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E-raamat: Analytical Techniques in Biosciences: From Basics to Applications

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Edited by Chukwuebuka Egbuna (Africa Centre of Excellence in Public Health and Toxicological Research, University of Port Harcourt, Nigeria), Edited by Jonathan C. Ifemeje, Edited by Kingsley C. Patrick-Iwuanyanwu (Africa Centre of Excellence, Centre for Public Health and Toxicological Research (ACE-PUTOR), University of Port-Harcourt,), Edited by Azhar Rasul, Edited by Muhammad Ajmal Shah

Formaat: EPUB+DRM
Ilmumisaeg: 21-Oct-2021
Kirjastus: Academic Press Inc
Keel: eng
ISBN-13: 9780128227992

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Molecular biology

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Formaat: EPUB+DRM
Ilmumisaeg: 21-Oct-2021
Kirjastus: Academic Press Inc
Keel: eng
ISBN-13: 9780128227992

Teised raamatud teemal:

Molecular biology

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Analytical Techniques in Biosciences: From Basics to Applications presents comprehensive and up-to-date information on the various analytical techniques obtainable in bioscience research laboratories across the world. This book contains chapters that discuss the basic bioanalytical protocols and sample preparation guidelines. Commonly encountered analytical techniques, their working principles, and applications were presented. Techniques, considered in this book, include centrifugation techniques, electrophoretic techniques, chromatography, titrimetry, spectrometry, and hyphenated techniques. Subsequent chapters emphasize molecular weight determination and electroanalytical techniques, biosensors, and enzyme assay protocols. Other chapters detail microbial techniques, statistical methods, computational modeling, and immunology and immunochemistry.

The book draws from experts from key institutions around the globe, who have simplified the chapters in a way that will be useful to early-stage researchers as well as advanced scientists. It is also carefully structured and integrated sequentially to aid flow, consistency, and continuity. This is a must-have reference for graduate students and researchers in the field of biosciences.

• Presents basic analytical protocols and sample-preparation guidelines
• Details the various analytical techniques, including centrifugation, spectrometry, chromatography, and titrimetry
• Describes advanced techniques such as hyphenated techniques, electroanalytical techniques, and the application of biosensors in biomedical research
• Presents biostatistical tools and methods and basic computational models in biosciences

List of contributors

About the editors

xxi

1 Bioanalysis: methods, techniques, and applications

(24)

Mithun Rudrapal

Aniket P. Kothawade

Shahira M. Ezzat

Chukwuebuka Egbuna

Abbreviations

(1)

1.1 Introduction

(1)

1.2 Bioanalytical methods

(1)

1.2.1 Sample preparation

(1)

1.2.2 Sample measurement

(1)

1.3 Sample preparation

(2)

1.3.1 Liquid---liquid extraction

(1)

1.3.2 Solid-phase extraction

(1)

1.3.3 Protein precipitation

(1)

1.3.4 Microextraction techniques

(1)

1.4 Bioanalytical techniques

(8)

1.4.1 Hyphenated techniques

(5)

1.4.2 Ligand binding assay

(1)

1.5 Method development

(1)

1.6 Bioanalytical method validation

(4)

1.6.1 Types of method validation

(1)

1.6.2 Objective and need for analytical method validation

(1)

1.6.3 Parameters of analytical method validation

(3)

1.7 Analytical challenges

(1)

1.8 Applications

(2)

1.9 Conclusion

(1)

References

(4)

2 Sample preparation techniques in biological and pharmaceutical sciences

(18)

Nait Bachir Yacine

Bouanani Hanane

Abbreviations

(1)

2.1 Introduction

(1)

2.2 Biological samples description

(1)

2.2.1 Types of samples on living subjects

(1)

2.2.2 Types of postmortem samples

(1)

2.3 Basic notions regarding biological samples preparation

(2)

2.3.1 Cell and tissue sample preparation

(1)

2.3.2 Biological liquid sample preparation

(1)

2.3.3 Medullar or blood sample preparation

(1)

2.3.4 Sample preparation for nucleic acid preparation

(1)

2.4 Benefits of sample preparation

(1)

2.5 Conventional extraction techniques

(5)

2.5.1 Solid-phase extraction

(2)

