Alistair Russell

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

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.

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)

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.

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

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...

🚨🚨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...

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.

#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/

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.

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!

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 ...

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/

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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...

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

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!

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.

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!

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...

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...

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...

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/...

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.

Junior, Assistant, or Associate Specialist – Xue Lab University of California, Irvine is hiring. Apply now!

The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more.
recruit.ap.uci.edu/JPF09601

This Thursday I will present the entirety of my PhD work (and a little bit more on the side) at #ASV2025 @amersocvirology.bsky.social . Be sure to be there if you'd like to know what is the hidden message of the coronavirus N gene!

Tiia is a superstar, and will be presenting not one, but two separate projects that are currently in the works. Make sure to check out her flash talk (W4-9) and posters (P1-28 and P21-1) on Tuesday. We welcome and appreciate your thoughts and feedback! #ASV2025

On our way to Montreal for #ASV2025. Make sure to come check out Matt’s (@mattmcfa17.bsky.social) work during W22-6. Can’t wait to see you all! @amersocvirology.bsky.social

Join our #DVGWorkshop2025 in Hamburg! Registration deadline: July 06. Take your chance to become part of the #DVGWorkshop2025 at @leibnizliv.bsky.social in Hamburg: www.leibniz-liv.de/aktuelles/ve...

#virusgenomics #defectivegenomes #DVGs #DIPs #antivirals #sequencing