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Items tagged with: phage
Systematic and scalable genome-wide essentiality mapping to identify nonessential genes in phages
In this work, authors use an arrayed genome-wide CRISPR interference assay to map gene essentiality landscape in the canonical coliphages λ and P1.plos.io
🎉 New preprint from the (MDM) lab:
🔗 https://www.biorxiv.org/content/10.1101/2023.11.22.567924v1
❓ How accurately can we predict diverse #bacteriophage bacteria-interactions from their #genomes only ?
🦠 We created a matrix of >38k #phage-#bacteria interactions to find out (=> AUROC 86%) & used our predictions to recommend tailored phage cocktails.
Predicting which phages infect which specific strains would allow to better fight bacterial infections and understand #microbial ecology.
1/n
#microbiology #virus #phagotherapy
Predicting phage-bacteria interactions at the strain level from genomes
Predicting how phages can selectively infect specific bacterial strains holds promise for developing novel approaches to combat bacterial infections and better understanding microbial ecology.bioRxiv
Doctoral student in in structural and functional protein bioinformatics
Description of the workplace In the Atkinson lab we are interested in making discoveries about protein function and structure, with a focus on bacterial immune system components that protect againstlu.varbi.com
Transient eco-evolutionary dynamics early in a phage epidemic have strong and lasting impact on the long-term evolution of bacterial defences
Organisms use a range of defence systems to protect against their parasites. Using a bacteria-phage model system, we investigate what drives the transient evolution of different systems, which has important implications for host ecology and pathogeni…plos.io
#USFCMS #microbiology #micro #virology #phage #virus
https://youtu.be/GOWEANUgzpw
Matters Microbial #2: Shock and awe microbiology and a chat with Mya Breitbart
Mark discusses some “shock and awe” concepts about the microbial world that he introduces to his microbiology students, and asks three important questions ab...YouTube
A Roadmap for Genome-Based Phage Taxonomy
Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy.MDPI
Studying some phage genes with scattered, partial alignments in varying degrees (40~+90%) of ID against closely related cousins (~93% ANI).
I'm thinking intragenic insertion/shuffling - but what kind of signals could I look for here? Common scars? Models to reference? #phage #bioinformatics #genomics
Happy to say I defended my dissertation "Methods and complexity in phage-bacteria ecology and evolution"!
Much thanks to all those who supported me throughout my PhD.
I'm glad to be sticking around the Turner Lab for another year as a post-doc to continue my work on multispecies phage-bacteria communities
#PhDone #AcademicChatter #AcademicMastodon #Academia #PhD #Ecology #Evolution #Phage #Phages
Happy to see the first experimental project I led finally out in the world! With Jeremy Moore, Sydney Olsen, and Mike Travisano
We combined experimental evolution and mathematical modeling to ask: do bacteria evolve to swim away from phages?
1/n
https://doi.org/10.1101/2023.04.29.538831
#microbiology #evolution #ecology #phages #phage #bacteria #MicrobialEvolution #MicrobialEcology
Fight not flight: parasites drive the bacterial evolution of resistance, not avoidance
In the face of ubiquitous threats from parasites, hosts often evolve strategies to resist infection or to altogether avoid contact with parasites. At the microbial scale, bacteria frequently encounter viral parasites, bacteriophages.bioRxiv
Phages... So many #phage and they are all #prophage integrated into a #bacteria #genome
A few million prophages from > million bacterial genomes
Are prophages good or bad for bacteria? The data shows they provide heaps of benefits
The paper is in #biorxiv and the data is on #figshare
https://www.biorxiv.org/content/10.1101/2023.04.20.537752v1
https://open.flinders.edu.au/projects/Prophage_predictions/162127
The Promise and Pitfalls of Prophages
Phages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through lysogenic conversion.bioRxiv
https://www.biorxiv.org/content/10.1101/2023.03.19.532758v1
Diverse and abundant viruses exploit conjugative plasmids
Viruses exert profound evolutionary pressure on bacteria by interacting with receptors on the cell surface to initiate infection.bioRxiv
Designed, built, trained, and tested with #phage genomes, it also works on #bacteria and #eukaryotes too.
https://www.biorxiv.org/content/10.1101/2023.04.10.536325v1
Programmed ribosomal frameshifts, and how to find them
One of the stranger phenomena that can occur during gene translation is where, as a ribosome reads along the mRNA, various cellular and molecular properties contribute to stalling the ribosome on a slippery sequence, shifting the ribosome into one of…bioRxiv
https://www.nature.com/articles/s41586-023-05862-7
Ubiquitin-like Conjugation by Bacterial cGAS Enhances Anti-phage Defence - Nature
Nature - Ubiquitin-like Conjugation by Bacterial cGAS Enhances Anti-phage DefenceNature
Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY
https://www.biorxiv.org/content/10.1101/2023.02.24.529968v1?rss=1
#phage #viruses
Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown.bioRxiv
It uses the degenerate codons to only give you the AA's you really want in any position.
https://github.com/retospect/phagetrix
Will add more statistics later.
