Entries by Dakota

Agaricus Bisporus DNA barcoding

We’ve finally acquired enough equipment from ebay, suppliers, and junk piles to conduct our own full scale test, so to speak, of our current makeshift DIY laboratory. The whole experiment involved DNA isolation, PCR, and a gel run with visualization in order to confirm that our equipment and reagents worked as intended. We managed to […]

Bacillus subtilis vs. homegrown penicillin

This is an update post on the quest to isolate a Penicillium strain from citrus fruit, in the hopes of at some point along the journey finding some penicillin.  A video was recently uploaded to our youtube channel that briefly explained the experimental conditions.  Basically, three different liquid cultures (not pure or sterile- they were grown in […]

Unboxing some new glassware & reagents

There are a few companies whose names get tossed around when it comes to getting decent equipment, glassware, and chemicals as a DIY’er; United Nuclear http://www.unitednuclear.com/ Elemental Scientific http://www.elementalscientific.net/ HMS Beagle http://www.hms-beagle.com/ …and today I think Home Science Tools http://www.homesciencetools.com/ can be added to the list. Though I have only ordered from Home Science Tools, I think it’s important […]

Penicillium isolation from citrus fruit

Natural product discovery is such an attractive field because it offers someone the chance to discover a new compound, not yet known to science, with potentially life saving medicinal properties.  Even most non-scientists will know about penicillin, its use as an antibiotic during World War II, and the numerous lives it has saved since then.  There […]

Ebay has everything you need – new RapidCycler PCR machine added to the bench

Although the goal was to get a conventional thermal cycler for PCR, this unique machine was too interesting to pass up doing a little more detective work on.  After reading a bit more about the RapidCycler system designed by Idaho Technology, it seemed to perfectly match what we wanted to do, amplify target sequences of […]

Primers for Fungal ID

Our next step for some of these fungal cultures is to be able to positively ID them by using DNA extraction methods along with PCR to amplify conserved regions of their genome. A couple of weeks ago, I was able to synthesize some common primers used for fungal barcoding. In general, some common regions that […]

Cool new gene-builder software

Been a while since I’ve updated.  We have a bunch of photos we need to upload of what happened to all the fungal cultures, so hopefully that will come within the next week.  In the meantime, I happened upon a pretty neat new piece of software, thanks to the diybio google group found at www.diybio.org called […]

What fungi (and bacteria) doth live here?

This is a follow up to this post, looking at what things are growing on our plates (and hopefully out of our samples).  We didn’t use antibiotics in our PDA growth media, so we expected some bacterial growth as chances are high that they would outgrow the fungi. We were not disappointed, many of our samples showed […]

The journey has begun…

After a long time of talking, we finally put a plan into action, leaving the world of theoretical microbiology behind and entering the world of practical application. The first part of our long journey (to be outlined at a later date) was to select some plant samples and sterilize their surface. Sterilizing their surface with […]