It’s been a while since the last lab note update – August 26th post on Halobacterium genome extraction was the last post, more than a month ago.

The Halobacterium genome extraction optimization for Nanopore Flongle sequencing continues. After a couple of weeks of some strange hectic schedules, I was finally able to sit down for the last couple of days to really think about the protocol at hand.

A quick update on the third high molecular weight extraction test on our Halobacterium – the culture used for this test is our ~80th subculture. With this we’ve been running continuous acidic media subculture of Halobacterium mutant strain for 551 days, or a little over a year and a half.

Last Halobacteria genome extraction test (for ONT Flongle sequencing) happened without using any real reagents like proteinase K and RNase – both to see how the skeleton protocol fares with the culture (which is a pretty standard way we do things around here) and because we’re completely out of the said reagents at the time.

EDIT: The author of the CoLoRd paper responded with clarification and some parts of the note were corrected with corresponding EDIT tag. His response is copied at the bottom of the post (also in the comments section way below). Thank you!

The Halobacterium flongle sequencing data is approaching rapidly – I decided to take the week to clean up our in house high-molecular weight DNA extraction protocol, adapt them for the S-layer membrane of Halobacterium (for example, the extensive freeze-thaw process we used for Deinococci and gram-negative microbes would not be necessary here) and test out […]

This is the first post under the ‘history’ heading on this online lab note, so I’ll start with a bit of a tangent on why there will be more science history related notes and posts on this site going forward.

As I’ve written about a couple of times in this lab note, I have ongoing still-cultures of Halobacterium NRC-1 control and its tentative acidotolerant mutant strain going on in our studio-lab.

The Flongle sequencing of our potentially mutant Halobacteria NRC-1 is right around the corner (as soon as we get that interminable computer hardware issue out of the way), and I’ve been busy catching up on literature and compiling tools and data we might need for post-sequencing analysis.

Tonight we’re continuing on with the weekly study of the Tree Thinking textbook, proceeding to chapter 2. “Tree thinking and its importance in the development of evolutionary thought.” The chapter covers the transition from ladder thinking around the concept of evolution to tree thinking, beginning with Jean-Baptiste Larmarck’s concept of Scala Naturae- the ladder of […]

I recently wrote about the 16S barcoding results for our mysterious East River bacteria – it’s quite likely that the bacteria is a novel Methylobacterium from class alphaproteobacteria, and we’re going to try a full genome sequencing soon.