Advances in Biological Science Research: A Practical Approach

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Advances in Biological Science Research: A Practical Approach
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Contributors
Preface
Acknowledgments
1. Bioinformatics methods: application toward analyses and interpretation of experimental data
	1.1 Aim of the chapter
	1.2 DNA sequencing
	1.3 Identification of organisms from nucleotide sequence
		1.3.1 What is BLAST?
		1.3.2 Methods for nucleotide BLAST
		1.3.3 Interpretation of BLAST results
		1.3.4 Construction and interpretation of phylogenetic tree
		1.3.5 Sequence deposition
	1.4 Microbial ecology statistics
		1.4.1 Species composition/species richness
		1.4.2 Species abundance
			1.4.2.1 Example 1: illustration for species abundance
			1.4.2.2 Example 2: comparison of species abundance with richness
		1.4.3 Species diversity
			1.4.3.1 Similarity indices
			1.4.3.2 Dissimilarity indices
	1.5 Biostatistics
		1.5.1 Sampling statistics
		1.5.2 Testing of hypothesis
		1.5.3 Probability distribution
			1.5.3.1 Example
	1.6 Advanced bioinformatics tools in biological sciences
		1.6.1 Sequence analysis
		1.6.2 Phylogenetic analysis
		1.6.3 Sequence databases
	1.7 Conclusion
	References
2. Genome sequence analysis for bioprospecting of marine bacterial polysaccharide-degrading enzymes
	2.1 Introduction
	2.2 Marine polysaccharides and polysaccharide-degrading bacteria: an overview
	2.3 Identification of polysaccharide-degrading genes through genome annotation
	2.4 Identification of polysaccharide-degrading genes in newly sequenced bacterial genome: a guide for beginners
	2.5 Genome sequence analysis unravels organization of polysaccharide-degrading genes as polysaccharide utilization loci
	2.6 Genome annotation: a potential tool for the elucidation of glycometabolism pathways
	2.7 CAZy database: a promising tool for the classification of polysaccharide-degrading genes/enzymes identified in newly sequen ...
	2.8 Validation of computationally identified polysaccharide-degrading genes in the genomes of marine bacteria
	Acknowledgments
	References
3. Proteomics analysis of Mycobacterium cells: challenges and progress
	3.1 Introduction
	3.2 Proteome analysis of axenic mycobacteria
	3.3 Proteome analysis of mycobacteria-infected cells
	3.4 Proteome analysis of mycobacteria-containing host vacuoles
	3.5 Conclusion
	References
4. Plant proteomics: a guide to improve the proteome coverage
	4.1 Introduction
	4.2 Hurdles associated with plant proteins sample preparation for mass spectrometry–based proteomics
	4.3 Primary considerations to design suitable workflows for plant proteomics
		4.3.1 Effective protein sample preparation: extraction and recovery from difficult plant samples
			4.3.1.1 Sample harvesting
			4.3.1.2 Tissue homogenization and sample integrity
			4.3.1.3 Protein extraction in denaturing conditions
			4.3.1.4 Removal of biological contaminants and re-solubilization of proteins
		4.3.2 Contaminant removal from or during protein digestion
		4.3.3 Overcoming the high-dynamic range of protein concentrations for the discovery of low-abundant proteins
		4.3.4 Digestion of plant proteins
		4.3.5 Overcoming technical and biological variations
	4.4 Advances and applications in plant proteomics
		4.4.1 Proteogenomics to help annotation of open reading frames (ORFs) in newly sequenced genomes
		4.4.2 Understanding plant development and responses to environmental clues
	4.5 Conclusion and future perspective
	References
5. Structural analysis of proteins using X-ray diffraction technique
