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Volume:3 Issue:14
July 20, 2013
Cancer Biology
Measurement of Endogenous MALT1 Activity
Authors:
Daniel Nagel
Daniel Nagel
Affiliation:
Cellular Signal Integration, Helmholtz Zentrum München, Munich, Germany
Bio-protocol author page:
a691
and
Daniel Krappmann
Daniel Krappmann
Affiliation:
Cellular Signal Integration, Helmholtz Zentrum München, Munich, Germany
For correspondence:
daniel.krappmann@helmholtz-muenchen.de
Bio-protocol author page:
a460
,
date: 7/20/2013, 4365 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.821
[Abstract] MALT1(Mucosa associated lymphoid tissue protein 1) is an important adapter protein for the NF-kB driven lymphocyte activation and the development and survival of distinct B-cell lymphoma entities. In addition MALT1 is a cysteine protease that structurally ...
Article identifier: bio-protocol.org/e821
Estradiol Receptor (ER) Chromatin Immunoprecipitation in MCF-7 Cells
Authors:
Pia Giovannelli
Pia Giovannelli
Affiliation:
Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy
For correspondence:
pia.giovannelli@unina2.it
Bio-protocol author page:
a696
,
Gabriella Castoria
Gabriella Castoria
Affiliation:
Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy
Bio-protocol author page:
a697
and
Antimo Migliaccio
Antimo Migliaccio
Affiliation:
Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy
Bio-protocol author page:
a392
,
date: 7/20/2013, 3515 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.831
[Abstract] Steroid hormone receptors, for example estradiol receptor, act like transcription factors. In the cell, steroids bind to a specific receptor. Upon ligand binding, many steroid receptors dimerize and enter nuclei where they bind specific DNA sequences ...
Article identifier: bio-protocol.org/e831
Immunology
Endosomal pH Measurement in Bone Marrow Derived Dendritic Cells
Authors:
Sophia Maschalidi
Sophia Maschalidi
Affiliation 1:
INSERM, Unité 1013, Paris, France
Affiliation 2:
Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
Bio-protocol author page:
a685
and
Bénédicte Manoury
Bénédicte Manoury
Affiliation 1:
INSERM, Unité 1013, Paris, France
Affiliation 2:
Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
For correspondence:
benedicte.manoury@inserm.fr
Bio-protocol author page:
a346
,
date: 7/20/2013, 3059 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.819
[Abstract] Endosomes embraces different set of compartments such as early endosomes, intermediate endosomes and late endosomes or lysosomes. They become acidic as they mature. This acidification is generated by the vacuolar membrane proton pump V-ATPase that is ...
Article identifier: bio-protocol.org/e819
Isolation of Phagosomes from Dendritic Cells by Using Magnetic Beads
Author:
Bénédicte Manoury
Bénédicte Manoury
Affiliation 1:
INSERM, Unité 1013, Paris, France
Affiliation 2:
Université Paris Descartes, Sorbonne Paris Cité, Faculté de Médecine, Paris, France
For correspondence:
benedicte.manoury@inserm.fr
Bio-protocol author page:
a346
,
date: 7/20/2013, 3041 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.820
[Abstract] Phagosomes are intracellular organelles in dendritic cells in which pathogens such as viruses, bacteria and parasites are internalised to be proteolysed and killed. Phagosomes are formed by fusion with the plasma membrane, some area of the endoplasmic ...
Article identifier: bio-protocol.org/e820
Microbiology
Preparation of
Candida albicans
Biofilms for Transmission Electron Microscopy
Authors:
Heather T. Taff
Heather T. Taff
Affiliation:
Department of Medicine, University of Wisconsin, Madison, USA
For correspondence:
htaff@wisc.edu
Bio-protocol author page:
a333
and
David R. Andes
David R. Andes
Affiliation:
Department of Medicine, University of Wisconsin, Madison, USA
For correspondence:
dra@medicine.wisc.edu
Bio-protocol author page:
a689
,
date: 7/20/2013, 4140 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.822
[Abstract] Transmission Electron Microscopy is a form of microscopy that allows for imaging of distinct portions of an individual cell. For
Candida albicans
biofilms, it is often used to visualize the cell walls of fixed samples of yeast and hyphae. This protocol ...
Article identifier: bio-protocol.org/e822
Preparation of
Candida albicans
Biofilms Using an
in vivo
Rat Central Venous Catheter Model
Authors:
Heather T. Taff
Heather T. Taff
Affiliation:
Department of Medicine, University of Wisconsin, Madison, USA
For correspondence:
htaff@wisc.edu
Bio-protocol author page:
a333
,
Karen Marchillo
Karen Marchillo
Affiliation:
Department of Medicine, University of Wisconsin, Madison, USA
Bio-protocol author page:
a690
and
David R. Andes
David R. Andes
Affiliation:
Department of Medicine, University of Wisconsin, Madison, USA
For correspondence:
dra@medicine.wisc.edu
Bio-protocol author page:
a689
,
date: 7/20/2013, 2895 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.823
[Abstract]
In vivo
biofilms grown on medical devices are necessary to understand the interactions of the fungal biofilm and the host environment in which it is most commonly found. This protocol describes a way to grow
Candida albicans
biofilms on the interior ...
