Chemical Tools in Microbiology 1
- 1st Edition, Volume 664 - March 22, 2022
- Imprint: Academic Press
- Editor: Erin E. Carlson
- Language: English
- Hardback ISBN:9 7 8 - 0 - 3 2 3 - 9 1 2 2 2 - 8
- eBook ISBN:9 7 8 - 0 - 3 2 3 - 9 1 1 3 0 - 6
Clinical Microbiology, Volume 664 in the Methods in Enzymology series, highlights new advances in the field with this new volume presenting interesting chapters on a variety of top… Read more
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Request a sales quoteClinical Microbiology, Volume 664 in the Methods in Enzymology series, highlights new advances in the field with this new volume presenting interesting chapters on a variety of topics, including Synthesis of chemical probes to study bacterial adenylating enzymes, Fluoroquinolone-derived fluorescent probes for studies of bacterial penetration and efflux, Combining informatics with ABPP to identify serine hydrolyses in bacteria, A Ligand Selection Strategy Identifies Chemical Probes Targeting the Proteases of SARS‐CoV‐2, Activity-based probes for bacterial histidine kinases, Metabolomic approaches to enzyme function and pathway discovery, Identification of bile salt hydrolase activity in gut microbiota, and much more.
Other chapters cover Multiplex fluorescence screening and identification using multiplex TMT, Customized Peptidoglycan Surfaces to Investigate Innate Immune Recognition via SPR, Site-Specific Siderocalin Binding to Ferric and Ferric-Free Enterobactin As Revealed by Mass Spectrometry, Proteomics of short-chain fatty acid probes in Salmonella, Development and application of highly sensitive labeling reagents for amino acids, and a variety of other timely topics.
- 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 Chemical Microbiology
Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists
- Cover image
- Table of Contents
- Series Page
- Copyright
- Contributors
- Preface
- Chapter One: Integration of bioinformatic and chemoproteomic tools for the study of enzyme conservation in closely related bacterial species
- Abstract
- 1: Introduction
- 2: Integration of bioinformatics with ABPP
- 3: Protocols
- 4: Summary
- References
- Chapter Two: A ligand selection strategy to customize small molecule probes for activity-based protein profiling (LS-ABPP)
- Abstract
- 1: Introduction
- 2: Ligand selection strategy for activity-based protein profiling (LS-ABPP)
- 3: Protocol
- 4: Summary
- Acknowledgments
- References
- Chapter Three: Activity-based ATP analog probes for bacterial histidine kinases
- Abstract
- 1: Introduction
- 2: ATP analog activity-based probes
- 3: Gel-based activity assays
- 4: Concentration-dependent kinetics assay
- 5: CuAAC reaction conditions
- 6: Conclusion
- Acknowledgments
- References
- Chapter Four: BSH-TRAP: Bile salt hydrolase tagging and retrieval with activity-based probes
- Abstract
- 1: Introduction
- 2: General methods
- 3: Synthesis of bile salt hydrolase (BSH) activity-based probe
- 4: Application of BSH-TRAP to cultured bacterial strains
- 5: Application of BSH-TRAP to mouse gut microbiome samples
- 6: General considerations for BSH-TRAP
- Acknowledgments
- References
- Chapter Five: Detecting and identifying glycoside hydrolases using cyclophellitol-derived activity-based probes
- Abstract
- 1: Introduction
- 2: Analytical tools for activity-based protein profiling
- 3: Sample preparation
- 4: In-gel fluorescence-based activity-based-protein profiling for glycoside hydrolase detection
- 5: Identification of activity-based probe targets by peptide mass spectrometry following affinity-based enrichment
- 6: Conclusion
- Acknowledgments
- References
- Chapter Six: Chemical proteomics for identifying short-chain fatty acid modified proteins in Salmonella
- Abstract
- 1: Introduction
- 2: In-gel profiling of SCFA-reporter labeled Salmonella total cell lysates
- 3: Label-free quantitative proteomics analysis of SCFA-reporter Salmonella total cell lysates
- 4: CRISPR-Cas9 editing and epitope-tagging of proteins in Salmonella
- 5: Validation of SCFA-reporter protein modification in Salmonella
- 6: Summary and outlook
- References
- Chapter Seven: Kinetic dissection of macromolecular complex formation with minimally perturbing fluorescent probes
- Abstract
- 1: Introduction
- 2: Experimental design and system considerations
- 3: Protocol and analysis
- 4: Summary
- References
- Chapter Eight: Mobilization of cryptic antibiotic biosynthesis loci from human-pathogenic Nocardia
