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Volume:5 Issue:11
June 05, 2015
Cell Biology
Dictyostelium
Cultivation, Transfection, Microscopy and Fractionation
Authors:
Jennifer Hirst
Jennifer Hirst
Affiliation:
Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
For correspondence:
jh228@cam.ac.uk
Bio-protocol author page:
a2250
,
Robert R Kay
Robert R Kay
Affiliation:
MRC Laboratory of Molecular Biology, Cambridge, UK
Bio-protocol author page:
a2251
and
David Traynor
David Traynor
Affiliation:
MRC Laboratory of Molecular Biology, Cambridge, UK
For correspondence:
dt101@mrc-lmb.cam.ac.uk
Bio-protocol author page:
a2252
,
date: 6/5/2015, 3337 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1485
[Abstract] The real time visualisation of fluorescently tagged proteins in live cells using ever more sophisticated microscopes has greatly increased our understanding of the dynamics of key proteins during fundamental physiological processes such as cell locomotion, ...
Article identifier: bio-protocol.org/e1485
FRAP Analysis of LET-23::GFP in the Vulval Epithelial Cells of Living
Caenorhabditis elegans
Larvae
Authors:
Michael Walser
Michael Walser
Affiliation:
University of Zurich, Institute of Molecular Life Sciences, Winterthurerstrasse, Zurich
Bio-protocol author page:
a2260
,
Alex Hajnal
Alex Hajnal
Affiliation:
University of Zurich, Institute of Molecular Life Sciences, Winterthurerstrasse, Zurich
Bio-protocol author page:
a2261
and
Juan M. Escobar-Restrepo
Juan M. Escobar-Restrepo
Affiliation:
University of Zurich, Institute of Molecular Life Sciences, Winterthurerstrasse, Zurich
For correspondence:
juan.escobar@imls.uzh.ch
Bio-protocol author page:
a2262
,
date: 6/5/2015, 1948 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1489
[Abstract] The
Caenorhabditis elegans
(
C. elegans
) vulva is a well-established system to study organ development as the molecular mechanisms that govern its formation are conserved in animals. Of special interest is the EGFR/RAS/MAPK signaling pathway that is required ...
Article identifier: bio-protocol.org/e1489
Immunology
Extraction and Identification of T Cell Stimulatory Self-lipid Antigens
Authors:
Marco Lepore
Marco Lepore
Affiliation:
Experimental Immunology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
Bio-protocol author page:
a2266
,
Sebastiano Sansano
Sebastiano Sansano
Affiliation:
Experimental Immunology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
Bio-protocol author page:
a2267
,
Claudia de Lalla
Claudia de Lalla
Affiliation:
Experimental Immunology Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy
Bio-protocol author page:
a2268
,
Paolo Dellabona
Paolo Dellabona
Affiliation:
Experimental Immunology Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy
Bio-protocol author page:
a2269
,
Giulia Casorati
Giulia Casorati
Affiliation:
Experimental Immunology Unit, Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milano, Italy
Bio-protocol author page:
a2270
,
Gennaro De Libero
Gennaro De Libero
Affiliation 1:
Experimental Immunology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
Affiliation 2:
Singapore Immunology Network (SIgN), Agency for Science, Technology, and Research, Singapore
Bio-protocol author page:
a2271
and
Lucia Mori
Lucia Mori
Affiliation 1:
Experimental Immunology, Department of Biomedicine, University Hospital Basel, Basel, Switzerland
Affiliation 2:
Singapore Immunology Network (SIgN), Agency for Science, Technology, and Research, Singapore
For correspondence:
lucia.mori@unibas.ch
Bio-protocol author page:
a2272
,
date: 6/5/2015, 2128 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1491
[Abstract] Autoreactive T cells restricted to CD1 molecules and specific for endogenous lipids are abundant in human blood (de Jong
et al.
, 2010; de Lalla
et al.
, 2011). A few self-lipid molecules recognized by diverse individual T cell clones and accumulated within ...
Article identifier: bio-protocol.org/e1491
Cytokine-Stimulated Phosphoflow of Whole Blood Using CyTOF Mass Cytometry
Authors:
Rosemary Fernandez
Rosemary Fernandez
Affiliation:
Human Immune Monitoring Center, Stanford University, Stanford, USA
Bio-protocol author page:
a2282
and
Holden Maecker
Holden Maecker
Affiliation:
Human Immune Monitoring Core, Institute of Immunity, Transplantation & Infection, Stanford University School of Medicine, Stanford, USA
For correspondence:
maecker@stanford.edu
Bio-protocol author page:
a1861
,
date: 6/5/2015, 3270 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1495
[Abstract] The ability to assess the function of a range of cytokine, antigen receptor, and Toll-like receptor (TLR) signaling pathways in a range of immune cells could provide a kind of fingerprint of the state of the human immune system. The mass cytometry or ...