Article identifier: bio-protocol.org/e823
High-throughput β-galactosidase and β-glucuronidase Assays Using Fluorogenic Substrates
Author:
Joshua P. Ramsay
Joshua P. Ramsay
Affiliation:
School of Biomedical Sciences, Curtin University, Perth, Australia
For correspondence:
josh.ramsay@curtin.edu.au
Bio-protocol author page:
a450
,
date: 7/20/2013, 5330 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.827
[Abstract] β-galactosidase and β-glucuronidase enzymes are commonly used as reporters for gene expression from gene promoter-
lacZ
or
uidA
fusions (respectively). The protocol described here is a high-throughput alternative to the commonly used Miller assay (Miller, ...
Article identifier: bio-protocol.org/e827
Extraction and Quantification of Cyclic Di-GMP from
Pseudomonas aeruginosa
Authors:
Ankita Basu Roy
Ankita Basu Roy
Affiliation:
Biological Sciences Department, Binghamton University, State University of New York at Binghamton, Binghamton, USA
Bio-protocol author page:
a699
,
Olga E. Petrova
Olga E. Petrova
Affiliation:
Biological Sciences Department, Binghamton University, State University of New York at Binghamton, Binghamton, USA
Bio-protocol author page:
a700
and
Karin Sauer
Karin Sauer
Affiliation:
Biological Sciences Department, Binghamton University, State University of New York at Binghamton, Binghamton, USA
For correspondence:
ksauer@binghamton.edu
Bio-protocol author page:
a701
,
date: 7/20/2013, 4969 views,
1 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.828
[Abstract] Cyclic di-GMP (c-di-GMP) has emerged as an important intracellular signaling molecule, controlling the transitions between planktonic (free-living) and sessile lifestyles, biofilm formation, and virulence in a wide variety of microorganisms. The following ...
Article identifier: bio-protocol.org/e828
Analyzing Inhibitory Effects of Reagents on
Mycoplasma
Gliding and Adhesion
Authors:
Taishi Kasai
Taishi Kasai
Affiliation:
Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
Bio-protocol author page:
a712
and
Makoto Miyata
Makoto Miyata
Affiliation:
Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan
For correspondence:
miyata@sci.osaka-cu.ac.jp
Bio-protocol author page:
a711
,
date: 7/20/2013, 4235 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.829
[Abstract] Dozens of
Mycoplasma
species bind to solid surfaces and glide in the direction of the membrane protrusion at a pole. In gliding,
Mycoplasma
legs catch, pull and release sialylated oligosaccharides fixed on a solid surface. The analyses of inhibitory ...
Article identifier: bio-protocol.org/e829
HIV-1 Virus-like Particle Budding Assay
Authors:
Nathan H Vande Burgt
Nathan H Vande Burgt
Affiliation:
Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
Bio-protocol author page:
a693
,
Luis J Cocka
Luis J Cocka
Affiliation:
Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
For correspondence:
lcocka@mail.med.upenn.edu
Bio-protocol author page:
a694
and
Paul Bates
Paul Bates
Affiliation:
Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
Bio-protocol author page:
a344
,
date: 7/20/2013, 3657 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.830
[Abstract] Viral replication culminates with the egress of the mature virion from the host cell. This step of the viral life cycle has recently garnered increased attention with the discovery of the cellular restriction factor, Tetherin, which tethers budded virions ...
Article identifier: bio-protocol.org/e830
Molecular Biology
DNase I Footprinting to Identify Protein Binding Sites
Authors:
Isabelle Gaugué
Isabelle Gaugué
Affiliation:
FRE3630-CNRS (ex UPR9073), Institut de Biologie Physico-Chimique, Paris, France
Bio-protocol author page:
a686
,
Dominique Bréchemier-Baey
Dominique Bréchemier-Baey
Affiliation:
FRE3630-CNRS (ex UPR9073), Institut de Biologie Physico-Chimique, Paris, France
Bio-protocol author page:
a687
and
Jacqueline Plumbridge
Jacqueline Plumbridge
Affiliation:
FRE3630-CNRS (ex UPR9073), Institut de Biologie Physico-Chimique, Paris, France
For correspondence:
jackie.plumbridge@ibpc.fr
Bio-protocol author page:
a688
,
date: 7/20/2013, 5925 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.824
[Abstract] DNase I footprinting is used to precisely localise the position that a DNA binding protein,
e.g.
a transcription factor, binds to a DNA fragment. A DNA fragment of a few hundred bp is labelled at one end and then incubated with the proteins suspected ...
