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Biochemical Pathways and Environmental Responses in Plants: Part B
- 1st Edition, Volume 680 - January 27, 2023
- Editor: Joseph Jez
- Language: English
- Hardback ISBN:9 7 8 - 0 - 4 4 3 - 1 8 5 8 4 - 7
- eBook ISBN:9 7 8 - 0 - 4 4 3 - 1 8 5 8 5 - 4
Biochemical Pathways and Environmental Responses in Plants, Part B, Volume 682 in the Methods in Enzymology series, highlights advances in the field with this new volume presentin… Read more
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Request a sales quoteBiochemical Pathways and Environmental Responses in Plants, Part B, Volume 682 in the Methods in Enzymology series, highlights advances in the field with this new volume presenting chapters on MIE 681/682: Biochemical pathways and environmental responses in plants, Structure, function, and engineering of plant polyketide synthases, A sensitive LC-MS/MS assay for enzymatic characterization of methylthioalkylmalate synthase involved in glucosinolate side-chain elongation, Assaying formate-tetrahydrofolate ligase with monoglutamylated and polyglutamylated substrates using a fluorescence-HPLC based assay, An Approach to Nearest Neighbor Analysis of Pigmented Protein Complexes by Using Chemical Crosslinking in Combination with Mass Spectrometry, Biochemical characterization of plant aromatic aminotransferases, and much more.
Other chapters focus on Functional Analysis of Phosphoethanolamine N-methyltransferase (PMT) in Plants and Parasites, A structure-guided computational screening approach for predicting plant enzyme-metabolite interactions, Plant metacaspase: an example of microcrystal structure determination and analysis, Biocatalytic system for comparative assessment of functional association of cytochrome P450 monooxygenases with their redox partners, Dirigent Protein Family Function and Structure, and more.
- Provides the authority and expertise of leading contributors from an international board of authors
- Presents the latest release in Methods in Enzymology series
- Includes the latest information on Biochemical pathways and environmental responses in plants
Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists
- Cover
- Title page
- Table of Contents
- Copyright
- Contributors
- Preface
- Section I: Protein
- Chapter One: Systems and strategies for plant protein expression
- Abstract
- 1: Introduction
- 2: Transit peptide prediction
- 3: Cloning NAXD and NAXE expression vectors
- 4: Optimizing expression
- 5: Purification and storage of recombinant enzymes
- 6: Troubleshooting and additional considerations for plant protein expression
- 7: Conclusions
- Acknowledgments
- References
- Chapter Two: Biochemical characterization of plant aromatic aminotransferases
- Abstract
- 1: Introduction
- 2: Heterologous production of Aro AT proteins
- 3: Conducting Aro AT catalyzed enzymatic reactions
- 4: Detection methods for Aro AT product formation or substrate consumption
- Acknowledgments
- References
- Chapter Three: Assaying plant formate-tetrahydrofolate ligase with monoglutamylated and polyglutamylated substrates using a fluorescence-HPLC based method
- Abstract
- 1: Introduction
- 2: Methods
- 3: Summary
- Acknowledgment
- References
- Further reading
- Chapter Four: Functional analysis of phosphoethanolamine N-methyltransferase in plants and parasites: Essential S-adenosylmethionine-dependent methyltransferase in choline and phospholipid metabolism
- Abstract
- 1: Introduction
- 2: Genomic and structural analysis of PMTs
- 3: Cloning, expression, and purification of PMTs
- 4: In vitro functional analysis of PMTs
- 5: Conclusion
- Acknowledgments
- References
- Chapter Five: An approach to nearest neighbor analysis of pigment-protein complexes using chemical cross-linking in combination with mass spectrometry
- Abstract
- 1: Introduction
- 2: Protein sample preparation
- 3: Mass spectrometry sample preparation
- 4: LC-MS/MS instrumentation
- 5: Identification of chemically cross-linked peptides
- 6: Network analysis of cross-linked sites
- 7: Conclusion and perspectives
- References
- Chapter Six: Structural characterization of protein–DNA complexes using small angle X-ray scattering (SAXS) with contrast variation
- Abstract
- 1: Introduction
- 2: Sample preparation for SAXS contrast variation
- 3: SAXS data collection and analysis
- 4: Summary of procedures
- 5: Expected outcomes
- 6: Conclusion
- 7: Optimization and troubleshooting
- References
- Chapter Seven: A fast and cost-effective procedure for reliable measurement of trypsin inhibitor activity in soy and soy products
- Abstract
- 1: Introduction
- 2: Development of a simplified trypsin inhibitor assay
- 3: Calculation of trypsin inhibitor activity
- 4: Immunoblot analysis of soybean lines with contrasting trypsin inhibitor content
- 5: Measurement of KTi activity in soybean lines with contrasting trypsin inhibitor content
- 6: Comparison of the 10 mL, 5 mL and the simplified 1 mL assay procedures
- 7: Measurement of trypsin inhibitor activity of hexane defatted SBM samples
- 8: Measurement of trypsin inhibitor activity of select commercial SBM samples
- 9: Measurement of TI activity using a microtiter plate
- 10: Conclusions
- Acknowledgments
- References
- Section II: Metabolite
- Chapter Eight: Strategies to study the metabolic origins of specialized plant metabolites: The specialized 1,4-naphthoquinones
- Abstract
- 1: Introduction
- 2: Strategies to study the metabolic origins of specialized metabolites
- 3: Conclusions and future directions
- Acknowledgments
- References
- Chapter Nine: A liquid chromatography-mass spectrometry-based metabolomics strategy to explore plant metabolic diversity
- Abstract
- 1: Introduction
- 2: Sample harvesting and homogenization
- 3: Metabolite extraction
- 4: Data acquisition
- 5: Data analysis
- Acknowledgments
