Laboratory Protocols in Fungal Biology (eBook)

EditorsVijai 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 EditorsDr. 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. GuptaDr. 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.

1.          Safety Norms and Regulations in Handling Fungal SpecimensFinola E. Cliffe  2.          Methods of Cryopreservation in FungiLadislav Homolka 3.          Long Term Preservation of Fungal Cultures in All-Russian Collection of Microorganisms (VKM): Protocols and ResultsSvetlana 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 CropsS. 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 FungiJayabalan Sangeetha and Devarajan Thangadurai 7.          Microscopic Methods for Analytical Studies of FungiDe-Wei Li 8.          Scanning Electron Microscopy for Fungal Sample ExaminationEduardo 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 MicroscopyTanya 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 MicroscopyTélesphore 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 PlantsVijai Kumar Gupta and Brejesh Kumar Pandey  14.      Development of Media for Growth and Enumeration of Fungi from WaterSegula Masaphy 15.      Sabouraud Agar for Fungal GrowthJanelle M. Hare 16.      A Method for the Formation of Candida Biofilms in 96 Well Microtiter Plates and its Application to Antifungal Susceptibility TestingChristopher G. Pierce, Priya Uppuluri, and Jose L. Lopez-Ribot 17.      Screening for Compounds Exerting Antifungal ActivitiesJean-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 FungiTélesphore 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 AnalysisJeannette Vogt, Frank Stahl, Thomas Scheper, and Susann Müller 22.      Quantitative PCR Analysis of Double-Stranded RNA-Mediated Gene Silencing in FungiJosé 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 CommunitiesMiruna Oros-Sichler and Kornelia Smalla 24.      Proteomic Protocols for the Study of Filamentous FungiRaquel González Fernández and Jesús V. Jorrín Novo 25.      Detection and Quantification of Endoprotease Activity Using a Coomassie Dye-Binding AssayAnthony 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 FungiK. Lily Therese, R. Bagyalakshmi, and H. N. Madhavan  28.      Real-Time PCR Assay in FungiNaomichi Yamamoto 29.      Quantitative Sampling Methods for the Analysis of Fungi: Air SamplingMary C. O’Loughlin, Katherine D. Turner, and Kevin M. Turner  30.      Transformation of Filamentous Fungi in Microtiter PlateBianca Gielesen and Marco van den Berg 31.      Molecular Fingerprinting of Fungal Communities in SoilRoberto A. Geremia and Lucie Zinger 32.      Development of Microsatellite Markers from Fungal DNA Based on Shotgun PyrosequencingShaobin Zhong 33.      Multiplex and Quantifiable Detection of Infectious Fungi Using Padlock Probes, General qPCR and Suspension Microarray ReadoutMagnus Jobs, Ronnie Eriksson, and Jonas Blomberg 34.      Rapid Deletion Plasmid Construction Methods for Protoplast and Agrobacterium-based Fungal Transformation SystemsMaría D. García-Pedrajas, Zahi Paz, David L. Andrews, Lourdes Baeza-Montañez, and Scott E. Gold 35.      Improved Transformation Method for Alternaria brassicicola and its ApplicationsYangrae 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 ChromatographyBerend 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 FungiTélesphore Sime-Ngando and Marlène Jobard  39.      Nucleic and Protein Extraction Methods for Fungal Exopolysaccharide ProducersJochen 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 stipitisParamjit 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-MSBernhard 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 biomassManimaran Ayyachamy, Vijai Kumar Gupta, Finola E. Cliffe, and Maria G. Tuohy 45.      Protoplast Fusion Techniques in FungiAnnie Juliet Gnanam  46.      Large Scale Production of Lignocellulolytic Enzymes in Thermophilic FungiManimaran Ayyachamy, Mary Shier, and Maria G. Tuohy 47.      Panfungal PCR Method for Detection of Aflatoxigenic MoldsMalik M. Ahmad, Pravej Alam, M. Z. Abdin, and Saleem Javed 48.      Protocols for the Quantification of dsDNA and Its Fragmentation Status in FungiIoannis Papapostolou, Konstantinos Grintzalis, and Christos Georgiou 49.      Rapid Identification and Detection of Pathogenic Fungi by Padlock ProbesClement K. M. Tsui, Bin Wang, Cor D. Schoen, and Richard C. Hamelin 50.      Drug-Induced Permeabilization in FungiMaria D. Mayan, Alexandra MacAleenan, and Priscilla Braglia 51.      Extraction and Characterization of Taxol: An Anticancer Drug from an Endophytic And Pathogenic FungiM. Pandi P. Rajapriya and P. T. Manoharan 52.      Identification of Mycotoxigenic Fungi using an Oligonucleotide MicroarrayEugenia Barros 53.      DNA Microarray-Based Detection and Identification of Fungal SpecimensMinna Mäki 54.      Bioinformatic Protocols and the Knowledge-Base for Secretomes in FungiGengkon Lum and Xiang Jia Min 55.      High-Throughput Functional Annotation and Data Mining of Fungal Genomes to Identify Therapeutic TargetsGagan Garg and Shoba Ranganathan 56.      Application of Support Vector Machines in Fungal Genome and Proteome AnnotationSonal Modak, Shimantika Sharma, Prashant Prabhakar, Akshay Yadav, and V. K. Jayaraman 57.      Bioinformatics Tools for the Multilocus Phylogenetic Analysis of FungiDevarajan Thangadurai and Jayabalan Sangeetha