	5.1 Introduction
	5.2 Historical background
	5.3 X-ray crystallography
	5.4 Protein X-ray crystallography
	5.5 Advances in protein crystallography
	5.6 Case study: extended spectrum β-lactamases
	5.7 Conclusion
	Acknowledgments
	References
6. Technological advancements in industrial enzyme research
	6.1 Introduction
	6.2 Enzyme discovery
	6.3 Enzyme customization
	6.4 Improvement of existing enzymes through mutagenic approaches
		6.4.1 By site-directed mutagenesis
		6.4.2 By random mutagenesis
	6.5 High-throughput screening of genetic variants for novel enzyme production
	6.6 Immobilization of enzymes
	6.7 Enzyme inhibitor studies
	6.8 Enzyme promiscuity and multifunctional enzyme studies
	6.9 Sequence-dependent approach of the novel gene encoding the target enzyme/protein
	6.10 Function-based identification of the novel gene
	6.11 Identification of the novel gene by sequencing techniques
	6.12 Improvement of enzymatic catalysis by microbial cell surface display
	6.13 Conclusion
	References
7. Biotechnological implications of hydrolytic enzymes from marine microbes
	7.1 Introduction
	7.2 Applications of marine hydrolases
		7.2.1 Biorefineries
		7.2.2 Pharmaceuticals and cosmeceuticals
		7.2.3 Food industry
		7.2.4 Feed industry
		7.2.5 Biopolymer industry
		7.2.6 Detergent industry
		7.2.7 Textile industry
		7.2.8 Leather industry
		7.2.9 Paper and pulp industry
		7.2.10 Organic synthesis
		7.2.11 Waste treatment
		7.2.12 Nanoparticle synthesis
	7.3 Prospecting the use of hydrolytic enzymes from marine microbes
	References
	Further reading
8. Recent advances in bioanalytical techniques using enzymatic assay
	8.1 Introduction
		8.1.1 Why biosensors?
		8.1.2 Emergence of biosensors
	8.2 Classification of biosensors
		8.2.1 Enzyme biosensor
			8.2.1.1 Enzyme inhibition biosensor
		8.2.2 Overcoming limitations in enzyme-based biosensors
		8.2.3 Application of enzyme biosensor
	8.3 Enzyme biosensors for environmental monitoring
	8.4 Enzyme biosensors for food quality monitoring
	8.5 Future prospects and conclusions
	References
	Further reading
9. Microbial lectins: roles and applications
	9.1 Introduction
	9.2 Roles and mechanism of lectin action
	9.3 Applications of microbial lectins
		9.3.1 Lectins in diagnostics
		9.3.2 Lectins in bioremediation
		9.3.3 Lectins in bioflocculation
		9.3.4 Lectins in fluorescent staining
		9.3.5 Lectin and probiotics
	9.4 Conclusion
	References
	Further reading
10. Biodegradation of seafood waste by seaweed-associated bacteria and application of seafood waste for ethanol production
	10.1 Introduction
	10.2 Materials and methods
		10.2.1 Collection of marine seaweed samples
		10.2.2 Enrichment of Ulva-associated bacteria
		10.2.3 Isolation of calcium carbonate solubilizing marine Ulva-associated bacteria
		10.2.4 Investigating seafood waste (fish, crab, prawn waste) utilizing potential of selected calcium carbonate–solubilizing bacteria
			10.2.4.1 Preparation of crab/prawn shell and fish scale powder
			10.2.4.2 Microbial utilization of seafood waste as a sole source of carbon
		10.2.5 Agarase production by marine Ulva sp.–associated bacteria
		10.2.6 Production of protease by Ulva sp.–associated bacteria
		10.2.7 Phosphate solubilization by acid-producing Ulva sp.–associated bacteria
		10.2.8 Cellulase production by Ulva sp.–associated bacteria
		10.2.9 Production of chitinase by Ulva sp.–associated bacteria
		10.2.10 Degradation of fish/crab/prawn waste using microbial consortia developed using Ulva sp.–associated bacteria
		10.2.11 Identification of seaweed-associated bacteria
	10.3 Results and discussion
