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Active Cdk5 Immunoprecipitation and Kinase Assay

Authors: Andrew N. Bankston
Andrew N. BankstonAffiliation 1: Department of Pharmacology, Emory University, Atlanta, GA
Affiliation 2: Department of Neurological Surgery, University of Louisville, Louisville, KY
Bio-protocol author page: a4746
Li Ku
Li KuAffiliation: Department of Pharmacology, Emory University, Atlanta, GA
Bio-protocol author page: a4747
 and Yue Feng
Yue FengAffiliation: Department of Pharmacology, Emory University, Atlanta, GA
For correspondence: yfeng@emory.edu
Bio-protocol author page: a4748
date: 7/5/2017, 113 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2363.

[Abstract] Cdk5 activity is regulated by the amounts of two activator proteins, p35 and p39 (Tsai et al., 1994; Zheng et al., 1998; Humbert et al., 2000). The p35-Cdk5 and p39-Cdk5 complexes have differing sensitivity to salt and detergent concentrations (Hisanaga and Saito, 2003; Sato et al., 2007; Yamada et ...

Fluorometric Estimation of Glutathione in Cultured Microglial Cell Lysate

Authors: Vikas Singh
Vikas SinghAffiliation 1: Immunotoxicology Laboratory, Food Drug and Chemical Toxicology Group and Nanotherapeutics & Nanomaterial Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), 31-Vishvigyan Bhawan, MG Marg, Lucknow, Uttar Pradesh-226001, India
Affiliation 2: Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, 31-Vishvigyan Bhawan, MG Marg, Lucknow, Uttar Pradesh, India
Bio-protocol author page: a4575
Ruchi Gera
Ruchi GeraAffiliation 1: Immunotoxicology Laboratory, Food Drug and Chemical Toxicology Group and Nanotherapeutics & Nanomaterial Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), 31-Vishvigyan Bhawan, MG Marg, Lucknow, Uttar Pradesh-226001, India
Affiliation 2: Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, 31-Vishvigyan Bhawan, MG Marg, Lucknow, Uttar Pradesh, India
Bio-protocol author page: a4576
Mahaveer Prasad Purohit
Mahaveer Prasad PurohitAffiliation 1: Water Analysis Laboratory, Nanotherapeutics and Nanomaterial Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow-226001, Uttar Pradesh, India
Affiliation 2: Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, 31-Vishvigyan Bhawan, MG Marg, Lucknow, Uttar Pradesh, India
Bio-protocol author page: a4577
Satyakam Patnaik
Satyakam PatnaikAffiliation: Water Analysis Laboratory, Nanotherapeutics and Nanomaterial Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow-226001, Uttar Pradesh, India
Bio-protocol author page: a4578
 and Debabrata Ghosh
Debabrata GhoshAffiliation 1: Immunotoxicology Laboratory, Food Drug and Chemical Toxicology Group and Nanotherapeutics & Nanomaterial Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), 31-Vishvigyan Bhawan, MG Marg, Lucknow, Uttar Pradesh-226001, India
Affiliation 2: Academy of Scientific and Innovative Research (AcSIR), CSIR-IITR Campus, 31-Vishvigyan Bhawan, MG Marg, Lucknow, Uttar Pradesh, India
For correspondence: debabrata.ghosh@iitr.res.in
Bio-protocol author page: a4579
date: 6/5/2017, 298 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2304.

[Abstract] Glutathione is one of the major antioxidant defense components present in cells. It is predominantly present as reduced glutathione (GSH) and converted into oxidized glutathione (GSSG) while reducing the free radicals like hydroxyl ions (OH-). For the measurement of GSH and GSSG, o-phthalaldehyde (OPT) ...