- References
- Chapter Ten: Quantification of plant cardenolides by HPLC, measurement of Na+/K+-ATPase inhibition activity, and characterization of target enzymes
- Abstract
- 1: Introduction
- 2: Rationale
- 3: Plant sample preparation
- 4: HPLC analysis of cardenolide abundance
- 5: Assays of Na+/K+-ATPase inhibition by plant extracts
- 6: Inhibition of Na+/K+-ATPase from insect nervous tissue
- Acknowledgments
- References
- Chapter Eleven: Ex vivo metabolomics—A hypothesis-free approach to identify native substrate(s) and product(s) of orphan enzymes
- Abstract
- 1: Introduction
- 2: Materials
- 3: Methods
- 4: Notes
- Acknowledgments
- References
- Chapter Twelve: Metabolite fingerprinting: A powerful metabolomics approach for marker identification and functional gene annotation
- Abstract
- 1: Introduction
- 2: Materials
- 3: Methods
- 4: Notes
- Acknowledgments
- References
- Section III: Environment
- Chapter Thirteen: Controlled environments for cannabis cultivation to support “omics” research studies and production
- Abstract
- 1: Introduction
- 2: Equipment and other resources
- 3: Reagents
- 4: Supplies
- 5: Preparing growing areas
- 6: Preparing mother plants
- 7: Obtaining clones and initial aeroponic propagation
- 8: Hardening clones prior to greenhouse growth
- 9: Vegetative growth period in the greenhouse
- 10: Early flowering period in the greenhouse
- 11: Late flowering period in the greenhouse
- 12: Flower harvest
- 13: Conclusions and additional comments
- References
- Chapter Fourteen: Standard operating procedures for the comprehensive and reliable analysis of cannabis terpenes
- Abstract
- 1: Introduction
- 2: Equipment
- 3: Equipment, accessories and consumables
- 4: Equipment, supplies, and reagents for sample processing
- 5: Sample processing for headspace analysis without tissue homogenization
- 6: Sample processing for headspace analysis with tissue homogenization
- 7: Sample processing for solvent extraction with tissue homogenization
- 8: Autosampler settings for headspace analysis
- 9: Autosampler settings for headspace SPME analysis
- 10: Autosampler settings for liquid sample injection
- 11: GC settings for separating terpenes over an HP5-MS column
- 12: GC settings for separating terpenes over a DB-WAX column
- 13: GC settings for separating terpene enantiomers over a Cyclodex-B column
- 14: Settings for GC–MSD data acquisition
- 15: Settings for FID data acquisition
- 16: Generating calibration curves with authentic standards
- 17: Setting up an automated data analysis method
- 18: Application Example 1: Impact of different sample processing methods on terpene profiles
- 19: Application Example 2: Using comprehensive terpene analyses to address common peak mis-annotations
- 20: Conclusions and outlook
- References
- Chapter Fifteen: Isolation of novel chemical components and their plant target proteins under selenium stress
- Abstract
- 1: Introduction
- 2: Chemical screening under selenate stress conditions
- 3: Characterizing the selected candidate chemicals
- 4: Identification of chemical-binding target proteins in plants
- 5: Characterization of the interaction between selected chemical compounds and target proteins
- 6: Summary
- Acknowledgments
- References
- Chapter Sixteen: Imaging systemic calcium response and its molecular dissection using virus-induced gene silencing
- Abstract
- 1: Introduction
- 2: Before you begin
- 3: Materials and equipment
- 4: Cloning with VIGS vectors, the tobacco rattle virus
- 5: Agroinfiltration into N. benthamiana and A. thaliana and silencing confirmation
- 6: GCaMP imaging
- 7: GCaMP analysis
- 8: Summary and conclusions
- Acknowledgments
- References
- Chapter Seventeen: Analysis of plant flooding response
- Abstract
- 1: Introduction
- 2: Partial and full submergence with plants grown in pots
- 3: Partial and full submergence in petri dishes
- 4: Waterlogging in pots
- 5: Measurement of growth-related parameters from leaves
- 6: Measurement of chlorophyll and carotenoid from leaves
- 7: Measurement of anthocyanin from leaves
- 8: Measurement of malondialdehyde from leaves
- 9: Measurement of molecular markers for flooding stress
- 10: Summary and conclusions
- Acknowledgments
- References
- No. of pages: 504
- Language: English
- Edition: 1
- Volume: 680
- Published: January 27, 2023
- Imprint: Academic Press
- Hardback ISBN: 9780443185847
- eBook ISBN: 9780443185854
JJ
Joseph Jez
Prof. Jez received his B.S. in biochemistry from Penn State University (1992), a Ph.D. in biochemistry & molecular biophysics from the University of Pennsylvania (1998), and was an NIH-NRSA postdoctoral fellow at the Salk Institute for Biological Studies (1998-2001). After working as a research scientist at Kosan Biosciences (2001-2002), he started his research group at the Donald Danforth Plant Science Center and moved to the Department of Biology at Washington University in 2008. He has authored more than 160 papers and received a Presidential Early Career Award for Scientists and Engineers (2005), the Phytochemical Society of North America's Arthur Neish Young Investigator Award (2007), and a Fulbright Senior Specialist Award (2012) and was named as Howard Hughes Medical Institute Professor in 2014. Research in the Jez lab seeks to understand how environmental changes re-model biochemical pathways in plants at the molecular, cellular, and organism levels with the aim of engineering these systems to address agricultural and environmental problems. Current work in the lab employs a combination of structural biology, protein chemistry, and plant biology. He also launched the Biotech Explorers Program, which aims to introduce undergraduates to how teams in science can tackle real world problems using cross-disciplinary approaches.
Affiliations and expertise
Department of Biology, Washington University in St. Louis, USA