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1-MCP (1-methylcyclopropene) Treatment Protocol for Fruit or Vegetables

Featured protocol,  Authors: Gamrasni Dan
Gamrasni DanAffiliation 1: Fruit Storage Research Laboratory, Israel Fruit Growers’ Association, Kiryat Shmona, Israel
Affiliation 2: Tel Hai Academic College, Tel Hai, Israel
Affiliation 3: Migal Institute, Kiryat Shmona, Israel
For correspondence: danny.gamrasni@gmail.com
Bio-protocol author page: a4422
Goldway Martin
Goldway MartinAffiliation 1: Tel Hai Academic College, Tel Hai, Israel
Affiliation 2: Migal Institute, Kiryat Shmona, Israel
Bio-protocol author page: a4423
Stern Yosi
Stern YosiAffiliation: RIMI, Petah Tikva, Israel
Bio-protocol author page: a4424
Breitel Dario
Breitel DarioAffiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
Bio-protocol author page: a4425
 and Aharoni Asaph
Aharoni AsaphAffiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
Bio-protocol author page: a4426
date: 5/20/2017, 114 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2278.

Brief version appeared in PLoS Genet, Mar 2016
1-MCP (1-methylcyclopropene) is a simple synthetic hydrocarbon molecule that interacts with the ethylene receptor and inhibits the response of fruit or plant to ethylene. 1-MCP has opened new opportunities in handling harvested crops and serves as a powerful tool to learn about plant response to ethylene (Watkins and Miller, 2006). 1-MCP is manufactured by Agrofresh and known by its commercial name SmartfreshSM.

Simple Spectroscopic Determination of Nitrate, Nitrite, and Ammonium in Arabidopsis thaliana

Featured protocol,  Authors: Takushi Hachiya
Takushi HachiyaAffiliation 1: Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences,, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
Affiliation 2: Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
For correspondence: takushi@agr.nagoya-u.ac.jp
Bio-protocol author page: a4507
 and Yuki Okamoto
Yuki OkamotoAffiliation: Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
Bio-protocol author page: a4508
date: 5/20/2017, 129 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2280.

Brief version appeared in Plant Cell Physiol, Nov 2016
Plants use nitrate, nitrite, and ammonium as inorganic nitrogen (N) sources. These N compounds are included in plant tissues at various concentrations depending on the balance between their uptake and assimilation. Thus, the contents of nitrate, nitrite, and ammonium are physiological indicators of plant N economy. Here, we describe a protocol for measurement of these inorganic N species in A. thaliana shoots or roots.

Protein Isolation from Plasma Membrane, Digestion and Processing for Strong Cation Exchange Fractionation

Featured protocol,  Authors: Ning Yang
Ning YangAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4554
Bing Han
Bing HanAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4555
 and Tai Wang
Tai WangAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
For correspondence: twang@ibcas.ac.cn
Bio-protocol author page: a4558
date: 5/20/2017, 114 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2298.

Brief version appeared in J Integr Plant Biol, Dec 2010
Plasma membrane (PM) proteins play crucial roles in diverse biological processes. But their low abundance, alkalinity and hydrophobicity make their isolation a difficult task. This protocol describes an efficient method for PM proteins isolation, digestion and fractionation so that they can be well prepared for mass spectrometry analysis.

Plasma Membrane Preparation from Lilium davidii and Oryza sativa Mature and Germinated Pollen

Featured protocol,  Authors: Ning Yang
Ning YangAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4554
Bing Han
Bing HanAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4555
Lingtong Liu
Lingtong LiuAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4556
Hao Yang
Hao YangAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4557
 and Tai Wang
Tai WangAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
For correspondence: twang@ibcas.ac.cn
Bio-protocol author page: a4558
date: 5/20/2017, 91 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2297.

Brief version appeared in J Integr Plant Biol, Dec 2010
Pollen germination is an excellent process to study cell polarity establishment. During this process, the tip-growing pollen tube will start elongating. The plasma membrane as the selectively permeable barrier that separate the inner and outer cell environment plays crucial roles in this process. This protocol described an efficient aqueous polymer two-phase system followed by alkaline solution washing to prepare Lilium davidii or Oryza sativa plasma membrane with high purity.

