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Reposted by Alistair Russell

Kristen DeAngelis 🏳️‍🌈🏳️‍⚧️🍉 @kristenobacter.bsky.social · 7d

UMass Amherst Microbiology is hiring a tenure-track virologist. Come work with me! 🦠🧪
careers.umass.edu/amherst/en-u...

Details - Assistant Professor - Virology | Human Resources | UMass Amherst

careers.umass.edu

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Reposted by Alistair Russell

Tiffany Lowe-Power 🌱🦠 @tlowepower.bsky.social · 17d

Please repost -- The Univ. California Davis dept of Plant Pathology is hiring a Fungal biologist / Mycologist

Applications due Dec 1

Application portal: recruit.ucdavis.edu/JPF07339

Screenshot shows part of the job posting (with alt-text of the same text)

he Department of Plant Pathology at the University of California, Davis is seeking applications for a fulltime, tenure-track Assistant Professor position in Mycology, with a focus on plant pathogenic, symbiotic,
or mycotoxigenic fungi and fungal-like organisms (e.g., oomycetes). We are looking for a highly
motivated and creative scientist with a strong background in mycology and/or the biology of fungi and
fungal-like organisms that interact with plants. The successful candidate will be expected to develop a
world-class, externally funded research program that integrates both fundamental and applied aspects
of fungal biology within the context of plant pathology. We welcome applicants pursuing a wide range
of research topics related to plant-associated fungi, including but not limited to mechanisms of fungal
pathogenesis or symbiosis with plants, population genomics and evolution of fungal plant pathogens,
plant-associated fungal microbiomes and plant-microbe interactions, and/or one health approaches to
fungal diseases and antifungal resistance. Applicants working in other relevant research areas involving
pathogenic, symbiotic, or mycotoxigenic fungi or fungal-like organisms that affect plant health are also
encouraged to apply. The successful candidate will have significant opportunities for collaboration with
faculty in plant pathology, microbiology, genomics, and agricultural sciences, and to contribute to
addressing issues of importance to California’s agricultural and natural ecosystems.
The appointee primary teaching responsibilities will be teaching Introductory Mycology, an upperdivision lab class, and SAS 30, Mushroom, Molds & Society, a general education class for non-majors.
Additional graduate and undergraduate teaching responsibilities may be assigned based on
departmental needs and the candidate’s expertise. The department offers modern instructional
facilities, including a newly renovated teaching laboratory.

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Reposted by Alistair Russell

PLOS Biology @plosbiology.org · Sep 3

What causes viral transmission bottlenecks? This study uses barcoded virions to show that in the case of #influenza A #virus, early within-host replication dynamics (rather than a reduced inoculum population) drive loss of diversity during transmission @plosbiology.org 🧪 plos.io/4ngicDK

Population diversity declines between inoculated and exposed guinea pigs. Viral titers in nasal lavage samples are indicated by the overall height of the bar. Red lines show LOD (50 PFU/mL). Colors within the bars represent unique barcodes, and the height of each color indicates barcode frequency within the sample. Plots for individual animals are paired with those of their cage mate. Representative pairs for direct contact (top half) and aerosol (bottom half) exposure are shown from three experimental replicates. Guinea pig ID numbers are shown in the upper right corner of each plot.

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Reposted by Alistair Russell

Jacob Yount @yountlabosu.bsky.social · Sep 1

🚨🚨Our new preprint establishes the first robust model of severe influenza cardiac complications in WT immunocompetent mice. Heart transcriptomics implicated a potential therapeutic metabolic intervention that indeed shows beneficial heart/survival effects. 🦠🧫🧬🫁🫀🐀
www.biorxiv.org/content/10.1...

Cardioprotective effects of AMPK activation in H1N1 influenza virus infection

Cardiac complications are among the most common and severe extrapulmonary manifestations of influenza virus infection, yet they are rarely recapitulated in mouse models without immunodeficiency. We fo...

www.biorxiv.org

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Reposted by Alistair Russell

NiceLab @nicelab.bsky.social · Aug 30

Excited to share the most recent work from our lab! In which we seek out the cellular source of homeostatic IFNL in the gut and find that gut pDC are ‘rewired’ to produce IFNL over type I IFNs.