	10.4 Application of seafood waste for bioethanol production
	Acknowledgments
	References
11. Phosphate solubilization by microorganisms: overview, mechanisms, applications and advances
	11.1 Introduction
	11.2 Phosphate-solubilizing microorganisms: an overview
		11.2.1 Screening microorganisms for phosphate solubilization
	11.3 Phosphate solubilizing microorganisms: mechanisms
		11.3.1 Inorganic phosphate-solubilization mechanisms
			11.3.1.1 Organic acid production
			11.3.1.2 Chelation
			11.3.1.3 Inorganic acid production
			11.3.1.4 Proton extrusion
			11.3.1.5 Exopolysaccharide production
			11.3.1.6 Siderophore production
		11.3.2 Organic phosphate solubilization mechanisms
			11.3.2.1 Enzyme production
	11.4 Phosphate-solubilizing microorganisms: applications and advances
		11.4.1 Biofertilizer
		11.4.2 Phytoremediation
	11.5 Conclusion
	References
12. Metagenomics a modern approach to reveal the secrets of unculturable microbes
	12.1 Introduction
	12.2 History of metagenomic approach
	12.3 Approach, strategies, and tools used in the metagenomic analysis
		12.3.1 Isolation of metagenomic DNA
		12.3.2 Cloning vector and host
		12.3.3 Screening of metagenomic clones
		12.3.4 Sequencing and bioinformatics analysis of the metagenomic clones
	12.4 Application of the metagenomic approach
	12.5 Conclusion remarks
	Acknowledgments
	References
13. Halophilic archaea as beacon for exobiology: recent advances and future challenges
	13.1 Introduction
	13.2 Missions with exobiological significance
		13.2.1 1960–2000
		13.2.2 2000–10
		13.2.3 2010–18
	13.3 Extremophiles–a general overview
	13.4 Halophiles in the universe
	13.5 Modes of energy generation in halophilic archaea
	13.6 Radiation resistance in halophilic archaea
	13.7 Halophilic archaea from ancient halite crystals
	13.8 Adaptation of halophilic archaea to extreme temperatures and pH
	13.9 Growth of halophilic archaea in the presence of perchlorates
	13.10 Saline environments in space
		13.10.1 Mars
		13.10.2 Europa
		13.10.3 Enceladus
	13.11 Methods for detecting halophilic archaea in saline econiches
	13.12 Conclusion
	References
14. Bacterial probiotics over antibiotics: a boon to aquaculture
	14.1 Introduction
	14.2 The probiotic approach
	14.3 Antimicrobial mechanism of probiotics
		14.3.1 Production of antagonistic compounds
		14.3.2 Competitive exclusion
		14.3.3 Immunomodulation
		14.3.4 Production of other beneficiary compounds
	14.4 Screening and development of probiotics
		14.4.1 In vitro screening for antimicrobial activity
		14.4.2 Mucus adhesion, colonization, and growth profile
		14.4.3 Pathogenicity test
		14.4.4 Organism identification
		14.4.5 Route of delivery, dosage, and frequency
		14.4.6 In vivo validation
		14.4.7 Shelf life
		14.4.8 Economic evaluation
	14.5 Recent probiotics used in aquaculture
	14.6 Conclusion and future perspectives
	Acknowledgments
	References
15. Recent advances in quorum quenching of plant pathogenic bacteria
	15.1 Introduction
	15.2 Overview of the different quorum sensing molecules of plant pathogenic bacteria
	15.3 Mechanisms of quorum quenching
		15.3.1 Inhibition of synthesis of quorum sensing signal
		15.3.2 Inhibition of sensing of quorum sensing signal
		15.3.3 Degradation of quorum sensing molecules
			15.3.3.1 Acyl homoserine lactone degradation
			15.3.3.2 3-Hydroxy palmitic acid methyl ester hydrolase
			15.3.3.3 Degradation of the diffusible signal factor
			15.3.3.4 Other mechanisms for quorum quenching
	15.4 Quorum quenching against plant pathogens
	15.5 Transgenic plants expressing quorum quenching molecules
	15.6 Summary and future research needs
