Happy Gypsy
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happygypsy.bsky.social
Happy Gypsy
@happygypsy.bsky.social
37 followers 180 following 2 posts
I'm a very boring bear-like person focusing on food safety, microbial genomics, bioinformatics, zoonoses, European union, getting easily angry when reading stupid things from stupid people
Posts Replies Media Videos
Reposted by Happy Gypsy
who.int
We see you.

WHO is grateful for the love 💙 and messages of support we received.

We stand by you. #HealthForAll
January 28, 2025 at 11:23 AM
Reposted by Happy Gypsy
andrewjpage.bsky.social
At @theiagen.bsky.social we are hiring a fully remote IT/Cloud security operations manager, based in the US. You'll get to work with me in public health and microbial bioinformatics which I find is very personally rewarding!
theiagen.pinpointhq.com/en/postings/...
IT/Cloud Security Operations Manager
Job Opening: IT/Cloud Security Operations Manager at Theiagen Genomics in Remote-US.
theiagen.pinpointhq.com
January 28, 2025 at 12:13 PM
Reposted by Happy Gypsy
stcmicrobeblog.bsky.social
a timely love letter 👏 which we fully endorse.
...and wonder if large data centers in Europe – we don't have to name them – might be on hand to mirror PubMed/GenBank if the new US administration continues as it has started and eventually shuts down the NIH completely.
c0nc0rdance.bsky.social c0nc0rdance @c0nc0rdance.bsky.social · Jan 27
This is just a short love letter to PubMed:
absolutely one of the best things US agencies have ever done for science.

'When I were a lad': we had databases of articles (Science Citation Index Expanded or Medline) but the only way to access text was to find the physical journal then photocopy it.
National Library of Medicine's PubMed search engine.
January 27, 2025 at 7:12 PM
Reposted by Happy Gypsy
nanoporetech.com
Recent #birdflu cases highlight the need for proactive #pathogen monitoring. Read how researchers using nanopore sequencing in wastewater detected surges in #influenza A, showing its potential as an early warning system.

Read here: www.the-microbiologist.com/news/sewage-... #H5N1
Sewage could act as early warning system for influenza A outbreaks
Researchers monitoring wastewater for avian and human influenza A virus have detected a surge in virus as the flu season got underway, showing that the technique could act as an early warning system f...
www.the-microbiologist.com
January 27, 2025 at 6:08 PM
Reposted by Happy Gypsy
natachacouto.bsky.social
Registration for #IMMEM14 is now open! Don't forget it is limited to 350 participants so secure your spot. @escmid.bsky.social @esgem.bsky.social escmid.org/congress-eve...
Registration & Information
Learn more about the congress and events hosted by ESCMID in the fields of Clinical Microbiology (CM) and Infectious Disease (ID).
escmid.org
January 28, 2025 at 11:16 AM
Reposted by Happy Gypsy
astrokatie.com
Withdrawing US funding from the World Health Organization is a potential disaster for public health worldwide, due to the impact it will have on the important work the WHO does. Preventing the CDC from even *talking* with WHO personnel is a step much farther toward undermining global health & safety
CDC ordered to stop working with WHO immediately, upending expectations of an extended withdrawal
U.S. public health officials have been told to stop working with the World Health Organization, effective immediately. The surprise decision is focused on the U.S.
apnews.com
January 27, 2025 at 10:31 PM
Reposted by Happy Gypsy
adamjkucharski.bsky.social
Our recent pre-preprint rapid review of epidemiological parameters for H5N1 influenza in humans, and implications for potential outbreak clusters: www.medrxiv.org/content/10.1...
January 27, 2025 at 9:21 PM
Reposted by Happy Gypsy
epcrocha.bsky.social
The contribution of natural transformation for the acquisition of novel genes has been notoriously difficult to quantify because it relies on recombination (which is affected by other processes). Here's a first estimate : doi.org/10.1101/2025... (for the very busy: 1-6% of gene gains) #MicroSky
Transformation, Recombination and horizontal transfer
January 27, 2025 at 1:11 PM
Reposted by Happy Gypsy
vscooper.micropopbio.org
Excellent article by colleague and mirror biology expert Michael Kay about the promises of mirror peptides and the perils of synthesizing mirror bacteria. undark.org/2025/01/16/o...
Reflecting on the Risks of ‘Mirror Life’
Opinion | Scientists are considering the threats posed by creating bacteria that are chemical mirror images of natural ones.
undark.org
January 27, 2025 at 4:00 PM
Reposted by Happy Gypsy
c0nc0rdance.bsky.social
This is just a short love letter to PubMed:
absolutely one of the best things US agencies have ever done for science.

'When I were a lad': we had databases of articles (Science Citation Index Expanded or Medline) but the only way to access text was to find the physical journal then photocopy it.
National Library of Medicine's PubMed search engine.
January 27, 2025 at 5:14 PM
Reposted by Happy Gypsy
duncanrobertson.bsky.social
"UKHSA has confirmed a case of influenza A(H5N1) in a person in the West Midlands region. Bird-to-human transmission of avian influenza is rare and has previously occurred a small number of times in the UK."

