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Cell Biology

Generation of a Cellular Reporter for Functional BRD4 Inhibition

Authors: Sara Sdelci
Sara SdelciAffiliation: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna, Austria
Bio-protocol author page: a4753
 and Stefan Kubicek
Stefan KubicekAffiliation 1: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, Vienna, Austria
Affiliation 2: Christian Doppler Laboratory for Chemical Epigenetics and Antiinfectives, CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
For correspondence: skubicek@cemm.oeaw.ac.at
Bio-protocol author page: a4754
date: 7/5/2017, 128 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2368.

[Abstract] The ubiquitously expressed bromodomain-containing protein 4 (BRD4) is an epigenetic reader, which recruits transcriptional regulatory complexes to acetylated chromatin. Because of its role in enhancing proliferation, BRD4 has become a therapeutic target in oncology, as the inhibition of this protein leads to the reduction of the growth of many tumours. ...

Microvesicle Isolation from Rat Brain Extract Treated Human Mesenchymal Stem Cells

Authors: Ji Yong Lee
Ji Yong LeeAffiliation: Institute for BioMedical Convergence, Catholic Kwandong University-International St. Mary’s Hospital, Incheon-si, Republic of Korea
Bio-protocol author page: a4768
Seong-Mi Choi
Seong-Mi ChoiAffiliation: Institute for BioMedical Convergence, Catholic Kwandong University-International St. Mary’s Hospital, Incheon-si, Republic of Korea
Bio-protocol author page: a4769
 and Han-Soo Kim
Han-Soo KimAffiliation: Department of Biomedical Sciences, College of Medical Convergence, Catholic Kwandong University, Gangneung-si, Gangwon-do, Republic of Korea
For correspondence: hankim63@gmail.com
Bio-protocol author page: a4770
date: 7/5/2017, 146 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2375.

[Abstract] Microvesicle (MVs) are submicron-sized membranous vesicles that are either actively released from cells via secretory compartments or shed from cell surface membranes. MVs are generated by many cell types and serve as vehicles that transfer biological information (e.g., protein, mRNA, and miRNA) to distant cells, thereby affecting their gene expression, ...

Soft Agar Colony Formation Assay as a Hallmark of Carcinogenesis

Authors: Feng Du
Feng DuAffiliation: State key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, China
Bio-protocol author page: a4714
Xiaodi Zhao
Xiaodi ZhaoAffiliation: State key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, China
For correspondence: leedyzhao@fmmu.edu.cn
Bio-protocol author page: a4715
 and Daiming Fan
Daiming FanAffiliation: State key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi’an, China
Bio-protocol author page: a4716
date: 6/20/2017, 284 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2351.

[Abstract] Soft agar colony formation assay is established to estimate the anchorage-independent growth ability of cells. In this assay, a bottom layer of agar with complete media is poured and solidified first, followed by an upper layer containing a specified number of cells suspended in medium-agar mixture. After two weeks of incubation, the number of colonies ...

ELISPOT Assay to Measure Peptide-specific IFN-γ Production

Authors: Michelle N. Wykes
Michelle N. WykesAffiliation: QIMR Berghofer Medical Research Institute, Brisbane, Australia
For correspondence: michelle.wykes@qimrberghofer.edu.au
Bio-protocol author page: a4571
 and Laurent Renia
Laurent ReniaAffiliation 1: Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
Affiliation 2: Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
For correspondence: renia_laurent@immunol.a-star.edu.sg
Bio-protocol author page: a4572
date: 6/5/2017, 286 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2302.

[Abstract] Interferon-gamma (IFN-γ) is crucial for immunity against intracellular pathogens and for tumor control. It is produced predominantly by natural killer (NK) and natural killer T cells (NKT) as well as by antigen-specific Th1 CD4+ and CD8+ effector T cells. When investigating immune responses against pathogens and cancer cells, measuring antigen-specific ...

