Mycology

12.

Research Methods in Mycology

12.1.

Collection and Isolation

12.1.1.

Field Collection

12.1.1.1.

Sampling Strategies

12.1.1.2.

Collection Techniques

12.1.1.3.

Field Documentation

12.1.1.4.

Preservation Methods

12.1.2.

Isolation Techniques

12.1.2.1.

Direct Isolation

12.1.2.2.

Dilution Plating

12.1.2.3.

Selective Isolation

12.1.2.4.

Single Spore Isolation

12.1.3.

Environmental Sampling

12.1.3.1.

12.1.3.2.

12.1.3.3.

12.1.3.4.

Plant Tissue Sampling

12.2.

Culture Methods

12.2.1.

12.2.1.1.

General Purpose Media

12.2.1.2.

Selective Media

12.2.1.3.

Differential Media

12.2.1.4.

Specialized Media

12.2.2.

Culture Conditions

12.2.2.1.

Temperature Requirements

12.2.2.2.

pH Requirements

12.2.2.3.

Atmospheric Conditions

12.2.2.4.

Light Requirements

12.2.3.

Culture Maintenance

12.2.3.1.

Short-term Storage

12.2.3.2.

Long-term Preservation

12.2.3.2.1.

Cryopreservation

12.2.3.2.2.

12.2.3.2.3.

12.2.3.2.4.

Silica Gel Storage

12.3.

Microscopy and Imaging

12.3.1.

Light Microscopy

12.3.1.1.

Brightfield Microscopy

12.3.1.2.

Phase Contrast Microscopy

12.3.1.3.

Differential Interference Contrast

12.3.1.4.

Fluorescence Microscopy

12.3.1.4.1.

Fluorescent Stains

12.3.1.4.2.

Fluorescent Proteins

12.3.2.

Electron Microscopy

12.3.2.1.

Scanning Electron Microscopy

12.3.2.1.1.

Sample Preparation

12.3.2.2.

Transmission Electron Microscopy

12.3.2.2.1.

Sample Preparation

12.3.3.

Specialized Imaging

12.3.3.1.

Confocal Microscopy

12.3.3.2.

Time-Lapse Microscopy

12.3.4.

Staining Techniques

12.3.4.1.

12.3.4.2.

Structural Stains

12.3.4.2.1.

Lactophenol Cotton Blue

12.3.4.2.2.

Calcofluor White

12.3.4.2.3.

12.3.4.3.

Functional Stains

12.4.

Molecular Methods

12.4.1.

DNA Extraction and Purification

12.4.1.1.

Extraction Methods

12.4.1.2.

Quality Assessment

12.4.2.

PCR-Based Methods

12.4.2.1.

12.4.2.2.

12.4.2.3.

12.4.2.4.

12.4.3.

12.4.3.1.

Sanger Sequencing

12.4.3.2.

Next-Generation Sequencing

12.4.3.2.1.

Illumina Sequencing

12.4.3.2.2.

PacBio Sequencing

12.4.3.2.3.

Oxford Nanopore

12.4.4.

Phylogenetic Analysis

12.4.4.1.

Sequence Alignment

12.4.4.2.

Tree Construction Methods

12.4.4.3.

Statistical Support

12.4.5.

Genomic Approaches

12.4.5.1.

Whole Genome Sequencing

12.4.5.2.

Comparative Genomics

12.4.5.3.

Transcriptomics

12.4.5.4.

12.4.5.5.

12.4.6.

Molecular Identification

12.4.6.1.

12.4.6.1.1.

12.4.6.1.2.

Other Barcode Regions

12.4.6.2.

MALDI-TOF Mass Spectrometry

12.5.

Experimental Design and Analysis

12.5.1.

Experimental Design Principles

12.5.1.1.

12.5.1.2.

12.5.1.3.

12.5.2.

Statistical Analysis

12.5.2.1.

Descriptive Statistics

12.5.2.2.

Hypothesis Testing

12.5.2.3.

Multivariate Analysis

12.5.3.

Data Management

12.5.3.1.

Database Systems

12.5.3.2.

12.5.3.3.

Reproducibility

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11. Plant Pathology and Phytopathogenic Fungi

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1. Introduction to Mycology