Advances in Biological Science Research A Practical Approach Edited by Surya Nandan Meena Biological Oceanography Division, National Institute of Oceanography, Dona Paula, Goa, India Milind Mohan Naik Department of Microbiology, Goa University, Goa, India AcademicPressisanimprintofElsevier 125LondonWall,LondonEC2Y5AS,UnitedKingdom 525BStreet,Suite1650,SanDiego,CA92101,UnitedStates 50HampshireStreet,5thFloor,Cambridge,MA02139,UnitedStates TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UnitedKingdom Copyright(cid:1)2019ElsevierInc.Allrightsreserved. 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LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress BritishLibraryCataloguing-in-PublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary ISBN:978-0-12-817497-5 ForinformationonallAcademicPresspublicationsvisitourwebsiteat https://www.elsevier.com/books-and-journals Publisher:AndreG.Wolff AcquisitionEditor:LindaVersteeg-buschman EditorialProjectManager:SandraHarron ProductionProjectManager:PoulouseJoseph CoverDesigner:VickyPearsonEsser TypesetbyTNQTechnologies Contributors GauriA.Achari,DepartmentofBiologicalSciences,BirlaInstituteofTechnologyand Science Pilani,KKBirlaGoaCampus,Zuarinagar,India LaurenceV.Bindschedler,SchoolofBiologicalSciences,RoyalHollowayUniversity ofLondon, Egham,Surrey,UnitedKingdom Sunita Borkar, Department of Microbiology, P.E.S’s R.S.N. College of Arts and Science,Goa, India JudithM.Braganc¸a,DepartmentofBiologicalSciences,BirlaInstituteofTechnology and Science(BITS)Pilani,KKBirla,GoaCampus,Zuarinagar,Goa,India SandeshT.Bugde,DepartmentofChemistry,GoaUniversity,TaleigaoPlateau,Goa, India LakshangyS.Charya,DepartmentofMicrobiology,GoaUniversity,TaleigaoPlateau, Goa, India AvelynoD’Costa,DepartmentofZoology,GoaUniversity,TaleigaoPlateau,Goa,India Priya M. D’Costa, Department of Microbiology, Goa University, Taleigao Plateau, Goa, India Varada S. Damare, Department of Microbiology, Goa University, Taleigao Plateau, Goa, India Kanchanmala Deshpande, Department of Chemistry, Goa University, Taleigao Plateau, Goa,India ShantiN.Dessai,DepartmentofZoology,GoaUniversity,TaleigaoPlateau,Goa,India Vazhakatt Lilly Anne Devasia, Department of Biotechnology, Goa University, Goa, India; Present address: Department of Biotechnology, Hindustan College of Arts and Science,Padur,Kelambakkam, Chennai,India Sunder N. Dhuri, Department of Chemistry, Goa University, Taleigao Plateau, Goa, India JamesDsouza,St.Xavier College,Mapusa,Goa, India Samantha Fernandes, Department of Biotechnology, Goa University, Taleigao Plateau, Goa,India SandeepGarg,DepartmentofMicrobiology,GoaUniversity,TaleigaoPlateau, Goa, India Umesh B. Gawas, Department of Chemistry, Dnyanprassarak Mandal’s College and Research Centre,Assagao,Goa,India xxi xxii Contributors Sanjeev C. Ghadi, Department of Biotechnology, Goa University, Taleigao Plateau, Goa,India Shyamalina Haldar, Department of Microbiology, Goa University, Taleigao Plateau, Goa,India Sarvesh S. Harmalkar, Department of Chemistry, Goa University, Taleigao Plateau, Goa,India Md Imran, Department of Biotechnology, Goa University, Taleigao Plateau, Goa, India SrijayKamat, Department of Biotechnology,Goa University,TaleigaoPlateau, Goa, India R.Kanchana,DepartmentofBiotechnology,ParvatibaiChowguleCollegeofArtsand Science-Autonomous,Margao,Goa,India SavitaKerkar,DepartmentofBiotechnology,GoaUniversity,TaleigaoPlateau,Goa, India HetikaKotecha,DepartmentofBiotechnology,GoaUniversity,TaleigaoPlateau,Goa, India M.K. Praveen Kumar, Department of Zoology, Goa University, Taleigao Plateau, Goa,India R.K. Kunkalekar, Department of Chemistry, Goa University, Taleigao Plateau, Goa, India Mahesh S. Majik, Department of Chemistry, Goa University, Taleigao Plateau, Goa, India VinodK.Mandrekar,DepartmentofChemistry,St.Xavier’sCollege,Mapusa,Goa, India Kabilan Mani, Department of Biotechnology, PSG College of Technology, Coimbatore,India Surya Nandan Meena, Biological Oceanography Division, National Institute of Oceanography,DonaPaula,Goa,India AbhishekMishra,DixaEducationand Research,AltoPorvorim,Goa,India Geetesh K. Mishra, Multiscale Fluid Mechanics Lab, School of Mechanical