Note: Intro -- Contents -- List of Contributors -- Chapter-1 -- Introduction -- Mass Spectrometry and Microbiology -- Chapters Included in This Book -- Emerging MS Methods and Technologies Not Covered Here -- Perspective -- Disclaimer -- References -- Part I -- Methodology and Techniques -- Chapter-2 -- Methods and Instrumentation inMass Spectrometry for the Differentiation of Closely Related Microorganisms -- Introduction -- Selectivity and Specificity in the Analysis of Microorganisms with MS -- MS Instrumentation -- MALDI and MALDI-MS Instrumentation -- TOF Mass Analyzer -- ESI and ESI-MS Instrumentation -- Quadrupole-Based Mass Analyzers -- Orbitrap Mass Analyzer -- MS-Based Methods and Instrumentation for the Differentiation of Closely Related Bacteria: Strain Level and Antibiotic Resistant -- Profile-Based Techniques for Strain-Level Differentiation -- Increasing the Reproducibility of the MALDI-MS Measurement -- Increasing the Selectivity in Protein Biomarkers Detection -- Top-Down Proteomic Approaches -- Differentiation and Detection of Antibiotic-Resistant Bacteria -- Conclusions -- References -- Chapter-3 -- Sample Preparation Methods for the Rapid MS Analysis of Microorganisms -- Enrichment Methods -- Enrichment of Microbial Cells/Biomarkers Involving Non-covalent Interactions -- Cells -- Biomarkers -- Enrichment of Cells/Biomarkers Involving Covalent Interactions -- Cells -- Biomarkers -- Immuno-Affinity Enrichment of Microbial Cells/Biomarkers -- Cells -- Biomarkers -- Cell Lysis -- Chemical Methods -- Physical Methods -- Separation of Cells and Biomarkers -- Intact Cells -- Biomarkers -- Sample Preparation for MALDI-MS -- References -- Chapter-4 -- Advantages Offered by Proteomic Strategies for Rapid Biodetection -- Identification of Components in Mixtures -- Rapid Detection of Genetic Engineering in Bacteria. , Characterizing Bacteria with Unsequenced Genomes -- Going Forward -- References -- Chapter-5 -- Bottom-Up Proteomics Methods for Strain-Level Typing and Identification of Bacteria -- Introduction -- Cell Harvesting and Protein Extraction -- Cell Lysis and the Preparation of Whole Cell Protein Extracts -- Preparation of Subcellular Fractions -- Outer Membrane Proteins -- Surface Layer Proteins -- Preparation of Flagella -- Extracellular Proteins -- Processing of Bacterial Proteins for Bottom-Up Proteomics Analysis -- Cell Shaving -- Protein Digestion Methods -- Solubilization and Denaturation of Proteins -- Reduction of Disulfide Bonds and Alkylation of Reduced Cysteines -- Protein Digestion Conditions -- Sample Digestion Strategies -- Liquid Phase Separation and Ionization of Peptides Followed by Acquisition of Tandem Mass Spectra -- Liquid Chromatography-ESI-MS -- Capillary Electrophoresis-ESI-MS -- Liquid Chromatography MALDI-MS/MS -- Database (DB) Construction and Searching -- Bacterial DBs -- DBs of Virulence Factors, Toxins, and Antibiotic Resistance Determinants -- Creation/Correction of Microbial Protein DBs Through Re-sequencing and Analysis of Genomes -- Custom DBs of E. coli and Salmonella Flagellins -- Search Engines -- Setting Search Parameters -- DB Searches -- Processing of DB Search Results -- Subspecies Differentiation and Strain-Level Typing of Bacteria Based on Searching Protein DBs with Peptide MS/MS Spectra -- Classification and Identification of Bacteria Based on the Number of Shared Peptides -- Peptide-to-Taxa Assignments: Determination of the Closest Neighbor -- Analysis of Subproteomes -- Confirmation of the Taxonomic Position of an Unknown Strain -- Relationship Between the Fraction of Shared Peptides (FSP) and Conservation of the Genome/Proteome. , Genomic Interrelationships Among Unknown Strains Revealed by Shotgun Proteomics -- Discrimination of Microbial Strains Based on Typing of Flagellin and Surface