Haustorium Induction Assay of the Parasitic Plant Phtheirospermum japonicum

Featured protocol,  Authors: Juliane K. Ishida
Juliane K. IshidaAffiliation 1: RIKEN Center for Sustainable Resource Science, Yokohama, Japan
Affiliation 2: Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
Bio-protocol author page: a4459
Satoko Yoshida
Satoko YoshidaAffiliation 1: RIKEN Center for Sustainable Resource Science, Yokohama, Japan
Affiliation 2: Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Nara, Japan
Bio-protocol author page: a4460
 and Ken Shirasu
Ken ShirasuAffiliation 1: RIKEN Center for Sustainable Resource Science, Yokohama, Japan
Affiliation 2: Graduate School of Science, The University of Tokyo, Tokyo, Japan
For correspondence: ken.shirasu@riken.jp
Bio-protocol author page: a2656
date: 5/5/2017, 173 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2260.

Brief version appeared in Plant Cell, Aug 2016
Phtheirospermum japonicum is a facultative root parasitic plant in the Orobanchaceae family used as a model parasitic plant. Facultative root parasites form an invasive organ called haustorium on the lateral parts of their roots. To functionally characterize parasitic abilities, quantification of haustorium numbers is required. However, this task is quite laborious and time consuming. Here we describe an efficient protocol to induce haustorium in vitro by haustorium-inducing chemicals and host root exudate treatments in P. japonicum.

Mating Based Split-ubiquitin Assay for Detection of Protein Interactions

Featured protocol,  Authors: Wijitra Horaruang
Wijitra HoraruangAffiliation: Laboratory of Plant Physiology and Biophysics, Bower Building, University of Glasgow, Glasgow, UK
Bio-protocol author page: a4456
 and Ben Zhang
Ben ZhangAffiliation: Laboratory of Plant Physiology and Biophysics, Bower Building, University of Glasgow, Glasgow, UK
For correspondence: Ben.Zhang@glasgow.ac.uk
Bio-protocol author page: a4457
date: 5/5/2017, 312 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2258.

Brief version appeared in Plant Cell, Jun 2015
The mating based split-ubiquitin (mbSUS) assay is an alternative method to the classical yeast two-hybrid system with a number of advantages. The mbSUS assay relies on the ubiquitin-degradation pathway as a sensor for protein-protein interactions, and it is suitable for the determination of interactions between full-length proteins that are cytosolic or membrane-bound. Here we describe the mbSUS assay protocol which has been used for detecting the interaction between K+ channel and SNARE proteins (Grefen et al., 2010 and 2015; Zhang et al., 2015 and 2016)

Comprehensive Methods for Leaf Geometric Morphometric Analyses

Featured protocol,  Authors: Laura L. Klein
Laura L. KleinAffiliation: Department of Biology, Saint Louis University, St. Louis, Missouri, USA
For correspondence: lklein10@slu.edu
Bio-protocol author page: a4481
 and Harlan T. Svoboda
Harlan T. SvobodaAffiliation: Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, USA
For correspondence: hs923311@ohio.edu
Bio-protocol author page: a4482
date: 5/5/2017, 396 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2269.

Brief version appeared in Plant Physiol, Mar 2016
Leaf morphometrics are used frequently by several disciplines, including taxonomists, systematists, developmental biologists, morphologists, agronomists, and plant breeders to name just a few. Leaf shape is highly variable and can be used for identifying species or genotypes, developmental patterning within and among individuals, assessing plant health, and measuring environmental impacts on plant phenotype. Traditional leaf morphometrics require hand tools and access to specimens, but modern efforts to digitize botanical collections make digital morphometrics a readily accessible and scientifically rigorous option. Here we provide detailed instructions for performing some of the most informative digital geometric morphometric analyses available: generalized Procrustes analysis, elliptical Fourier analysis, and shape features. This comprehensive procedure for leaf shape analysis is comprised of six main sections: A) scanning of material, B) acquiring landmarks, C) analysis of landmark data, D) isolating leaf outlines, E) analysis of leaf outlines, and F) shape features. This protocol provides a detailed reference for applying landmark and outline analysis to leaf shape as well as describing leaf shape features, thus empowering researchers to perform high throughput phenotyping for diverse applications.

