Concluded my research trip to Belgium & Wales today, and had the privilege of giving a seminar at Swansea University yesterday about some of my past and my ongoing research!
Very grateful to @royalsocietynz.bsky.social and @isme-microbes.bsky.social for making this trip possible!
An upward angled photo of the historic Leuven town hall
Have arrived in Leuven today to spend a few weeks learning from some fantastic collaborations at @kuleuvenuniversity.bsky.social - huge thanks to @isme-microbes.bsky.social for making this trip possible!
We thought about it, but the dna wasn't usually particularly high molecular weight nor was it viscous so we never tried shearing
Yeah absolutely - so in kelp DNA for example we did some LCMS and found the likely culprit for blockages was polyphenols bound to the DNA onlinelibrary.wiley.com/doi/full/10....
But in the case of some of this data, it was supposedly 'pure' DNA from the zymo mock community.
I did try to see if the signal or quality change before the blockage - funnily enough the quality tended to be higher at the end of the read when it terminated due to a block, than when it terminated due to completing the read. But really just haven't had motivation recently do the proper deep dive.
Granted, this was from a quick and dirty analysis I did a year or so ago, but I tried it with the zymo mock community and also observed the same sort of thing. So i'm just curious as to whether the GC-rich sequences are more likely to block. Just for context, the 'combined' is all reads together.
Curious as to your thoughts - if I look at metagenomic datasets from ONT sequencing, and separate them based on end reason (i.e., blocked pore vs completely navigated the poor) - I find two very different communities. The grouping is based on the terminal base of DNA sequence (misc metagenomic data)
Anyone on here ever tried using a laser to break open really tough samples for DNA extraction? I'm working on some tough chitinous tissues which nothing seems to reliably lyse them - and thought I might take some inspiration from laser microdissection (which is a tad overkill/$$)
Has anyone here got much experience with microbial ecology and experimental pre-registration? I'm embarking on a new project, and would like to pre-register & peer review the experimental design - but I have no idea where to start.
🚨 Free one-week in person workshop on SLiM from 24th - 28th March at the University of Auckland. 📉🧬
Hands on tutorials will be lead by experienced SLiM users Dr @williampearman.bsky.social and Anna Clark.
Some ECR travel funds available.🎉
Register here 👉 docs.google.com/forms/d/e/1F...
Very glad to have this paper out - one of the cooler things to come out of my PhD. This also happens to be (likely) the last publication to come out of my PhD as well!
I don't understand why people don't sequence negative extraction controls. I've spent more time recently managing reagent contamination for low biomass extractions than i've spent doing the actual extractions. Extensive sterile filtering, UV, and EMA treatment seemed to be the only way that worked.
Am I right in assuming that blunting our humanities and social sciences research will dull our understanding of inequities suffered by Māori, and the role that a just Te Tiriti interpretation would play in resolving this?
Because if so, it's hard not to connect the dots to the true intent here.