Layer Proteins -- Typing of E. coli and Salmonella Strains Based on Flagellin H Antigen Sequences -- Typing of Lactobacillus Strains Based on Surface Layer (S-Layer) Protein Sequences -- Discrimination of Strains Based on Antibiotic Resistance -- Concluding Remarks -- References -- Chapter-6 -- Maximizing the Taxonomic Resolution of MALDI-TOF-MS-Based Approaches to Bacterial Characterization: From Culture Conditions Through Data Analysis -- Introduction -- Overview of MALDI-TOF MS Profiling of Bacteria -- Library-Based Approaches -- Bioinformatics-Enabled Approaches -- Successes at the Genus and Species Levels -- Strain-Level Characterization: Successes, Challenges, and Strategies -- Commercially Available Software -- Assessing Strain-Level Performance -- Objectives -- Reproducibility -- Group Separation/Performance Metrics -- Score -- Jackknife/Bootstrapping/Threshold Cutoffs -- Culture Conditions -- Medium Type -- Medium Form (Broth/Agar) -- Sample Preparation -- Intact Cells -- Protein Extracts -- Pretreatment to Enhance Taxonomic Resolution -- Data Acquisition -- Data Analysis -- Summary -- Acknowledgments -- References -- Part II -- Subspecies Discrimination -- Chapter-7 -- Modulation of the Discriminatory Power of MALDI-TOF MS Profiling for Distinguishing Between Closely Related Bacterial Strains -- Introduction -- Differentiation Between Strains of L. acidophilus Group Grown under Different Cultivation Conditions -- Background -- Protocol -- Results -- Summary -- The Influence of Cultivation Conditions on Distinguishing Between Strains of Selected Mycobacterium spp. -- Background -- Protocol -- Results -- Summary. , Modulation of the Discriminatory Power Using an Alternative Matrix Solution -- Background -- Protocol -- Results -- Summary -- Modulation of the Discriminatory Power Using Microwave-Assisted Proteolysis -- Background -- Protocol -- Results -- Summary -- Conclusions -- References -- Chapter-8 -- Discriminatory Power of MALDI-TOF Mass Spectrometry for Phylogenetically Closely Related Microbial Strains -- Introduction -- Materials and Methods -- Sample Preparation -- MALDI-TOF Mass Spectrometry -- Data Analysis -- Staphylococcus Aureus -- Population Structure and Typing of S. aureus (Clonal Complexes) -- MS Biomarkers for Strain or CC Allocation of S. aureus/MRSA -- MS Biomarkers for Predicting Virulence Genes and Methicillin Resistance of S. aureus/MRSA -- Enterococcus faecium -- Population Structure and Typing of E. faecium -- MS Biomarkers for Strain or CC Allocation of E. faecium and Prediction of Vancomycin Resistance -- Differentiation of Bacillus anthracis, Bacillus cereus sensu stricto and Bacillus thuringiensis -- Summary and Outlook -- References -- Chapter-9 -- MALDI-TOF MS As a Novel Tool for Dereplication and Characterization of Microbiota in Bacterial Diversity Studies -- An Introduction to Dereplication in Bacterial Diversity Studies -- The Use of MALDI-TOF MS for Dereplication in Environmental Microbiology -- The Use of MALDI-TOF MS for Dereplication in Food Microbiology -- MALDI-TOF MS Can Combine Dereplication and Identification -- Detection of Taxonomic Novelty -- MALDI-TOF MS As a Dereplication Tool in Culturomics -- The Influence of Experimental Factors on MALDI-TOF Mass Spectra Generated -- Dereplication at an Infraspecific Level? -- Future Perspectives -- References -- Chapter-10 -- Bacterial Identification at the Serovar Level by Top-Down Mass Spectrometry -- Introduction -- Methods -- Bacterial Strains. , Extraction of Cellular Proteins -- HPLC of Intact Proteins -- LC-MS and Data Analysis -- MS Data Analysis -- Top-Down LC-MS/MS -- Top-Down Data Analysis -- Results and Discussion -- Intact Protein Expression Profiles -- Top-Down Protein Identification -- Proteogenomics -- Multiplexed Serovar Identification