Engineering,SungkyunkwanUniversity,Suwon,SouthKorea Chellandi Mohandass, Biological Oceanography Division, National Institute of Oceanography,DonaPaula,Goa,India Pranay P. Morajkar, Department of Chemistry, Goa University, Taleigao Plateau, Goa,India Sajiya Yusuf Mujawar, Laboratory of Bacterial Genetics and Environmental Biotechnology,Department ofMicrobiology,GoaUniversity,Goa,India UshaD.Muraleedharan,Department ofBiotechnology,GoaUniversity,Goa,India Contributors xxiii MilindMutnale,NationalCentreforPolarandOceanResearch(NCPOR),Vasco-da- Gama, Goa,India Srikanth Mutnuri, Applied and Environmental Biotechnology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, KKBirla GoaCampus,Zuarinagar,Goa, India Amarja P. Naik, Department of Chemistry, Goa University, Taleigao Plateau, Goa, India Kiran Suresh Naik, Department of Chemistry, P.E.S.’s R.S.N. College of Arts & Science,Farmagudi,Ponda,Goa, India MilindMohanNaik,DepartmentofMicrobiology,GoaUniversity,Goa,India Ravidas K. Naik,ESSO-National Centre forPolarand Ocean Research, Vasco, Goa, India Bhanudas R. Naik, Department of Chemistry, Goa University, Taleigao Plateau, Goa, India PrachiParab,Department ofMicrobiology,GoaUniversity,Goa,India Chhaya Patole, Proteomics Division, National Centre for Biological Sciences, Bengaluru, India FloryPereira,PES’sRaviSitaramNaikCollegeofArtsandScience,Department of Microbiology,Ponda,Goa,India PreethiB.Poduval,DepartmentofBiotechnology,GoaUniversity,TaleigaoPlateau, Goa, India MeghanathShambhuPrabhu,PorterSchooloftheEnvironmentandEarthSciences, Tel Aviv University, Tel Aviv, Israel; Applied and Environmental Biotechnology Laboratory, Department of Biological Sciences, Birla Institute of Technology and Science,Pilani, KKBirlaGoaCampus,Zuarinagar,Goa,India Neha Prabhu, Department of Microbiology, Goa University, Taleigao Plateau, Goa, India R. Ramesh, Crop Improvement and Protection Section, ICAR-Central Coastal AgriculturalResearch Institute,Old Goa,India Gouri Raut,Bioenergydivision,AgharkarResearch Institute,Pune,India AmeetaRaviKumar,InstituteofBioinformaticsandBiotechnology(IBB),Savitribai PhulePuneUniversity,Pune,India Bhakti B. Salgaonkar, Department of Biological Sciences, Birla Institute of Tech- nologyandScience(BITS)Pilani,KKBirla,GoaCampus,Zuarinagar,Goa,India SanikaSamant,Department ofBiotechnology,GoaUniversity,Goa,India SuvidhaSamant,Dixa EducationandResearch,AltoPorvorim,Goa,India KashifShamim,LaboratoryofBacterialGeneticsandEnvironmentalBiotechnology, Department ofMicrobiology,GoaUniversity,Goa,India xxiv Contributors PriyankaV.Shirodkar,DepartmentofBiotechnology,GoaUniversity,Goa, India S.K.Shyama,Department ofZoology,GoaUniversity,TaleigaoPlateau, Goa,India Akshaya Sridhar, Department of Biotechnology, PSG College of Technology, Coimbatore,India Abhilash Sundarasami, Department of Biotechnology, PSG College of Technology, Coimbatore,India Diviya Chandrakant Vaingankar, Department of Microbiology, Goa University, Goa,India PoonamVashist,Department ofBiotechnology,GoaUniversity,Goa,India Preface Biologicalsciencesarethestudyoflifeandlivingorganisms,theirlifecycles, adaptationsandenvironment.“AdvancesinBiologicalSciencese A Practical Approach”describes recent progress in various rapidly growing biological sciences, such as bioinformatics, genomics, metagenomics, proteomics, enzy- mology, agriculture and marine microbiology, bioremediation, medicinal chemistry, and nanotechnology. This book consists of a total of thirty one chapters,eachofwhichhasbeencontributedbyhighlyqualifiedprofessionals (professors, assistant professors, scientists, postdoctoral fellows, and senior researchscholars)intherespectivefieldsofresearch. The chapter on bioinformatics describes the analysis and interpretation of biologicalexperimentaldatausingonlinebioinformaticstoolsorsoftware.The genomicschapterdescribesthestep-by-stepstrategyforidentifyingthegeneof interest in the newly sequenced bacterial genome. Recent advances in metagenomics-basedapproacheshaverevolutionizedmicrobialecologyscience and have led to the discovery of some of the new biocatalytic molecules. In addition, metagenomics is undoubtedly the key to the discovery of secondary metabolites that can