Series: Fungal Biology

Gupta, V.K., Tuohy, M.G., Ayyachamy, M., Turner, K.M., O’Donovan, A. (Eds.)

2013, XXV, 604 p. 117 illus., 43 illus. in color.

• Consolidates the most widely used mycological methods available in the fields of biochemistry, biotechnology and microbiology
• Features the work of the foremost authorities on fungal biology
• Multi-purpose book for a diverse audience

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.

Contents

1 Safety Norms and Regulations in Handling
Fungal Specimens......................................................................... 1
Finola E. Cliffe

2 Methods of Cryopreservation in Fungi ...................................... 9
Ladislav Homolka

3 Long-Term Preservation of Fungal Cultures in All-Russian
Collection of Microorganisms (VKM): Protocols
and Results .................................................................................... 17
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 ............................. 67
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 .............................................................. 73
S. Chandra Nayaka, M. Venkata Ramana, A.C. Udayashankar,
S.R. Niranjana, C.N. Mortensen, and H.S. Prakash

6 Identification Key for the Major Growth Forms
of Lichenized Fungi...................................................................... 91
Jeyabalan Sangeetha and Devarajan Thangadurai

7 Microscopic Methods for Analytical Studies of Fungi .............. 113
De-Wei Li

8 Scanning Electron Microscopy for Fungal
Sample Examination .................................................................... 133
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 .............. 151
Biplab C. Paul, Hui Ma, Laelie A. Snook, and Tanya E.S. Dahms

10 Use of Fourier-Transform Infrared (FTIR)
Microscopy Method for Detection of Phyto-Fungal
Pathogens ...................................................................................... 161
Vitaly Erukhimovitch and Mahmoud Huleihel

11 Diagnosis of Parasitic Fungi in the Plankton: Technique
for Identifying and Counting Infective Chytrids Using
Epifluorescence Microscopy ........................................................ 169
Télesphore Sime-Ngando, Serena Rasconi,
and Mélanie Gerphagnon

12 Fungal Cell Wall Analysis ........................................................... 175
Pilar Pérez and Juan C. Ribas

13 Histopathological Technique for Detection of Fungal
Infections in Plants ....................................................................... 197
Vijai Kumar Gupta and Brejesh Kumar Pandey

14 Development of Media for Growth and Enumeration
of Fungi from Water .................................................................... 201
Segula Masaphy

15 Sabouraud Agar for Fungal Growth .......................................... 211
Janelle M. Hare

16 A Method for the Formation of Candida Biofilms
in 96 Well Microtiter Plates and Its Application
to Antifungal Susceptibility Testing ............................................ 217
Christopher G. Pierce, Priya Uppuluri, and Jose L. Lopez-Ribot

17 Screening for Compounds Exerting Antifungal Activities ....... 225
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 ................................................... 231
Télesphore Sime-Ngando, Marlène Jobard, and Serena Rasconi

19 Staining Techniques and Biochemical Methods
for the Identification of Fungi ..................................................... 237
Jeyabalan Sangeetha and Devarajan Thangadurai

20 Protocol for the In Vivo Quantification of Superoxide
Radical in Fungi ........................................................................... 259
Konstantinos Grintzalis, Ioannis Papapostolou,
and Christos Georgiou

21 Isolation of Intact RNA from Sorted S. cerevisiae Cells
for Differential Gene Expression Analysis ................................. 265
Jeannette Vogt, Frank Stahl, Thomas Scheper, and Susann Müller

22 Quantitative PCR Analysis of Double-Stranded
RNA-Mediated Gene Silencing in Fungi.................................... 279
José J. de Vega-Bartol, Vega Tello, Jonathan Niño, Virginia Casado,
and José M. Díaz-Mínguez

23 Semi-Nested PCR Approach to Amplify Large
18S rRNA Gene Fragments for PCR-DGGE Analysis
of Soil Fungal Communities ........................................................ 289
Miruna Oros-Sichler and Kornelia Smalla

24 Proteomic Protocols for the Study of Filamentous Fungi ........ 299
Raquel González Fernández and Jesús V. Jorrín Novo

25 Detection and Quantification of Endoprotease Activity
Using a Coomassie Dye-Binding Assay ...................................... 309
Anthony J. O’Donoghue and Cathal S. Mahon

26 Protocol of a LightCycler™ PCR Assay for Detection
and Quantification of Aspergillus fumigatus DNA
in Clinical Samples of Neutropenic Patients.............................. 315
Birgit Spiess and Dieter Buchheidt

27 Application of Polymerase Chain Reaction and PCR-Based
Methods Targeting Internal Transcribed Spacer Region
for Detection and Species-Level Identification of Fungi........... 321
K. Lily Therese, R. Bagyalakshmi, and H.N. Madhavan