of Semi-blinded Isolates -- Conclusion -- References -- Part III -- Drug Resistance Monitoring and Assays -- Chapter-11 -- Rapid Profiling of Human Pathogenic Bacteria and Antibiotic Resistance Employing Specific Tryptic Peptides as Biomarkers -- Introduction -- Library-Based Approaches -- Proteomics-Based Approaches -- Approaches Based on Tryptic Peptides Toward Identification and Typing of Pathogens Below the Species Level -- Exploiting MALDI-TOF/TOF MS for Discrimination of Subspecies: In Search of Microorganism-Specific Tryptic Peptides -- Experimental Procedure -- Identification of Antibiotic Resistance Mechanisms in Bacteria Using Tryptic Peptides -- Limitations and Future Perspectives -- References -- Chapter-12 -- Detection of β-Lactamases and Their Activity Using MALDI-TOF MS -- β-Lactamases -- Detection of β-Lactam Hydrolysis -- Identification of β-Lactamases Using Inhibitors -- Comparison with Carba NP and Spectrophotometric Assays -- Automated Detection -- Detection of β-Lactamase Types -- Conclusion -- References -- Chapter-13 -- Stable-Isotope-Based Strategies for Rapid Determination of Drug Resistance by Mass Spectrometry -- Introduction -- Functional Assays for Establishing Drug Resistance -- Conclusion -- References -- Index.

Note: Intro -- Foreword -- Acknowledgments -- Contents -- Part I: Introduction -- Chapter 1: Collateral Values: The Natural Capital Created by Landscapes of War -- 1.1 A Proposal -- 1.2 Battlefields -- 1.3 Borderlands -- References -- Part II: Battlefields -- Chapter 2: Rethinking Resources in Our National Battlefields -- 2.1 Battlefields' Natural Capital -- 2.2 Identifying Priorities: Why Protect Public Lands -- 2.3 The Early Years of Preservation: Battlefields for Historical Preservation -- 2.4 The Early Years of Preservation: National Parks for Conservation and Recreation -- 2.5 National Battlefields: Renewed Attention During the Civil War's Semicentennial -- 2.6 National Parks: Negotiating Two World Wars -- 2.7 The Civil War Centennial: The Battle Over Historical Memory Intensifies -- 2.8 A Consumer's Republic: Tourism and Its Discontents -- 2.9 NPS Changing Course -- 2.10 Battlefields: Historic Preservation Meets Environmental Protection -- 2.11 The Future -- References -- Chapter 3: Registering English Battlefields: The Constructive Conservation of Historic Environments -- 3.1 Introduction -- 3.2 A Brief Overview of England's Military History -- 3.3 Conservation Policy and the Realization of Battlefield Significance -- 3.3.1 The Ambiguities of Battlefield Protection -- 3.3.2 Constructive Conservation -- 3.4 Registration Criteria and Battlefield Designation -- 3.5 Naseby Battlefield -- 3.5.1 Ecosystems & -- Services Provided -- 3.5.1.1 Hedges -- 3.5.1.2 Wetlands -- 3.5.2 Management -- 3.5.2.1 Ownership -- 3.5.2.2 Interpretive Features -- 3.5.3 Threats -- 3.5.4 Naseby Land Cover Assessment -- 3.6 Bosworth Battlefield -- 3.6.1 Ecosystems & -- Services Provided -- 3.6.1.1 Grasslands -- 3.6.1.2 Woodlands -- 3.6.1.3 Wetlands -- 3.6.2 Management -- 3.6.2.1 Ownership -- 3.6.2.2 Attractions and Amenities -- 3.6.3 Threats. , 3.6.4 Land Cover Assessment -- 3.7 Maldon Battlefield -- 3.7.1 Ecosystems & -- Services Provided -- 3.7.1.1 Mudflats -- 3.7.1.2 Salt Marsh -- 3.7.1.3 Estuary -- 3.7.1.4 Intertidal Zone -- 3.7.2 Management -- 3.7.2.1 Ownership -- 3.7.2.2 Visitation -- 3.7.3 Threats -- 3.7.4 Land Cover Assessment -- 3.8 Conclusions -- References -- Chapter 4: Old Forts and New Amenities in the Southern Plains -- 4.1 Introduction -- 4.1.1 Forts Are Valuable Protected Places -- 4.1.2 Background on Indian Wars and Forts -- 4.1.3 How the Forts Became Protected Places -- 4.2 Physical Geography, Land Use, and Ecoregions of the Forts -- 4.3 Current Ecosystem Services of the Southern Plains Forts -- 4.3.1 Classification