meet the urgent demand for new medicines from natural sources. Proteomics chapters provide an overview of appropriate experimental workflows for plant proteomics, suggestions to improve the extraction and preparation of plant protein samples. Further current proteomic analysis is underway to better understand intracellular pathogen survival and disease persistence.AnoverviewofX-raydiffractiontechniquetheworkingprinciple, the instrumentation, and its usefulness in the structural characterization of the proteinhasbeendetailed.Thissectiondescribethevarioustypesoflectinpro- teins from different microbial source and also describe their role and action mechanisms. The section on enzymology explains bioanalytical techniques; principlesofvariousenzymeinhibitionassay’sparametersrequiredtooptimize enzyme testing; and analytical merit characteristics for enzyme testing and its applicabilitytorealsampleanalysis.Furtheremphasisisplacedoninformation onroutineprotocols,aimedathighlightingandbetterunderstandingsomeofthe challengesfacedduringtheenzymecharacterization/purificationstudies. xxv xxvi Preface The section on microbiology presents an overview of microorganisms that solubilize phosphates, recent progress and future challenges with halophilic archaeaasabeaconforexobiology,theuseofprobioticsandtheirmechanismsto control aquatic pathogens, and recent new research findings on the control of plant pathogenic diseases through various quorum quenching strategies. The reader will also be briefed about the advances in microbial techniques for the recovery of phosphorus in sustainable wastewater management, advances in ectomycorrhizal research methods, and techniques for the mass production of fungalarbuscularmycorrhiza. Some chapters describe the photocatalytic and microbial degradation of amaranth dye, biodegradation of seafood waste by bacteria associated with seaweed and the use of seafood waste for the production of ethanol, the pro- duction of Polyhydroxyalkanoates by microorganisms in extreme econiches, withaparticularfocusontheuseofcheaplyavailablewastematerialssuchas carbonsubstratesforPolyhydroxyalkanoatessynthesis. Chapters on medicinal chemistry present the various analytical techniques fortheextraction,purification,andcharacterizationofmetabolitesfromnatural sources. Specialattention is focused on a discussion on case studies involving isolation ofmarine,microbial,andterrestrialnaturalproductswiththehelp of suitable examples. Another chapter discusses the advances in bioceramics, their biocompatibility, classification, application, and further research on bioceramics. Latest advancement in application of various 3D reconstructed human skin models for the screening of natural chemical compounds of cosmeceuticalpotentialhavebeenincluded. Theaquaticsciencesectiondiscussestheadvancesinsamplingstrategiesand analysisofphytoplanktonandcurrentstrategiesfortheisolationandpreserva- tionofecologicallyimportantmarineprotists.Further,somechaptersdescribe theroleofnanoparticlesinadvancedbiomedicalresearchwithreferencetodrug deliveryandanticancertherapy. Forbetterunderstandingofthemechanismof DNA damage as well as regions of the genome that are prone to alterations, micronucleus test and the single-cell gel electrophoresis assay techniques are describedwiththelatestmodifications. This bookdescribes theupdates on themethodologiesandprotocols being usedbyresearchersintheirroutineexperimentsofbiologicalsciences.Greater emphasishasbeengiventothebasicfundamentalsandthelatesttechniquesor methods in routine experiments. We have given equal importance to text and illustrations, therefore, sincere efforts have been made to support the textual clarificationsandexplanationswiththehelpofflowcharts,tables,andfigures.It iswritteninaclearandconciselanguagetoenhancetheself-motivationofthe researchers. Preface xxvii The book will help graduate and postgraduate students to explore their researchcareers.Inaddition,recentlyupdatedinformationonvariousresearch fields and techniques in biological sciences will definitely benefit university professors, university lecturers, and scientists from different life sciences institutionsworldwide. SuryaNandanMeena MilindMohanNaik