You can try it in google colab.
GitHub - retospect/phagetrix: Optimizer for degenerate codon use in phage library generation.
Optimizer for degenerate codon use in phage library generation. - GitHub - retospect/phagetrix: Optimizer for degenerate codon use in phage library generation.GitHub
The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice
https://www.nature.com/articles/s41467-023-36526-9
#phage #viruses
The ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice - Nature Communications
To protect from host attack, numerous jumbo bacteriophages establish a micron-scale, protein-based structure to enclose their replicating DNA.Nature
https://www.nature.com/articles/s41564-022-01318-2
#phage #bacteria #crispr
Restriction endonuclease cleavage of phage DNA enables resuscitation from Cas13-induced bacterial dormancy - Nature Microbiology
Deployment of some CRISPR-Cas systems stunts host growth by degrading all transcripts, but Listeria seeligeri reverses dormancy using restriction-modification-based phage DNA targeting.Nature
"This transcriptomics-driven characterization of LUZ100 supports recent evidence that T7-like phages should not automatically be assumed to have a strictly lytic life cycle."
https://journals.asm.org/doi/full/10.1128/msystems.01189-22?af=R
#phage #viruses
"Collectively, our data support a model where suppression of quorum-regulated virulence factors by Pf4 allows P. aeruginosa to evade detection by innate host immune responses."
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010925
#viruses #virology #symbiosis #phage
Tripartite interactions between filamentous Pf4 bacteriophage, Pseudomonas aeruginosa, and bacterivorous nematodes
Author summary Pseudomonas aeruginosa is an opportunistic bacterial pathogen that infects wounds, lungs, and medical hardware. P. aeruginosa strains are often themselves infected by a filamentous virus (phage) called Pf.journals.plos.org
Need a #virus or #phage bioinformatics tool?
Have a #virus or #phage bioinformatics tool?
Check out this google sheet and add your new tools
https://docs.google.com/spreadsheets/d/1ClNgip08olKK-oBMMlPHBwIcilqSxsan8MEaYphUei4/edit#gid=0
Viral Bioinformatics Tools
Sheet1 Name,Category,Phage, Virus, or Both,Methods,Citation,URL,Last update (YYYMMDD),Notes,Install from conda,Install from pip,Install from source,Database size if required for download,Dependencies,Runs on a laptop,Runs on a cluster MaGplotR,CRISP…Google Docs
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0281769
Unusual prophages in Mycobacterium abscessus genomes and strain variations in phage susceptibilities
Mycobacterium abscessus infections are relatively common in patients with cystic fibrosis and are clinically challenging, with frequent intrinsic resistance to antibiotics.journals.plos.org
Have a #virus or #phage bioinformatics tool?
Check out this google sheet and add your new tools
https://docs.google.com/spreadsheets/d/1ClNgip08olKK-oBMMlPHBwIcilqSxsan8MEaYphUei4/edit?usp=sharing
Viral Bioinformatics Tools
Sheet1 Tool name,Category,Phage, Virus, or Both,Methods,Citation,URL,Last update,Notes,Install from conda,Install from pip,Install from source,Database size if required for download,Dependencies,Runs on a laptop,Runs on a cluster Pharokka,Annotation…Google Docs
https://www.nature.com/articles/s41598-023-27734-w
Monitoring phage-induced lysis of gram-negatives in real time using a fluorescent DNA dye - Scientific Reports
Scientific Reports - Monitoring phage-induced lysis of gram-negatives in real time using a fluorescent DNA dyeNature
https://www.nature.com/articles/s41396-023-01358-4
Congrats to all !
CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice - The ISME Journal
The ISME Journal - CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic miceNature
I was a #postdoc at the time and I had 1 evening to produce something around the idea that virulence in #bacteria is often 'all about the #phage ... '
A lucky break for me!
#MastoArt #Introduction
