Laboratory Protocols in Fungal Biology: Current Methods in Fungal Biology

ISBN-13: 9781493941971 / Angielski / Miękka / 2016 / 604 str.

Vijai Kumar Gupta; Maria G. Tuohy; Manimaran Ayyachamy

Opis

Fungi and their biomolecules are today being explored in a variety of scientific endeavors. This manual is an invaluable source of laboratory protocols for standard and applied research applications in a range of fields such as biotechnology and microbiology.

Recenzje

From the book reviews:

"The book 'Laboratory Protocols in Fungal Biology' written by international researchers, offers diverse modern laboratory techniques in the field of fungal biology. ... Each chapter is comprehensive, provides readily reproducible protocols and is easy to grasp by beginners. This book is a valuable guide to budding mycologists as well as professionals. It is recommended to all the Universities. A crucial Laboratory Manual for Fungal Biologists, Taxonomists, Fungal Biotechnologists, Biochemists, Histochemists, Plant Pathologists and Laboratory technicians." (Melvina D'souza and Samantha C. Karunarathna, Fungal Diversity, December, 2014)

"This new book is very much hands-on, and covers an extraordinarily diverse range of topics. ... Chapters are well-referenced to primary literature, and there are numerous links to website. There are numerous illustrations, most clearly presented, and in some cases using colour. This is a reference work that deserves to be accessible in all mycology laboratories ... ." (IMA Fungus, Vol. 4 (1), 2013)

Spis treści

1.          Safety Norms and Regulations in Handling Fungal Specimens

Finola E. Cliffe

 

2.          Methods of Cryopreservation in Fungi

Ladislav Homolka

 

3.          Long Term Preservation of Fungal Cultures in All-Russian Collection of Microorganisms (VKM): Protocols and Results

Svetlana M. Ozerskaya, Natalya E. Ivanushkina, Galina A. Kochkina, Svetlana S. Eremina, Alexander N. Vasilenko, and Nadezhda I. Chigineva

 

4.          Fungal Specimen Collection and Processing.

Anthonia O’Donovan, Vijai Kumar Gupta, and Maria G. Tuohy

 

5.          Chemical and Molecular Methods for Detection of Toxigenic Fungi and Their Mycotoxins from Major Food Crops

S. Chandra Nayaka, A.C. Udayashankar, M.Venkata Ramana, S.R. Niranjana, C. N. Mortensen,  and H.S. Prakash

 

6.          Identification Key for the Major Growth Forms of Lichenized Fungi

Jayabalan Sangeetha and Devarajan Thangadurai

 

7.          Microscopic Methods for Analytical Studies of Fungi

De-Wei Li

 

8.          Scanning Electron Microscopy for Fungal Sample Examination

Eduardo Alves, Gilvaine Ciavareli Lucas, Edson Ampélio Pozza, and Marcelo de Carvalho Alves

 

9.          High Resolution Imaging and Force Spectroscopy of Fungal Hyphal Cells by Atomic Force Microscopy

Tanya Dahms

 

10.      Use of Fourier-Transform Infrared (FTIR) Microscopy Method For Detection of Phyto-Fungal Pathogens

        Vitaly Erukhimovitch and Mahmoud Huleihel

 

11.      Diagnose of Parasitic Fungi in The Plankton:  Technique for Identifying And Counting Infective Chytrids Using Epifluorescence Microscopy

Télesphore Sime-Ngando, Serena Rasconi, and Mélanie Gerphagnon

 

12.      Fungal Cell Wall Analysis

        Pilar Pérez and Juan C. Ribas

 

13.      Histopathological Technique for Detection of Fungal Infections in Plants

Vijai Kumar Gupta and Brejesh Kumar Pandey

 

14.      Development of Media for Growth and Enumeration of Fungi from Water

Segula Masaphy

 

15.      Sabouraud Agar for Fungal Growth

Janelle M. Hare

 

16.      A Method for the Formation of Candida Biofilms in 96 Well Microtiter Plates and its Application to Antifungal Susceptibility Testing

Christopher G. Pierce, Priya Uppuluri, and Jose L. Lopez-Ribot

 

17.      Screening for Compounds Exerting Antifungal Activities

Jean-Paul Ouedraogo, Ellen L. Lagendijk, Cees A.M.J.J van den Hondel, Arthur F.J. Ram, and Vera Meyer

 

18.      Fluorescence In situ Hybridization of Uncultured Zoosporic Fungi

Télesphore Sime-Ngando, Marlène Jobard, and Serena Rasconi

 

19.      Staining Techniques and Biochemical Methods for the Identification of Fungi

Jayabalan Sangeetha and Devarajan Thangadurai

 

20.      Protocol for the In vivo Quantification of Superoxide Radical in Fungi

Grintzalis Konstantinos, Papapostolou Ioannis, and Christos Georgiou

 

21.      Isolation of Intact RNA from Sorted S. cerevisiae Cells for Differential Gene Expression Analysis

Jeannette Vogt, Frank Stahl, Thomas Scheper, and Susann Müller

 

