Entries by Dakota

DNA Barcoding of fungal endophytes followed by DNA sequencing

So while we’re waiting for some reagents to come in for the synthesis of our first chemical product, I’ve been helping to run a class on the natural products of fungal endophytes.  Most of the work we’ve been doing the past few years on our own has been surrounding bio-active secondary metabolites originating from fungal endophytes, inspired […]

Cultivate friendship and do cool science

So the past two weeks have been pretty crazy, in a good way.  I’ve managed to meet up with people from MIT, BOSSLab, and a few local biotechs on the North Shore.  It’s been strange not having to wake up to go to a 9-5.  I wouldn’t say it’s good, because distractions abound, but I […]

Quitting my job to start a biotech company in the basement

So after years upon years of talk, planning, more talk, and more empty promises to myself and others, I finally took a leap of faith.  At a certain point, you realize that there isn’t anymore time for planning and writing down ideas, action needs to be taken.  Many people, myself included, have let this unattainable […]

Endophyte isolation followup

  A few samples were selected for hyphal tipping and pure culture isolation.  Shown, in no particular order, are some of the samples to be taken and re-plated on fresh PDA.   Small pieces of the mycelia were excised with a sterile scalpel and placed in the center of fresh plates.  In some instances, like […]

Down n’ Dirty sequencing

We’ve done enough PCR on fungal cultures and samples to know that our PCR program, enzymes, and primers are working as intended.  In order to give us confidence in the ITS amplification of  unknown endophytic fungal samples, we wanted to amplify a known species and confirm that we can get clean sequencing reads. We performed […]

Basic endophyte isolation – testing the lower limits of aseptic technique

In the quest to isolate new endophytic fungi and build a strain library for screening, one of the main issues we face is still being unable to afford a laminar flow hood.  Sterility is a big concern in endophyte isolation, as it is very important to assure that any microorganisms found in the petri dish […]

Turning failure into success

After many gels that looked like the picture above, with only primer dimers, we had to reconsider our approach to PCR. Often times in the sciences, experiments don’t go as planned, and what we’ve come to learn is that it is incredibly important how you handle those situations, as neglecting sources of error can lead […]

Honing in on fungal DNA barcoding

We have successfully shown that we are able to barcode an unknown fungal sample, but the question now is, can we reproduce it? We have gathered the necessary tools and now face the task of making sure that our protocols are thorough, easy to follow and most importantly, reproducible. Over the past week we have […]

Simple Disc Diffusion Assay

                             This is a simple disc diffusion assay that we conjured up. The aim here is to see the effects an antibiotic has on a bacterial colony. In this case, we plated E.coli on PDA plates with no antibiotics in the media. We made […]

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 […]