Phos-tag Immunoblot Analysis for Detecting IRF5 Phosphorylation

Authors: Go R. Sato
Go R. SatoAffiliation: Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
Bio-protocol author page: a4548
Tatsuma Ban
Tatsuma BanAffiliation: Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
For correspondence: tatban@yokohama-cu.ac.jp
Bio-protocol author page: a4549
 and Tomohiko Tamura
Tomohiko TamuraAffiliation: Department of Immunology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
For correspondence: tamurat@yokohama-cu.ac.jp
Bio-protocol author page: a4550
date: 5/20/2017, 553 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2295.

[Abstract] While the activation of the transcription factor interferon regulatory factor 5 (IRF5) is critical for the induction of innate immune responses, it also contributes to the pathogenesis of the autoimmune disease systemic lupus erythematosus (SLE). IRF5 phosphorylation is a hallmark of its activation ...

Analysis of in vivo Interaction between RNA Binding Proteins and Their RNA Targets by UV Cross-linking and Immunoprecipitation (CLIP) Method

Authors: Pamela Bielli
Pamela BielliAffiliation 1: Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
Affiliation 2: Laboratory of Neuroembriology, Fondazione Santa Lucia, Rome, Italy
Bio-protocol author page: a4492
 and Claudio Sette
Claudio SetteAffiliation 1: Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
Affiliation 2: Laboratory of Neuroembriology, Fondazione Santa Lucia, Rome, Italy
For correspondence: claudio.sette@uniroma2.it
Bio-protocol author page: a4493
date: 5/20/2017, 472 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2274.

[Abstract] RNA metabolism is tightly controlled across different tissues and developmental stages, and its dysregulation is one of the molecular hallmarks of cancer. Through direct binding to specific sequence element(s), RNA binding proteins (RBPs) play a pivotal role in co- and post-transcriptional RNA regulatory ...

Semi-quantitative Analysis of H4K20me1 Levels in Living Cells Using Mintbody

Authors: Yuko Sato
Yuko SatoAffiliation: Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
For correspondence: satoy@bio.titech.ac.jp
Bio-protocol author page: a4494
 and Hiroshi Kimura
Hiroshi KimuraAffiliation: Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
For correspondence: hkimura@bio.titech.ac.jp
Bio-protocol author page: a4495
date: 5/20/2017, 428 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2276.

[Abstract] Eukaryotic nuclear DNA wraps around histone proteins to form a nucleosome, a basic unit of chromatin. Posttranslational modification of histones play an important role in gene regulation and chromosome duplication. Some modifications are quite stable to be an epigenetic memory, and others exhibit rapid ...

Virtual Screening of Transmembrane Serine Protease Inhibitors

Authors: Antti Poso*
Antti PosoAffiliation 1: School of Pharmacy, University of Eastern Finland, Kuopio, Finland
Affiliation 2: Department of Internal Medicine VIII, University Hospital Tübingen, Tübingen, Germany
Bio-protocol author page: a4406
Topi Tervonen*
Topi TervonenAffiliation: Cancer Cell Circuitry Laboratory, Research Programs Unit/Translational Cancer Biology, University of Helsinki, Helsinki, Finland
Bio-protocol author page: a4407
 and Juha Klefström*
Juha KlefströmAffiliation: Cancer Cell Circuitry Laboratory, Research Programs Unit/Translational Cancer Biology, University of Helsinki, Helsinki, Finland
For correspondence: juha.klefstrom@helsinki.fi
Bio-protocol author page: a3835
 (*contributed equally to this work) date: 4/20/2017, 570 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2246.

[Abstract] The human family of type II transmembrane serine proteases includes 17 members. The defining features of these proteases are an N-terminal transmembrane domain and a C-terminal serine protease of the chymotrypsin (S1) fold, separated from each other by a variable stem region. Recently accumulated evidence ...

