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Volume:3 Issue:21
November 05, 2013
Biochemistry
Quantification of Bacterial Fatty Acids by Extraction and Methylation
Authors:
Mark Politz
Mark Politz
Affiliation:
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, USA
Bio-protocol author page:
a938
,
Rebecca Lennen
Rebecca Lennen
Affiliation:
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, USA
Bio-protocol author page:
a939
and
Brian Pfleger
Brian Pfleger
Affiliation:
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, USA
For correspondence:
pfleger@engr.wisc.edu
Bio-protocol author page:
a557
,
date: 11/5/2013, 5537 views,
1 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.950
[Abstract] This protocol describes two similar methods for the extraction and methylation of fatty acids from bacterial cultures. The acid derivatization protocol (Lennen
et al.
, 2013; Bligh and Dyer, 1959) results in the extraction and methylation of all fatty ...
Article identifier: bio-protocol.org/e950
β1 Integrin Cell-surface Immunoprecipitation (Selective Immunoprecipitation)
Author:
Ralph T. Böttcher
Ralph T. Böttcher
Affiliation:
Molecular Medicine Division, Max Planck Institute for Biochemistry, Martinsried, Germany
For correspondence:
rboettch@biochem.mpg.de
Bio-protocol author page:
a962
,
date: 11/5/2013, 3803 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.962
[Abstract] Immunoprecipitation (IP) is a widely used method to isolate a specific protein from a mixed protein sample using an antibody that exclusively binds to that particular protein. This technique allows studying protein-protein and protein-nucleic acid interactions ...
Article identifier: bio-protocol.org/e962
Cell Biology
Ki67 Immunofluorescence on Bovine Cell Lines
Authors:
Justine Marsolier
Justine Marsolier
Affiliation:
Epigenetics and Cell Fate, UMR 7216 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
Bio-protocol author page:
a945
,
Souhila Medjkane
Souhila Medjkane
Affiliation:
Epigenetics and Cell Fate, UMR 7216 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
Bio-protocol author page:
a946
,
Martine Perichon
Martine Perichon
Affiliation:
Epigenetics and Cell Fate, UMR 7216 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
Bio-protocol author page:
a947
and
Jonathan B. Weitzman
Jonathan B. Weitzman
Affiliation:
Epigenetics and Cell Fate, UMR 7216 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
For correspondence:
jonathan.weitzman@univ-paris-diderot.fr
Bio-protocol author page:
a948
,
date: 11/5/2013, 2794 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.958
[Abstract] This is a rapid protocol to test the effects of drugs treatment on bovine cell replication using Ki67 staining. Ki67 is associated with cell proliferation and is present during all active phases of the cell cycle (G1, S, G2, and mitosis), but is absent ...
Article identifier: bio-protocol.org/e958
Immunology
Bacterial Counts in Spleen
Authors:
Elías Barquero-Calvo
Elías Barquero-Calvo
Affiliation:
Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
Bio-protocol author page:
a954
,
Carlos Chacón-Díaz
Carlos Chacón-Díaz
Affiliation:
Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
Bio-protocol author page:
a958
,
Esteban Chaves-Olarte
Esteban Chaves-Olarte
Affiliation:
Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
Bio-protocol author page:
a960
and
Edgardo Moreno
Edgardo Moreno
Affiliation:
Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
For correspondence:
emoreno@racsa.co.cr
Bio-protocol author page:
a961
,
date: 11/5/2013, 8029 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.954
[Abstract] Bacterial loads can be determined as colony forming units (CFU) at any point of the infection by culturing spleen homogenates on agar plates. This is a reliable method for comparing the kinetics of infection in various mouse strains, estimating the virulence ...
Article identifier: bio-protocol.org/e954
Microbiology
H
2
O
2
Kill Assays of Biofilm Bacteria
Authors:
Malika Khakimova
Malika Khakimova
Affiliation:
Department of Microbiology, McGill University, Montreal, Canada
Bio-protocol author page:
a951
and
Dao Nguyen
Dao Nguyen
Affiliation:
Department of Medicine, McGill University, Montreal, Canada
For correspondence:
dao.nguyen@mcgill.ca
Bio-protocol author page:
a952
,
date: 11/5/2013, 3537 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.952
[Abstract] Ubiquitous in nature and often surface associated, biofilms cause numerous chronic human infections. Biofilms are structured multicellular bacterial communities where cells are entrapped in a polymer matrix. Bacteria growing as biofilms are characterized ...
