Matthew Croxen

Amplicon sequencing of pasteurized retail dairy enables genomic surveillance of H5N1 avian influenza virus in United States cattle Highly pathogenic avian influenza (HPAI) viruses with H5 hemagglutinin (HA) genes (clade 2.3.4.4b) are causing an ongoing panzootic in wild birds. Circulation of these viruses is associated with spill...

New in @plosone.org : Amplicon sequencing of pasteurized retail dairy reveals H5N1 avian influenza virus in U.S. cattle milk. Tiled-amplicon NGS achieved >90% genome coverage from pasteurized milk samples, enabling genomic surveillance of H5N1 spillover in cattle. journals.plos.org/plosone/arti...

Black Microbiologists Association Moving Microbiology Forward

It’s Black Inclusion Week this week. If you are a Black microbiologist we would recommend connecting with the Black Microbiologists Association. They are working hard to increase visibility and facilitate connections: blackinmicrobiology.org #BlackInMicro #BIW2025

T7 is short enough that they can be designed at the 5' end of an oligo

I think it's a good idea, otherwise you are liking driving overexpression of downstream genes, or their antisense RNA (which may prevent translation). Or could mess up plasmid stability if it's replication is based on RNA like ColE1

T7 terminator or rrnB T1T2 I used to use frequently

Are these optimized promoter sequences for strong constitutive expression? Perhaps you don't need as much product made, and can use a less efficient sequence?

Conversely clone into a lower copy number plasmid?

Transcriptional terminators may help.

The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation a...

A new version of our Mtb pangenome preprint is out! Expanded analysis of the full pangenome data and answering all those questions the reviewers asked for ;). Great working with
@mabi-behruznia.bsky.social @danwhiley.bsky.social @blackpassiflora.bsky.social and others
www.biorxiv.org/content/10.1...

The Matthew effect in science funding | PNAS A classic thesis is that scientific achievement exhibits a “Matthew effect”: Scientists who have previously been successful are more likely to succ...

Mathew effect

“…early funding success introduces a growing rift, with winners just above the funding threshold accumulating more than twice as much research funding (€180,000) during the following eight years as nonwinners just below it.”

www.pnas.org/doi/10.1073/...

Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons. Published #OpenAccess and fee-free in #MGen using a #PublishAndRead agreement: https://doi.org/10.1099/mgen.0.001312

Home A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
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Pathoplexus| Home Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.

One of the reasons I've been quiet on Bluesky for a few months is because I've been working on something big - something I'm really happy to share now! Pathoplexus.org
A new, open-source database for pathogen sequence sharing. 👐🧬🌎

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Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosqu... The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and pr...

This is v impressive from @pathogenomenick.bsky.social and Co. Trap mosquitoes with CO2 (dry ice), and by sequencing them+bloodmeal+viruses, you get information on host, vector and arboviruses. Piloted in Sao Paolo.
www.microbiologyresearch.org/content/jour...

1. Canadian researchers publish the first estimates of 2023-24 #flu vaccine effectiveness that I've seen to date, in Eurosurveillance. The VE is pretty good — 61% overall against H1N1, which was responsible for the vast majority of cases.
#EpiSky www.eurosurveillance.org/content/10.2...

My attempt