Steve Baker

Steve Baker

@sfbkr.bsky.social

sfbkr lab | influenza and alternative RNA splicing loyola university chicago

72 followers111 following15 posts

Steve Baker
@sfbkr.bsky.social

lab 2.0 in Chicago in search of a postdoc! Pursue virus-host interactions, post-translational modifications, and RNA splicing. Excellent in oral and written communication, lab and project management, and an ability to supervise and mentor trainees. sfbkrlab.org www.careers.luc.edu/postings/35620

sfbkrlab.org sfbkr lab We study how host alternative splicing shapes the outcome of influenza virus infection — from cryptic isoforms that antagonize the polymerase to the ANP32 proteins that support it.

Steve Baker reposted

Daniel Blanco-Melo
@dbm003.bsky.social

Excited to share our work on #AncientRNA from alcohol-preserved lungs, recovering the oldest human RNA virus genome (an 18th-century rhinovirus). Our study shows that viral RNA remnants persist in centuries-old tissue, opening new ways to study virus evolution and historical disease #Paleovirology🫁🦠

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Steve Baker
@sfbkr.bsky.social

Now live! Nearly all human genes contain multiple transcript isoforms - and the genes that predominantly control infection, ISGs, are no different. Using PacBio with analysis help from Yan Guo, Himadri noticed a never-before-seen transcript isoform of ISG15 that potently restricts flu 1/4

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Steve Baker
@sfbkr.bsky.social

Seminal work by Lenschow, Krug, and Bogunovic found that ISG15 is antiviral against influenza A and B virus in mice, but in humans ISG15 antagonizes influenza B virus and less so A. This is in part explained by ISG15’s ability to dampen inflammation 3/4

Steve Baker
@sfbkr.bsky.social

Using transcript-aware knockdown we found that endogenous ncISG15, and not ISG15, is antiviral against influenza A virus through polymerase restriction. But life finds a way, and influenza A NS1 antagonizes ncISG15. ncISG15 seems widely conserved- we’re excited how this finding shapes the field! 4/4

Steve Baker
@sfbkr.bsky.social

Now live! Nearly all human genes contain multiple transcript isoforms - and the genes that predominantly control infection, ISGs, are no different. Using PacBio with analysis help from Yan Guo, Himadri noticed a never-before-seen transcript isoform of ISG15 that potently restricts flu 1/4

biorxiv.orgbiorxiv.org
Steve Baker
@sfbkr.bsky.social

Non-canonical ISG15 (ncISG15) encodes an 8 aa N-terminal truncation. Like ISG15 it post-translationally modifies proteins and is secreted, but ISG15 is 100X more abundant (explaining its lack of ID). Things got spicy when we tested ncISG15’s function during influenza A viral infection 2/4

Steve Baker reposted

Karishma Bisht
@karishmabisht.bsky.social

Ever wondered how fever helps fight flu? Our research shows that fever-like temperature tip the scales in the battle between the influenza virus and the immune system by enhancing antiviral responses and altering viral RNA dynamics. Check out the full article here: www.science.org/doi/10.1126/...

science.orgFebrile temperature activates the innate immune response by promoting aberrant influenza A virus RNA synthesisFever promotes aberrant influenza A virus RNA synthesis and innate immune activation.

Steve Baker reposted

Stephanie L. Williams
@stephlwilliams.bsky.social

Very happy to have been able to contribute to this study that was published today in Science, which was truly a great collaborative effort. Avian PB1 provides a fitness advantage to IAV at febrile-range temperatures both in vitro and a hyperthermic nouse model 🦠 www.science.org/doi/10.1126/... #flu

science.orgAvian-origin influenza A viruses tolerate elevated pyrexic temperatures in mammalsHost body temperature can define a virus’s replicative profile—influenza A viruses (IAVs) adapted to 40° to 42°C in birds are less temperature sensitive in vitro compared with human isolates adapted t...

Steve Baker reposted

hanckslab.bsky.social
@hanckslab.bsky.social

Switches: New..lots of protein-coding mRNAs encode #miRNA ..former Ph.D. student's last hurrah building on our #mitochondria C15orf48/miR-147b stuff bmcgenomics.biomedcentral.com/articles/10....

bmcgenomics.biomedcentral.comA subclass of small RNAs is encoded by exons of protein-coding genes - BMC GenomicsBackground Small RNAs regulate gene expression in species across the tree of life. miRNAs, which impact a variety of cellular and physiological processes ranging from development and stress adaptation to host defense, are one of the best characterized classes of small RNA. Many miRNAs are produced from longer non-coding transcripts generated from host genes via a series of RNA cleavage reactions. The location of a small RNA within a host gene can shape the processing of the mature small RNA. For example, a type of miRNAs derived from host gene intronic sequence, referred to as miRtrons, are Drosha-independent and reliant on splicing for biogenesis. Relatedly, processing of a small RNA from an exon of a protein-coding mRNA, in principle, may destabilize it and compromise translation of the host gene. Prior to extensive transcriptome analysis, informatics analyses identified six human miRNAs embedded in exons of protein-coding genes and experimental studies have characterized additional anecdotal examples. Still, whether protein-coding mRNAs encoding small RNAs represent an appreciable class of host genes given the now recognized complexity of the transcriptome is unclear. Results Our analysis finds 201 small RNAs (118 human and 83 mouse) encoded by expressed exons of protein-coding genes (5’-UTR, CDS, 3’-UTR). Forty-six of these cases (29 human and 17 mouse) are also present in MirGeneDB which includes the most up-to-date miRNA classifications. Many of these small RNAs are poorly characterized with 96% of the protein-coding host gene relationships identified here not previously known. Furthermore, the identification of nearly fifty human and mouse small RNAs embedded within coding exons of canonical ORFs suggests that overlapping hybrid genes might be more common than previously appreciated in higher organisms. Expression analysis for a subset of these small RNAs indicates that many display differential expression across human tissues with the pattern correlating significantly with the expression of the candidate protein-coding host gene. Significance Overall, our analysis suggests that the number of protein-coding transcripts serving as host genes is greater than previously recognized. Our small RNA host gene classifications may serve as a resource to shed new light on small RNA biology, specific host genes, and gene regulation.

Steve Baker reposted

Chris Brooke
@christopherbrooke.bsky.social

Check out @mfarjo.bsky.social's new preprint where she uses a simulation-based approach to explore the evolutionary consequences of genetic mixing through co-infection for segmented viruses: www.biorxiv.org/content/10.1... hope you like it!

biorxiv.orgThe fitness consequences of coinfection and reassortment for segmented viruses depend upon viral genetic structureCellular coinfection between multiple virions is a common feature of viral infections. The collective virus-virus interactions enabled by these coinfections can influence the fitness of viral populati...

Steve Baker reposted

Erik Karlsson
@eakarlsson.bsky.social

**JOBS ALERT** The Virology Unit at @PasteurCambodia hiring 1 Scientist and 2 Postdocs to join our fast-moving, field-connected, research-driven team on emerging viruses and zoonoses. 🧪🧬🥼🦠🔬🐓💉🦇😷 Limited time to apply — and we need people to start ASAP.**👇

Steve Baker
@sfbkr.bsky.social

Looking for a good PDF reader app that will sync library across devices and allow for simple annotation. I don't need the reference manager aspect. Is there anything better than Paperpile?

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