	Acknowledgments
	References
16. Trends in production and fuel properties of biodiesel from heterotrophic microbes
	16.1 Introduction
	16.2 Growth of different sources of biodiesel on various substrates
		16.2.1 Screening of lipid-producing microorganisms
	16.3 Harvesting of cellular biomass from fermentation broth
	16.4 Cell lysis
	16.5 Lipid extraction
	16.6 Transesterification/FAME preparation—conventional two-step, one-step, use of lipases
		16.6.1 Transesterification process
			16.6.1.1 Homogeneous catalyzed transesterification
			16.6.1.2 Heterogeneous catalysts for transesterification
			16.6.1.3 Direct or in situ transesterification
			16.6.1.4 Lipase-catalyzed transesterification
			16.6.1.5 Other methods of transesterification
	16.7 Determination of fuel properties of heterotrophic microbes
		16.7.1 Cetane number
		16.7.2 Viscosity
		16.7.3 Density
		16.7.4 Higher heating value
	16.8 Conclusions and future perspectives
	Acknowledgments
	References
17. Advances and microbial techniques for phosphorus recovery in sustainable wastewater management
	17.1 Introduction
	17.2 Technologies for phosphorus recovery
		17.2.1 The process of struvite crystallization
		17.2.2 Recovery of struvite from wastes
		17.2.3 Source of magnesium for struvite formation
	17.3 Struvite crystallization technologies
		17.3.1 Lab-scale studies
		17.3.2 Biological struvite precipitation
		17.3.3 Struvite formation within wastewater treatment plants: pilot-scale studies
	17.4 Use of struvite as fertilizer and its potential market
		17.4.1 Use of struvite to increase soil fertility
		17.4.2 World and India's fertilizer requirements
	17.5 Economic feasibility of struvite recovery process
	17.6 Conclusion
	References
18. Genotoxicity assays: the micronucleus test and the single-cell gel electrophoresis assay
	18.1 Introduction
		18.1.1 Micronucleus test
		18.1.2 Comet assay (single-cell gel electrophoresis)
	18.2 Conclusion
	References
19. Advances in methods and practices of ectomycorrhizal research
	19.1 Introduction
	19.2 Benefits of ECM association
	19.3 Cultivation and physiology of ECM fungi
		19.3.1 Cultivation media for ECM fungi
		19.3.2 Isolation methods of ECM fungi
	19.4 Identification methods of ECM fungi
		19.4.1 Conventional methods
		19.4.2 Case study
		19.4.3 Challenges in the identification of ECM
		19.4.4 Advances in identification of ECM
	19.5 Assessment and quantification of ECM
		19.5.1 Conventional methods of assessment and quantification of ECM
		19.5.2 Molecular tools of assessment and quantification of ECM
			19.5.2.1 Nucleic acid–based molecular methods
			19.5.2.2 Transcriptome analysis
			19.5.2.3 Proteomic analysis
	19.6 Stress response and pigments/phenolics in ECM fungi
	19.7 Application in forestry: ECM fungi as bioinoculants
		19.7.1 Types of ectomycorrhizal inoculants
			19.7.1.1 Solid-state fermentation
			19.7.1.2 Submerged cultivation
		19.7.2 Ectomycorrhizal inoculants in field applications
	19.8 Conclusion
	19.9 Future prospects
	Acknowledgments
	References
	Further reading
20. Photocatalytic and microbial degradation of Amaranth dye
	20.1 Introduction
	20.2 Advanced photocatalytic amaranth degradation using titanium dioxide
		20.2.1 Characterization of TiO2 supported mesoporous Al2O3 catalyst
		20.2.2 Amaranth adsorption versus photocatalytic-degradation kinetics
		20.2.3 Identification of photodegradation products using LC-ESI-HRMS technique
		20.2.4 Toxicity of photodegradation products
	20.3 Bioremediation of amaranth dye
	20.4 Coupling of photocatalysis with bioremediation methods
	References