2.5.2 Liquid-liquid extraction

(2)

2.5.3 Protein precipitation technique

(1)

2.5.4 Column switching

(1)

2.6 Techniques based on microextraction technologies

(3)

2.6.1 Microextraction with packed sorbent

(1)

2.6.2 Monolithic packed 96-tips

(1)

2.6.3 Solid-phase microextraction

(1)

2.6.4 Hollow fiber liquid-phase microextraction

(1)

2.7 Common mistakes during sample preparation

(1)

2.8 Conclusion and perspectives

(1)

References

(4)

3 Centrifugation techniques

(16)

Ahmed Olatunde

Mayowa Shakirdeen Obidola

Habibu Tijjani

Abbreviations

(1)

3.1 Introduction

(1)

3.2 Principles of centrifugation

(1)

3.3 Types of centrifugation

(6)

3.3.1 Differential centrifugation

(1)

3.3.2 Density gradient centrifugation

(3)

3.3.3 Ultracentrifugation

(2)

3.4 Centrifuge

(4)

3.4.1 Types of centrifuge

(3)

3.4.2 Centrifuge rotors

(1)

3.5 Maintenance and care of centrifugation equipments

(1)

3.6 Applications of centrifugation

(1)

3.7 Conclusion

(1)

References

(2)

4 Electrophoretic techniques

(14)

Apratim Maity

Shyam Sundar Kesh

Santwana Palai

Chukwuebuka Egbuna

4.1 Introduction

(1)

4.2 Electrophoresis

(1)

4.2.1 Principle of electrophoresis

(1)

4.2.2 Milestones in the development of electrophoretic techniques

(1)

4.3 Gel electrophoresis

(1)

4.4 Agarose gel electrophoresis

(2)

4.4.1 Protein electrophoresis

(1)

4.4.2 DNA electrophoresis

(1)

4.5 Polyacrylamide gel electrophoresis

(1)

4.5.1 Protein electrophoresis

(1)

4.5.2 DNA electrophoresis

(1)

4.6 Staining procedures

(1)

4.7 Isoelectric focusing

(1)

4.8 Immobilized pH gradients

(1)

4.9 Proteome analysis

(1)

4.10 Functional proteomics

(1)

4.11 Gradient gel

(1)

4.12 Two-dimensional electrophoresis

(1)

4.13 Two-dimensional differential gel electrophoresis

(1)

4.14 Conclusion and future direction

(1)

References

(2)

5 Chromatographic techniques: types, principles, and applications

(30)

V.B. Chandana Kumari

Shashank M. Patil

Ramith Ramu

Prithvi S. Shirahatti

Naveen Kumar

B.P. Sowmya

Chukwuebuka Egbuna

Chukwuemelie Zedech Uche

Kingsley C. Patrick-Iwuanyanwu

Abbreviations

(1)

5.1 Introduction

(3)

5.1.1 History

(1)

5.1.2 General principle

(2)

5.2 Chromatographic techniques based on the bed shape

(5)

5.2.1 Column chromatography

(2)

5.2.2 Planar chromatography

(3)

5.3 Chromatographic techniques based on the physical state of mobile phase

(3)

5.3.1 Gas chromatography

(1)

5.3.2 Liquid chromatography

(2)

5.4 Chromatographic techniques based on the separation mechanism

(4)

5.4.1 Affinity chromatography

(2)

5.4.2 Ion-exchange chromatography

(1)

5.4.3 Gel-filtration chromatography

(1)

5.5 Specialized techniques of chromatography

(4)

5.5.1 Displacement chromatography

(1)

5.5.2 Hydrophobic interaction chromatography

(1)

5.5.3 Expanded bed adsorption chromatography

(1)

5.5.4 Hydrodynamic chromatography

(1)

5.5.5 Two-dimensional chromatography

(1)

5.5.6 Simulated moving-bed chromatography

(1)

5.5.7 Pyrolysis gas chromatography

(1)

5.5.8 Fast protein liquid chromatography

(1)

5.5.9 Counter-current chromatography

(1)

5.5.10 Periodic counter-current chromatography

(1)

5.5.11 Chiral chromatography

(1)

5.5.12 Aqueous normal-phase chromatography

(1)