"The birds were infected with the DI.2 genotype"

ukhsa-newsroom.prgloo.com/news/human-c...
Human case of avian flu detected in England
UK Health Security Agency News and Media
ukhsa-newsroom.prgloo.com
January 27, 2025 at 2:41 PM
Reposted by Happy Gypsy
efsa.europa.eu
Applications for the #EFSAFellowship via #EUFORA are open!

Join 100+ professionals in shaping #EUFoodSafety & #RiskAssessment. Be a sending organisation and collaborate with top experts.

⏰ Deadline: 20 March 2025

🔗 Apply now: europa.eu/!ubnNQy

#EFSA #FoodSafety #Collaboration
January 21, 2025 at 1:46 PM
Reposted by Happy Gypsy
mgalactus.bsky.social
My go-to song for days in which morons and bullies gloat over their "victories" is this one from Italian alternative hip hop band Uochi Toki ⚔️
youtu.be/piCyRYd224I?...
Uochi Toki - Lo Spadaccino
YouTube video by Angelskiller666
youtu.be
January 21, 2025 at 4:02 PM
Reposted by Happy Gypsy
who.int
WHO comments on United States announcement of intent to withdraw bit.ly/4hrbeJ7
WHO comments on United States announcement of intent to withdraw The World Health Organization regrets the announcement that the United States of America intends to withdraw from the Organization. WHO plays a crucial role in protecting the health and security of the world’s people, including Americans, by addressing the root causes of disease, building stronger health systems, and detecting, preventing and responding to health emergencies, including disease outbreaks, often in dangerous places where others cannot go. The United States was a founding member of WHO in 1948 and has participated in shaping and governing WHO’s work ever since, alongside 193 other Member States, including through its active participation in the World Health Assembly and Executive Board. For over seven decades, WHO and the USA have saved countless lives and protected Americans and all people from health threats. Together, we ended smallpox, and together we have brought polio to the brink of eradication. American institutions have contributed to and benefited from membership in WHO. With the participation of the United States and other Member States, WHO has over the past 7 years implemented the largest set of reforms in its history, to transform our accountability, cost-effectiveness, and impact in countries. This work continues. We hope the United States will reconsider and we look forward to engaging in constructive dialogue to maintain the partnership between the USA and WHO, for the benefit of the health and well-being of millions of people around the globe.
January 21, 2025 at 10:38 AM
Reposted by Happy Gypsy
arambaut.bsky.social
I am amazed that what we now know likely happened in the market on the basis of substantially more data (and from multiple sources) lies squarely within the informed speculation based on 11 sequences and some assumptions about the evolutionary rate made 10 days after the first genome.
flodebarre.bsky.social Flo Débarre @flodebarre.bsky.social · Jan 20
That day, @arambaut.bsky.social posted an analysis of the first few available genomes of the new coronavirus.
Reading it given what we now know, it is amazing how much could already be inferred at the time. ▫️3/3

virological.org/t/preliminar...
Screenshot of part of the linked webpage. Text: The estimated date for the most recent common ancestor (and the 95% credible interval) are: Assumed rate Estimated date of MRCA 95% interval 1x10-3 27-Nov-2019 06-Nov-2019 – 16-Dec-2019 0.5x10-3 28-Oct-2019 13-Sep-2019 – 03-Dec-2019 Both these estimates are compatible with the TMRCA at the beginning of December. Observations From the available data it is not possible to tell whether the TMRCA of the sampled cases was in a human or a non-human animal (the reservoir). The sampled human viruses may be the result of multiple independent zoonotic introductions from a non-human animal source, a few introductions and then limited human-to-human transmission or a single introduction into the human population and spread. Determining which of these scenarios is more likely will depend on the assessment of other information (dates of onset, locations of likely non-human animal sources, epidemiological links between cases). However, the phylogenetic data thus far suggests that the jump or jumps from non-human animals occurred relatively soon before the earliest identified cases. If multiple zoonotic jumps occurred, these did not come from a virus reservoir that was genetically diverse. That, in turn, would suggest that the virus had only recently become established in the direct non-human source or that the initial human patients had been exposed to a non-human animal source that had a genetically limited population of viruses. This might be the case if one or a group of infected animals had been brought into Wuhan city from elsewhere and was in a position to expose multiple individuals.
January 21, 2025 at 1:17 PM
Reposted by Happy Gypsy
alanmcn1.bsky.social
Some Editors picks from @microbiologysociety.org MGen this week.