22.      Quantitative PCR Analysis of Double-Stranded RNA-Mediated Gene Silencing in Fungi

José Javiar de Vega-Bartol, María Vega Tello Hernández, Jonathan Niño Sánchez, Virginia Casado del Castillo, and José M. Díaz-Mínguez

 

23.      Semi-nested PCR Approach to Amplify Large 8S rRNA Gene Fragments for PCR-DGGE Analysis of Soil Fungal Communities

Miruna Oros-Sichler and Kornelia Smalla

 

24.      Proteomic Protocols for the Study of Filamentous Fungi

Raquel González Fernández and Jesús V. Jorrín Novo

 

25.      Detection and Quantification of Endoprotease Activity Using a Coomassie Dye-Binding Assay

Anthony J. O’Donoghue and Cathal S. Mahon

 

26.      Protocol of a LightCyclerÔ PCR Assay for Detection and Quantification of Aspergillus fumigatus DNA in Clinical Samples of Neutropenic Patients

        Birgit Spiess and Dieter Buchheidt

 

27.      Application of Polymerase Chain Reaction (PCR) and PCR Based Methods Targeting Internal Transcribed Spacer (ITS) for Detection and Species Level  Identification of Fungi

K. Lily Therese, R. Bagyalakshmi, and H. N. Madhavan

 

28.      Real-Time PCR Assay in Fungi

Naomichi Yamamoto

 

29.      Quantitative Sampling Methods for the Analysis of Fungi: Air Sampling

Mary C. O’Loughlin, Katherine D. Turner, and Kevin M. Turner 

 

30.      Transformation of Filamentous Fungi in Microtiter Plate

Bianca Gielesen and Marco van den Berg

 

31.      Molecular Fingerprinting of Fungal Communities in Soil

Roberto A. Geremia and Lucie Zinger

 

32.      Development of Microsatellite Markers from Fungal DNA Based on Shotgun Pyrosequencing

Shaobin Zhong

 

33.      Multiplex and Quantifiable Detection of Infectious Fungi Using Padlock Probes, General qPCR and Suspension Microarray Readout

Magnus Jobs, Ronnie Eriksson, and Jonas Blomberg

 

34.      Rapid Deletion Plasmid Construction Methods for Protoplast and Agrobacterium-based Fungal Transformation Systems

María D. García-Pedrajas, Zahi Paz, David L. Andrews, Lourdes Baeza-Montañez, and Scott E. Gold

 

35.      Improved Transformation Method for Alternaria brassicicola and its Applications

Yangrae Cho, Akhil Srivastava, and Christopher Nguyen

 

36.      Methods for High Quality DNA Extraction from Fungi

        Vijai Kumar Gupta, Maria G. Tuohy and Rajeeva Gaur

 

37.      Production of Recombinant Proteins from Pichia pastoris: Interfacing Fermentation and Immobilized Metal Ion Affinity Chromatography

Berend Tolner, Gaurav Bhavsar, Bride Foster, Kim Vigor, and Kerry Chester

 

38.      Development of a Real-Time Quantitative PCR Assay for the Assessment of Uncultured Zoosporic Fungi

Télesphore Sime-Ngando and Marlène Jobard

 

39.      Nucleic and Protein Extraction Methods for Fungal Exopolysaccharide Producers

Jochen Schmid, Dirk Mueller-Hagen, Volker Sieber, and Vera Meyer

 

40.      Directed Evolution of A Fungal Xylanase for Improvement of Thermal and Alkaline Stability

        Dawn Elizabeth Stephens, Suren Singh, and Kugen Permaul

 

41.      Genome Shuffling Protocol for the Pentose-Fermenting Yeast Scheffersomyces stipitis

Paramjit K. Bajwa, Nicole K. Harner, Terri L. Richardson, Sukhdeep Sidhu, Marc B. Habash, Jack T. Trevors, and Hung Lee

 42.      Detection and Identification of Fungal Microbial Volatile Organic Compounds by HS-SPME-GC-MS

Bernhard Kluger, Susanne Zeilinger, Gerlinde Wiesenberger, Denise Schöfbeck, and Rainer Schuhmacher

 

43.      Transformation Methods for Slow Growing Fungi

        Suman Mukherjee and Rebecca Creamer

 

44.      Enzymatic Saccharification of lignocellulosic biomass

Manimaran Ayyachamy, Vijai Kumar Gupta, Finola E. Cliffe, and Maria G. Tuohy

 

45.      Protoplast Fusion Techniques in Fungi

Annie Juliet Gnanam

 

46.      Large Scale Production of Lignocellulolytic Enzymes in Thermophilic Fungi

Manimaran Ayyachamy, Mary Shier, and Maria G. Tuohy

 

47.      Panfungal PCR Method for Detection of Aflatoxigenic Molds

Malik M. Ahmad, Pravej Alam, M. Z. Abdin, and Saleem Javed

 

48.      Protocols for the Quantification of dsDNA and Its Fragmentation Status in Fungi

Ioannis Papapostolou, Konstantinos Grintzalis, and Christos Georgiou

 