5.6 Future perspectives

(1)

5.7 Conclusion

(1)

References

(8)

6 Titrimetry

103

(12)

Andrew G. Mtewa

Duncan C. Sesaazi

Senyo K. Botchie

Emanuel L. Peter

Serawit Deyno

Belay Akino Neme

Davies Mweta

6.1 Introduction

103

(1)

6.2 Instrumentation in titrimetry

103

(2)

6.3 Categorization of titrimetric methods

105

(5)

6.3.1 Analyte direction determination

105

(1)

6.3.2 Solvents and type of reactions involved

106

(4)

6.4 Challenges associated with titrimetry

110

(1)

6.4.1 Determining end point

110

(1)

6.4.2 Accuracy of the measuring instruments

111

(1)

6.4.3 Uncertainty value

111

(1)

6.4.4 Human error

111

(1)

6.5 Modern application of titrimetry

111

(1)

6.6 Conclusion

112

(1)

References

112

(3)

7 Mass spectrometry

115

(10)

Abdallah Habbab

7.1 Introduction

115

(1)

7.2 Instrumentation

115

(2)

7.3 Ionization processes

117

(4)

7.3.1 Gas-phase ionization processes

117

(1)

7.3.2 Desorption ionization processes

118

(2)

7.3.3 Evaporative ionization processes

120

(1)

7.4 Application

121

(1)

7.5 Conclusion

122

(1)

References

123

(2)

8 Hyphenated techniques

125

(22)

Chinaza Godswill Awuchi

Hannington Twinomuhwezi

Chibueze Gospel Awuchi

Abbreviations

125

(1)

8.1 Introduction

125

(2)

8.2 Gas chromatography tandem mass spectroscopy

127

(5)

8.3 Liquid chromatography tandem mass spectroscopy

132

(2)

8.3.1 Construction of LC-MS interface

133

(1)

8.4 Liquid chromatography tandem nuclear magnetic resonance

134

(2)

8.5 Liquid chromatography tandem infrared spectroscopy

136

(1)

8.6 Gas chromatography tandem infrared spectroscopy

137

(2)

8.6.1 Measurement of spectra of light-pipe GC-IR/FTIR instrument

138

(1)

8.6.2 Matrix-isolation gas chromatography tandem infrared spectroscopy

138

(1)

8.7 Capillary electrophoresis tandem mass spectrometry

139

(2)

8.8 Differential scanning calorimetry tandem Raman spectroscopy

141

(1)

8.9 Thermogravimetry tandem GC-MS

141

(1)

8.9.1 Analysis of coffee beans using TG-GC-MS

142

(1)

8.10 Conclusion and future prospects

142

(1)

References

143

(4)

9 Molecular weight determination of nucleic acids and proteins

147

(10)

Ravi Prakash

Pramod Kumar Singh

Santosh Kumar Jatav

Ajay Kumar Gautam

9.1 Introduction

147

(1)

9.2 Molecular weight determination of nucleic acid

148

(3)

9.2.1 Molecular weight determination of DNA

148

(1)

9.2.2 Molecular weight determination of RNA

149

(1)

9.2.3 Molecular weight determination of plasmid DNA

150

(1)

9.2.4 Molecular weight determination of DNA-bound protein(s)

151

(1)

9.3 Molecular weight determination of protein

151

(4)

9.3.1 Protein precipitation

152

(3)

9.4 Conclusion

155

(1)

References

155

(2)

10 Electroanalytical techniques in biosciences: conductometry, coulometry, voltammetry, and electrochemical sensors

157

(22)

Saadat Majeed

Sayed Tayyab Raza Naqvi

Muhammad Najam ul Haq

Muhammad Naeem Ashiq

10.1 Introduction

157

(1)

10.2 Electrochemical cell and cell potential measurements

158

(5)

10.3 Reference electrodes and electrochemical measurements

163

(3)

10.4 Conductometry

166

(1)

10.5 Coulometry

167

(1)

10.6 Voltametric techniques

167

(5)

10.6.1 Linear sweep voltammetry

168

(2)

10.6.2 Cyclic voltammetry

170

(2)

10.6.3 Stripping voltammetry (anodic and cathodic)

172

(1)

10.7 Microelectrodes

172

(1)