Pathogenicity Assay of Penicillium expansum on Apple Fruits

Featured protocol,  Authors: Yong Chen
Yong ChenAffiliation: Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4471
Boqiang Li
Boqiang LiAffiliation: Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a1847
Zhanquan Zhang
Zhanquan ZhangAffiliation: Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a1845
 and Shiping Tian
Shiping TianAffiliation: Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
For correspondence: tsp@ibcas.ac.cn
Bio-protocol author page: a1848
date: 5/5/2017, 167 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2264.

Brief version appeared in Mol Plant Microbe Interact, Jun 2015
Penicillium expansum, a widespread filamentous fungus, is a major causative agent of fruit decay and leads to huge economic losses during postharvest storage and shipping. Furthermore, it produces mycotoxin on the infected fruits that may cause harmful effects to human health. This pathogenicity assay involves a stab inoculation procedure of P. expansum on apple fruit, an important experimental technique to study fungal pathogenesis. This assay can be applied to analyze the virulence of postharvest pathogen on other fruits such as orange, pear and kiwifruit.

1-MCP (1-methylcyclopropene) Treatment Protocol for Fruit or Vegetables

Authors: Gamrasni Dan
Gamrasni DanAffiliation 1: Fruit Storage Research Laboratory, Israel Fruit Growers’ Association, Kiryat Shmona, Israel
Affiliation 2: Tel Hai Academic College, Tel Hai, Israel
Affiliation 3: Migal Institute, Kiryat Shmona, Israel
For correspondence: danny.gamrasni@gmail.com
Bio-protocol author page: a4422
Goldway Martin
Goldway MartinAffiliation 1: Tel Hai Academic College, Tel Hai, Israel
Affiliation 2: Migal Institute, Kiryat Shmona, Israel
Bio-protocol author page: a4423
Stern Yosi
Stern YosiAffiliation: RIMI, Petah Tikva, Israel
Bio-protocol author page: a4424
Breitel Dario
Breitel DarioAffiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
Bio-protocol author page: a4425
 and Aharoni Asaph
Aharoni AsaphAffiliation: Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
Bio-protocol author page: a4426
date: 5/20/2017, 114 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2278.

[Abstract] 1-MCP (1-methylcyclopropene) is a simple synthetic hydrocarbon molecule that interacts with the ethylene receptor and inhibits the response of fruit or plant to ethylene. 1-MCP has opened new opportunities in handling harvested crops and serves as a powerful tool to learn about plant response to ethylene ...

Simple Spectroscopic Determination of Nitrate, Nitrite, and Ammonium in Arabidopsis thaliana

Authors: Takushi Hachiya
Takushi HachiyaAffiliation 1: Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences,, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
Affiliation 2: Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
For correspondence: takushi@agr.nagoya-u.ac.jp
Bio-protocol author page: a4507
 and Yuki Okamoto
Yuki OkamotoAffiliation: Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
Bio-protocol author page: a4508
date: 5/20/2017, 129 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2280.

[Abstract] Plants use nitrate, nitrite, and ammonium as inorganic nitrogen (N) sources. These N compounds are included in plant tissues at various concentrations depending on the balance between their uptake and assimilation. Thus, the contents of nitrate, nitrite, and ammonium are physiological indicators of ...

Protein Isolation from Plasma Membrane, Digestion and Processing for Strong Cation Exchange Fractionation

Authors: Ning Yang
Ning YangAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4554
Bing Han
Bing HanAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4555
 and Tai Wang
Tai WangAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
For correspondence: twang@ibcas.ac.cn
Bio-protocol author page: a4558
date: 5/20/2017, 114 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2298.

[Abstract] Plasma membrane (PM) proteins play crucial roles in diverse biological processes. But their low abundance, alkalinity and hydrophobicity make their isolation a difficult task. This protocol describes an efficient method for PM proteins isolation, digestion and fractionation so that they can be well ...

Plasma Membrane Preparation from Lilium davidii and Oryza sativa Mature and Germinated Pollen

Authors: Ning Yang
Ning YangAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4554
Bing Han
Bing HanAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4555
Lingtong Liu
Lingtong LiuAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4556
Hao Yang
Hao YangAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4557
 and Tai Wang
Tai WangAffiliation: Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
For correspondence: twang@ibcas.ac.cn
Bio-protocol author page: a4558
date: 5/20/2017, 91 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2297.