Murine Bronchoalveolar Lavage

Authors: Fan Sun
Fan SunAffiliation 1: University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, USA
Affiliation 2: Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, USA
Bio-protocol author page: a4527
Gutian Xiao
Gutian XiaoAffiliation 1: University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, USA
Affiliation 2: Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, USA
Bio-protocol author page: a4528
 and Zhaoxia Qu
Zhaoxia QuAffiliation 1: University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, USA
Affiliation 2: Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, USA
For correspondence: quz@upmc.edu
Bio-protocol author page: a4529
date: 5/20/2017, 420 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2287.

[Abstract] A basic Bronchoalveolar lavage (BAL) procedure in mouse is described here. Cells and fluids obtained from BAL can be analyzed by Hema3-staining, immunostaining, Fluorescence-activated cell sorting (FACS), PCR, bicinchoninic acid protein assay, enzyme-linked immunosorbent assay (ELISA), luminex assays, etc., to examine the immune cells, pathogens, proteins ...

Analysis of Mitochondrial Transfer in Direct Co-cultures of Human Monocyte-derived Macrophages (MDM) and Mesenchymal Stem Cells (MSC)

Authors: Megan V. Jackson
Megan V. JacksonAffiliation: Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast , Northern Ireland
Bio-protocol author page: a4447
 and Anna D. Krasnodembskaya
Anna D. KrasnodembskayaAffiliation: Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast , Northern Ireland
For correspondence: a.krasnodembskaya@qub.ac.uk
Bio-protocol author page: a4449
date: 5/5/2017, 559 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2255.

[Abstract] Mesenchymal stem/stromal cells (MSC) are adult stem cells which have been shown to improve survival, enhance bacterial clearance and alleviate inflammation in pre-clinical models of acute respiratory distress syndrome (ARDS) and sepsis. These diseases are characterised by uncontrolled inflammation often underpinned by bacterial infection. The mechanisms ...

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, 531 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. Here, we provide transwell permeability assay and ...

Adhesion and Invasion Assay Procedure Using Caco-2 Cells for Listeria monocytogenes

Authors: Swetha Reddy
Swetha ReddyAffiliation: College of Veterinary Science, Mississippi State University, Starkville, USA
For correspondence: mswethareddy@gmail.com
Bio-protocol author page: a4476
 and Frank Austin
Frank AustinAffiliation: College of Veterinary Science, Mississippi State University, Starkville, USA
Bio-protocol author page: a4477
date: 5/5/2017, 488 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2267.

[Abstract] Listeria monocytogenes is an important Gram-positive foodborne pathogen that is a particular problem in ready-to-eat food. It has an ability to survive in harsh conditions like refrigeration temperatures and high salt concentrations and is known to cross intestinal, placental and blood-brain barriers. Several cancerous cell lines like cervical, liver, ...

Melanoma Stem Cell Sphere Formation Assay

Authors: Alessandra Tuccitto
Alessandra TuccittoAffiliation: Department of Experimental Oncology and Molecular Medicine, Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
Bio-protocol author page: a4374
Valeria Beretta
Valeria BerettaAffiliation: Department of Experimental Oncology and Molecular Medicine, Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
Bio-protocol author page: a4375
Francesca Rini
Francesca RiniAffiliation: Department of Experimental Oncology and Molecular Medicine, Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
Bio-protocol author page: a4376
Chiara Castelli
Chiara CastelliAffiliation: Department of Experimental Oncology and Molecular Medicine, Unit of Immunotherapy of Human Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
For correspondence: chiara.castelli@istitutotumori.mi.it
Bio-protocol author page: a4377
 and Michela Perego
Michela PeregoAffiliation: The Wistar Institute, Philadelphia, USA
For correspondence: mperego@wistar.org
Bio-protocol author page: a4378
date: 4/20/2017, 574 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2233.

[Abstract] Self-renewal is the ability of cells to replicate themselves at every cell cycle. Throughout self-renewal in normal tissue homeostasis, stem cell number is maintained constant throughout life. Cancer stem cells (CSCs) share this ability with normal tissue stem cells and the sphere formation assay (SFA) is the gold standard assay to assess stem cells ...