RNA Degradation Assay Using RNA Exosome Complexes, Affinity-purified from HEK-293 Cells

Authors: Michal Domanski
Michal DomanskiAffiliation: Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
Bio-protocol author page: a4413
 and John LaCava
John LaCavaAffiliation 1: Laboratory of Cellular and Structural Biology, Rockefeller University, New York, USA
Affiliation 2: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA
For correspondence: jlacava@rockefeller.edu
Bio-protocol author page: a4414
date: 4/20/2017, 537 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2239.

[Abstract] The RNA exosome complex plays a central role in RNA processing and regulated turnover. Present both in cytoplasm and nucleus, the exosome functions through associations with ribonucleases and various adapter proteins (reviewed in [Kilchert et al., 2016]). The RNA exosome-associated EXOSC10 protein is ...

Affinity Purification of the RNA Degradation Complex, the Exosome, from HEK-293 Cells

Authors: Michal Domanski
Michal DomanskiAffiliation: Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
Bio-protocol author page: a4413
 and John LaCava
John LaCavaAffiliation 1: Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA
Affiliation 2: Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA
For correspondence: jlacava@rockefeller.edu
Bio-protocol author page: a4414
date: 4/20/2017, 490 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2238.

[Abstract] The RNA exosome complex plays a central role in RNA processing and regulated turnover. Present both in cytoplasm and nucleus, the exosome functions through associations with ribonucleases and various adapter proteins (reviewed in [Kilchert et al., 2016]). The following protocol describes an approach ...

RNA-protein UV-crosslinking Assay

Authors: Dipak Kumar Poria
Dipak Kumar PoriaAffiliation: Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
Bio-protocol author page: a4215
 and Partho Sarothi Ray
Partho Sarothi RayAffiliation: Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
For correspondence: psray@iiserkol.ac.in
Bio-protocol author page: a4216
date: 3/20/2017, 949 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2193.

[Abstract] RNA-protein interactions play a crucial role in every aspect of RNA metabolism, and also plays a major role in post-transcriptional gene regulation. RNA-binding proteins have been implicated in viral gene expression (Ray and Das, 2002) and microRNA-mediated gene regulation (Poria et al., 2016). Here ...

Polysome Analysis

Authors: Dipak Kumar Poria
Dipak Kumar PoriaAffiliation: Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
Bio-protocol author page: a4215
 and Partho Sarothi Ray
Partho Sarothi RayAffiliation: Department of Biological Sciences, Indian Institute of Science Education and Research, Kolkata, India
For correspondence: psray@iiserkol.ac.in
Bio-protocol author page: a4216
date: 3/20/2017, 677 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2192.

[Abstract] Polysome analysis is a method to separate mRNAs from a cell into actively translating and non-translating fractions depending on their association with polysomes. By this protocol, cell lysates are fractionated by sucrose density gradient ultracentrifugation. Free mRNA fraction and various ribosomal ...
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Analysis of Protein Stability by the Cycloheximide Chase Assay