- Abstract
- 1: Introduction
- 2: Materials and equipment
- 3: TAR cloning
- 4: Conclusions
- Acknowledgments
- References
- Chapter Nine: Assessing and utilizing esterase specificity in antimicrobial prodrug development
- Abstract
- 1: Introduction
- 2: Esterase activity assays with a variable alcohol component
- 3: Antimicrobial prodrug development
- 4: Prospectus
- References
- Chapter Ten: Identification of volatile producing enzymes in higher fungi: Combining analytical and bioinformatic methods
- Abstract
- 1: Volatile organic compound (VOC) analysis in fungi
- 2: Bioinformatic-aided identification of biosynthetic pathways of fungal VOCs
- References
- Chapter Eleven: Bile salt hydrolase profiling by fluorogenic probes in the human gut microbiome
- Abstract
- 1: Introduction
- 2: Existing ways of measuring BSH activity
- 3: Fluorogenic probes for BSH quantitation
- 4: Probe validation protocols
- 5: Fecal sample preparation
- 6: Fluorogenic assay protocol
- 7: Conclusions
- Acknowledgments
- References
- Chapter Twelve: Optimized APEX2 peroxidase-mediated proximity labeling in fast- and slow-growing mycobacteria
- Abstract
- 1: Introduction
- 2: Before you begin
- 3: Key resources table
- 4: Equipment
- 5: Step-by-step method details
- 6: Quantification and statistical analysis
- 7: Advantages
- 8: Limitations
- 9: Safety considerations and standards
- References
- Edition: 1
- Volume: 664
- Published: March 22, 2022
- No. of pages (Hardback): 306
- No. of pages (eBook): 306
- Imprint: Academic Press
- Language: English
- Hardback ISBN: 9780323912228
- eBook ISBN: 9780323911306
EC
Erin E. Carlson
Erin E. Carlson received her B.A. at St. Olaf College (Northfield, MN) in 2000. She went on to graduate studies funded by the NIH Predoctoral Biotechnology Training Program at the University of Wisconsin - Madison and earned a Ph.D. in organic chemistry in 2005 under the direction of Professor Laura L. Kiessling. Her graduate career focused on the design and synthesis of mechanistic probes and inhibitors for carbohydrate-binding proteins, concentrating on the study of UDP-galactopyranose mutase (UGM), an enzyme involved in cell wall biosynthesis of Mycobacterium tuberculosis.
Subsequently, Dr. Carlson was awarded an American Cancer Society Postdoctoral Fellowship for studies at The Scripps Research Institute with Professor Benjamin F. Cravatt. Carlson and Cravatt developed a global metabolite profiling strategy that utilizes chemoselective probes to enable enrichment and profiling of metabolites from complex biological systems. This technology, referred to as Metabolite Enrichment by Tagging and Proteolytic Release (METPR), facilitates the rigorous characterization of biochemical pathways through their most sensitive reporter, endogenous small molecules. In 2007, Dr. Carlson received an NIH Pathway to Independence Award (K99/R00) and joined the faculty at Indiana University in 2008. In the summer of 2014, she joined the faculty in the Chemistry Department at the University of Minnesota and was appointed as a Graduate Faculty member of the Department of Medicinal Chemistry, the Department of Biochemistry, Molecular Biology and Biophysics and the graduate program in Biomedical Informatics and Computational Biology in 2015.
Since the start of her independent career, she has won numerous awards including being named a Presidential Early Career Awards for Scientists and Engineers (PECASE) recipient, a Pew Biomedical Scholar, the NIH Director’s New Innovator Award, the Indiana University Outstanding Junior Faculty Award, the NSF CAREER Award, the Cottrell Scholar Award and was named a Sloan Research Fellow and an Indiana University Dean's Fellow. Professor Carlson has been highlighted in several videos including one produced by NBC in their Science Behind The News series, a fast-paced video series supported by the National Science Foundation. This piece was one of five videos highlighting work funded by NSF's Directorate for Mathematical and Physical Sciences. She was also featured in a "Brilliant Minds" video. Dr. Carlson was also named one of "Tomorrow's PIs" in the sixth annual issue of Genome Technology and received the Outstanding Postdoctoral Mentor Award from the University of Minnesota Postdoctoral Association in 2017.
Affiliations and expertise
Associate Professor, Department of Chemistry, University of Minnesota, USARead Chemical Tools in Microbiology 1 on ScienceDirect