Secretion of Adipsin as an Assay to Measure Flux from the Endoplasmic Reticulum (ER)

Authors: Alexandria Brumfield
Alexandria BrumfieldAffiliation: Department of Biochemistry, Weill Cornell Medicine, New York, USA
Bio-protocol author page: a4307
Natasha Chaudhary
Natasha ChaudharyAffiliation: Department of Biochemistry, Weill Cornell Medicine, New York, USA
Bio-protocol author page: a4308
 and Timothy E. McGraw
Timothy E. McGrawAffiliation 1: Department of Biochemistry, Weill Cornell Medicine, New York, USA
Affiliation 2: Department of Cardiothoracic Surgery, Weill Cornell Medicine, New York, USA
For correspondence: temcgraw@med.cornell.edu
Bio-protocol author page: a4309
date: 4/5/2017, 604 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2204.

[Abstract] In this protocol we describe a quantitative biochemical assay to assess the efficiency of endoplasmic reticulum (ER) to Golgi protein transport in adipocytes (Bruno et al., 2016). The assay takes advantage of the fact that adipocytes secrete various bioactive proteins, known as adipokines. As a measure of ER to Golgi flux we determine the rate of bulk ...
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[Bio101] Cell Proliferation Assay by Flow Cytometry (BrdU and PI Staining)

Author: Hui Zhu
Hui ZhuAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: huizhu@stanford.edu
Bio-protocol author page: a32
date: 4/5/2012, 40591 views, 2 Q&A
DOI: https://doi.org/10.21769/BioProtoc.198.

[Abstract] Cell Proliferation assays include an important set of fluorescence-based tests that can monitor cell health and cell division by evaluating DNA synthesis through thymidine incorporation. Bromodeoxyuridine (5-bromo-2'-deoxyuridine, BrdU) is a synthetic nucleoside that is an analogue of thymidine. BrdU ...

[Bio101] Calcium Phosphate Transfection of Eukaryotic Cells

Author: Yanling Chen
Yanling ChenAffiliation: Department of Immunology, The Scripps Research Institute, La Jolla, USA
For correspondence: ylchen@scripps.edu
Bio-protocol author page: a27
date: 2/5/2012, 28873 views, 2 Q&A
DOI: https://doi.org/10.21769/BioProtoc.86.

[Abstract] Transfection of DNA into cells is an indispensible protocol in molecular biology. While plenty of lipid-based transfection reagents are commercially available nowadays, a quick, simple, efficient and inexpensive method is to transfect eukaryotic cells via calcium phosphate co-precipitation with DNA ...

[Bio101] Calcium Imaging

Author: Mingye Feng
Mingye FengAffiliation: Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, USA
For correspondence: mfeng@jhmi.edu
Bio-protocol author page: a47
date: 4/5/2012, 19662 views, 4 Q&A
DOI: https://doi.org/10.21769/BioProtoc.200.

[Abstract] This is a protocol of Ca2+ imaging experiment using Ca2+ indicator Fura-2. Ca2+ imaging is an efficient and quantitative method for measuring cytosolic and internal store Ca2+ levels, as well as their dynamic changes....

[Bio101] Sucrose Gradient Analysis

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, 16500 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.194.

[Abstract] The sedimentation rate of a protein in a linear sucrose gradient can be used to determine its S value when compared to proteins of known S values which are run in a parallel gradient. This can be used to estimate an approximate molecular weight of the protein and test the potential interaction of two ...

Flow Cytometric Detection of Reactive Oxygen Species

Authors: Hsin-Yi Chang
Hsin-Yi ChangAffiliation: Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
Bio-protocol author page: a571
Hsuan-Cheng Huang
Hsuan-Cheng HuangAffiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
Bio-protocol author page: a572
Tsui-Chin Huang
Tsui-Chin HuangAffiliation: Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
Bio-protocol author page: a573
Pan-Chyr Yang
Pan-Chyr YangAffiliation: Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
Bio-protocol author page: a574
Yi-Ching Wang
Yi-Ching WangAffiliation: Department of Pharmacology, National Cheng Kung University, Tainan, Taiwan
Bio-protocol author page: a575
 and Hsueh-Fen Juan
Hsueh-Fen JuanAffiliation: Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
For correspondence: yukijuan@ntu.edu.tw
Bio-protocol author page: a324
date: 4/20/2013, 15812 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.431.