Authors: Shih-Han Kao
Shih-Han KaoAffiliation: Research Center for Tumor Medical Science, China Medical University, Taichung, Taiwan
Bio-protocol author page: a1920
Wen-Lung Wang
Wen-Lung WangAffiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
Bio-protocol author page: a1921
Chi-Yuan Chen
Chi-Yuan ChenAffiliation: Department of Nutrition and Health Sciences, Chang Gung University of Science and Technology, Taoyuan, Taiwan
Bio-protocol author page: a1922
Yih-Leong Chang
Yih-Leong ChangAffiliation: Department of Pathology and Graduate Institute of Pathology, National Taiwan University, Taipei, Taiwan
Bio-protocol author page: a1923
Yi-Ying Wu
Yi-Ying WuAffiliation: Graduate Institute of Clinical Medicine, National Cheng Kung University, Taipei, Taiwan
Bio-protocol author page: a1924
Yi-Ting Wang
Yi-Ting WangAffiliation 1: Chemical Biology and Molecular Biophysics Program, Academia Sinica, Taipei, Taiwan
Affiliation 2: Institute of Chemistry, Academia Sinica, Taipei, Taiwan
Affiliation 3: Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
Bio-protocol author page: a1925
Shu-Ping Wang
Shu-Ping WangAffiliation: Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, USA
Bio-protocol author page: a1926
Alexey I Nesvizhskii
Alexey I NesvizhskiiAffiliation 1: Department of Pathology, University of Michigan, Ann Arbor, USA
Affiliation 2: Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, USA
Bio-protocol author page: a1927
Yu-Ju Chen
Yu-Ju ChenAffiliation 1: Chemical Biology and Molecular Biophysics Program, Academia Sinica, Taipei, Taiwan
Affiliation 2: Institute of Chemistry, Academia Sinica, Taipei, Taiwan
Bio-protocol author page: a1928
Tse-Ming Hong
Tse-Ming HongAffiliation: Graduate Institute of Clinical Medicine, National Cheng Kung University, Taipei, Taiwan
Bio-protocol author page: a1929
 and Pan-Chyr Yang
Pan-Chyr YangAffiliation 1: Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
Affiliation 2: Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
Affiliation 3: NTU Center of Genomic Medicine, National Taiwan University, Taipei, Taiwan
Present address: Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
For correspondence: pcyang@ntu.edu.tw
Bio-protocol author page: a574
date: 1/5/2015, 24053 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1374.

[Abstract] Comparison of protein stability in eukaryotic cells has been achieved by cycloheximide, which is an inhibitor of protein biosynthesis due to its prevention in translational elongation. It is broadly used in cell biology in terms of determining the half-life of a given protein and has gained much popularity ...

Biotinylation of Cell Surface Proteins

Author: Guo N. Huang
Guo N. HuangAffiliation: Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, USA
For correspondence: guo.n.huang@gmail.com
Bio-protocol author page: a30
date: 5/5/2012, 18394 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.170.

[Abstract] Membrane proteins are major sensors of extracellular stimuli and initiators of intracellular signal transduction, and their abundance on the cell surface in particular is often dynamically regulated even when there are no significant changes of their total abundance in a cell. This protocol is designed ...

ImmunoPrecipitation of Nuclear Protein with Antibody Affinity Columns

Authors: Saïda Dadi
Saïda DadiAffiliation: Centre d'Immunology de Marseille Luminy (CIML), Aix-Marseille UM2, INSERM UMR1104, CNRS UMR7280, Marseille, France
Bio-protocol author page: a215
Dominique Payet-Bornet
Dominique Payet-BornetAffiliation: Centre d'Immunology de Marseille Luminy (CIML), Aix-Marseille UM2, INSERM UMR1104, CNRS UMR7280, Marseille, France
Bio-protocol author page: a216
 and Pierre Ferrier
Pierre FerrierAffiliation: Centre d'Immunology de Marseille Luminy (CIML), Aix-Marseille UM2, INSERM UMR1104, CNRS UMR7280, Marseille, France
For correspondence: ferrier@ciml.univ-mrs.fr
Bio-protocol author page: a217
date: 2/5/2013, 15733 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.319.

[Abstract] Co-Immunoprecipitation (Co-IP) is the method used to pull down protein partners of a protein of interest using an antibody that specifically binds to this specific protein in order to test protein-protein interaction. “Pulled down” proteins can be analyzed by western blot for suspected protein partner, ...

[Bio101] Western Blot for Detecting Phosphorylated STAT3

Author: Huagang Zhang
Huagang ZhangAffiliation: Albert Einstein College of Medicine, Yeshiva University, New York City, USA
For correspondence: huagangzhang@gmail.com
Bio-protocol author page: a21
date: 8/20/2011, 12684 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.125.

[Abstract] The STAT3 transcription factor is an important signaling molecule for many cytokines and growth factor receptors and is constitutively activated in a number of human tumors and possesses oncogenic potential and anti-apoptotic activities. STAT3 is activated by phosphorylation at Tyr705, which induces ...

