Pia Sen

I gave a department seminar talk on Friday and the amazing art by @elliejameson.bsky.social made it so much easier for ecologists and systematists in the department to conceptualize necessary background for my work!

Check out our paper on intricate nested interactions between viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts. Excellent collaboration with @deemteam.bsky.social, @anagtz.bsky.social and Michail Yakimov
Free access link: rdcu.be/eLtCH
🧵 by @yifanzhou.bsky.social 👇

A Statement from NPR’s Editor in Chief on the Pentagon’s Press Policy.
Read More: www.npr.org/2025/10/13/g...

Ink drawing challenges During October I have been taking on an art challenge to develop drawing skills and habits through undertaking an ink drawing every day in October, based on a prompt word. After posting some microb…

This year I submitted a big transdisciplinary grant at the end of September and have now started the new semester’s teaching. I lacked a bit of motivation to draw and started a couple of days late! If I miss any days you can check out previous October art here: elliejameson.wordpress.com/inktober/

Published in Current Biology! P. aeruginosa can use its filamentous phage to inhibit competitors but high phage production is susceptible to cheater miniphage invasion. Subsequent phage tragedy of the commons can lower bacteria and phage fitness. Link: authors.elsevier.com/c/1lt5I3QW8S...

Filamentous cheater phages drive bacterial and phage populations to lower fitness Kubota et al. show that bacteria can use their filamentous phage to outcompete other bacteria, but increased phage production enables the evolution of cheater miniphages with truncated genomes. Miniphages exploit full-length phages and lower total phage production, causing some bacteria to lose their prophages and any associated fitness benefits.

Filamentous cheater phages drive bacterial and phage populations to lower fitness: Current Biology https://www.cell.com/current-biology/fulltext/S0960-9822(25)01198-4?rss=yes

Thread: Introducing GCUA v2.0 (General Codon Usage Analysis) - a Python tool for analysing codon usage patterns in DNA sequences! Originally developed in 1998, now completely rewritten with modern features. Let me walk you through what I like about this version (PLS RT) github.com/mol-evol/gcu...

ASM Issues Joint Statement Calling For Secretary Kennedy Resignation The American Society for Microbiology joined national medical, scientific, public health and patient organizations to call for the resignation of HHS Secretary Robert F. Kennedy Jr. to ensure the health of the American people. Protecting public health is our responsibility as physicians, scientists and patient advocates. It is also the responsibility of our elected officials, and we call for their support at this critical moment to protect the health of the nation.

Thanks to @asm.org and colleagues for stadning up for public health. Call Congress today and demand Kennedy's resignation
asm.org/press-releas...

Phage defence-system abundances vary across environments and increase with viral density | Philosophical Transactions of the Royal Society B: Biological Sciences The defence systems bacteria use to protect themselves from their viruses are mechanistically and genetically diverse. Yet the ecological conditions that predict when defences are selected for remain ...

Phage defence-system abundances vary across environments and increase with viral density

Phil. Trans. R. Soc. B by @seanmeaden.bsky.social, Edze Westra and @peterfineran.bsky.social

royalsocietypublishing.org/doi/10.1098/...

Every few months the "good lab hands" thing comes up and it misses a key point: you can learn to have good hands. Training matters.

Good hands aren't some magic gift from the PCR gods, you have to develop them through directed repetitive practice, like any other skill

What tool do folks use to make circular synteny plots for phage (or pretty mosaic) genomes? I’m running into the problem where most synteny tools I’m seeing don’t let you import your own annotations and ORFs 🥲

Synteny and linkage decay in bacteriophage pangenomes Bacteriophages are rich in genetic diversity, due to frequent horizontal transfer and recombination. This makes traditional microbial phylogenetic analyses, often based on the assumption of vertical inheritance, not suitable for interpreting this diversity. Here, inspired by recent work on bacterial pangenomes, we investigate the evolution of a collection of 3425 actinobacteriophage genomes. We find that synteny is strongly conserved: core genes have a well-defined order, and most accessory genes are localized in a few locations along the core genome backbone. Within the core genome alignment, linkage disequilibrium decays rapidly with distance in some groups, while phylogenetic structure in other groups causes long-range linkage. Our quantitative characterizations extend across many groups of phages and indicate widespread homologous recombination restricted by strong gene order conservation. ### Competing Interest Statement The authors have declared no competing interest. National Science Foundation, https://ror.org/021nxhr62, PHY-2309135 Gordon and Betty Moore Foundation, https://ror.org/006wxqw41, 2919.02 Chan Zuckerberg Initiative (United States), https://ror.org/02qenvm24, DAF grant to the Kavli Institute for Theoretical Physics (KITP) Swiss National Science Foundation, https://ror.org/00yjd3n13, 310030_188547

Synteny and linkage decay in bacteriophage pangenomes | bioRxiv https://www.biorxiv.org/content/10.1101/2025.08.12.669904v1?rss=1

Expression level of anti-phage defence systems controls a trade-off between protection range and autoimmunity - Nature Microbiology The authors examine several defense systems and find that increased expression enhances their protection range, albeit at a cost of autoimmunity.

Expression level of anti-phage defence systems controls a trade-off between protection range and autoimmunity | Nature Microbiology https://www.nature.com/articles/s41564-025-02063-y

The science was cutting edge, and the company was unparalleled- thank you everyone for such a welcoming and thrilling #GRCMicroPop! Looking forward to cyberstalking all your google scholar profiles ❤️

Incredible time at my first GRC! Thank you so much to everyone who made my experience at Microbial Populations so special :) I learned so much, saw amazing people (both ones I’ve known and new folks)! Left feeling inspired and reminded how much I love microbial ecology & its ppl 🧫🦠

Excited for my first Microbial Population Biology GRS + GRC!