21. Role of nanoparticles in advanced biomedical research
	21.1 Introduction
	21.2 Cancer therapy
	21.3 Metal nanoparticles as drug delivery and anticancer agents
		21.3.1 Gold nanoparticles
		21.3.2 Silver nanoparticles
	21.4 Metal oxide nanoparticles as drug delivery and anticancer agent
		21.4.1 Iron oxide nanoparticles
		21.4.2 Miscellaneous
	21.5 Carbon-based nanoparticles as drug delivery and anticancer agents
		21.5.1 Graphene oxide/reduced graphene oxide for drug delivery
	21.6 Conclusions
	Acknowledgments
	References
22. Iron-oxygen intermediates and their applications in biomimetic studies
	22.1 Introduction
	22.2 Mononuclear nonheme iron(III)-superoxo complexes
	22.3 Mononuclear nonheme iron(III)-peroxo complex
	22.4 Mononuclear nonheme iron(III)-hydroperoxo complex
	22.5 Mononuclear high-valent iron(IV)-oxo complex
	22.6 Mononuclear nonheme iron(V)-oxo complex
	22.7 Application of iron-oxygen intermediates in biomimetics
	22.8 Summary
	Acknowledgments
	References
23. Frontiers in developmental neurogenesis
	23.1 Introduction to neurogenesis
		23.1.1 Developmental neurogenesis
	23.2 Signaling pathway cross talk of developmental neurogenesis
		23.2.1 Notch
		23.2.2 Wingless/Integrated
		23.2.3 Hedgehog/Sonic hedgehogs
		23.2.4 Fibroblast growth factor
		23.2.5 Neuronal progenitor cell environment
	23.3 Tools to study developmental neurogenesis
		23.3.1 In vitro models
		23.3.2 Time-lapse analysis
		23.3.3 Transcriptome, metabolomics, and single-cell “omics”
		23.3.4 Real-time analysis of progenitors in both embryonic and postnatal studies by tissue explants/slice assays
	23.4 Conclusion
	References
24. Analytical methods for natural products isolation: principles and applications
	24.1 Introduction
	24.2 Extraction techniques
	24.3 Isolation and purification techniques
	24.4 High-performance liquid chromatography
		24.4.1 Analysis of chromatograms obtained from HPLC/GC
	24.5 Spectroscopic methods for characterization
		24.5.1 Ultraviolet-visible spectroscopy
		24.5.2 Infrared spectroscopy
		24.5.3 Mass spectrometry
		24.5.4 Nuclear magnetic resonance spectroscopy
	24.6 Chemical profiling of marine sponges: case studies
		24.6.1 Marine sponge, Haliclona cribricutis
		24.6.2 Marine sponge, Fasciospongia cavernosa
		24.6.3 Marine sponge, Axinella donnani
	24.7 Conclusion
	Acknowledgments
	References
25. Advanced bioceramics
	25.1 Introduction
	25.2 Classification of biomaterials
	25.3 Applications and properties of bioceramics
		25.3.1 Hydroxyapatite
		25.3.2 β-Tricalcium phosphate (β-TCP)
		25.3.3 Alumina (Al2O3)
		25.3.4 Zirconia
		25.3.5 Bioglass and glass ceramics
	25.4 Conclusion and future perspectives
	Acknowledgments
	References
26. Production of polyhydroxyalkanoates by extremophilic microorganisms through valorization of waste materials
	26.1 Introduction
	26.2 Synthesis of polyhydroxyalkanoates
	26.3 Classification of PHAs
		26.3.1 Biosynthetic origin
		26.3.2 Monomer size
		26.3.3 Monomers units
		26.3.4 Nature of the monomers
	26.4 Screening, extraction, and characterization of polyhydroxyalkanoates
		26.4.1 Screening for PHA
		26.4.2 PHA extraction
		26.4.3 PHA characterization
	26.5 Advances in the applications of PHAs
		26.5.1 Food industry
		26.5.2 Medical industry
		26.5.3 Agricultural industry
	26.6 Extremophilic microorganisms
	26.7 Extremophilic microorganisms producing PHAs
	26.8 PHAs from renewable resources and agroindustrial wastes
	26.9 Conclusions
	Acknowledgments
	References
27. Techniques for the mass production of Arbuscular Mycorrhizal fungal species
	27.1 Introduction
	27.2 Pot/substrate-based mass production system
