دانلود کتاب Microbial Proteomics: Development in Technologies and Applications

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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
Western Blotting
Enzyme-Linked Immuno Sorbent Assay
Immunohistochemistry
Mass Spectrometry
Isotope-coded Affinity Tag Labeling
Stable Isotope Labeling by/with Amino Acids in Cell Culture
Isobaric Tags for Relative and Absolute Quantitation
X-ray Crystallography
Nuclear Magnetic Resonance Spectroscopy
PROSPECTIVE DIRECTION
CONSENT FOR PUBLICATION
CONFLICT OF INTEREST
ACKNOWLEDGEMENTS
REFERENCES
Subject Index