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Zone88 Zone88
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9 years ago
I am trying to isolate fungi grown on an insect and identify them. Usually, for bacteria that we used in the class, I isolated the strain, extracted DNA, ran and amplified PCR and sent it to nearby university to sequence it. I know the general process but, I am still confused with the details. Now, I am working with fungus. So, how do I know which primers I should use for the fungus? And, let's say PCR is amplified. When they sequence the DNA, is the whole genome sequenced? (I really don't think so. Specific primer will bind to specific fragment of DNA, right? If you can correct me on this, I truly appreciate it) Then, if the whole DNA strand was not sequenced, how do they make identification for sure from one fragment of DNA? What makes one primer set work for multiple strains? If I am using different set of primer for fungus, how can I find out which primer to use?
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wrote...
Staff Member
9 years ago
In other words, you're looking for a protocol to isolate fungi? I've been out of the lab for three years now, so my help is limited here, though I did provide a protocol that will show you how to isolate fungi.

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- Master of Science in Biology
- Bachelor of Science
wrote...
Staff Member
9 years ago
THERE'S A GREAT METHOD IM USING IT FOR FUNGAL DNA EXTRACTION

To a 1.5-mL Eppendorf tube containing 500 mL of lysis buffer (400 mM Tris-HCl [pH 8.0], 60 mM ethylene diaminetetra acetic acid [EDTA] [pH 8.0], 150 mM NaCl, 1% sodium dodecyl sulfate), a small lump of mycelia from young culture is added by using a sterile toothpick, with which the lump of mycelia is disrupted. The tube is then left at room temperature for 10 min. After adding 150 mL of potassium acetate (pH 4.8; which is made of 60 mL of 5 M potassium acetate, 11.5 mL of glacial acetic acid, and 28.5 mL of distilled water), the tube is vortexed briefly and spun at 10000 × g for 1 min. The supernatant is transferred to another 1.5-mL Eppendorf tube and centrifuged again as described above. After transferring the supernatant to a new 1.5-mL Eppendorf tube, an equal volume of isopropyl alcohol is added. The tube is mixed by inversion briefly. The tube is spun at 10000 × g for 2 min, and the supernatant is discarded. The resultant DNA pellet is washed in 300 mL of 70% ethanol. After the pellet is spun at 10000 rpm for 1 min, the supernatant is discarded. The DNA pellet is air dried and dissolved in 50 mL of deionized H2O, and 1 mL of the purified DNA is used in 25 to 50 mL of PCR mixture. The extractions were done in duplicate assays for each sample.
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