of Ecosystem Services -- 4.3.2 Provisioning Services -- 4.3.2.1 Habitat -- 4.3.2.2 Food -- 4.3.2.3 Raw Materials and Energy -- 4.3.2.4 Fresh Water -- 4.3.3 Regulating Services -- 4.3.3.1 Climate and Air Quality -- 4.3.3.2 Water Quality and Flood Control -- 4.3.3.3 Soil Protection/Fertility -- 4.3.3.4 Pollinaton -- 4.3.4 Cultural Services -- 4.3.4.1 Recreation for Mental and Physical Health -- 4.3.4.2 Aesthetics and Inspiration -- 4.3.4.3 Identity and Spirituality -- 4.3.4.4 Tourism -- 4.4 Concluding Remarks: Forts Then and Now -- References -- Chapter 5: The Conflict Landscape of Verdun, France: Conserving Cultural and Natural Heritage After WWI -- 5.1 Introduction -- 5.2 Disturbance and Divergent Paths of Recovery: The Western Front of the Great War -- 5.3 The Verdun Battlefield as an Object of Study -- 5.3.1 Verdun: Study Area -- 5.3.2 Verdun: History -- 5.4 Effects of the Fighting on Local Environment -- 5.5 Land Management in the Aftermath of the War -- 5.6 Present-Day Landscapes Seen by Airborne LiDAR -- 5.7 Modern Recognition of Verdun's Environmental Value -- 5.8 Conservation and Valorization Issues -- 5.9 Conclusions -- References. , Chapter 6: The Ecosystem Service Impacts from Invasive Plants in Antietam National Battlefield -- 6.1 Introduction -- 6.2 Stressor-Response Functions -- 6.2.1 Ailanthus altissima -- 6.2.2 Rosa multiflora -- 6.2.3 Celastrus orbiculatus -- 6.2.4 Alliaria petiolata -- 6.3 Ecosystem Services Impacted by Invasive Plants -- 6.3.1 Casual Visitors -- 6.3.2 Avid Recreationists -- 6.3.3 Neighbors -- 6.3.4 Distant and Non-use Beneficiaries -- 6.4 Conclusions: Managing Biological Invasions to Promote Ecosystem Services in Battlefield Landscapes -- References -- Part III: Borderlands -- Chapter 7: Valuing the Wounds of War: Korea's DMZ as Nature Preserve -- 7.1 Introduction -- 7.2 Making the DMZ -- 7.3 Life in the DMZ -- 7.4 DMZ to TBPP -- 7.5 Out of War, Peace -- References -- Chapter 8: A Casualty of Peace? Lessons on De-militarizing Conservation in the Cordillera del Condor Corridor -- 8.1 Conflict Background -- 8.2 The Key Stakeholders -- 8.3 From Macro-conflicts to Micro-conflicts -- 8.4 The Mining Enclaves -- 8.5 Conclusion -- References -- Chapter 9: Legitimizing Militarization or Legitimate Conservation? Collateral Value and Landscapes of the Iron Curtain Borderlands -- 9.1 Introduction -- 9.2 From Death Strip to Green Belt -- 9.3 Military Environmentalism, or Ecological Militarization -- 9.4 Pulling Back the Curtain on Green Militarization -- 9.5 Critiquing Military Environmentalism -- 9.6 Collateral Values and Militarized Landscapes -- 9.7 Memory, Meaning, and Conservation -- 9.8 Curation of Cultural Landscapes -- References -- Chapter 10: From Buffer Zone to National Park: Afghanistan's Wakhan National Park -- 10.1 Introduction -- 10.2 How the Wakhan Corridor Came to Be -- 10.3 From Buffer Zone to National Park -- 10.4 The People of Wakhan National Park -- 10.5 Current Environment -- 10.6 Wildlife -- 10.7 Development of Wakhan National Park. , 10.8 Benefits of Wakhan National Park to Local People -- 10.9 Challenges -- References -- Chapter 11: Guantánamo 2.0: Transforming Gitmo into a Peace Park and Ecological Research Center -- 11.1 Introduction -- 11.2 History -- 11.3 Natural Assessment -- 11.3.1 Plants and Habitats -- 11.3.2 Reptiles -- 11.3.3 Mammals -- 11.3.4 Birds -- 11.3.5 Marine Species -- 11.3.6 Ecosystem Services -- 11.3.7 Conservation Concerns -- 11.4 Future Scenarios -- 11.4.1 Research Center -- 11.4.2 Peace Park -- 11.5 Proposal Response -- References -- Part IV: Synthesis -- Chapter 12: Battlefields and Borderlands: The Past, Present and Future of Collateral Values -- 12.1 Collateral Values -- 12.2 The Past and Present of Collateral Values -- 12.3 The Future of Collateral Values -- References -- Index.