10.8 Chemically modified electrodes and electrochemical sensors

173

(2)

10.8.1 Potentiometric sensors

174

(1)

10.8.2 Amperometric sensors

174

(1)

10.8.3 Conductometric sensors

175

(1)

10.9 Conclusion

175

(1)

10.11 Electrochemistry general questions

176

(1)

References

176

(3)

11 Biosensors: components, mechanisms, and applications

179

(12)

Rohini Karunakaran

Merve Keskin

11.1 Introduction

179

(1)

11.2 Biosensors

179

(1)

11.3 History of biosensors

180

(1)

11.4 Biocomponents

181

(1)

11.5 Characteristics of biosensors

181

(1)

11.6 The working mechanism of biosensors

182

(2)

11.6.1 Amperometric biosensors

183

(1)

11.6.2 Potentiometric biosensors

184

(1)

11.7 Designing of biosensor

184

(1)

11.8 Three generations of biosensors

185

(1)

11.9 Bioreceptor molecules and biosensing techniques

185

(3)

11.9.1 Enzymes

185

(1)

11.9.2 Proteins

186

(1)

11.9.3 Nucleic acid bioreceptors

186

(1)

11.9.4 Surface plasmon resonance biosensors

187

(1)

11.9.5 Gold nanoparticle biosensors

187

(1)

11.10 Clinical application areas of biosensors

188

(1)

11.11 Conclusion and prospects

189

(1)

References

189

(2)

12 Enzyme assay techniques and protocols

191

(10)

Iqra Sarfraz

Azhar Rasul

Ilknur Ucak

Ngit Shin Lai

Muhammad Asrar

Sevki Adem

12.1 Introduction

191

(1)

12.2 Enzymatic assays in drug discovery

192

(4)

12.2.1 Nicotinamide adenine dinucleotide assays

192

(2)

12.2.2 Measurement of adenine dinucleotide's activity by fluorescence spectroscopy

194

(1)

12.2.3 Measurement of adenine dinucleotide's activity by bioluminescence

194

(1)

12.2.4 ATP-based enzymatic assays

195

(1)

12.3 Enzymatic assays as diagnostic tools for diseases

196

(1)

12.3.1 Enzymatic assays for diagnosis of liver diseases

196

(1)

12.3.2 Enzymatic assays for cancer diagnosis

197

(1)

12.4 Conclusions and future recommendation

197

(1)

References

198

(3)

13 Microbial techniques and methods: basic techniques and microscopy

201

(20)

Alloysius Chibuike Ogodo

Dawn Ify Agwaranze

Morumda Daji

Rufus Emamoge Aso

Abbreviations

201

(1)

13.1 Introduction

201

(1)

13.2 Culturing microorganisms; preparation and sterilization of microbiological media

202

(3)

13.2.1 Microbiological media

203

(2)

13.3 Determination of microbial numbers

205

(2)

13.3.1 Standard plate count (SPC) or Viable Count (VC)

205

(1)

13.3.2 Direct microscopic count

206

(1)

13.3.3 Turbidimetric method

207

(1)

13.3.4 Drop-plate method

207

(1)

13.4 Pure culture techniques

207

(2)

13.4.1 Aseptic techniques

207

(1)

13.4.2 Spread-plate technique

208

(1)

13.4.3 The streak-plate technique

208

(1)

13.4.4 Pour-plate techniques

209

(1)

13.5 Stains and staining techniques

209

(2)

13.5.1 Some staining techniques

209

(2)

13.6 Identification of microorganisms

211

(4)

13.6.1 Cultural characteristics

211

(1)

13.6.2 Microscopic identification

212

(1)

13.6.3 Biochemical procedures

212

(2)

13.6.4 Carbohydrates fermentation test

214

(1)

13.6.5 Molecular identification of microorganisms

215

(1)

13.6.6 Serological tests for microbial identification

215

(1)

13.7 Antimicrobial susceptibility testing

215

(1)

13.7.1 Broth dilution test

216

(1)

13.7.2 Disk diffusion test

216

(1)

13.8 Microscopy

216

(2)

13.8.1 Types of microscope

216

(1)

13.8.2 The compound microscope

217

(1)

