a4288
 and Els Henckaerts
Els HenckaertsAffiliation: Department of Infectious Diseases, King's College London, London, United Kingdom
For correspondence: els.henckaerts@kcl.ac.uk
Bio-protocol author page: a4289
date: 5/5/2017, 458 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2271.

[Abstract] Adeno-associated virus (AAV) is a small single-stranded DNA virus that requires the presence of a helper virus, such as adenovirus or herpes virus, to efficiently replicate its genome. AAV DNA is replicated by a rolling-hairpin mechanism (Ward, 2006), and during replication several DNA intermediates ...

In vitro Assays for Measuring Endothelial Permeability by Transwells and Electrical Impedance Systems

Authors: Hong-Ru Chen
Hong-Ru ChenAffiliation: The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
Bio-protocol author page: a4488
 and Trai-Ming Yeh
Trai-Ming YehAffiliation 1: The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
Affiliation 2: Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
For correspondence: today@mail.ncku.edu.tw
Bio-protocol author page: a4489
date: 5/5/2017, 585 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2273.

[Abstract] Vascular leakage is an important feature in several diseases, such as septic shock, viral hemorrhagic fever, cancer metastasis and ischemia-reperfusion injuries. Thus establishing assays for measuring endothelial permeability will provide insight into the establishment or progression of such diseases. ...

RNA-dependent RNA Polymerase Assay for Hepatitis E Virus

Authors: Vidya P. Nair
Vidya P. NairAffiliation: Virology Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
Bio-protocol author page: a4217
Saumya Anang
Saumya AnangAffiliation: Virology Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
Bio-protocol author page: a4292
Akriti Srivastava
Akriti SrivastavaAffiliation: Virology Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
Bio-protocol author page: a4293
 and Milan Surjit
Milan SurjitAffiliation: Virology Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
For correspondence: milan@thsti.res.in
Bio-protocol author page: a4218
date: 4/5/2017, 774 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2199.

[Abstract] RNA-dependent RNA polymerase (RdRp) is essential for the replication of viral RNA for RNA viruses. It synthesizes the complementary strand of viral genomic RNA, which is used subsequently as a template to generate more copies of viral genome. This assay measures activity of the hepatitis E virus (HEV) ...

RNA Strand Displacement Assay for Hepatitis E Virus Helicase

Authors: Vidya P. Nair
Vidya P. NairAffiliation: Virology Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
Bio-protocol author page: a4217
 and Milan Surjit
Milan SurjitAffiliation: Virology Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
For correspondence: milan@thsti.res.in
Bio-protocol author page: a4218
date: 4/5/2017, 701 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2198.

[Abstract] The hepatitis E virus (HEV) helicase uses ATP to unwind the RNA duplexes. This is an essential step for viral replication. This protocol aims to measure the double strand RNA unwinding activity of the HEV helicase....
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[Bio101] Lentivirus Production

Author: Nabila Aboulaich date: 3/5/2011, 24419 views, 6 Q&A
DOI: https://doi.org/10.21769/BioProtoc.39.

[Abstract] Lentivirus is a common tool used to introduce a gene into mammalian or other animal cells.This protocol is to produce lentivirus stocks from hairpin-pLKO.1 plasmid....

[Bio101] Purification of Adenovirus by Cesium Chloride Density Gradients

Author: Huan Pang
Huan PangAffiliation: Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, USA
For correspondence: pang_huan@hotmail.com
Bio-protocol author page: a48
date: 4/5/2012, 18627 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.201.

[Abstract] Adenovirus are efficient gene delivery systems. The standard method for purification of adenoviral vectors is based on using a cesium chloride (CsCl) density gradient combined with ultracentrifugation. This method is suitable for small-scale purification and is less expensive than column chromatography ...

Infectious Focus Assays and Multiplicity of Infection (MOI) Calculations for Alpha-herpesviruses

Authors: Anna Sloutskin
Anna SloutskinAffiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
Bio-protocol author page: a1808
 and Ronald S. Goldstein
Ronald S. GoldsteinAffiliation: Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
For correspondence: ron.goldstein@biu.ac.il
Bio-protocol author page: a1809
date: 11/20/2014, 11718 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1295.

[Abstract] Titration of viral stocks is a critical process before any experimental use of the virus. Here we describe an infectious focus assay for several alphaherpesviruses, a titration method for fluorescently labeled viruses, based on the original plaque assay. In addition, the calculation of multiplicity ...

ADCC Assay Protocol

Authors: Vikram Srivastava
Vikram SrivastavaAffiliation: Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
Bio-protocol author page: a1115
Zheng Yang
Zheng YangAffiliation: Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
Bio-protocol author page: a1116
Ivan Fan Ngai Hung
Ivan Fan Ngai HungAffiliation: Department of Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
Bio-protocol author page: a1117
Jianqing Xu
Jianqing XuAffiliation: Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
Bio-protocol author page: a1118
Bojian Zheng
Bojian ZhengAffiliation: Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
Bio-protocol author page: a1119
 and Mei-Yun Zhang
Mei-Yun ZhangAffiliation: Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China
For correspondence: zhangmy@hku.hk
Bio-protocol author page: a1120
date: 1/20/2014, 10206 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1029.

[Abstract] Antibody-dependent cell-mediated cytotoxicity (ADCC) bridges innate and adaptive immunity, and it involves both humoral and cellular immune responses. ADCC has been found to be a main route of immune protection against viral infections and cancers in vivo. Here we developed a flow cytometry based protocol ...