Protein Translation Study – Label Protein with S35 Methionine in Cells

Authors: Salma Hasan
Salma HasanAffiliation: INSERM U1009, Gustave Roussy, Villejuif, France
Bio-protocol author page: a140
 and Isabelle Plo
Isabelle PloAffiliation: INSERM U1009, Gustave Roussy, Villejuif, France
For correspondence: isabelle.plo@gustaveroussy.fr
Bio-protocol author page: a141
date: 11/5/2012, 11999 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.282.

[Abstract] To follow protein synthesis, cells should be incubated with radioactive amino acid such as [35S] methionine during mRNA translation. Then, the neosynthetized protein will be identified by an autoradiography after immunoprecipitation with a specific antibody and separation on a polyacrylamide denaturing ...

[Bio101] Cell Culture Transfection for Production and Purification of Wnt Ligands

Author: Lili Jing
Lili JingAffiliation: Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, USA
For correspondence: lilijingcn@gmail.com
Bio-protocol author page: a38
date: 1/20/2012, 9860 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.176.

[Abstract] Wnt ligand proteins are extremely difficult to purify and enrich in vitro. This protocol uses Wnt11r protein as an example to illustrate how to use 293T cells to produce secreted Wnt11r and collect it in vitro for further biochemical experiments....

Autophagy Assays (LC3B immunofluorescence, LC3B western blot, acridine orange assay)

Authors: Xin Zhang
Xin ZhangAffiliation: High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, China
Bio-protocol author page: a1093
 and Qingsong Liu
Qingsong LiuAffiliation: High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, Anhui, China
For correspondence: qsliu97@hmfl.ac.cn
Bio-protocol author page: a1094
date: 12/20/2013, 9429 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1012.

[Abstract] Autophagy is a dynamic cellular event that is involved in the degradation of long lived proteins and organelles in cells. Biochemical methods such as western blot to measure autophagic proteins have been increasingly used in autophagy studies because it is convenient and objective. Among them, the total ...

Purification of His-ubiquitin Proteins from Mammalian Cells

Authors: Vanesa Olivares Illana
Vanesa Olivares IllanaAffiliation: Interacciones Biomoleculares y Cancer, Instituto de Fisica, San Luis Potosi, Mexico
For correspondence: vanesa@ifisica.uaslp.mx
Bio-protocol author page: a98
 and Robin Farhaeus
Robin FarhaeusAffiliation: Cibles Therapeutiques, INSERM Unite 940, Universite Paris 7, Paris, France
For correspondence: robin.fahraeus@inserm.fr
Bio-protocol author page: a99
date: 9/5/2012, 9240 views, 6 Q&A
DOI: https://doi.org/10.21769/BioProtoc.258.

[Abstract] This protocol is used to purify His-tag ubiquitin conjugated protein. In this particular case, cells were transfected with His-tag ubiquitin and p53 which allowed us to purify using His-tag and reveal the WB using antibodies against p53 to see just the p53-ubiquitinate. The present protocol can be used ...

[Bio101] Immunofluorescence Detection /F-actin Staining of MTLn3 Cells

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: 4/20/2012, 8413 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.206.

[Abstract] Epidermal growth factor (EGF)-stimulated MTLn3 cells protrusion play an important role in cell migration. Phalloidin which binds F-actin in cells is an imaging tool used with light microscopy to investigate the distribution of actin. The protocol described here can be useful for observing signaling ...

Immunoprecipitation for Cell Culture

Author: Hui Zhu
Hui ZhuAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: huizhu@stanford.edu
Bio-protocol author page: a32
date: 2/5/2012, 8203 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.72.

[Abstract] Immunoprecipitation (IP) is a method to pull down a protein out of solution using an antibody that specifically binds to that particular protein. Immunoprecipitation is a powerful technique to isolate and concentrate a particular protein from a sample containing many thousands of different proteins, ...
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