49.      Rapid Identification and Detection of Pathogenic Fungi by Padlock Probes

Clement K. M. Tsui, Bin Wang, Cor D. Schoen, and Richard C. Hamelin

 

50.      Drug-Induced Permeabilization in Fungi

Maria D. Mayan, Alexandra MacAleenan, and Priscilla Braglia

 

51.      Extraction and Characterization of Taxol: An Anticancer Drug from an Endophytic And Pathogenic Fungi

M. Pandi P. Rajapriya and P. T. Manoharan

 

52.      Identification of Mycotoxigenic Fungi using an Oligonucleotide Microarray

Eugenia Barros

 

53.      DNA Microarray-Based Detection and Identification of Fungal Specimens

Minna Mäki

 

54.      Bioinformatic Protocols and the Knowledge-Base for Secretomes in Fungi

Gengkon Lum and Xiang Jia Min

 

55.      High-Throughput Functional Annotation and Data Mining of Fungal Genomes to Identify Therapeutic Targets

Gagan Garg and Shoba Ranganathan

 

56.      Application of Support Vector Machines in Fungal Genome and Proteome Annotation

Sonal Modak, Shimantika Sharma, Prashant Prabhakar, Akshay Yadav, and V. K. Jayaraman

 

57.      Bioinformatics Tools for the Multilocus Phylogenetic Analysis of Fungi

Devarajan Thangadurai and Jayabalan Sangeetha

O autorze

Editors

Vijai Kumar Gupta is Assistant Professor of Biotechnology at MITS University, India. Presently, he is working as a Post Doctoral Research Scientist, at NUIG, Ireland. He obtained his Ph.D. in Microbiology from Dr. R.M.L. Avadh University, India. He has been honoured with several awards, including the prestigious Indian ICAR Senior Research Fellowship and Young Scientist Award-2009, 2011. He has over seven years of research experience in Applied Microbiology and Biotechnology with a special interest in fungal biology.  He has edited books published from Lambert Academic Publishing, Germany; Nova Science Publishers, USA; Science Publisher, CRC Press, Taylor & Francis, USA; and Springer, USA.

Dr. Maria G. Tuohy is the Head of the Molecular Glycobiotechnology Research Group, NUI Galway. She has more than 20 years experience in the molecular biochemistry, genetics and biotechnology of fungi, with a special interest in thermophilic ascomycetes and the characterization of these fungi as cell factories for protein production, including novel thermostable enzymes/enzyme systems. Dr. Tuohy has authored 132 research publications. She is also a reviewer for international journals and funding agencies, an associate editor for Microbiology and co-editor of four books with Dr. V. K. Gupta.

Associate Editors

Dr. Manimaran Ayyachamy is a Research Scientist with NUIG, Ireland. He obtained his PhD in Microbiology from the University of Madras, India. He has twelve years of research experience in microbial biotechnology with a special interest in microbial enzymes and biofuels technology. He has co-edited books published from Lambert Academic Publishing, Germany; Nova Science Publishers, USA; Science Publisher, CRC Press, Taylor & Francis, USA; and Springer, USA with Dr. V.K. Gupta

Dr. Kevin M. Turner is a Research Scientist in the division of Manufacturing Sciences and Technology in Pfizer Ireland Pharmaceuticals, Dublin. He obtained his PhD from the University of Limerick, Ireland. He has three years of research experience in microbial biotechnology.

Dr. Anthonia O’Donovan is a Postdoctoral Research Scientist with NUIG, Ireland. She obtained her PhD in Biochemistry from the National University of Ireland Galway, Ireland. She has seven years of research experience in microbial enzymes and biofuels technology.

Blurb

Laboratory Protocols in Fungal Biology presents the latest techniques in fungal biology. This book analyzes information derived through real experiments, and focuses on cutting edge techniques in the field. The book comprises 57 chapters contributed from internationally recognised scientists and researchers. Experts in the field have provided up-to-date protocols covering a range of frequently used methods in fungal biology. Almost all important methods available in the area of fungal biology viz. taxonomic keys in fungi; histopathological and microscopy techniques; proteomics methods; genomics methods; industrial applications and related techniques; and bioinformatics tools in fungi are covered and complied in one book. Chapters include introductions to their respective topics, list of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting. Each chapter is self-contained and written in a style that enables the reader to progress from elementary concepts to advanced research techniques.  Laboratory Protocols in Fungal Biology is a valuable tool for both beginner research workers and experienced professionals.

Coming Soon in the Fungal Biology series:

Goyal, Manoharachary / Future Challenges in Crop Protection Against Fungal Pathogens

Martín, García-Estrada, Zeilinger / Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites

Zeilinger, Martín, García-Estrada / Biosynthesis and Molecular Genetics of Fungal Secondary Metabolites, Volume 2

van den Berg, Maruthachalam / Genetic Transformation Systems in Fungi

Schmoll, Dattenbock / Gene Expression Systems in Fungi

Dahms / Advanced Microscopy in Mycology