bioRxivpreprint @biorxivpreprint.bsky.social · Aug 29

Plasmacytoid dendritic cells in the intestine preferentially produce interferon lambda at homeostasis contributing to tonic localized innate immune responses https://www.biorxiv.org/content/10.1101/2025.08.25.672167v1

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Reposted by Alistair Russell

Gregg Gonsalves @gregggonsalves.bsky.social · Aug 28

#NIH is hanging by a thread. The #CDC has been decimated. #RFK Jr. and Russell #Vought are psychopaths--I don't say this frivolously--they are cold, calculating, inflicting violence on millions through public policy. It is where we are right now. These men are not normal. 1/

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Reposted by Alistair Russell

Isabel @isabelott.bsky.social · Aug 28

Please read all three senior officials’ resignation letters in full. I couldn’t even find quotes to pull. All three are cornerstones of modern public health. Dan Jernigan’s been at CDC longer than I’ve been alive. Department leadership left them in an impossible position.

Chris Geidner @chrisgeidner.bsky.social · Aug 28

All three are here: insidemedicine.substack.com/p/breaking-n...

Breaking News: Read three top CDC officials' resignation emails.

The end of an era.

insidemedicine.substack.com

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Alistair Russell @alistairrussell.bsky.social · Aug 27

There are other hits in our dataset, so I hope this may help others working on the same questions. I also hope our method is broadly useful to others!

Alistair Russell @alistairrussell.bsky.social · Aug 27

We further characterize the importance of transcription to an interferon response, consistent with prior work from Richard Randall, and newer work from AJ te Velthuis and Jonathan Yewdell.
pubmed.ncbi.nlm.nih.gov/24478437/
www.science.org/doi/10.1126/...
pubmed.ncbi.nlm.nih.gov/39605425/

Influenza A virus transcription generates capped cRNAs that activate RIG-I - PubMed

During influenza A virus (IAV) infection, host pathogen receptor retinoic acid-inducible gene I (RIG-I) detects the partially complementary, 5'-triphosphorylated ends of the viral genome segments and ...

pubmed.ncbi.nlm.nih.gov

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Alistair Russell @alistairrussell.bsky.social · Aug 27

Applying our system to infection with flu virus lacking an innate immune antagonist, we identify the NELF complex as significantly enhancing interferon transcription. Digging in mechanistically we find that inactivating this complex increases flu transcription, increasing viral RNA.

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Alistair Russell @alistairrussell.bsky.social · Aug 27

By taking the ratio of the signal RNA to the integration events (sequencing the DNA) we can infer if an edit increases, decreases, or does nothing to our test promoter.

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Alistair Russell @alistairrussell.bsky.social · Aug 27

By hooking up our promoter of interest upstream of a promoter driving a CRISPR guide, when our promoter is active a longer "signal" RNA is generated.

Description of CRITR-seq approach. A reporter promoter upstream of the U6 promoter for guide production drives the production of an mRNA that also contains the guide sequence. Sequencing is used to identify integration events, and activity of the test promoter (gDNA and mRNA, respectively). The effect of the guide at that test promoter can then be read out as the ratio of mRNA to gDNA. Edits that decrease activity at the test promoter decrease this ratio, increase, increase.

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Alistair Russell @alistairrussell.bsky.social · Aug 27

There are prior genome-wide screens, but they are pretty labor intensive and involve cell sorting. Taking a note from a method developed in yeast called CiBER-Seq developed by Nicholas Ingolia's group, and CROP-seq, developed by Christopher Bock's group, we developed a sequencing-only approach.

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Alistair Russell @alistairrussell.bsky.social · Aug 27

So what did we do? We are deeply interested into the inputs of the cellular event of viral detection and the production of interferons. Our prior work largely focused on viral variation, but we wanted to look into host processes that influence this event.

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Alistair Russell @alistairrussell.bsky.social · Aug 27

I also want to thank all three anonymous reviewers. If you saw the first preprint I hope you will agree it was much improved by their careful critiques. The review process was everything one could want.

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Alistair Russell @alistairrussell.bsky.social · Aug 27

As a still somewhat junior PI (less every day) I feel so incredibly lucky to have had the support and patience of my more senior colleagues.

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Alistair Russell @alistairrussell.bsky.social · Aug 27

I also want to thank our editor, Anice Lowen, and editorial board member Harmit Malik. Anice was also the editor on Alison's other paper in PLoS Pathogens. Her willingness to shepherd our papers through the review process is deeply appreciated.

