Molecular Cloning: A Laboratory Manual

Growth and Storage

Quantitative preservation of viability of Aspergillus fumigatus

Media for growth of Aspergillus

Manipulation of Aspergillus

Strain identification

Colony identification key: A key for the identification of species via colony morphology on standard media.

Microsatellite typing for Aspergillus fumigatus

Random Amplification of Polymorphic DNA (RAPD) Typing and Fingerprinting

FGSC strains and mutants

ATTC: Fungi & Yeast strains

DNA & RNA Extraction

Achilles cleavage of fungal chromosomes

Differential display from infected and uninfected tissue

Differential screening of cDNAs from infected and uninfected tissue

REMI and transformation of Septoria nodorum (Stagonospora)

REMI and transformation in Magnaporthe grisea

RNA miniprep (N.crassa)

RNA preperation

Large scale DNA preperation

Fungal DNA miniprep3

Fungal DNA miniprep2

Fungal DNA miniprep1

Guanadinium extraction of fungal RNA

Transformation

Protoplast preparation for A.nidulans

Protoplast preparation

FGSC: Plasmids and gene libraries

Total lipid extraction

Protein/Antigen extraction

List of A.nidulans mutants

In vitro killing assays

SOP's for the Preparation of Aspergillus test strains for inhalation pulmonary aspergillosis studies including : Processing tissue samples for PCR , Galactomannan; DNA extraction for quantitative real-time PCR , and of tissue fungal burden

A rapid method for generating gene deletions in Aspergillus fumigatus

Random subclone generation - Sonication

Random subclone generation - Nebulization

Random subclone generation - Random fragment end-repair, size selection, and phosphorylation

Random subclone generation - DNA ligation

Random subclone generation - Competent cell preparation

Random subclone generation - Bacterial cell transformation

Random subclone generation - Rubidium Chloride method for Transformation Competent E. coli

Random subclone generation - CaCl competent cells

Random subclone generation - Microcentrifuge tube transformation

CsCL RNA preps

RNase protection assay

Nick translations

Southerns with oligo probes

Southern blots

Phenol extraction of DNA samples

Midiprep double-stranded DNA isolation

Glyoxal gels

Large scale double-stranded DNA isolation

Concentration of DNA by ethanol precipitation

Bacterial cell maintenance

Restriction digestion

Kinase end-labeling of DNA

Agarose gel electrophoresis

Elution of DNA fragments from agarose

Notes on Restriction/Modification Bacterial Strains

Fragment purification on Sephacryl S-500 spin columns

Methods for DNA isolation (E.coli) - Genomic DNA isolation from blood

Methods for DNA isolation (E.coli) - 96 well double-stranded template isolation

Methods for DNA isolation (E.coli) - Biomek-automated modified-Eperon isolation procedure for single-stranded M13DNA

Methods for DNA isolation (E.coli) - Single-stranded M13 DNA isolation using phenol

Methods for DNA isolation (E.coli) - Large scale M13RF isolation

Methods for DNA isolation (E.coli) - Miniprep double-stranded DNA isolation

Methods for DNA isolation (E.coli) - Biomek protocol for 96 DNA preps

Polymerase Chain Reaction (PCR)

Purification of PCR fragments for cloning

Preparation of SmaI-linearized, dephosphorylated double-stranded M13 replicative form cloning vector

Long PCR

Synthesis and purification of oligonucleotides

Bst-catalyzed radiolabeled DNA sequencing

Old sequencing protocols

ABI sequencing protocols

cDNA sequencing based on PCR and random shotgun cloning

Double-stranded sequencing of cDNA clones containing long poly(A) tails using anchored poly(dT) primers

Fluorescent-labeled sequencing gel preparation, pre-electrophoresis, sample loading, electrophoresis, data collection, and analysis on the ABI 373A DNA sequencer

Sequenase[TM] catalyzed sequencing with dye-labeled terminators

Taq-polymerase catalyzed cycle sequencing using fluorescent-labeled dye terminator reactions

Taq-polymerase catalyzed cycle sequencing using fluorescent-labeled dye primers

Radiolabeled sequencing gel preparation, loading, and electrophoresis

Old sequencing gels

Rapid hybridization of complementary M13 inserts

Taq polymerase purification

Cosmid packaging protocol

SDS-PAGE

Tricine gels

Eosinophilic fungal rhinosinusitis - Clinical material collection and culture technique

Detection of fungi using fluorescent brighteners

Detection of medically important fungi using PCR

Preparation of Solid Tissue for Aspergillus Galactomannan

Recommended protocol for extracting Aspergillus DNA from whole blood.

Measurement of serum drug level

HPLC assay method for determining Amphotericin B levels in serum and tissue specimens

Bioassay for Determining Itraconazole Levels in Blood

Bioassay for Determining Voriconazole Levels in Blood

Reference method for antifungal susceptibility testing of filamentous fungi.

Susceptibility testing of amphotericin B and itraconazole

Methods for assaying gliotoxin production in Aspergillus fumigatus

EUCAST Technical Note on the method for the determination of broth dilution minimum inhibitory concentrations of antifungal agents for conidia-forming moulds

Sampling Aspergillus spores in air

Sampling Aspergillus spores in water

Solutions

Physical constants

Poisson calculations

Codon chart and amino acid symbols

DNA mobility in gels

Units and formulas

Bacterial Transformation and Transfection: A summary

Commonly used restriction enzymes and assay buffers

Listing of M13 (pUC) cloning sites

Oligonucleotide universal primers used for DNA sequencing

Taq Cycle Sequencing Reagent Preparation

Primers

References

NOTE: Protocols are credited to the person who donated it or the original source of the protocol if it is known - the person donating is NOT necessarily the person who originally wrote the protocol. If anyone wishes to claim credit for a protocol please contact us