[Bio101] VSVG Psudotyped Retrovirus Production

Author: Jia Li
Jia LiAffiliation: Department of Immunology, Medical Center, Duke University, Durham, North Carolina, USA
For correspondence: jiali.email@gmail.com
Bio-protocol author page: a16
date: 12/5/2011, 9305 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.158.

[Abstract] Retrovirus vector pseudotyped with vesicular stomatitis virus G (VSV-G) protein has been proven to exhibit high efficiency to deliver genes in a variety of cells. Efficiency is affected by relative cell growth rate and phosphatidylserine level on the cell membrane....

Assay to Evaluate Vascular Permeability Induction in Mice

Authors: Henry Puerta-Guardo
Henry Puerta-GuardoAffiliation: Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies, Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, México
Bio-protocol author page: a980
Arturo Raya-Sandino
Arturo Raya-SandinoAffiliation: Department of Physiolology, Biophysics and Neurosciences, Center for Research and Advanced Studies, Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, México
Bio-protocol author page: a981
Lorenza González-Mariscal
Lorenza González-MariscalAffiliation: Department of Physiolology, Biophysics and Neurosciences, Center for Research and Advanced Studies, Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, México
Bio-protocol author page: a982
Victor H. Rosales
Victor H. RosalesAffiliation: General Services Laboratory, Center for Research and Advanced Studies, Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, México
Bio-protocol author page: a983
José Ayala-Dávila
José Ayala-DávilaAffiliation: Department of Physiolology, Biophysics and Neurosciences, Center for Research and Advanced Studies, Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, México
Bio-protocol author page: a984
Bibiana Chávez-Mungía
Bibiana Chávez-MungíaAffiliation: Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies, Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, México
Bio-protocol author page: a985
Daniel Martínez-Fong
Daniel Martínez-FongAffiliation: Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies, Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, México
Bio-protocol author page: a986
Fernando Medina
Fernando MedinaAffiliation: Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies, Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, México
Bio-protocol author page: a987
Juan E. Ludert
Juan E. LudertAffiliation: Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies, Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, México
For correspondence: jludert@cinvestav.mx
Bio-protocol author page: a988
 and Rosa María del Angel
Rosa María del AngelAffiliation: Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies, Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, México
For correspondence: rmangel@cinvestav.mx
Bio-protocol author page: a989
date: 11/20/2013, 9183 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.977.

[Abstract] Dengue virus infection usually courses as a benign self-limited fever, called dengue fever. However, on occasions it can progress to a life-threatening complication known as severe dengue (SD). A hallmark of SD is a sharp increase in vascular permeability. Secondary infections are considered a risk ...

Immunoplaque Assay (Influenza Virus)

Authors: Longping V. Tse
Longping V. TseAffiliation: Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, USA
For correspondence: lt273@cornell.edu
Bio-protocol author page: a940
Yueting Zhang
Yueting ZhangAffiliation: Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, USA
Bio-protocol author page: a941
 and Gary R. Whittaker
Gary R. WhittakerAffiliation: Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, USA
For correspondence: grw7@cornell.edu
Bio-protocol author page: a942
date: 11/5/2013, 7292 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.959.

[Abstract] Despite developed long time ago, plaque assay is still the gold standard for viral titer quantification in modern virology. The standard crystal violet-based plaque assay relies on virus’ ability to induce cytopathic effect (CPE) which limits the assay to lytic viruses. Alternative viral quantification ...

Amplification of HIV-1 Infectious Virus in BL3 Lab

Author: Xin Wang
Xin WangAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: xinwang73@hotmail.com
Bio-protocol author page: a26
date: 3/5/2012, 6429 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.102.

[Abstract] This method is used for making high titer human immunodeficiency virus type-1 (HIV-1) virus stock for subsequent infection assays. The amplification of T-tropic HIV-1 virus (IIIB strain) uses the CD4+ T cell line H9....

Packaging of Retroviral RNA into Viral Particles Analyzed by Quantitative Reverse Transcriptase-PCR

Authors: Bianca Hoffmann
Bianca HoffmannAffiliation: Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
Bio-protocol author page: a446
 and Bastian Grewe
Bastian GreweAffiliation: Department of Molecular and Medical Virology, Ruhr-University Bochum, Bochum, Germany
For correspondence: bastian.grewe@rub.de
Bio-protocol author page: a371
date: 4/20/2013, 6331 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.684.

[Abstract] Formation of viral particles and packaging of genomic retroviral RNA into these particles are important steps in the late phase of the viral replication cycle. The efficiency of the incorporation of viral or cellular RNAs into viral particles can be studied using a quantitative Reverse Transcriptase-PCR ...

RNA Isolation and Northern Blot Analysis

Authors: Ying Liao
Ying LiaoAffiliation: School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
Bio-protocol author page: a1236
To Sing Fung
To Sing FungAffiliation: School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
Bio-protocol author page: a1237
Mei Huang
Mei HuangAffiliation: School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
Bio-protocol author page: a1238
Shouguo Fang
Shouguo FangAffiliation: School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
Bio-protocol author page: a1239
Yanxin Zhong
Yanxin ZhongAffiliation: School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
Bio-protocol author page: a1240
 and Dingxiang Liu
Dingxiang LiuAffiliation: School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
For correspondence: dxliu@ntu.edu.sg
Bio-protocol author page: a1241
date: 3/20/2014, 5608 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1077.

[Abstract] The northern blot is a technique used in molecular biology research to study gene expression by detection of RNA in a sample. With northern blotting it is possible to observe particular gene expression levels during differentiation, morphogenesis, as well as abnormal or diseased conditions. Here, we ...
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