Issue 267
C&T Round Up for May 2024!
Round up time! This month we covered why phage researchers are flocking to Australia in July (and California in June!), discussed our 'phage picks' for this month, and shared a very special story from one of the researchers that make up the front lines of our 'Phage Alert' system.
Community digest1alert5updates7jobs1post
Phage alert
Urgent need for Klebsiella pneumoniae phages for a patient in Nepal
We are urgently seeking Klebsiella pneumoniae phages for a patient in Nepal.
Ways to help at this stage:
- By sending your phages for testing on the patient's strains
- By receiving the patient's strain and testing your phages
- By helping spread the word about this request
- By providing us with names/email addresses of labs you think we should contact
Please email staff@phage.directory if you can help in any way, or if you would like further details/clarification.
Let’s make a difference, Phage Directory
Updates
Meow! A cat named Squeaks needed phage therapy after falling 3 stories, and thanks to Ronen Hazan’s lab in Jerusalem, she got it, and it saved her leg!
Stephen Tang (Columbia University, USA) and colleagues published a new preprint on de novo gene synthesis by an antiviral reverse transcriptase. They demonstrate bacterial creation of extrachromosomal genes via rolling-circle reverse transcription of non-coding RNA, and how it results in antiviral immunity.
Toomas Mets (Lund University, Sweden) and colleagues published a new paper on the mechanism of phage sensing and restriction by toxin-antitoxin-chaperone systems. They show how E. coli TAC systems detect and neutralize phages by targeting major tail proteins and modifying mRNA, representing a novel hybrid antiphage defense mechanism.
Toshiki Nagakubo (University of Tsukuba, Japan) and colleagues published a new paper on how contractile injection systems promote Streptomyces spore formation via a phage tapemeasure-related protein.
Phages spotted on the big screen! "The Good Doctor" TV series finale apparently involves treatment of an important character with phage therapy!
Jobs
Elena Gómez-Sanz (University of Bern, Switzerland) is hiring 1) a postdoc in phages and AMR to develop strategies to visualize transduction dynamics; 2) a PhD student to characterize a unique staphylococcal phage-host library to assess and measure transduction and to select phage candidates with potential translational applications; and 3) a PhD student to measure contribution of staphylococcal temperate phages to bacterial adaptation to antibiotics.
Elena Gómez-Sanz (University of Bern, Switzerland) is hiring:
- a postdoc in phages and AMR to develop strategies to visualize transduction dynamics
- a PhD student to characterize a unique staphylococcal phage-host library to assess and measure transduction and to select phage candidates with potential translational applications
- a PhD student to measure contribution of staphylococcal temperate phages (and prophages) to bacterial adaptation to antibiotics
The Bordenstein lab (Penn State University) is hiring a Research Technologist to conduct research in host-microbe symbioses and the microbiome sciences, spanning insect endosymbionts, phages, and animal-associated microbiomes.
University of Greifswald, Germany is hiring a research assistant to work on the ‘UtiliPhage’ project, establishing protocols for phage isolation, purify phages, determine immunogenicity and more.
University of Otago, New Zealand is hiring a postdoc to contribute to research on enhancing seed inoculants with phages, adaptable phage solutions for biocontrol, and understanding phage-pathogen specificity for phage therapy.
The Luque Lab at the University of Miami is hiring a postdoc to contribute to an innovative project combining structural virology, multi-scale modeling, and environmental virology.
University of Toronto, Canada is hiring a Sessional Lecturer to teach the Principles of Genetic Analysis I Laboratory.
Community board
Registration is now open for the 2024 International Soil Virus Conference!
Soil virologists and enthusiasts will gather to explore the multifaceted roles of soil viruses within a One Health framework, with a special focus on meta-omics characterization of soil viruses and their connections with biogeochemistry, food web dynamics, and soil health.
The meeting takes place June 25 to June 27 at the University of California Livermore Collaboration Center (virtual option available).
Register by June 14!
