C&T Round Up for September 2023!

Issue 240 | September 29, 2023
8 min read
Capsid and Tail

This month we heard about the ICBRAR phage conference in India, got an excerpt from The Good Virus by Tom Ireland, had a look behind the scenes of a Swiss team battling UTIs with engineered phages, and learned about speeding up the phage therapy lab process from Jessica.

What’s New

The first patient in Armata Pharmaceuticals’ newest trial has been treated. This is part of the Phase 2a portion of their diSArm study, which evaluates the potential treatment of S. aureus bacteremia.

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Clinical trialsPhage therapyBiotech news

Jason Wilson (University of Sheffield) and colleagues published a new preprint on the molecular mechanism of phage tail contraction, shedding light on the structure of an S-layer-penetrating phage.

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Molecular MechanismsPreprintPhage-host interactions

In a new Current Opinion in Microbiology piece, Jochen Klumpp, Matthew Dunne, and Martin Loessner explore the potential of phage receptor-binding proteins for diagnostic and therapeutic applications.

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ReviewReceptor-Binding Proteins

Juergen Eckhardt, writing for Forbes magazine, recently wrote an article on phage therapy.

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Popular newsPhage therapy

Min Wang (Ocean University of China) and colleagues have identified a new Halomonas phage in the Mariana Trench. This is the deepest known phage isolation.

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Virus DiscoveryDeep-Sea PhageMariana Trench

Latest Jobs

PhD projectPhage defense
The Frunzke lab (Forschungszentrum Jülich, Germany) is seeking a PhD student to study bacterial antiviral immunity.
Gut phagesMolecular BiologyMetagenomicsPhD project
Eugen Pfeifer (Jouy-en-Josas, France) is hiring a PhD student to study phages in the human gut using molecular biology and metagenomics.
Phage EcologyMicrobial CommunitiesPhD Project
PhD Position in Phage Ecology in Microbial Communities at VU Amsterdam.
TechnicianBiotech
Oxford Silk Phage Technologies Limited (Oxford, UK) is hiring a phage technician.

Community Board

Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!

Medical-grade phage is now available for expanded access through Tolka.ai’s waitlist, after a year of hard work by Johan Wikstrom, Keqing Li, Thomas Hunt, Volodymyr Kulchytskyi, and the broader phage community; phage researchers can learn more at tolka.ai/expandedaccess.

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Medical-grade PhageInvestigational TreatmentExpanded Access

BBC Radio 4, a popular radio station in the United Kingdom, published a podcast episode titled “Bacteria: The Tiny Giants, Forests, Pharma and Phages” that explores various aspects of phage research and their impact on ecosystems.

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PodcastPopular science

From @scientiff via Twitter: Hey #scitwitter! I’m troubleshooting some #phage DNA extraction woes with our undergrads. We use phenol-chloroform-isoamyl and phase-lock gels for the process but we’re still getting high 260/230 after elution. Any advice on DNA clean up would be much appreciated!

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Phage twitterMethods

C&T Round Up for September 2023!

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Product designer and co-founder of Phage Directory
Co-founderProduct Designer
Iredell Lab, Phage Directory, The Westmead Institute for Medical Research, Sydney, Australia, Phage Australia
Twitter @yawnxyz
Skills

Bioinformatics, Data Science, UX Design, Full-stack Engineering

I am a co-founder of Phage Directory, and have a Master of Human-Computer Interaction degree from Carnegie Mellon University and a computer science and psychology background from UMBC.

For Phage Directory, I take care of the product design, full-stack engineering, and business / operations aspects.

As of Feb 2022, I’ve recently joined Jon Iredell’s group in Sydney, Australia to build informatics systems for Phage Australia. I’m helping get Phage Australia’s phage therapy system up and running here, working to streamline workflows for phage sourcing, biobanking and collection of phage/bacteria/patient matching and monitoring data, and integrating it all with Phage Directory’s phage exchange, phage alerts and phage atlas systems.

Hi everyone! Summer is right around the corner (or fall if you don’t live in the Upside Down), and we’ve had some great posts this month. It’s been so great hearing from various labs around the world, and reading about their cool phage work (even though it’s sometimes over my head).

If you’re working on some cool phage research and you want to tell the rest of the phage community, don’t hesitate to email me ([email protected]) or check out the Guest Writer’s Guide! There’s still a couple of more spots left for the rest of the year’s Capsid schedule.