[Abstract] Pollen germination is an excellent process to study cell polarity establishment. During this process, the tip-growing pollen tube will start elongating. The plasma membrane as the selectively permeable barrier that separate the inner and outer cell environment plays crucial roles in this process. This ...

Haustorium Induction Assay of the Parasitic Plant Phtheirospermum japonicum

Authors: Juliane K. Ishida
Juliane K. IshidaAffiliation 1: RIKEN Center for Sustainable Resource Science, Yokohama, Japan
Affiliation 2: Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
Bio-protocol author page: a4459
Satoko Yoshida
Satoko YoshidaAffiliation 1: RIKEN Center for Sustainable Resource Science, Yokohama, Japan
Affiliation 2: Institute for Research Initiatives, Division for Research Strategy, Nara Institute of Science and Technology, Nara, Japan
Bio-protocol author page: a4460
 and Ken Shirasu
Ken ShirasuAffiliation 1: RIKEN Center for Sustainable Resource Science, Yokohama, Japan
Affiliation 2: Graduate School of Science, The University of Tokyo, Tokyo, Japan
For correspondence: ken.shirasu@riken.jp
Bio-protocol author page: a2656
date: 5/5/2017, 173 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2260.

[Abstract] Phtheirospermum japonicum is a facultative root parasitic plant in the Orobanchaceae family used as a model parasitic plant. Facultative root parasites form an invasive organ called haustorium on the lateral parts of their roots. To functionally characterize parasitic abilities, quantification of haustorium ...

Mating Based Split-ubiquitin Assay for Detection of Protein Interactions

Authors: Wijitra Horaruang
Wijitra HoraruangAffiliation: Laboratory of Plant Physiology and Biophysics, Bower Building, University of Glasgow, Glasgow, UK
Bio-protocol author page: a4456
 and Ben Zhang
Ben ZhangAffiliation: Laboratory of Plant Physiology and Biophysics, Bower Building, University of Glasgow, Glasgow, UK
For correspondence: Ben.Zhang@glasgow.ac.uk
Bio-protocol author page: a4457
date: 5/5/2017, 312 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2258.

[Abstract] The mating based split-ubiquitin (mbSUS) assay is an alternative method to the classical yeast two-hybrid system with a number of advantages. The mbSUS assay relies on the ubiquitin-degradation pathway as a sensor for protein-protein interactions, and it is suitable for the determination of interactions ...

Comprehensive Methods for Leaf Geometric Morphometric Analyses

Authors: Laura L. Klein
Laura L. KleinAffiliation: Department of Biology, Saint Louis University, St. Louis, Missouri, USA
For correspondence: lklein10@slu.edu
Bio-protocol author page: a4481
 and Harlan T. Svoboda
Harlan T. SvobodaAffiliation: Department of Environmental and Plant Biology, Ohio University, Athens, Ohio, USA
For correspondence: hs923311@ohio.edu
Bio-protocol author page: a4482
date: 5/5/2017, 396 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2269.

[Abstract] Leaf morphometrics are used frequently by several disciplines, including taxonomists, systematists, developmental biologists, morphologists, agronomists, and plant breeders to name just a few. Leaf shape is highly variable and can be used for identifying species or genotypes, developmental patterning ...

Pathogenicity Assay of Penicillium expansum on Apple Fruits

Authors: Yong Chen
Yong ChenAffiliation: Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a4471
Boqiang Li
Boqiang LiAffiliation: Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a1847
Zhanquan Zhang
Zhanquan ZhangAffiliation: Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
Bio-protocol author page: a1845
 and Shiping Tian
Shiping TianAffiliation: Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, China
For correspondence: tsp@ibcas.ac.cn
Bio-protocol author page: a1848
date: 5/5/2017, 167 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2264.

[Abstract] Penicillium expansum, a widespread filamentous fungus, is a major causative agent of fruit decay and leads to huge economic losses during postharvest storage and shipping. Furthermore, it produces mycotoxin on the infected fruits that may cause harmful effects to human health. This pathogenicity assay ...

