Microbial Proteomics : Development in Technologies and Applications.

Cover -- Title -- Copyright -- End User License Agreement -- Contents -- Foreword -- Preface -- ACKNOWLEDGEMENTS -- About the Editor -- Dedication -- List of Contributors -- Microbial Biofilm and Drug Resistance: A Proteomic Approach -- Sarika Sharma1 and Sandeep Sharma2,* -- INTRODUCTION -- The Process of Biofilm Formation -- Attachment -- Micro-Colony Formation -- Detachment -- Mechanism of Biofilm Resistance against Antimicrobials -- Limited Penetration of Drugs Due to Glycocalyx -- Enzyme-Mediated Resistance -- State of Metabolism and Rate of Growth in Biofilms -- Genetic Adaptations -- Efflux Pumps -- Quorum Sensing -- TARGET PROTEINS TO STUDY BIOFILM -- Proteins Involved in Cellular Metabolism -- Transporter Proteins -- Stress-responsive Proteins -- Proteomic Techniques to Study Biofilm -- Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) -- Isotope-coded Affinity Tags (ICAT) -- Isobaric Tags for Relative and Absolute Quantification (iTRAQ) -- Tandem Mass Tags (TMT) -- Isotope-coded Protein Label (ICPL) -- Bioorthogonal Noncanonical Amino Acid Tagging (BONCAT) -- Future Prospectus -- CONCLUSION -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES -- Past, Present, and Future of Gel-Based Microbial Proteomics -- Munna Lal Yadav1,*, Arvind K. Verma1, Preeti Rawat1, Abhishek Parashar1, Divakar Sharma2, Sudarshan Kumar1 and Ashok K. Mohanty1,* -- INTRODUCTION -- PROTEIN SAMPLE PREPARATION FROM MICROBIAL SOURCE -- CLEAN-UP AND QUANTIFICATION OF PROTEINS -- GEL ELECTROPHORESIS OF PROTEINS -- TYPES OF PAGE -- SDS-PAGE (Sodium Dodecyl Sulphate-polyacrylamide Gel Electrophoresis) -- Tricine SDS-PAGE -- Native Page -- SDD-AGE (Semi Denaturing Detergent-agarose Gel Electrophoresis) -- 2D-PAGE (Two-dimensional Gel Electrophoresis) -- Isoelectric Focusing (First Dimension) -- SDS-PAGE (Second Dimension).

2D-DIGE (TWO DIMENSIONAL DIFFERENCE IN-GEL ELECTROPHORESIS) -- ANALYSIS OF 2D GEL AND DIGE GEL BY DIFFERENT SOFTWARE -- 2D Gel Analysis using Image Master 2D Platinum -- Evaluation of DIGE Gels using DeCyder -- COMPARISON BETWEEN IEF, SDS-PAGE, 2D-PAGE, AND DIGE -- MICROBIAL PROTEOMICS IN DAIRY PROCESSING -- FUTURE PERSPECTIVES OF GEL BASED MICROBIAL PROTEOMICS -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES -- Liquid Chromatography-Mass Spectrometry (LCMS): An Advanced Tool for the Microbial Proteomics Analysis -- Pranav Kumar Prabhakar* -- INTRODUCTION -- MASS SPECTROSCOPY (MS) -- Shotgun MS-Based Proteomics -- Shotgun MS-Based Quantitative Proteomics -- EXPERIMENTAL PROCEDURE -- i. Sample Preparation -- ii. Mass Spectrometry -- DATA ACCOMPLISHMENT -- PROTEIN IDENTIFICATION -- USE OF MALDI-TOF IN MICROBIAL IDENTIFICATION AND ANTIMICROBIAL RESISTANCE -- CONCLUSION -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES -- Functional Annotation and Enrichment of Microbial Proteins Using Systems Biology: Tools and Applications -- Aditya Arya* and Vivek Dhar Dwivedi -- INTRODUCTION -- IMPORTANCE OF ANNOTATION AND ENRICHMENT -- EMERGING TRENDS IN GENOMICS -- EMERGING TRENDS IN PROTEOMICS -- ANNOTATION OF MICROBIAL PROTEINS -- SYSTEMS BIOLOGY AND ANNOTATIONS -- FUTURE GUIDELINES -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES -- Emerging Paradigm of Post-translational Modifications in Microbes: An Undefeatable Weapon -- Arpana Sharma1,2, Chandrajeet Singh1, Gopika Raval2, Kruti Dave2, Ankita Mathur3, Juhi Sharma4 and Divakar Sharma5,* -- INTRODUCTION -- What are the General Characteristics of Bacteria and the Significance of the Study? -- What are the Post-translation Modifications?.

The Biological Significance of Post Translation Modifications and their Implications -- PTM Stories Unfolded in Some Pathogenic Organisms -- Role of PTMs in Host-pathogen Interactions -- PTM Role in Drug Resistance -- Mechanisms of Bacterial Drug Resistance -- Different PTMs Present in Bacteria -- Acetylation -- Phosphorylation -- Hydroxylation -- Lipidation -- AMPylation -- ADP-Ribosylation -- Glycosylation -- Carboxylation -- Nitrosylation -- Protein Pupylation and ubiquitin- like Modifications -- Proteomic Approaches Used in Exploration of Microbial PTMs -- Technical Challenges in the PTM Which Needs Immediate Attention -- The Lessons Learned from the Past and Giving Way to Future Solutions -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES -- Pupylation: A Novel Proteolysis Pathway in Prokaryotes Functionally Reminiscent to Eukaryotic Ubiquitination -- Yogesh K. Dhuriya1 and Divakar Sharma2,* -- INTRODUCTION -- Bacterial Proteasome: An Evolutionary Precursor of Eukaryotic Proteasome -- Structure - Mycobacterium Proteasome -- Mpa -Mycobacterium Proteasome ATPase -- Pupylation -Mark of Intrinsic Protein Demolition -- Reversed Pupylation -Depupylation -- Recycling of Pup - Proteasome Regulation -- Pup-proteasome System (PPS) - Bacterial Physiology -- Proteasome - Stress Sensor Machine -- Cpa (Cdc48-like protein of actinobacteria) -A Novel Proteasome Interacting Molecule -- CONCLUSION AND FUTURE PROSPECTS -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES -- Overview and Challenges in Proteins Sample Preparation for 2-DGE in Bacterial Proteomics -- Divakar Sharma1 ,*, Juhi Sharma2, Nirmala Deo3 and Deepa Bisht3 -- INTRODUCTION -- Overview, Challenges and Probable Solutions -- Enrichment and Extraction of the Complete Proteome from Bacteria -- Protein Precipitation Strategies.