[Abstract] Reactive oxygen species (ROS) are molecules containing hydroxyl radicals or peroxides with unpaired electrons. In healthy aerobic cells, ROS are produced naturally as a byproduct of oxidative phosphorylation, oxidoreductase enzymes, or metal catalyzed oxidation at a controlled rate. However, ROS can ...

Isolation of Dendritic Cells and Macrophages from the Murine Kidneys of Lupus by Cell Sorter

Authors: Ramalingam Bethunaickan
Ramalingam BethunaickanAffiliation: Center for Autoimmunity and Musculoskeletal Diseases, Feinstein Institute for Medical Research, New York, USA
For correspondence: bramalingam@gmail.com
Bio-protocol author page: a24
 and Anne Davidson
Anne DavidsonAffiliation: Center for Autoimmunity and Musculoskeletal Diseases, Feinstein Institute for Medical Research, New York, USA
Bio-protocol author page: a1712
Anne Davidson Lab, date: 4/20/2012, 13614 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.168.

[Abstract] Methods for the isolation and characterization of mononuclear phagocytes from the kidneys of mice with SLE are essential to understand the patho-physiology of the disease. Activation of these cells is associated with the onset of clinical disease in mice and infiltration with these cells is associated ...

Protocol for Apoptosis Assay by Flow Cytometry Using Annexin V Staining Method

Authors: Imayavaramban Lakshmanan
Imayavaramban LakshmananAffiliation: Biochemistry and Molecular Biology, Nebraska Medical Center, Omaha, USA
Bio-protocol author page: a276
 and Surinder K Batra
Surinder K BatraAffiliation: Biochemistry and Molecular Biology, Nebraska Medical Center, Omaha, USA
For correspondence: sbatra@unmc.edu
Bio-protocol author page: a445
date: 3/20/2013, 12757 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.374.

[Abstract] This assay is used to count the number of cells that have undergone apoptosis. Apoptosis will be detected by initially staining the cells with Annexin V and propidium iodide solution followed by flow cytometry analysis. It is based on the principle that normal cells are hydrophobic in nature as they ...

Flow Cytometric Detection of Mitochondrial Membrane Potential

Authors: Hsin-Yi Chang
Hsin-Yi ChangAffiliation: Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taipei
Bio-protocol author page: a571
Hsuan-Cheng Huang
Hsuan-Cheng HuangAffiliation: Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
Bio-protocol author page: a572
Tsui-Chin Huang
Tsui-Chin HuangAffiliation: Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
Bio-protocol author page: a573
Pan-Chyr Yang
Pan-Chyr YangAffiliation: Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
Bio-protocol author page: a574
Yi-Ching Wang
Yi-Ching WangAffiliation: Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
Bio-protocol author page: a575
 and Hsueh-Fen Juan
Hsueh-Fen JuanAffiliation: Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
For correspondence: yukijuan@ntu.edu.tw
Bio-protocol author page: a324
date: 4/20/2013, 10257 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.430.

[Abstract] Mitochondrial membrane potential (Δψm) is an important parameter of mitochondrial function and an indicator of cell health. Depletion of Δψm suggests the loss of mitochondrial membrane integrity reflecting the initiation of the proapoptotic signal. Recently, lipophilic cationic fluorescent dyes have ...

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, 10141 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] Mitotic Index Determined by FACS Protocol

Author: Hui Zhu
Hui ZhuAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: huizhu@stanford.edu
Bio-protocol author page: a32
date: 3/20/2012, 10067 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.196.

[Abstract] Fluorescence Activated Cell Sorting (FACS) is a sensitive method to count mitotic cells. Cells are stained with an antibody that recognizes an antigen present only in mitotic cells, combined with propidium iodide (PI) to stain DNA. Two-dimensional FACS scanning allows the differential quantitation of ...
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