13.8.3 Examination of prepared slide under the microscope

217

(1)

13.8.4 Care of the microscope

218

(1)

13.9 Conclusion

218

(1)

References

218

(3)

14 Computational modeling and tools in biosciences: bioinformatics approach

221

(12)

K. Stavelin Abhinandithe

Chandan Shivamallu

Chukwuebuka Egbuna

Shiva Prasad Kollur

14.1 Introduction

221

(1)

14.2 Enabling biological discovery with computational modeling and simulation

222

(2)

14.2.1 Usefulness of biological models

222

(1)

14.2.2 Types of models

223

(1)

14.3 Computational tools

224

(6)

14.3.1 Functions of computational tools

225

(1)

14.3.2 Tools for data integration

225

(3)

14.3.3 Data presentation

228

(1)

14.3.4 Algorithms for operating on biological data

229

(1)

14.3.5 Data mining and discovery

229

(1)

14.4 Conclusion

230

(1)

References

230

(3)

15 Statistical methods and tools in biosciences

233

(18)

Ethelbert Chinaka Nduka

Uchenna Petronilla Ogoke

15.1 Introduction

233

(1)

15.2 Preliminary statistical methods

233

(2)

15.2.1 Data collection

233

(1)

15.2.2 Data preparation

234

(1)

15.2.3 Data presentation

234

(1)

15.2.4 Data analysis

234

(1)

15.2.5 Result interpretation and conclusion

235

(1)

15.3 Methods of data analysis

235

(9)

15.3.1 Parametric statistics

235

(2)

15.3.2 Regression analysis

237

(6)

15.3.3 Correlation coefficients

243

(1)

15.3.4 Major types of correlation

243

(1)

15.4 Conclusion

244

(1)

15.5 Sample exercises

245

(3)

15.5.1 Sample exercise 1: simple linear regression

245

(1)

15.5.2 Sample exercise 2: multiple linear regression

246

(2)

References

248

(1)

Further reading

249

(2)

16 Immunology and immunochemistry

251

(18)

Muhammad Riaz

Fatima Yousaf

Muhammad Akram

Muhammad Irfan Ullah

Ghulam Rasool

Chukwuebuka Egbuna

Kingsley C. Patrick-Iwuanyanwu

Chukwuemelie Zedech Uche

Jonathan C. Ifemeje

16.1 Introduction

251

(2)

16.2 Immunochemistry

253

(9)

16.2.1 Immunohistochemistry

254

(4)

16.2.2 Immunohistochemical methods

258

(3)

16.2.3 Antigen retrieval

261

(1)

16.2.4 Proteolytic enzyme digestion

261

(1)

16.2.5 Heat-mediated antigen retrieval techniques

261

(1)

16.3 Immunocytochemistry

262

(1)

16.3.1 Protocol for immunocytochemistry

262

(1)

16.4 Applications of immunochemistry

262

(3)

16.4.1 Prognostic markers in cancer

263

(1)

16.4.2 Neurodegenerative disorders

263

(1)

16.4.3 Brain trauma

263

(1)

16.4.4 Muscle diseases

263

(1)

16.4.5 Infections

263

(1)

16.4.6 Bacterial infections

263

(1)

16.4.7 Viral infections

264

(1)

16.4.8 Fungal infections

264

(1)

16.4.9 Parasitic infections

264

(1)

16.4.10 Immunohistochemistry, emerging infections, and bioterrorism

264

(1)

16.4.11 Research

264

(1)

16.4.12 Novel uses

265

(1)

16.5 Conclusion

265

(1)

References

265

(4)

Index

269

Chukwuebuka Egbuna (PhD) is a chartered chemist and academic researcher. He is a member of the Institute of Chartered Chemists of Nigeria (ICCON), the Nigerian Society of Biochemistry and Molecular Biology (NSBMB), and the Royal Society of Chemistry (RSC) (United Kingdom). Dr. Egbuna is the founder and editor of the Elsevier book series on Drug Discovery Update. The series includes books, monographs, and edited collections from all areas of drug discovery including emerging therapeutic claims for the treatment of diseases. He has published research articles in many international journals of repute and is ranked among the top 500 Nigerian scientists in SciVal/SCOPUS. He has edited more than 25 books with Elsevier, Springer, Wiley, and Taylor & Francis. His most recent book is the three volume Coronavirus Drug Discovery, published by Elsevier. Dr. Egbuna is the founder and the publishing director of IPS Intelligentsia Publishing Services.