(6/7) We highlight a few stories: evidence for retroposition into phage-specific loci, unique CapR domains not reported in group II intron-encoded homing endonucleases, and the presence of a group II intron in an annotated Inovirus, the first group II intron noted in a single stranded DNA organism.

PHAGE ICON!!!

(5/7) We use three lines of evidence along with Infernal hits. (1) The presence of full-length intronless homologs of genes the group II’s are inserted in. (2) Identification of pseudoknotted tertiary base-pairing not modeled by Infernal. (3) Similarity of intron-encoded ORFs to known group II ORFs.

(4/7) Recent accelerations in Infernal, a profile SCFG-based search and alignment tool from our lab, allow us to find these large RNAs across large genomic and metagenomic datasets.

(3/7) We wondered if they haven’t been widely identified in phage because they are challenging to find — they have low primary sequence similarity. Luckily, their splicing mechanism dictates strong conservation in parts of their secondary structure.

Group II intron mechanism

(2/7) Group II introns are self-splicing RNAs and the speculative ancestor of our own nuclear spliceosomal introns. They are widely known in bacterial, archaeal, and eukaryotic orgenallar genomes, but considered absent in phage.

Prevalence of Group II Introns in Phage Genomes Although bacteriophage genomes are under strong selective pressure for high coding density, they are still frequently invaded by mobile genetic elements (MGEs). Group II introns are MGEs that reduce h...

(1/7) Very excited to share my first PhD preprint on the interactions of two of my favorite mobile genetic elements: phages and group II introns!

www.biorxiv.org/content/10.1...

Escherichia coli phage-inducible chromosomal island aids helper phage replication and represses the locus of enterocyte effacement pathogenicity island Abstract. In this study, we identify and characterize a novel phage-inducible chromosomal island (PICI) found in commensal Escherichia coli MP1. This novel

An ICE, a PICI, and a phage walk into a cell… and start crosstalking. Interesting read on how MGEs juggle interactions like pros! 🦠

academic.oup.com/ismej/articl...

Interactions and evolutionary relationships among bacterial mobile genetic elements Nature Reviews Microbiology, Published online: 11 March 2025; doi:10.1038/s41579-025-01157-yIn this Review, Lang and colleagues present an overview of the current knowledge landscape regarding mobile genetic elements in bacteria, with a focus on their…

New online! Interactions and evolutionary relationships among bacterial mobile genetic elements

Biology’s Saw, Engineering’s Xu Win CAREER Awards | Columbian College of Arts & Sciences | The George Washington University Microbiology professor Jimmy Saw and civil and environmental engineering professor Zhengtian Xu were recognized with the National Science Foundation honor.

That’s my advisor!!!
columbian.gwu.edu/biologys-saw...

This is so true

Update: They were removed from our reviewer assignments completely. I'm so sorry to all those graduate students. Anonymous to protect the identity of the NIH employee I spoke to...I am on study section next month to discuss F awards. We were just instructed to put the F31-Diversity applications on the bottom of our priority list for review because there is a chance we may not be able to review them. My heart is breaking for the grad students and their mentors that put so much work into these just for them to be disqualified and thrown out.

Just in case you thought that removing DEI criteria would mean that everyone is competing equally: NIH is removing grad students from underrepresented backgrounds from the applicant pool altogether. Their applications will not be considered. Other students, not from these backgrounds, will be.

The statement reads: We are disappointed in the rapid capitulation by some U.S. institutions and organizations to recent attacks on diversity, equity, inclusion, and access. At their core, these weak arguments are fueled by the familiar underlying assumption that people from Black, Indigenous, and other marginalized identities cannot be excellent and therefore have not ‘earned’ our place in public intellectual life. However, we have always been competent, hardworking, and creative people who have contributed positively to society at large, across sectors but especially in science. We reject these attempts at silencing and erasure and will continue to be a place of respite and community in these turbulent times. To our members, your talent, skills, and safety are important! To our friends and allies, you may be feeling like everything happening is out of your control, but we want you to know that your voice and actions can make a difference. We want to point you towards some immediate actions that you can take. These are the top 3 issues we are concerned about and what you can do about it if you mirror our concerns. Freezing of federal funding and cutting grant programs for scientific research that have any connotation of being “DEI.” The potential confirmation of RFK Jr., a vocal anti-vaccination proponent, as the head of HHS. The American Society for Microbiology (ASM) removed their ABRCMS and IDEAAS webpages in addition to some scientist spotlights and written articles highlighting the current and historic contributions of microbiologists who are a part of marginalized communities including LGBTQIA+, Women, Indigenous and Black, as well as others page that could be considered “‘DEI”. Many have now been reinstated with changes to language (i.e. removing terms like “equity” and “marginalized”), and the statements released by ASM did not acknowledge the harm that they have caused to their members and showed no remorse for their actions.

A statement from the BMA Board Members to the BMA Community and Beyond.

Additional alt text to follow due to the character limit.

Federal health workers terrified after ‘DEI’ website publishes list of ‘targets’ The site calls out workers who have been involved with DEI initiatives. A majority are Black.

Federal health workers are expressing fear and alarm after a website called “DEI Watch List” published the photos, names and public information of a number of workers across health agencies, describing them as “targets.”