Article identifier: bio-protocol.org/e952
H
2
O
2
Kill Assays of Planktonic Stationary Phase Bacteria
Authors:
Malika Khakimova
Malika Khakimova
Affiliation:
Department of Microbiology, McGill University, Montreal, Canada
Bio-protocol author page:
a951
and
Dao Nguyen
Dao Nguyen
Affiliation:
Department of Medicine, McGill University, Montreal, Canada
For correspondence:
dao.nguyen@mcgill.ca
Bio-protocol author page:
a952
,
date: 11/5/2013, 3553 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.953
[Abstract] Stationary phase bacteria are highly tolerant to hydrogen peroxide. This protocol was developed to test the susceptibility to hydrogen peroxide killing in different
Pseudomonas aeruginosa
strains. This assay provides a reliable way to measure killing ...
Article identifier: bio-protocol.org/e953
Adhesion of
Moraxella catarrhalis
to Respiratory Tract Epithelial Cells
Authors:
Stefan P.W. de Vries
Stefan P.W. de Vries
Affiliation:
Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
Bio-protocol author page:
a949
and
Hester J. Bootsma
Hester J. Bootsma
Affiliation:
Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
For correspondence:
hester.bootsma@radboudumc.nl
Bio-protocol author page:
a950
,
date: 11/5/2013, 3700 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.956
[Abstract]
Moraxella catarrhalis
is a human-restricted pathogen that is responsible for respiratory tract infections such as childhood otitis media (OM) and exacerbation of chronic obstructive pulmonary disease (COPD) in adults. Successful colonization and infection ...
Article identifier: bio-protocol.org/e956
Analysis of
Moraxella catarrhalis
Outer Membrane Protein Profiles
Authors:
Stefan P.W. de Vries
Stefan P.W. de Vries
Affiliation:
Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
Bio-protocol author page:
a949
and
Hester J. Bootsma
Hester J. Bootsma
Affiliation:
Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
For correspondence:
hester.bootsma@radboudumc.nl
Bio-protocol author page:
a950
,
date: 11/5/2013, 3184 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.957
[Abstract] Phenotypes observed for certain
Moraxella catarrhalis
wild-type strains or mutants may be caused by a variety of factors including alteration of outer membrane protein composition. Examination of the outer membrane protein profiles may be a valuable ...
Article identifier: bio-protocol.org/e957
Immunoplaque Assay (Influenza Virus)
Authors:
Longping V. Tse
Longping V. Tse
Affiliation:
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 Zhang
Affiliation:
Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, USA
Bio-protocol author page:
a941
and
Gary R. Whittaker
Gary R. Whittaker
Affiliation:
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, 7217 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 ...
Article identifier: bio-protocol.org/e959
Neuroscience
Dissection of Different Areas from Mouse Hippocampus
Author:
Faraz A. Sultan
Faraz A. Sultan
Affiliation:
Neurobiology Department, University of Alabama at Birmingham, Birmingham, USA
For correspondence:
faraz@uab.edu
Bio-protocol author page:
a953
,
date: 11/5/2013, 6581 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.955
[Abstract] The hippocampus modulates a number of modules including memory consolidation, spatial navigation, temporal processing and emotion. A banana-shaped structure, the hippocampus is constituted of morphologically distinct subregions including the dentate ...
Article identifier: bio-protocol.org/e955
Mitochondrial Isolation and Purification from Mouse Spinal Cord
Authors:
Philippe A. Parone
Philippe A. Parone
Affiliation:
Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego (UCSD), La Jolla, CA, USA
For correspondence:
philippeparone@gmail.com
Bio-protocol author page:
a933
,
Sandrine Da Cruz
Sandrine Da Cruz
Affiliation:
Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego (UCSD), La Jolla, CA, USA
Bio-protocol author page:
a934
and
Don W. Cleveland
Don W. Cleveland
Affiliation:
Ludwig Institute for Cancer Research and Department of Cellular and Molecular Medicine, University of California at San Diego (UCSD), La Jolla, CA, USA
Bio-protocol author page:
a935
,
date: 11/5/2013, 3604 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.961
[Abstract] Mitochondria are eukaryotic organelles that play a crucial role in several cellular processes, including energy production, β-oxidation of fatty acids and regulation of calcium homeostasis. In the last 20 years there has been a hightened interest in ...