Dr. Kingsley Chukwuemeka Patrick-Iwuanyanwu is a Senior Lecturer in the Department of Biochemistry. Dr. Patrick-Iwuanyanwu is a recipient of The World Academy of Science- International Centre for Chemical and Biological Sciences (TWAS-ICCBS) Postgraduate fellowship award in 2009 to University of Karachi, Pakistan. He was among the 100 young scientists from around the world selected to attend The World Life Sciences Forum by BioVision (Lyon, France); He is a recipient of Society of Toxicology (SOT) /AstraZenecca IUTOX fellowship award in 2009. He served as a pioneer African representative and one of the founding Executive Members of Student Advisory Council (SAC) of Society of Environmental Toxicology and Chemistry (SETAC, EUROPE) from 2009-2011. Dr. Patrick-Iwuanyanwu is a member of several professional bodies including Nigerian Society of Biochemistry and Molecular Biology (NSBMB); Africa Education Initiative (NEF, CT. USA); West African Society of Toxicology (WASOT); Society of Environmental Toxicology and Chemistry (SETAC, Europe); Society of Toxicology (SOT, Reston, USA); Society for Experimental Biology (SEB, UK). Dr. Muhammad Ajmal Shah is a registered pharmacist and an academic researcher. He obtained his PharmD and MPhil in Pharmacognosy degrees from Federal Urdu University of Arts, Science & Technology, Pakistan. He obtained his PhD in Pharmaceutical Sciences from Prince of Songkla University Thailand by securing Thailand Education Hub for ASEAN Countries PhD Scholarship Award (TEH-AC 2014-17). He has published over 60 articles in well reputed international journals and has authored over 20 chapters in different books published by Elsevier and Springer. He is a reviewer and editorial board member of various reputed international journals. Dr. Shah is an active member of the American Society of Pharmacognosy, Phytochemical Society of Europe, American Society of Microbiology and GA Society for Medicinal Plant and Natural Product Research Germany. Currently, he is working as an Assistant Professor and Incharge at Department of Pharmacognosy, Faculty of Pharmaceutical Sciences, Government College University Faisalabad, Pakistan. His primary research interests include green extraction and enrichment of bioactive compounds, their isolation and bioevaluation in metabolic and aging associated diseases. Dr. Jonathan Chinenye Ifemeje, PhD, is an Associate Professor (Reader) in the Department of Biochemistry, Faculty of Natural Sciences, Chukwuemeka Odumegwu Ojukwu University, Nigeria. He has published over 40 articles with international publishers and has attended series of workshops and conferences. He has also served as an external examiner for various institutions. He is the managing editor of the Tropical Journal of Applied Natural Sciences and a reviewer and an editorial board member for various reputable journals. He has worked extensively in the areas of phytochemistry, environment, and nutritional toxicology. He is a member of various institutes, including the Institute of Chartered Chemists of Nigeria, the Nigerian Society of Biochemistry and Molecular Biology, and Society of Quality Assurance. Dr. Ifemeje is presently the Director of Student Industrial Work Experience Scheme (SIWES), COOU and the Department of Biochemistry Postgraduate Coordinator, COOU. He has also served as the department and faculty staff adviser. He obtained his PhD in applied biochemistry from Nnamdi Azikiwe University, Awka, Nigeria, and his MSc degree in nutrition and toxicology from the University of Port-Harcourt, Nigeria. Dr. Azhar Rasul is an Assistant Professor at Faculty of Life Sciences, Government College University. He has published over 79 peer-reviewed articles and 4 book chapters. Dr. Rasul has presented several invited talks at National and International level and has attended more than 20 International conferences in Japan, China, South Korea, Dubai, Sri Lanka, Qatar, Turkey, Thailand, Malaysia and France. He has obtained several national and international research grants (HEC-Pak Turk Mobility Grant, ISSESCO RG, HEC-NRPU RG(s), The Nagai Foundation Tokyo RG(s) and COMSTECH-TWAS RG).

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