Growth Assay for the Stem Parasitic Plants of the Genus Cuscuta

Authors: Volker Hegenauer
Volker Hegenauer Affiliation: Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
For correspondence: volker.hegenauer@zmbp.uni-tuebingen.de
Bio-protocol author page: a4396
Max Welz
Max WelzAffiliation: Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
Bio-protocol author page: a4397
Max Körner
Max KörnerAffiliation: Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
Bio-protocol author page: a4398
 and Markus Albert
Markus AlbertAffiliation: Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
Bio-protocol author page: a2064
date: 4/20/2017, 262 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2243.

[Abstract] Cuscuta spp. are widespread obligate holoparasitic plants with a broad host spectrum. Rootless Cuscuta penetrates host stems with so called haustoria to form a direct connection to the host vascular tissue (Dawson et al., 1994; Lanini and Kogan, 2005; Kaiser et al., 2015). This connection allows a steady ...

Single Molecule RNA FISH in Arabidopsis Root Cells

Authors: Susan Duncan
Susan DuncanAffiliation: Earlham Institute, Norwich Research Park, Norwich, United Kingdom
Bio-protocol author page: a4387
Tjelvar S. G. Olsson
Tjelvar S. G. OlssonAffiliation: John Innes Centre, Norwich Research Park, Norwich, United Kingdom
Bio-protocol author page: a4388
Matthew Hartley
Matthew HartleyAffiliation: John Innes Centre, Norwich Research Park, Norwich, United Kingdom
Bio-protocol author page: a4389
Caroline Dean
Caroline DeanAffiliation: John Innes Centre, Norwich Research Park, Norwich, United Kingdom
Bio-protocol author page: a4390
 and Stefanie Rosa
Stefanie RosaAffiliation: John Innes Centre, Norwich Research Park, Norwich, United Kingdom
Present address: Institute of Biochemistry and Biology, Plant Physiology, University of Potsdam, DE-14476 Potsdam-Golm, Germany
For correspondence: srosa@uni-potsdam.de
Bio-protocol author page: a2658
date: 4/20/2017, 413 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2240.

[Abstract] Methods that allow the study of gene expression regulation are continually advancing. Here, we present an in situ hybridization protocol capable of detecting individual mRNA molecules in plant root cells, thus permitting the accurate quantification and localization of mRNA within fixed samples (Duncan ...
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Detection of Hydrogen Peroxide by DAB Staining in Arabidopsis Leaves Updates
The author made some updates (highlighted in blue) to the protocol on 09/19/2016.

Authors: Arsalan Daudi
Arsalan DaudiAffiliation 1: Department of Biological Sciences, Royal Holloway University of London, Egham, UK
Affiliation 2: Department of Plant Pathology, University of California, Davis, CA, USA
For correspondence: aadaudi@ucdavis.edu
Bio-protocol author page: a107
 and Jose A. O’Brien
Jose A. O’BrienAffiliation: Department of Biological Sciences, Royal Holloway University of London, Egham, UK
Bio-protocol author page: a108
date: 9/20/2012, 33156 views, 16 Q&A
DOI: https://doi.org/10.21769/BioProtoc.263.

[Abstract] In this protocol, the in situ detection of hydrogen peroxide (one of several reactive oxygen species) is described in mature Arabidopsis rosette leaves by staining with 3,3'-diaminobenzidine (DAB) using an adaptation of previous methods (Thordal-Christensen et al., 1997; Bindschedler et al., 2006; Daudi ...

[Bio101] Infiltration of Nicotiana benthamiana Protocol for Transient Expression via Agrobacterium

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 7/20/2011, 31987 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.95.

[Abstract] Transient expression in tobacco plant (Nicotiana benthamiana) is used to determine the subcellular location of a protein of interest when tagged with a reporter such as green fluorescent protein (GFP), or to mass produce proteins without making transgenic plants. The root tumor bacteria, Agrobacteria, ...

[Bio101] Pollen Fertility/viability Assay Using FDA Staining

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 5/20/2011, 16834 views, 2 Q&A
DOI: https://doi.org/10.21769/BioProtoc.75.

[Abstract] Pollen grains can be fertile or sterile by nature. This method stains pollen grains for an enzyme as the vital indicator of membrane integrity. Only fertile grains fluoresce under microscopic examination....