Article identifier: bio-protocol.org/e1495
Cytokine-stimulated Phosphoflow of PBMC Using CyTOF Mass Cytometry
Authors:
Rosemary Fernandez
Rosemary Fernandez
Affiliation:
Human Immune Monitoring Center, Stanford University, Stanford, USA
Bio-protocol author page:
a2282
and
Holden Maecker
Holden Maecker
Affiliation:
Human Immune Monitoring Center, Stanford University , Stanford, USA
For correspondence:
maecker@stanford.edu
Bio-protocol author page:
a1861
,
date: 6/5/2015, 3844 views,
1 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1496
[Abstract] Phosphorylation of tyrosine, serine, and threonine residues is critical for the control of protein activity involved in various cellular events. An assortment of kinases and phosphatases regulate intracellular protein phosphorylation in many different ...
Article identifier: bio-protocol.org/e1496
Microbiology
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Quantification of Total and 2-LTR (Long terminal repeat) HIV DNA, HIV RNA and Herpesvirus DNA in PBMCs
Authors:
Marta Massanella
Marta Massanella
Affiliation:
University of California San Diego, La Jolla, USA
For correspondence:
mmassanellaluna@ucsd.edu
Bio-protocol author page:
a2185
,
Sara Gianella
Sara Gianella
Affiliation:
University of California San Diego, La Jolla, USA
Bio-protocol author page:
a2187
,
Steven M. Lada
Steven M. Lada
Affiliation:
University of California San Diego, La Jolla, USA
Bio-protocol author page:
a2274
,
Douglas D. Richman
Douglas D. Richman
Affiliation 1:
University of California San Diego, La Jolla, USA
Affiliation 2:
Veterans Affairs San Diego Healthcare System, La Jolla, USA
Bio-protocol author page:
a2275
and
Matthew C. Strain
Matthew C. Strain
Affiliation:
University of California San Diego, La Jolla, USA
For correspondence:
mstrain@ucsd.edu
Bio-protocol author page:
a2276
,
date: 6/5/2015, 3131 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1492
[Abstract] Almost all individuals infected with human immunodeficiency virus (HIV) are also infected with cytomegalovirus (CMV) and Epstein Barr virus (EBV). The aims of our studies have included characterizing and measuring the latent HIV reservoir and understanding ...
Article identifier: bio-protocol.org/e1492
Molecular Biology
DNA Damage Sensitivity Assays in
Caenorhabditis elegans
Authors:
Hyun-Min Kim
Hyun-Min Kim
Affiliation:
Department of Genetics, Harvard Medical School, Boston, USA
For correspondence:
hkim@genetics.med.harvard.edu
Bio-protocol author page:
a2256
and
Monica P. Colaiácovo
Monica P. Colaiácovo
Affiliation:
Department of Genetics, Harvard Medical School, Boston, USA
For correspondence:
mcolaiacovo@genetics.med.harvard.edu
Bio-protocol author page:
a2257
,
date: 6/5/2015, 2822 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1487
[Abstract]
C. elegans
has served as a genetically tractable multicellular model system to examine DNA damage-induced genotoxic stress which threatens genome integrity. Importantly, the high degree of conservation shared between worms and humans offers the advantage ...
Article identifier: bio-protocol.org/e1487
Enzymatic Activity Assays for Base Excision Repair Enzymes in Cell Extracts from Vertebrate Cells
Authors:
Melike Çağlayan
Melike Çağlayan
Affiliation:
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
Bio-protocol author page:
a1849
,
Julie K. Horton
Julie K. Horton
Affiliation:
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
Bio-protocol author page:
a2278
and
Samuel H. Wilson
Samuel H. Wilson
Affiliation:
Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
For correspondence:
wilson5@niehs.nih.gov
Bio-protocol author page:
a1850
,
date: 6/5/2015, 1816 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1493
[Abstract] We previously reported enzymatic activity assays for the base excision repair (BER) enzymes DNA polymerase β (pol β), aprataxin (APTX), and flap endonuclease 1 (FEN1) in cell extracts from
Saccharomyces cerevisiae
(Çağlayan and Wilson, 2014). Here, we ...
Article identifier: bio-protocol.org/e1493
Plant Science
Determination of the Developmental Origin of Seeds Containing Endosperm Using Flow Cytometric Analysis
Authors:
Christian Sailer
Christian Sailer
Affiliation:
Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
For correspondence:
christian.sailer@access.uzh.ch
Bio-protocol author page:
a2246
,
Anja Schmidt
Anja Schmidt
Affiliation:
Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
Bio-protocol author page:
a2247
and
Ueli Grossniklaus
Ueli Grossniklaus
Affiliation:
Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland
For correspondence:
grossnik@botinst.uzh.ch
Bio-protocol author page:
a2248
,
date: 6/5/2015, 2080 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1484
[Abstract] Seeds derived from a diploid, sexual plant typically contain a 2n embryo (n+n) and 3n endosperm, a ratio characteristic for most flowering plants. However, this ratio is altered in apomictic species, which reproduce asexually through seeds (Koltunow ...