28 Real-Time PCR Assay in Fungi .................................................. 331
Naomichi Yamamoto

29 Quantitative Sampling Methods for the Analysis
of Fungi: Air Sampling ................................................................ 337
Mary C. O’Loughlin, Katherine D. Turner, and Kevin M. Turner

30 Transformation of Filamentous Fungi in Microtiter Plate....... 343
Bianca Gielesen and Marco van den Berg

31 Molecular Fingerprinting of Fungal Communities in Soil ....... 349
Roberto A. Geremia and Lucie Zinger

32 Development of Microsatellite Markers from Fungal
DNA Based on Shotgun Pyrosequencing ................................... 357
Shaobin Zhong

33 Multiplex and Quantifiable Detection of Infectious
Fungi Using Padlock Probes, General qPCR,
and Suspension Microarray Readout ......................................... 363
Magnus Jobs, Ronnie Eriksson and Jonas Blomberg

34 Rapid Deletion Plasmid Construction Methods
for Protoplast and Agrobacterium-based Fungal
Transformation Systems .............................................................. 375
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 ................................................ 395
Yangrae Cho, Akhil Srivastava, and Christopher Nguyen

36 Methods for High-Quality DNA Extraction from Fungi .......... 403
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 ............................................................ 407
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 .................. 421
Télesphore Sime-Ngando and Marlène Jobard

39 Nucleic and Protein Extraction Methods for Fungal
Exopolysaccharide Producers ..................................................... 427
Jochen Schmid, Dirk Mueller-Hagen, Volker Sieber,
and Vera Meyer

40 Directed Evolution of a Fungal Xylanase for Improvement
of Thermal and Alkaline Stability .............................................. 435
Dawn Elizabeth Stephens, Suren Singh, and Kugen Permaul

41 Genome Shuffling Protocol for the Pentose-Fermenting
Yeast Scheffersomyces stipitis ...................................................... 447
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 ............... 455
Bernhard Kluger, Susanne Zeilinger, Gerlinde Wiesenberger,
Denise Schöfbeck, and Rainer Schuhmacher

43 Transformation Methods for Slow-Growing Fungi .................. 467
Suman Mukherjee and Rebecca Creamer

44 Enzymatic Saccharification of Lignocellulosic Biomass ........... 475
Manimaran Ayyachamy, Vijai Kumar Gupta,
Finola E. Cliffe, and Maria G. Tuohy

45 Protoplast Fusion Techniques in Fungi ...................................... 483
Annie Juliet Gnanam

46 Large-Scale Production of Lignocellulolytic Enzymes
in Thermophilic Fungi ................................................................. 489
Manimaran Ayyachamy, Mary Shier, and Maria G. Tuohy

47 Panfungal PCR Method for Detection
of Aflatoxigenic Molds ................................................................. 495
Malik M. Ahmad, Pravej Alam, M.Z. Abdin, and Saleem Javed

48 Protocols for the Quantification of dsDNA
and Its Fragmentation Status in Fungi ...................................... 501
Ioannis Papapostolou, Konstantinos Grintzalis,
and Christos Georgiou

49 Rapid Identification and Detection of Pathogenic
Fungi by Padlock Probes ............................................................. 505
Clement K.M. Tsui, Bin Wang, Cor D. Schoen,
and Richard C. Hamelin

50 Drug-Induced Permeabilization in Fungi .................................. 519
Maria D. Mayan, Alexandra McAleenan, and Priscilla Braglia

51 Extraction and Characterization of Taxol: An Anticancer
Drug from an Endophytic and Pathogenic Fungi ..................... 523
M. Pandi, P. Rajapriya, and P.T. Manoharan

52 Identification of Mycotoxigenic Fungi Using
an Oligonucleotide Microarray................................................... 529
Eugenia Barros

53 DNA Microarray-Based Detection and Identification
of Fungal Specimens .................................................................... 535
Minna Mäki

54 Bioinformatic Protocols and the Knowledge-Base
for Secretomes in Fungi ............................................................... 545
Gengkon Lum and Xiang Jia Min

55 High-Throughput Functional Annotation and Data Mining
of Fungal Genomes to Identify Therapeutic Targets ................ 559
Gagan Garg and Shoba Ranganathan

56 Application of Support Vector Machines in Fungal Genome
and Proteome Annotation ............................................................ 565
Sonal Modak, Shimantika Sharma, Prashant Prabhakar,
Akshay Yadav, and V.K. Jayaraman

57 Bioinformatics Tools for the Multilocus Phylogenetic
Analysis of Fungi .......................................................................... 579
Devarajan Thangadurai and Jeyabalan Sangeetha

Index ...................................................................................................... 593