Exploring SNP filtering strategies: the influence of strict vs soft core

www.microbiologyresearch.org/content/jour...
Exploring SNP filtering strategies: the influence of strict vs soft core
Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments, with SNPs as the fundamental ...
www.microbiologyresearch.org
January 17, 2025 at 2:11 PM
Reposted by Happy Gypsy
lskatz.github.io
Fasten v0.8.5 released for fastq analysis/manipulation - now includes adapter trimming and sorting by minimizers!
January 17, 2025 at 2:03 PM
Reposted by Happy Gypsy
bjesseshapiro.bsky.social
First paper of the year is "Within-host genetic diversity of SARS-CoV-2 across animal species."

TLDR: Deer contain more within-host viral diversity than humans! Why? Read on.

(brief 🧵; 1/n)

academic.oup.com/ve/article/1...
Within-host genetic diversity of SARS-CoV-2 across animal species
Abstract. Infectious disease transmission to different host species makes eradication very challenging and expands the diversity of evolutionary trajectori
academic.oup.com
January 17, 2025 at 4:56 PM
Reposted by Happy Gypsy
microbiologysociety.org
“It is really hard for infectious diseases to effectively stop being specialists and move over into a new species. So, when that happens, it is striking and concerning” — Microbiology Society member, Ed Hutchinson, in an important article published in the Guardian yesterday -
Age of the panzootic: scientists warn of more devastating diseases jumping between species
Experts believe H5N1 bird flu belongs in a growing category of infectious diseases that can cause pandemics across many species. But there are ways to reduce the risks
buff.ly
January 16, 2025 at 5:09 PM
Reposted by Happy Gypsy
bioinfoadv.bsky.social
🛠️ VAREANT is open-source and available on GitHub! Its modular design supports multi-platform use, large datasets, and efficient genomic data preparation.

Explore it here: https://github.com/drzeeshanahmed/Gene_VAREANT

#OpenScience #DataAnalysis #BioinformaticsTools
GitHub - drzeeshanahmed/Gene_VAREANT
Contribute to drzeeshanahmed/Gene_VAREANT development by creating an account on GitHub.
github.com
January 16, 2025 at 12:16 PM
Reposted by Happy Gypsy
rkmicrobes.bsky.social
We derive iron-siderophore interaction networks among Pseudomonas strains from sequencing data. One key insight: natural strains form dense networks, whereas pathogens are loners. With @frimanscience.bsky.social @zhiyuanli.bsky.social & Nanjing colleagues
www.science.org/doi/10.1126/...
Siderophore synthetase-receptor gene coevolution reveals habitat- and pathogen-specific bacterial iron interaction networks
Coevolving siderophore genes shape bacterial iron networks, unveiling the complexity of cheating across habitats and lifestyles.
www.science.org
January 16, 2025 at 9:29 AM
Reposted by Happy Gypsy
biology.ox.ac.uk
Many congratulations to Prof. Sam Sheppard, Professor of Microbial Genomics and Evolution in Oxford Biology on this recent award.
ineosoxford.bsky.social Ineos Oxford Institute for antimicrobial research @ineosoxford.bsky.social · Jan 16
Prof Sam Sheppard, Digital Microbiology and Bioinformatics lead at IOI, has been awarded a @wellcometrust.bsky.social Discovery Award of £5m to develop vaccines against the diarrhoea-causing bacteria, Campylobacter.

Read more▶️ www.ineosoxford.ox.ac.uk/news/wellcom...
@sheppardlab.bsky.social
Wellcome Discovery Award of £5m awarded to Prof Sam Sheppard at the Ineos Oxford Institute
www.ineosoxford.ox.ac.uk
January 16, 2025 at 11:13 AM
Reposted by Happy Gypsy
andrewjpage.bsky.social
I talked to @meganphillips.bsky.social from Emory on the Micro Binfie podcast about her work on MRSA. The most interesting part of the conversation was on digging into really old research papers, seems to have been a totally different style of debate back then
soundcloud.com/microbinfie/...
138 Decoding Tetracycline Resistance in MRSA
In this episode of the Micro Binfie Podcast, host Andrew Page takes listeners to the heart of the microbial genomics hackathon in Bethesda, Maryland, for an engaging conversation with special guest Me
soundcloud.com
January 16, 2025 at 3:01 PM
Reposted by Happy Gypsy
peacockflu.bsky.social
Wendy Barclay and I are recruiting a postdoc for a project investigating the evolution of swine influenza viruses and how this impacts future pandemic potential.

Job is based at Imperial's South Kensington campus. Drop me a DM/email for more details.
www.imperial.ac.uk/jobs/search-...
Description
Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...
www.imperial.ac.uk
January 16, 2025 at 2:29 PM
Reposted by Happy Gypsy
erictopol.bsky.social
Whoa! When a large language of life model generates a protein equivalent to ~500 million years of evolution.
@science.org
science.org/doi/10.1126/...
Simulating 500 million years of evolution with a language model
More than three billion years of evolution have produced an image of biology encoded into the space of natural proteins. Here we show that language models trained at scale on evolutionary data can gen...
science.org
January 16, 2025 at 7:01 PM