	27.3 The AM host plants
	27.4 Root trap cultures
	27.5 Plant trap cultures
	27.6 Soil as inoculum
	27.7 Microenvironment
	27.8 Conclusion
	References
28. Metagenomics: a gateway to drug discovery
	28.1 Introduction
	28.2 Approaches to accelerate antibiotic discovery
		28.2.1 Mining unusual habitats as a source of novel secondary metabolites
		28.2.2 Revolutionary cultivation techniques
			28.2.2.1 High-throughput cultivation of microorganisms using microcapsules technique
			28.2.2.2 Microfluidic bioreactor cultivation
			28.2.2.3 Diffusion chamber in situ cultivation
			28.2.2.4 The “isolation chip” or “ichip”
			28.2.2.5 Hollow-fiber membrane chamber
			28.2.2.6 I-TIP
			28.2.2.7 Co-culture technique
		28.2.3 Next-generation sequencing techniques in mining for bioactive compounds
			28.2.3.1 Single-cell genome sequencing
			28.2.3.2 Target sequencing or amplicon sequencing
			28.2.3.3 Whole-genome shotgun sequencing
	28.3 Metagenomic or environmental or community genomic sequencing
		28.3.1 Sequence-based metagenomics
		28.3.2 Function-based metagenomics
	28.4 How metagenomics facilitates drug discovery
	28.5 Conclusion
	Conflict of interests
	References
29. Application of 3D cell culture techniques in cosmeceutical research
	29.1 Introduction
	29.2 Two-dimensional cell system in cosmeceutical research
	29.3 Role of three-dimensional cell culture system in cosmeceutical research
	29.4 Key features of 3D cell culture
	29.5 Diverse application of 3D cell culture
	29.6 Preparation of 3D reconstructed human skin model
		29.6.1 The traditional approach for 3D skin model preparation
		29.6.2 Bioprinting technology for preparation of 3D skin models
	29.7 Application of 3D skin models in cosmeceutical research
		29.7.1 Skin whitening or melanin content
		29.7.2 Skin antiaging study using 3D in vitro skin model
		29.7.3 Antioxidant activity
		29.7.4 Antiinflammatory activity
		29.7.5 Wound healing assay
		29.7.6 Skin corrosion test
		29.7.7 Skin cell irritation test
		29.7.8 Skin penetration assay
		29.7.9 Phototoxicity study
		29.7.10 Genotoxicity assay
		29.7.11 Skin absorption assay
	29.8 Conclusion
	Acknowledgments
	References
30. Advances in isolation and preservation strategies of ecologically important marine protists, the thraustochytrids
	30.1 Introduction
	30.2 Occurrence and ecological significance
	30.3 Isolation
		30.3.1 Isolation of thraustochytrids
		30.3.2 Isolation of labyrinthulids
	30.4 Preservation of cultures
	30.5 Summary and future prospects
	Acknowledgments
	References
31. Advances in sampling strategies and analysis of phytoplankton
	31.1 Introduction
	31.2 Sampling strategies
		31.2.1 Choice of research vessel
		31.2.2 Sampling in coastal waters
		31.2.3 Aspects to be considered
	31.3 Analysis of phytoplankton
		31.3.1 Phytoplankton taxonomy
		31.3.2 Analysis of phytoplankton community structure
		31.3.3 Analysis of benthic diatoms
			31.3.3.1 Modifications of the extinction–dilution method
		31.3.4 Analysis of dinoflagellate cysts
		31.3.5 Study of fouling diatoms/biofilms
		31.3.6 Analysis of epibiotic phytoplankton
		31.3.7 Study of picophytoplankton
		31.3.8 Phytoplankton pigment analysis
		31.3.9 Analysis of viability and photosynthetic parameters of phytoplankton populations
		31.3.10 Toxin analysis
	31.4 Primary productivity
		31.4.1 Estimation of primary productivity using remote sensing
		31.4.2 Monitoring of HABs using remote sensing
	31.5 Future perspectives
	Acknowledgments
	References
Index
	A
	B
	C
	D
	E
	F
	G
	H
	I
	J
	K
	L
	M
	N
	O
	P
	Q
	R
	S
	T
	U
	V
	W
	X
	Y
	Z
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