Biochemical Pathways and Environmental Responses in Plants: Part C
- 1st Edition, Volume 683 - April 21, 2023
- Imprint: Academic Press
- Editor: Joseph Jez
- Language: English
- Hardback ISBN:9 7 8 - 0 - 4 4 3 - 1 3 1 9 7 - 4
- eBook ISBN:9 7 8 - 0 - 4 4 3 - 1 3 1 9 8 - 1
Biochemical Pathways and Environmental Responses in Plants: Part C, Volume 683 in the Methods in Enzymology series, highlights advances in the field. with this new volume presentin… Read more
Purchase options
Institutional subscription on ScienceDirect
Request a sales quoteBiochemical Pathways and Environmental Responses in Plants: Part C, Volume 683 in the Methods in Enzymology series, highlights advances in the field. with this new volume presenting chapters on topics including Preparation of hydroxycinnamoyl-CoA thioesters using recombinant 4-coumarate:coenzyme A ligase (4CL) for characterization of BAHD acyltransferases, Near-real time determination of BAHD acyl-coA transferase reaction rates, Bioinformatic tools for protein structure prediction and for molecular docking applied to enzyme active site analysis, Computational and biochemical methods to measure the activity of carboxysomes and protein organelles in vivo, Dirigent Proteins Family Function and Structure, Three-in-One Method for High-throughput plant multi-omics, amongst other timely topics.
Additional sections cover Analysis of isoprenyl-phosphates by liquid chromatography-mass spectrometry, Lignin/Lignan Biosynthesis Structure/Function, Comparison of TLC, HPLC, and direct infusion mass spectrometry methods for identification and quantification of diacylglycerol molecular species, Plant sphingolipid analysis, RNA-seq analysis of alternative pre-mRNA splicing mediated by photoreceptors in Physcomitrium patens, and much more.
- Provides the authority and expertise of leading contributors from an international board of authors
- Presents the latest release in Methods in Enzymology serials
- Updated release includes the latest information on Biochemical Pathways and Environmental Responses in Plants
Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists
- Cover image
- Title page
- Table of Contents
- Series Page
- Copyright
- Contributors
- Preface
- Section I: Protein
- Chapter One: Preparation of hydroxycinnamoyl-coenzyme A thioesters using recombinant 4-coumarate:coenzyme A ligase (4CL) for characterization of BAHD hydroxycinnamoyltransferase enzyme activities
- Abstract
- 1: Introduction
- 2: Preparation of hydroxycinnamoyl-CoA thioesters with recombinant 4CL1
- 3: Summary
- Acknowledgments
- References
- Chapter Two: Near-real time determination of BAHD acyl-coenzyme A transferase reaction rates and kinetic parameters using Ellman's reagent
- Abstract
- 1: Introduction
- 2: Measurement of BAHD hydroxycinnamoyltransferase reaction rates and determination of kinetic parameters
- 3: Summary
- Acknowledgments
- References
- Chapter Three: Tools for protein structure prediction and for molecular docking applied to enzyme active site analysis: A case study using a BAHD hydroxycinnamoyltransferase
- Abstract
- 1: Introduction
- 2: Protein structure prediction and model evaluation
- 3: Molecular docking of ligands into the protein model
- 4: Conclusions
- Acknowledgments
- References
- Chapter Four: Computational and biochemical methods to measure the activity of carboxysomes and protein organelles in vivo
- Abstract
- 1: Introduction
- 2: Molecular biology
- 3: Microscopy
- 4: Image analysis
- 5: Code repositories
- 6: Summary
- Acknowledgments
- References
- Chapter Five: Dirigent protein subfamily function and structure in terrestrial plant phenol metabolism
- Abstract
- 1: Introduction
- 2: Glycosylated DPs: Heterologous expression in yeast
- 3: Non-glycosylated DPs: Heterologous expression in E. coli
- 4: DP 3D crystallography
- 5: Summary and conclusions
- Acknowledgments
- References
- Section II: Metabolite
- Chapter Six: Three-in-one method for high throughput plant multi-omics
- Abstract
- 1: Introduction
- 2: Methods
- 3: Summary
- Funding and acknowledgements
- References
- Chapter Seven: Analysis of isoprenyl-phosphates by liquid chromatography-mass spectrometry
- Abstract
- 1: Introduction
- 2: Materials and equipment
- 3: Step-by-step method details
- 4: Expected outcomes
- 5: Quantification and statistical analysis
- 6: Advantages and limitations
- 7: Optimization and troubleshooting
- 8: Notes
- Acknowledgments
- References
- Chapter Eight: Comparison of TLC, HPLC, and direct-infusion ESI-MS methods for the identification and quantification of diacylglycerol molecular species
- Abstract
- 1: Introduction
- 2: Materials
- 3: Methods
- 4: Notes
- Acknowledgments
- References
- Section III: Environment
- Chapter Nine: RNA-seq analysis of alternative pre-mRNA splicing regulation mediated by photoreceptors in Physcomitrium patens
- Abstract
- 1: Introduction
- 2: Materials, reagents, and equipment
- 3: Methods
- 4: Data analysis and interpretation
- 5: Strengths and limitations of next-generation sequencing
- Acknowledgments
- References
- Chapter Ten: Monitoring lipid-protein interactions in planta using Förster resonance energy transfer
- Abstract
- 1: Introduction
- 2: FRET detection of the CFP-GAPC2 and TopFluor TMR-PA interaction in planta
- 3: Conclusion
- Acknowledgments
- References
- Chapter Eleven: Acetylene reduction assay for nitrogenase activity in root nodules under salinity stress
- Abstract
- 1: Introduction
- 2: Plant material preparation, including seed preparation, seed planting, watering conditions, harvesting, washing, and preparing roots for the assay
- 3: ARA assay setup
- 4: GC-FID/MS detection
- 5: Nitrogenase activity quantification
- Notes
- 6: Troubleshooting and Optimization
- 7: Conclusion
- Acknowledgments
- References
- Chapter Twelve: Using Hyper as a molecular probe to visualize hydrogen peroxide in living plant cells: An updated method
- Abstract
- 1: Introduction
- 2: Hyper stable expression in Arabidopsis and Tobacco with ratio-metric analysis
- 3: Hyper transient expression in tobacco leaves
- 4: Measuring intracellular H2O2 in Physcomitrium patens using the hyper ROS sensor
- Acknowledgments
- References
- Chapter Thirteen: Using DCP-Rho1 as a fluorescent probe to visualize sulfenic acid-containing proteins in living plant cells
- Abstract
- 1: Introduction
- 2: Use of a DCP-Rho1 probe to visualize in vivo sulfenylation in plants
- Acknowledgments
- References
- Edition: 1
- Volume: 683
- Published: April 21, 2023
- No. of pages (Hardback): 324
- No. of pages (eBook): 324
- Imprint: Academic Press
- Language: English
- Hardback ISBN: 9780443131974
- eBook ISBN: 9780443131981
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, USARead Biochemical Pathways and Environmental Responses in Plants: Part C on ScienceDirect