SDS-Tri Chloroacetic Acid (TCA)-Acetone Precipitation for Cell Lysate and Cytosolic Proteins -- Acetone Precipitation for Cell Lysate and Cytosolic Proteins -- Ammonium Sulfate Precipitation for Secretory/Culture Filtrate Proteins -- SDS-Tri Chloroacetic Acid (TCA)-Acetone Precipitation for Secretory/Culture Filtrate Proteins -- Isolation and Fractionation of Cell Membranes Proteins through Ultracentrifugation -- Effective Enrichment and Fractionation of Lipophilic Proteins without Ultracentrifugation -- CONCLUSION AND FUTURE PROSPECTS -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES -- Proteomics Based Biomarker Development Against Infections: An Overview -- M. Madhan Kumar1,*, Vivek Kumar Gupta1 and Divakar Sharma2 -- INTRODUCTION -- Proteins and Their Role in Infectious Diseases -- Life is the Mode of Action of Proteins - Friedrich Engels [1] -- Techniques Used for Studying Protein-protein Interactions (PPI) -- In Silico Methods for Studying Protein-protein Interactions -- A Note on Biomarkers and Their Role in Infectious Diseases -- Challenges in Studying Protein-protein Interactions -- Protein Markers in Bacterial and Viral Infections - Pathogen and Host Perspectives -- Influenza -- Hepatitis C -- Dengue -- Human Immunodeficiency Virus -1 (HIV-1) -- Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) -- Search for Protein Markers in Bacterial Infections - Host and Pathogen Perspectives -- Use of Bacterial Markers for Typing Bacteria -- Determining Antibiotic Resistance -- Proteomics in Biomarker Discovery and Diagnostics -- Biomarkers in Diagnosis, Treatment and Prevention of Infectious Diseases -- THE WAY AHEAD - FUTURE PERSPECTIVES -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES.

Microbial Metalloproteome: Approaches and Biomedical Application in Microbial Antibiotics Resistance -- Saroj Sharma, Monalisa Tiwari and Vishvanath Tiwari* -- INTRODUCTION -- EMERGENCE OF METALLOPROTEOMICS -- CURRENT APPROACHES TO METALLOPROTEOMICS -- ROLE OF METALLOPROTEINS IN MICROBIAL DRUG RESISTANCE -- METAL INDUCIBLE MICROBIAL PROTEOME AND HOST-PATHOGEN INTERACTION -- TARGETING METALLOPROTEINS TO TARGET MICROBE -- CONCLUDING REMARKS AND FUTURE ASPECTS -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES -- Proteomics of Mycobacterium Tuberculosis: An Overview -- Anil Kumar Gupta1,3, Divakar Sharma2 and Amit Singh1,3,* -- INTRODUCTION -- Advancement of Mycobacterial Research through Proteomics -- PROTEOMICS AND PHYSIOLOGY OF M. TUBERCULOSIS -- Identification of New Enzymes -- New Substrates -- New Metabolic Pathways -- PROTEOMICS IN DEVELOPING NOVEL BIOMARKERS -- PROTEOMICS AND VACCINE DISCOVERY OF MYCOBACTERIUM TUBERCULOSIS -- PATHWAY OF TB VACCINE DEVELOPMENT -- PROTEOMICS AND HOST-PATHOGEN INTERACTION -- Host Cells and Environments for M. tuberculosis -- PROTEOMIC ANALYSIS OF MYCOBACTERIUM TUBERCULOSIS-INFECTED CELLS -- PROTEOMICS AND STRUCTURAL BIOLOGY -- STRUCTURE-BASED DRUG DISCOVERY -- Relationship between Proteomics and Genomics -- Utility of Proteomics in Drug Discovery -- CONCLUSION -- CONSENT FOR PUBLICATION -- CONFLICT OF INTEREST -- ACKNOWLEDGEMENTS -- REFERENCES -- Proteome Based Insights in Drug-Resistant Mycobacterium tuberculosis -- Apoorva Narain1, Surya Kant1, Rikesh Kumar Dubey2, Kanchan Srivastava1 and Anand Kumar Maurya3,* -- INTRODUCTION -- DRUG RESISTANT TUBERCULOSIS -- CLINICALLY RELEVANT MTB PROTEINS -- Antigens of 85 Complex -- Mpt64 -- ESAT-6 and CFP-10 -- PROTEOMIC ANALYSIS IN MYCOBACTERIA -- Sodium Dodecyl Sulphate-Poly Acrylamide Gel Electrophoresis.

Two Dimensional Gel Electrophoresis.

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Electronic reproduction. Ann Arbor, Michigan : ProQuest Ebook Central, 2024. Available via World Wide Web. Access may be limited to ProQuest Ebook Central affiliated libraries.