Article identifier: bio-protocol.org/e961
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Implantation of Dkk-1-soaked Beads into the Neural Tube of Chicken Embryos
Authors:
Almudena Martinez-Ferre
Almudena Martinez-Ferre
Affiliation:
Institute of Neurosciences, Miguel Hernández University-Spanish National Research Council, San Juan, Alicante, Spain
Bio-protocol author page:
a967
,
Maria Navarro-Garberí
Maria Navarro-Garberí
Affiliation:
Institute of Neurosciences, Miguel Hernández University-Spanish National Research Council, San Juan, Alicante, Spain
Bio-protocol author page:
a968
,
Carlos Bueno
Carlos Bueno
Affiliation:
Institute of Neurosciences, Miguel Hernández University-Spanish National Research Council, San Juan, Alicante, Spain
Bio-protocol author page:
a969
and
Salvador Martinez
Salvador Martinez
Affiliation:
Institute of Neurosciences, Miguel Hernández University-Spanish National Research Council, San Juan, Alicante, Spain
For correspondence:
smartinez@umh.es
Bio-protocol author page:
a970
,
date: 11/5/2013, 4607 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.963
[Abstract] Chick embryos are known to be a powerful system to test gene function due to the “
in vivo
” accessibility, short time for results retrieval and the possibility to perform a large number of experiments. Synthetic micro-beads soaked in morphogenetic signals ...
Article identifier: bio-protocol.org/e963
NMDA-induced Excitotoxicity and Lactate Dehydrogenase Assay in Primary Cultured Neurons
Authors:
Shu Zhang
Shu Zhang
Affiliation:
Brain Research Centre, University of British Columbia, Vancouver, Canada
Bio-protocol author page:
a963
and
Yu Tian Wang
Yu Tian Wang
Affiliation:
Brain Research Centre, University of British Columbia, Vancouver, Canada
For correspondence:
ytwang@brain.ubc.ca
Bio-protocol author page:
a964
,
date: 11/5/2013, 4750 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.965
[Abstract] N-Methyl-D-aspartic acid receptor (NMDAR)-mediated excitotoxicity is thought to contribute to the pathogenesis of a large number of chronic neurodegenerative disorders (such as Alzheimer’s and Huntington’s diseases to mental illnesses) in addition to ...
Article identifier: bio-protocol.org/e965
Plant Science
Ovule Clearing Method for
Solanaceous
Species
Authors:
Audrey Loubert-Hudon
Audrey Loubert-Hudon
Affiliation:
Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
Bio-protocol author page:
a943
and
Daniel P. Matton
Daniel P. Matton
Affiliation:
Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, Québec, Canada
For correspondence:
dp.matton@umontreal.ca
Bio-protocol author page:
a944
,
date: 11/5/2013, 3129 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.951
[Abstract] Depending on the species, embryo sacs can be difficult to observe. Ovule clearing allows precise observation of whole tissues under Differential interference contrast (DIC) microscopy. The use of Methyl Salicylate as a clearing agent has proved to be ...
Article identifier: bio-protocol.org/e951
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Visualization and Quantification of Actin Dynamics in Rice Protoplasts
Authors:
Yurong Xie
Yurong Xie
Affiliation:
Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page:
a965
and
Shanjin Huang
Shanjin Huang
Affiliation:
Key laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
For correspondence:
sjhuang@ibcas.ac.cn
Bio-protocol author page:
a966
,
date: 11/5/2013, 2954 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.964
[Abstract] Direct visualization of the organization and dynamics of the actin cytoskeleton in rice cells is essential to understand its roles in regulating rice growth and development. Visualization of actin dynamics in protoplasts transformed with actin probe ...
Article identifier: bio-protocol.org/e964
Stem Cell
In vivo
BrdU Incorporation Assay for Murine Hematopioetic Stem Cells
Authors:
Ningfei An
Ningfei An
Affiliation:
Division of Hematology-Oncology, Department of Medicine, Medical University of South Carolina, Charleston, USA
Bio-protocol author page:
a936
and
Yubin Kang
Yubin Kang
Affiliation:
Division of Hematology-Oncology, Department of Medicine, Medical University of South Carolina, Charleston, USA
For correspondence:
kangy@musc.edu
Bio-protocol author page:
a937
,
date: 11/5/2013, 5100 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.960
[Abstract] Bromodeoxyuridine (BrdU) is a thymidine analog that is incorporated into DNA during the S-phase of the cell cycle. As such, BrdU incorporation can be used to quantify the number of cells that are in S-phase in the time period during which BrdU is available. ...
Article identifier: bio-protocol.org/e960
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