Article identifier: bio-protocol.org/e1484
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Magnaporthe oryzae
Inoculation of Rice Seedlings by Spraying with a Spore Suspension
Authors:
Aya Akagi
Aya Akagi
Affiliation:
Disease Resistant Crops Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan
Present address:
Bayer CropScience, Tokyo, Japan
Bio-protocol author page:
a2253
,
Chang-Jie Jiang
Chang-Jie Jiang
Affiliation:
Disease Resistant Crops Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan
Bio-protocol author page:
a2254
and
Hiroshi Takatsuji
Hiroshi Takatsuji
Affiliation:
Disease Resistant Crops Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan
For correspondence:
takatsuh@affrc.go.jp
Bio-protocol author page:
a2255
,
date: 6/5/2015, 2821 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1486
[Abstract] Fungal blast caused by
Magnaporthe oryzae
(
M. oryzae
) leads to a serious yield loss of rice. Appropriate assessment of disease occurrence is necessary to investigate the nature of the disease and plant strategies to resist the disease. We describe our ...
Article identifier: bio-protocol.org/e1486
Simple Digital Photography for Assessing Biomass and Leaf Area Index in Cereals
Authors:
Jaume Casadesús
Jaume Casadesús
Affiliation:
Institut de Recerca i Tecnologia Agroalimentàries, IRTA, Parc de Gardeny - Edifici Fruitcentre, Lleida, Spain
For correspondence:
jaume.casadesus@irta.cat
Bio-protocol author page:
a2258
and
Dolors Villegas
Dolors Villegas
Affiliation:
Institut de Recerca i Tecnologia Agroalimentàries, IRTA, Av. Rovira Roure, Lleida, Spain
For correspondence:
dolors.villegas@irta.cat
Bio-protocol author page:
a2259
,
date: 6/5/2015, 2689 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1488
[Abstract] These instructions refer to obtaining fast and low-labour estimates of ground cover, leaf area index and green biomass for a large number of plots, as those encountered in cereal breeding programs. The procedure includes obtaining the pictures in the ...
Article identifier: bio-protocol.org/e1488
Measurement of Net High-affinity Urea Uptake in Maize Plants
Authors:
Laura Zanin
Laura Zanin
Affiliation:
Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
For correspondence:
laura.zanin@uniud.it
Bio-protocol author page:
a2263
,
Nicola Tomasi
Nicola Tomasi
Affiliation:
Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
Bio-protocol author page:
a2264
and
Roberto Pinton
Roberto Pinton
Affiliation:
Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
Bio-protocol author page:
a2265
,
date: 6/5/2015, 1899 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1490
[Abstract] Despite its extensive use as a nitrogen fertilizer, the role of urea as a directly accessible nitrogen source for crop plants is still poorly understood. So far, the physiological and molecular aspects of urea acquisition have been investigated only ...
Article identifier: bio-protocol.org/e1490
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Cell Wall Biomass Preparation and Fourier Transform Mid-infrared (FTIR) Spectroscopy to Study Cell Wall Composition
Authors:
Ricardo M. F. da Costa
Ricardo M. F. da Costa
Affiliation:
Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, UK
For correspondence:
dacosta.rmf@gmail.com
Bio-protocol author page:
a2279
,
Gordon G. Allison
Gordon G. Allison
Affiliation:
Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, UK
For correspondence:
goa@aber.ac.uk
Bio-protocol author page:
a2280
and
Maurice Bosch
Maurice Bosch
Affiliation:
Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, UK
Bio-protocol author page:
a2281
,
date: 6/5/2015, 2038 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1494
[Abstract] Plant cell wall biomass is an abundant and renewable organic resource. Of the polymers it encloses, cellulose and hemicellulose are regarded as a raw material for the production of fuels and other products (Klemm
et al.
, 2005; Slavov
et al.
, 2013). Nonetheless, ...
Article identifier: bio-protocol.org/e1494
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Quantitative Image Analysis of Membrane Microdomains Labelled by Fluorescently Tagged Proteins in
Arabidopsis thaliana
and
Nicotiana benthamiana
Authors:
Iris K. Jarsch
Iris K. Jarsch
Affiliation:
Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
Present address:
Gurdon Institute, University of Cambridge, Cambridge, UK
Bio-protocol author page:
a2283
and
Thomas Ott
Thomas Ott
Affiliation:
Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
For correspondence:
Thomas.Ott@bio.lmu.de
Bio-protocol author page:
a2284
,
date: 6/5/2015, 2075 views,
0 Q&A
DOI:
https://doi.org/10.21769/BioProtoc.1497
[Abstract] We have recently characterized co-existing membrane microdomains that are labeled by different proteins in living plant cells (Jarsch
et al.
, 2014). For this approach we first created a digital fingerprint for each of the twenty marker proteins using ...
Article identifier: bio-protocol.org/e1497
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