I’ve mostly stumbled my way into the amateur pursuit of biology, lacking a realistic path to studying the topic in advanced settings.

Our last attempt at 16s barcode sequencing the East River bacteria wrapped up with out a solid conclusion, owing to the less than spectacular sequence fidelity, and the question of Methylobacterium hit from the salvaged sequence remaining suspicious on the account of it being a contaminant of sequencing reagents.

A particular midpoint rooted Deinoccoccus-Thermus phylogenetic tree I made during the last SCG hmm set curation have been on my mind for the last few days.

In a previous lab note entry I outlined a workflow for curating a subscreened single copy gene HMM set from a selection of genomes and pfam-HMM, courtesy of the GToTree pipeline. The process works quite robustly, and I was able to make more than a couple of very interesting datasets through it since then.

One thing I used to do with some of the environmental phage sampling runs in the past (both soil and liquid) was to simply crash them with cracking buffer and see what sort of bands I would get on a gel – of course, most of the time whole environmental samples would result in genomic […]

Sometimes availability of a good tool marks the beginnings of great research questions, just like the case with the wonderful GToTree– a phylogenetics tool I view as the gold standard for utility, ease of use and documentation for researchers and students alike.

In a past episode of our slow misadventures into nature-poking, we PCR’d out 16s barcoding sites from a East River bacterial sample and a peculiar branching bacteria sampled from an iridescent biofilm formed around a mangrove culture.

My initial attitude during the planning stages of Deinococcus radiophilus sequencing project was that the organism would provide a good first step for delving deeper into nitty gritty details of modern microbiology, and that I’ll eventually grow out of it. However, the more I study the genome of Deinococcus radiophilus, the more interesting the entirety […]

Prior to our deep dive into sequencing and assembling the Deinococcus radiophilus genome, we shared the common wisdom among the laypeople, and perhaps more people in the research community than most would like to admit;

The cultures of red-tinted bacteria (hopefully a bacteriochlorophyll utilizing species of some sort) from previous East River sampling run were getting a little long in the tooth, so I subcultured them into the new, smaller autoclavable plates with better seal using the last of the PPES-K media.

The initial test recorded in the blue shift DNA mutagenesis test II entry failed, most likely due to the state of the competent E.coli. We ran the same experiment described in the previous post again, with freshly prepared NEB turbo competent E.coli.