[Bio101] Histostaining for Tissue Expression Pattern of Promoter-driven GUS Activity in Arabidopsis

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 7/5/2011, 16011 views, 4 Q&A
DOI: https://doi.org/10.21769/BioProtoc.93.

[Abstract] Promoter-driven GUS (beta-glucuronidase) activity is the most commonly used technique for tissue-specific expression patterns in Arabidopsis. In this procedure, GUS enzyme converts 5-bromo-4-chloro-3-indolyl glucuronide (X-Gluc) to a blue product. The staining is very sensitive. Processed samples can ...

[Bio101] Arabidopsis Pollen Tube Aniline Blue Staining

Author: Yongxian Lu
Yongxian LuAffiliation: Carnegie Institution for Scienc, Stanford University, Stanford, USA
For correspondence: yxlu@stanford.edu
Bio-protocol author page: a28
date: 6/20/2011, 15533 views, 4 Q&A
DOI: https://doi.org/10.21769/BioProtoc.88.

[Abstract] The aim of this experiment is to track pollen tube growth in vivo in the female tissues after pollination. This can be used to phenotype pollen germination, tube growth and guidance, and reception....

In vitro Protein Ubiquitination Assays

Authors: Qingzhen Zhao
Qingzhen ZhaoAffiliation: College of Life Science, Liaocheng University, Liaocheng, China
Bio-protocol author page: a887
 and Qi Xie
Qi XieAffiliation: State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing, China
For correspondence: qxie@genetics.ac.cn
Bio-protocol author page: a888
date: 10/5/2013, 15153 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.928.

[Abstract] Ubiquitin can be added to substrate protein as a protein tag by the concerted actions of ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2) and ubiquitin protein ligase (E3). At the present of E1 and ubiquitin, E2 activity can be determined by the thio-ester formation. The E3 activity ...

[Bio101] Extract Genomic DNA from Arabidopsis Leaves (Can be Used for Other Tissues as Well)

Author: Yongxian Lu
Yongxian LuAffiliation: Carnegie Institution for Science, Stanford University, Stanford, USA
For correspondence: yxlu@stanford.edu
Bio-protocol author page: a28
date: 7/5/2011, 15132 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.90.

[Abstract] This is a simple protocol for isolating genomic DNA from fresh plant tissues. DNA from this experiment can be used for all kinds of genetics studies, including genotyping and mapping. This protocol uses Edward’s extraction buffer to isolate DNA....

Seed Germination and Viability Test in Tetrazolium (TZ) Assay

Authors: Pooja Verma
Pooja VermaAffiliation: NIPGR, National Institute of Plant Genome Research, New Delhi, India
Bio-protocol author page: a799
 and Manoj Majee
Manoj MajeeAffiliation: NIPGR, National Institute of Plant Genome Research, New Delhi, India
For correspondence: manojmajee@nipgr.ac.in
Bio-protocol author page: a800
date: 9/5/2013, 14283 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.884.

[Abstract] Tetrazolium (TZ) assay is the fast evaluation for seed viability and alternative quick method for seed’s germinability (Porter et al., 1947; Wharton, 1955). All respiring tissues are capable of converting a colourless compound, TZ (2,3,5 triphenyl tetrazolium chloride) to a carmine red coloured water-insoluble ...

[Bio101] Arabidopsis Growing Protocol – A General Guide

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 9/5/2011, 13790 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.126.

[Abstract] Arabidopsis as the model organism for higher plants is widely studied among plant biology labs around the world. However, taking care of this tiny plant may not be trivial. Here is a general guide used for the Heven Sze lab at the University of Maryland, College Park. A lot of efforts have been taken ...

[Bio101] A Transient Expression Assay Using Arabidopsis Mesophyll Protoplasts

Author: Xiyan Li
Xiyan LiAffiliation: Department of Genetics, Stanford University, Stanford, USA
For correspondence: lixiyan@stanford.edu
Bio-protocol author page: a13
date: 5/20/2011, 11505 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.70.

[Abstract] This method can be used to free and separate the mesophyll cells from Arabidopsis leaves. The protoplasts that are generated in this way can be used for transient expression for protein activity and subcellular localization assays....
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