Article identifier: bio-protocol.org/e824
Polysome Profiling Analysis
Authors:
Masahiro Morita
Masahiro Morita
Affiliation:
Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Canada
Bio-protocol author page:
a708
,
Tommy Alain
Tommy Alain
Affiliation:
Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Canada
Bio-protocol author page:
a709
,
Ivan Topisirovic
Ivan Topisirovic
Affiliation:
Department of Oncology and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, McGill University, Montreal, Canada
For correspondence:
ivan.topisirovic@mcgill.ca
Bio-protocol author page:
a707
and
Nahum Sonenberg
Nahum Sonenberg
Affiliation:
Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Canada
For correspondence:
nahum.sonenberg@mcgill.ca
Bio-protocol author page:
a710
,
date: 7/20/2013, 12962 views,
2 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.833
[Abstract] Polysome profiling is a method that allows monitoring of translation activity of mRNAs in cells and tissues. Once each polysome fractions are collected, the translation activity of each mRNA is analyzed using various molecular biology techniques such ...
Article identifier: bio-protocol.org/e833
Plant Science
Analysis of Malondialdehyde, Chlorophyll Proline, Soluble Sugar, and Glutathione Content in
Arabidopsis
seedling
Authors:
Zhijin Zhang
Zhijin Zhang
Affiliation:
Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China
Bio-protocol author page:
a684
and
Rongfeng Huang
Rongfeng Huang
Affiliation:
Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou, China
For correspondence:
rfhuang@caas.cn
Bio-protocol author page:
a362
,
date: 7/20/2013, 11118 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.817
[Abstract] The protocol has four sub-protocols, which are about the measurement of malondialdehyde, chlorophyll proline, soluble sugar, and glutathione content, respectively, in
Arabidopsis
seedling by using spectrophotometer. These methods are simple, effective ...
Article identifier: bio-protocol.org/e817
Determination of Enzyme Kinetic Parameters of UDP-glycosyltransferases
Authors:
Jörg M. Augustin
Jörg M. Augustin
Affiliation:
Faculty of Life Sciences - Department for Plant Biochemistry and Biotechnology, University of Copenhagen, Fredriksberg, Copenhagen, Denmark
For correspondence:
jmaug@gmx.de
Bio-protocol author page:
a403
and
Søren Bak
Søren Bak
Affiliation:
Faculty of Life Sciences - Department for Plant Biochemistry and Biotechnology, University of Copenhagen, Fredriksberg, Copenhagen, Denmark
Bio-protocol author page:
a404
,
date: 7/20/2013, 3776 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.825
[Abstract] The determination of enzyme kinetic parameters, such as the K
m
and k
cat
values, is an essential part of the characterization of newly discovered enzymes. This protocol describes the determination of enzyme kinetic parameters of the
Barbarea vulgaris
...
Article identifier: bio-protocol.org/e825
Extraction and Reglucosylation of
Barbarea vulgaris
Sapogenins
Authors:
Jörg M. Augustin
Jörg M. Augustin
Affiliation:
Faculty of Life Sciences - Department for Plant Biochemistry and Biotechnology, University of Copenhagen, Fredriksberg, Copenhagen, Denmark
For correspondence:
jmaug@gmx.de
Bio-protocol author page:
a403
,
Carl Erik Olsen
Carl Erik Olsen
Affiliation:
Faculty of Life Sciences - Department of Basic Science and Environment, University of Copenhagen, Fredriksberg, Copenhagen, Denmark
Bio-protocol author page:
a692
and
Søren Bak
Søren Bak
Affiliation:
Faculty of Life Sciences - Department for Plant Biochemistry and Biotechnology, University of Copenhagen, Fredriksberg, Copenhagen, Denmark
Bio-protocol author page:
a404
,
date: 7/20/2013, 3384 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.826
[Abstract] Plants produce a vast array of natural compounds. Many of them are not commercially available, and are thus lacking to be tested as substrates for enzymes. This protocol describes the extraction and acidic hydrolysis of metabolites from
Barbarea vulgaris
...
Article identifier: bio-protocol.org/e826
Maize Endosperm Protein Extraction and Analysis
Authors:
Xinze Chen
Xinze Chen
Affiliation:
School of Life Sciences, Shanghai University, Shanghai, China
Bio-protocol author page:
a704
,
Dongsheng Yao
Dongsheng Yao
Affiliation:
School of Life Sciences, Shanghai University, Shanghai, China
Bio-protocol author page:
a705
and
Rentao Song
Rentao Song
Affiliation:
School of Life Sciences, Shanghai University, Shanghai, China
For correspondence:
rentaosong@staff.shu.edu.cn
Bio-protocol author page:
a706
,
date: 7/20/2013, 3814 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.832
[Abstract] Alcohol-solubility is the most characteristic feature of the zein proteins, the major storage protein in maize. Using sodium borate buffer system with added reducing agent, total proteins are isolated, and zein proteins are separated from non-zein proteins. ...
Article identifier: bio-protocol.org/e832
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