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Alistair Russell @alistairrussell.bsky.social · Aug 27

Before giving a synopsis I want to give credit to the hard work of all of the authors (which I am fortunate enough to have them all from my group), particularly our lab alum, and my first graduate student, Alison Vicary.

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Alistair Russell @alistairrussell.bsky.social · Aug 27

Still worth celebrating things I think.
Our CRITR-Seq paper is now out online in PNAS
www.pnas.org/doi/10.1073/...

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

www.pnas.org

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Reposted by Alistair Russell

Fabian Rivera-Chávez @fabianrchavez.bsky.social · Aug 18

1/ Excited to share the first preprint from my lab! 🎉

My postdoc Paz asked how cholera toxin (CT) helps Vibrio cholerae thrive in the gut.

Turns out, CT rewires epithelial metabolism toward L-lactate production—fueling pathogen growth in the small intestine during disease

Cholera toxin-induced disease generates epithelial cell-derived L-lactate that promotes Vibrio cholerae growth in the small intestine

Cholera toxin (CT) promotes Vibrio cholerae colonization by altering gut metabolism to favor pathogen growth. We have previously found that CT-induced disease leads to increased concentrations of L-la...

www.biorxiv.org

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Reposted by Alistair Russell

Kristian G. Andersen @kgandersen.bsky.social · Aug 14

Just a reminder that if you want to do your postdoc in the best city in the world, well, you might be in luck - our position is still open and we're hoping to fill it within the next couple of weeks, so hurry up!

Kristian G. Andersen @kgandersen.bsky.social · Jul 15

Are you looking for a Postdoc or Research Programmer position? Want to work as part of highly collaborative infectious disease programs that have direct relevance to global health?

Well, we got you covered!

Learn more 👇

andersen-lab.com/about/

About - Andersen Lab

Learn more about the Andersen Lab, as well as jobs and career opportunities.

andersen-lab.com

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Reposted by Alistair Russell

Dr Jamie Gallagher @jamiebgall.co.uk · Aug 7

The Roslin Institute is looking for a full time Engagement Officer. Great to see them highlight that you don’t need a research background or PhD.
My research background is a massive help to me in my career, but that is just one of many routes that people can take into engagement. We need all voices!

Due to the amount of hands-on, lab-based engagement in our programme, we are looking for someone with at least basic (ideally biology-focused) lab skills, and we are very open to hearing about all relevant experience - a research background and/or PhD level qualifications are not required.

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Reposted by Alistair Russell

Tera Levin @teralevin.bsky.social · Aug 5

I'm excited to announce our new biorxiv preprint, wherein we investigate the evolution of the weirdest genetic locus I've ever seen! Behold the tgr genes of the social amoeba, which mediate self/non-self discrimination during facultative multicellularity 🐅 🧵 1/
www.biorxiv.org/content/10.1...

Hypermutable hotspot enables the rapid evolution of self/non-self recognition genes in Dictyostelium

Cells require highly polymorphic receptors to perform accurate self/non-self recognition. In the amoeba Dicytostelium discoideum, polymorphic TgrB1 & TgrC1 proteins are used to bind sister cells and e...

www.biorxiv.org

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Reposted by Alistair Russell

Carolina B. López @cblopezlab.bsky.social · Jul 31

Congratulations to SB Pye and team for validating several paramyxovirus copyback genomes by direct RNA-Seq (no PCR involved). Specially cool are species formed between nucleotide 1 of the genome and a sequence close to the trailer..these are real products! journals.asm.org/doi/10.1128/...

Validation of diverse and previously untraceable Sendai virus copyback viral genomes by direct RNA sequencing | Journal of Virology

Most viruses of the order Mononegavirales have been demonstrated to naturally generate copyback viral genomes. These genomes are critical determinants of infection outcomes; they interfere with standa...

journals.asm.org

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Reposted by Alistair Russell

Rob Finn @robdfinn.bsky.social · Jul 22

Great to see jackhammer is back! If you have not tried it please give it a go. We would welcome constructive feedback. We are still adding features.

HMMER @hmmer.bsky.social · Jul 11

📣 We’re pleased to announce the release of jackhmmer.
It’s now available for use, and we’d greatly value any feedback as we continue to improve the tool.

www.ebi.ac.uk/Tools/hmmer/...
Give it a try and share your thoughts!

#bioinformatics #hmmer

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