We’re juuust about getting rested from running Evergreen and just about getting caught up with our phage work down here. Jess is up to her neck with ÄKTA phage work, and I’m working on some data upload, management, and cleaning pipelines I can’t wait to share next month. Though the AI hype is real, ChatGPT, Code Interpreter, and OpenAI’s API endpoints have already drastically changed how we design protocols, record data, design databases, write code, etc. With the new GPT-4Vision around the corner (hopefully they’ll release an API endpoint), we’ll have even more superpowers under our fingertips. We’ll cover some of our tips, tricks, and prototypes next month!

But for now, here’s what we covered this month:

Unlocking the Power of Bacteriophages: Join Us at ICBRAR-2023

by Atif Khan

In the first issue of the month, Atif (who has been helping out on Capsid & Tail for years!) explores the rich history of phage research in India, highlighting the pioneering work of researchers like Ernest Hanbury Hankin and Dr. Felix d’Herelle. He then discusses the resurgence of phage therapy in the face of antibiotic-resistant bacteria, and the establishment of The Society for Bacteriophage Research and Therapy (SBRT) and its annual conference, the 4th International Conference on Bacteriophage Research and Antimicrobial Resistance (ICBRAR-2023). The theme is “Phage for Life” and explores phage use in not only therapy but in food preservation, aquaculture, agriculture, and other biotechnological fields. Jessica just gave a talk at ICBRAR last night about Phage Australia’s process, and I’m talking about using AI for data management tomorrow. Come join us!

The conference is happening right now! Register here: https://www.icbrar2023.com/

The Good Virus: A book about phages by Tom Ireland

by Jan Zheng

In this very special issue, we got to share a passage from Tom Ireland’s new book about phages, The Good Virus. This passage highlights the work of Forest Rohwer, a renowned viral ecologist, who has made significant contributions to understanding marine ecosystems and hunting viruses. The passage delves into Rohwer’s research on the diversity and role of phages in coral reefs and their potential in saving these delicate ecosystems — and how that relationships extends to mammals including humans. The writing is warm, approachable and welcoming, and I think would make a great gift to family members who wonder what it is we work with every day. If you’re interested in getting your own copy, there’s two editions, a US Edition and a UK Edition (the UK Edition has a nicer cover… so try to get that one!)

Urine Good Hands: Battling UTIs with Engineered Phages

by Matthew Dunne, Samuel Kilcher, Jiemin Du, and Susanne Meile

In this issue, the authors describe a phage-based diagnostic tool and a therapeutic approach for urinary tract infections (UTIs) using engineered phages. They reflect on the development of genetic tools, characterizing phages during lockdown, and their experiences working on the project, which was driven by the clinical need to establish new treatment paradigms for patients with recurrent, drug-resistant bladder infections. The interview-style article goes deep into their techniques to modify their genomes, the use of nanoluciferase as a reporter gene for point-of-care diagnostics, and challenges like determining the ideal effector payload, establishing a Zurich Uropathogen Collection during the COVID-19 pandemic. This is an incredible, technical read for those into the microbiology behind pahges.

Making our phage therapy process more efficient

by Jessica Sacher

In the last post of the month Jess provides some ideas of how we make our phage therapy process more efficient at Phage Australia, for our personalized phage therapy work. She covers how we scale up phage therapy as a personalized service, and how she set up the minimum viable pipeline for diagnostics, production, quality control, and monitoring. She discusses the division of labor, redundancy, and clear handoff points to ensure efficiency and patient safety. She also highlights the significance of managing expectations, establishing timelines, and holding recurring meetings to facilitate smooth operations. Additionally, she delves into the creation of standard operating procedures (SOPs) and logs to support lab documentation and maintain quality control. This is the second part in a continuing series; in the first part she gave a bird’s-eye overview of our phage therapy service at Phage Australia.

C&T Throwback!

To celebrate ICBRAR’s phage conference this week, we should all take a look at this interview with Pranav Johri, who who went from being an Eliava patient success case to becoming a powerful force for bringing access, diagnostics, and even regulatory pathways to phage therapy India. Here’s our interview: Improving access to phage therapy in India

Capsid & Tail

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Mary Ann Liebert PHAGE

Supported by

Leona M. and Harry B. Helmsley Charitable Trust

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