I can’t recommend this IMPACTT microbiome research meeting enough, so note the July 15th abstract deadline. Fantastic meeting. Amazing location. @SydneyMorgan is also one of the best meeting organizers I know. Plus 19 prizes for students/postdocs for this meeting size is also pretty good odds. :)
So humbly honoured to have this recognition. But as we all of know, it really does take a village. This is a tribute to many. It’s important we look wholistically at what enables research innovation.
I also invite you to think of all those who support you and be so grateful for them all - as I am.
In part by request, we are moving www.pseudomonas.com and other web-based resources back to being hosted in Canada. This distracts from moving forward with development/updates/research, but we're honouring user needs. Thank you @glwinsor.bsky.social and SFU Research Computing for tireless efforts!
@reactome.org - a leading, carefully curated, human-focused biological pathway database - has made impressive changes. This includes to their new chat bot, with still a focus on quality (have to mention quality is still a focus if anything involving LLMs is noted 😊). Worth checking out.
What’s really cool is that thanks to @xkcd.com I’m now further thinking about how Exceptionally Weird phage-mediated bacterial virulence is, and how it evolved. Art stimulating science.
(With thanks to @makemydna.bsky.social for earlier chats and @iddux.bsky.social for encouraging this)
Hmmm... Just realizing:
Eukaryotic viruses are normal. They evolved to infect their host.
Archaea are normal too.
It’s bacteria, and their phages, that are WEIRD - with phages and other mobile elements evolving genes that help infect the host of their host.
Basically: Bacterial virulence appears to be a complex arrangement, with phages evolving genes that facilitated infection of the eukayotic host of their bacterial host. Evolving to infect not just your host, but actually the-host-of-your-host is non-trivial. Likely not easily duplicated in archaea.
Indeed, we found the lack of archaeal pathogens so fascinating, we wrote a paper on it! Mutually-exclusive phage/virus populations infecting Bacteria and Archaea, and association of "offensive" bacterial virulence factors with phage/mobile elements, may be key. pmc.ncbi.nlm.nih.gov/articles/PMC...
People ask "who is the father of bioinformatics?" and google's response is Margaret Dayhoff.
Great to see the inspiring Margaret Dayhoff getting profiled: www.nature.com/articles/s43...
I also smiled at her (appropriately) being google's response to the question asked by people "who is the father of bioinformatics" 😊
Music streaming services like Spotify wonderfully have albums, but older album *sides* are lost. The sides were part of the experience. R.E.M. side names are so fun. Bauhaus "Press the eject and give me the tape out of it" line is the end of an album. Wiki documents sides (TY!). Could Spotify?...
This BA.3 saltation best fits a chronic infection mutation distribution - approximately 10^6 times more likely than the global Omicron distribution in the SMDP app.
Interesting. No alarm bells, but still Erin Gill @makemydna.bsky.social checked this saltation using her SMDP app eringill.shinyapps.io/covid_mutati... finding it most fits the mutation distribution of a chronic infection. Chronic infections are still a source of novelty (cc @sarperotto.bsky.social)
Re the #NIH downtimes (including #NCBI #genbank #pubmed etc) See tldr.nettime.org/@ww/11408997...
"Someone is doing networking... Badly..."
Really feel for all those dealing with this
(from NIH IT, to global users).
In general, the decimation of so much critical infrastructure is hard to fathom.
Re DNA sequence DBs: While sequence is shared across #INSDC databases #ENA #Genbank #DDBJ, the presentation and granularity of annotations/metadata can differ notably, with diff. benefits, impacting searches and downstream analyses. All INSDC databases must be maintained - annotations are important
I appreciate how scary it can be for young parents to give their baby vaccines - they hear so much about reactions. But as vaccination rates go down its becoming more and more important to vaccinate to protect your child.
- Imagine, given this history of meningitis impacts, how meaningful it was when my kids got the H. influenzae vaccine in the 2000s. No meningitis.
Very grateful for the science that led to this vaccine. So many kids (including in our family) are enjoying their lives now with no meningitis impacts
- My aunt's age 2 death was meaningful since in the 60’s I had meningitis (bacterial, likely H. influenzae) at age 2 - but survived thanks to antibiotics
- BUT a colleague’s son in the 80’s had such meningitis. Due to growing antibiotic resistance they had treatment failure: became deaf in one ear
A brief thread of a personal illustration of the benefits of science, antibiotics, and vaccines over this past century:
- I discovered in my twenties that I had an aunt I didn’t know had existed. They had died young, in the 1930’s, of meningitis at age 2 (no antibiotics/vaccines at the time)
I should clarify that I’m referring to microbial sequence data here! Human genome data is a whole other kettle of fish
Anyone know more re this “ #Starling removal ” to address a flu #H5N1 concern? Are they removing a whole flock? Culling migratory wild birds will have other impacts. I encourage tackling more the root of the problem, knowing it’s challenging (but I need more info) www.cidrap.umn.edu/avian-influe...
Funniest email I've received re @pseudomonas.com in over 20 yrs of hosting this DB:
"Hello There, Would you be open to get pseudomona com for 500 usd? I noticed that you're the owner of pseudomonas, the plural version, so I believe this could be of interest to you too."
Indeed NCBI is getting hammered due to all the download requests (likely due to concerns about POTUS Exec Order data deletion potential). A reminder that the @ebi.embl.org www.ebi.ac.uk/ena/browser/... has a daily sync of data. It’s not exactly the same, so maintaining both resources is important.
Grateful for @glwinsor.bsky.social and his tireless efforts to maintain this Pseudomonas.com resource for this WHO priority pathogen for over two decades! We encourage any feedback - still accepting responses... bsky.app/profile/pseu...
Also the cautionary note that I'll encourage them to handle Gram-positive with a membrane, like Mycobacteria, and avoid forcing predictions into "secreted" under certain scenarios. Forcing predictions, versus enabling a category of "unknown" can mislead and really drive down precision...
Thanks for this! I'm contacting the authors as we're funded to improve PSORTb (finally - with 3D data!) & perhaps we can collaborate! Am I going batty though, or did they compare against PSORTb gutted with no SCL-BLAST module?? Hardly a comparison? Note they force predictions. Will check it out...
Love that you are noting this built environment impact on infectious disease spread (i.e. rats not crossing busy roads!) but I'm afraid the DOI link to your paper in this thread isn't working??
Check out this soap made by my fantastic #SFU colleague @minisciencegirl.bsky.social. She said she was not happy with her streak plating, 😂 but I think it’s awesome. #microsky #IDsky #microbiology #sciart
I discovered this outhouse I walk by in the day on a trail near SFU has a motion-activated floodlight at night - even though the outhouse is always LOCKED at DUSK. Why??!
I don't see any #SARS-CoV-2 variants after #XEC of real note yet for the holiday season. 🎉
Thanks for making these valuable resources still available! Re "what's next" I find it key to look at a variant's background (other variants and immunity level) in a region specifically for those taking off. A variant can take off due to its background but not be a threat more globally/elsewhere...
Great and thank you! Let Erin and I know how well it works for you!
