Joe Bondy-Denomy

Joe Bondy-Denomy

@jbdsf.bsky.social

282 followers123 following19 posts

Joe Bondy-Denomy
@jbdsf.bsky.social

New experiment above! Once the phage library is made, one can spike in ~10^8 pfu of mutant pool into wild isolates, let phages replicate, sequence Tn and sensitively/quantitatively ID phage genes required in that isolate, not in lab strain. Phage phunctional genomics!

Joe Bondy-Denomy reposted

Cell Host & Microbe
@cp-cellhostmicrobe.bsky.social

Gut phage Acrs Type II CRISPR-Cas systems dominate human gut w/diverse phage Acrs targeting these systems. Widespread family, GutAcraca, adopts similar structures to inhibit Cas9 & regulate its own expression, highlighting phage adaptation to gut ecology www.cell.com/cell-host-mi...

cell.comDiscovery of human gut phage-encoded anti-CRISPR proteins unveils diverse mechanisms for phages to evade type II CRISPR immunityYuan and colleagues reveal that type II CRISPR-Cas systems dominate the human gut, and diverse gut phage-encoded anti-CRISPR (Acr) proteins target these systems. They identify a widespread family, Gut...
Joe Bondy-Denomy
@jbdsf.bsky.social
Erin Huiting@erinhuiting.bsky.social

Cell death is a fundamental mechanism of antiviral immunity across diverse organisms, including bacteria. As my final PhD project with @jbdsf.bsky.social, I was curious whether cell death is required for successful immunity with the ancient cGAS pathway known as ‘CBASS.’ Spoiler – the answer is no!

Joe Bondy-Denomy
@jbdsf.bsky.social

Woah love it! What a fun time Phage Phriends PhD

Adair Borges@adairb.bsky.social

A decade ago my benchmate Lina Leon and I were studying viruses and CRISPR together in grad school. Now Lina’s building immune assays at @dittobio.bsky.social to test our therapeutics proteins! Maybe the real PhD is the friends you make along the way [photo cred @jbdsf.bsky.social , 2016]

Joe Bondy-Denomy
@jbdsf.bsky.social

Wow!

Sorek Lab@soreklab.bsky.social

NLR-like immunity in bacteria A new study from the Alex Gao lab. The scope of this work is incredible!!! www.biorxiv.org/content/10.6...

biorxiv.orgDiverse bacterial pattern recognition receptors sense the conserved phage proteomeRecognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain ...
Joe Bondy-Denomy
@jbdsf.bsky.social

Phages are full of genes of unknown function that are likely adaptive in specific conditions. New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out tinyurl.com/bdcfrejh

Joe Bondy-Denomy
@jbdsf.bsky.social

Interested in phage defenses that natively block lytic phage used in therapies? Or do you want to figure out if a phage has a modified genome? Meet the END-nucleases, an enzyme family that can broadly restrict phages with many diverse modifications. From talented post-doc Wearn-Xin Yee!

Wearn Xin (Edeline)@wearnxin.bsky.social

We've identified a group of nucleases that can target multiple phages with hypermodified DNA, using a sensor domain present across many domains of life. We’ve even used this as a tool to find phages with hypermodified DNA! Really thankful to all the co-authors who have been such great help!

biorxiv.orgEND nucleases: Antiphage defense systems targeting multiple hypermodified phage genomesProkaryotes carry clusters of phage defense systems in defense islands that have been extensively exploited bioinformatically and experimentally for discovery of immune functions. However, little effo...
Joe Bondy-Denomy
@jbdsf.bsky.social

Thank you for moving it over here! Not yet up and running on bsky but learning :)

STCmicrobeblog@stcmicrobeblog.bsky.social

from 𝕏 for #phagesky #MicroSky @joeBondyDenomy The phiKZ jumbo phages build a protein based nucleus to protect their DNA(!), but what do they do before the nucleus is built? ... we identify host and phage proteins in an immediate early phage lipid vesicle. www.biorxiv.org/content/10.1...

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