Hello phage phans,
We’re at the end of May, and it’s been good for us! We just came back from a stint in Austria, where we visited Alpendorf for a wedding! It’s a beautiful place, and they have a stunning (and the world’s largest) ice cave. It’s well-worth a visit.
We’re getting settled in SF as Jessica’s starting her new position (we’ll share more details soon!) and I’m working to build AI-tools for biology (I promise to write more in this area, too).
Despite our new responsibilities, we’re still going strong on Capsid & Tail! We had a lot of great articles lined up in May, including introducing our new podcast interview series!
We’re still looking for guest posts for the rest of the year — we’d love to hear more about your deep phage research — anywhere from bioinformatics to phage engineering and phage/host molecular interactions. Both Jess and I and our audience absolutely love to read in-depth, behind-the-paper articles of some of your coolest findings.
If you’re looking for your next post-doc — or applying for a post-doc! — writing about your research will help you find that perfect match.
No idea is too small or too large — email me with your ideas: jan@phage.directory
This is what we covered in the month of May:
In this month’s Phage Picks, Jess and I picked four recent but diverse phage papers, that caught our attention in some way.
The first paper by Lin reviews the expanding universe of noncanonical contractile injection systems (CIS) in bacteria, which resemble phage tail fibers and have potential applications in programmable protein delivery. The second paper by Lugagne et al. demonstrates a deep learning model predictive control system that can predict and manipulate gene expression in thousands of individual E. coli cells by optimizing light stimuli, opening up exciting possibilities for phage-bacteria interaction studies and phage therapy cocktail design. The third paper by Sollier et al. introduces Figeno, a new open-source tool for visualizing multi-region genomic data with long-read support. The fourth paper by Rebula et al. provides a detailed guide to using CIM monolithic chromatography for effective phage purification, with a new technique called PATfix for real-time monitoring of phage concentration and impurity removal.
We’ve heard from some of you that you really like this format — our stats also show way tons of readership for Phage Picks! Please write us to let us know how we can improve it (or if you just have nice things to say you can tell us how much you like it)! We’re super proud of this format and can’t wait to share more papers with you.
In this announcement, Gary Trubl invites phage phans to attend the 2024 International Soil Virus Conference in Livermore, California from June 25-27. The conference will bring together soil virus researchers to foster collaboration, discuss cutting-edge research, and shape the trajectory of the field, and will feature a dynamic program of talks, discussions, poster presentations, and tours of National Lab facilities. The conference is limited to 60 in-person attendees (with virtual option available), and the objective is to explore soil viruses' roles in a One Health framework, with emphasis on meta-omics characterization and connections to biogeochemistry, food web dynamics, and soil health.
In this article, Gábor Apjok discusses his experiences volunteering to help with our Phage Alerts cases, despite the regulatory challenges surrounding phage therapy in his home country of Hungary. When responding to our Phage Alerts, Gábor attempts to match target pathogens with existing phages from his collection or isolate new phages from wastewater samples. The phage isolation process Gábor follows involves multiple rounds of purification, sequencing, bioinformatic analysis, and efficacy testing through killing curves and synergy assessments. While Gábor notes that phage isolation can be completed quickly, he highlights the regulatory hurdles that remain around phage production and purification in accredited labs before clinical use. Gábor argues that despite some challenges, phage therapy is a promising but underutilized tool that could help combat antibiotic resistance if given more governmental awareness and support to develop appropriate regulatory frameworks.
In this article (and brand new podcast!!), Jessica and Jeremy have a nice chat about the upcoming Viruses of Microbes (VoM). The team has been planning it since 2019, and this is the first VoM held outside of Europe, in Cairns, Australia (Ed. note: Just like Eurovision!). Right next to the Great Barrier Reef, it’s a tropical conference with lots of wildlife (crocs and drop bears!). It’s also shaping up with a diverse mix of 470 submitted abstracts, a sci-comm workshop for early career researchers, rainforest-themed socials with drop bears, and even an ECR-focused split session! It’s going to be the coolest VoM, so if you’re on the fence… definitely go. It’s a trip of a lifetime.