C&T Round Up for October 2023!

Issue 244 | October 27, 2023
7 min read
Capsid and Tail

Flinders Street Station in breezy, rainy Melbourne. At least the food and coffee is spectacular here! Generated by DALL-E 3.

This month, we heard about the Southeast Asia phage workshop, a few tidbits from Evergreen, and a brief intro on using ChatGPT for lab work!

What’s New

Michele Mutti and colleagues at BioNTech discovered that the activity of anti-staphylococcal phages is severely impaired in plasma or synovial fluid, hindering their potential as an alternative treatment for S. aureus infections inside the body.

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Research PaperStaphylococcus AureusPlasma Inhibition

Shawna McCallin and colleagues from ESGNTA-ESCMID study group published an overview of the current status and emerging use of phage therapy and phage-based products, as well as the socioeconomic and regulatory issues surrounding their development.

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ReviewPhage therapy

Rafael Gonzalez-Serrano (Universidad Miguel Hernández, Spain) and colleagues have discovered that distantly related Alteromonas mediterranea phages shares its host recognition module with phages from distantly related families, shedding light on the process of horizontal gene transfer among Caudoviricetes phages.

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Research paperHorizontal gene transferPhage-host interactions

Giada Finocchio (University of Zurich) and colleagues have discovered the target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA, shedding light on the structural architecture and catalytic activation of the system.

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Prokaryotic Immune SystemResearch paper

Tomoyoshi Kaneko (Waseda University, Tokyo) and colleagues isolated 28 phages infecting E. coli and evaluated factors like lysis activity, adsorption rate and burst size. They found that variation in lysis onset time and duration was higher between phages from different clusters.

Research paperPhage characterization

Latest Jobs

Phage TherapyPostdoc
FDA, USA is hiring a Postdoctoral Fellow to develop and characterize a phage therapy to decolonize vancomycin-resistant Enterococci.
Phage in agriculture
Huvepharma, Norwich, UK is hiring a phage researcher to study phage-based antimicrobial products for agriculture and veterinary pharmaceutical development.
TechnicianMolecularCellular biology
Eligo Bioscience is hiring a Technician - Molecular and Cellular Biology to study phage-related mechanisms in molecular and cellular biology.
ScientistPhage engineering
Research Technician
Baylor College of Medicine, Houston, USA is hiring a Research Technician II to study phage mechanisms in various organisms.
PhD project
Lucy Bock at University of Southampton is seeking a PhD researcher to study phages in the field of Translational Science.

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!

Workshop on personalized phage therapy: from lab to the patient - Join the 2nd edition of this exciting workshop Nov 30-Dec 2 in Brussels, Belgium hosted by BSVoM and coordinated by Dr. Jean-Paul Pirnay, Dr. Maya Merabishvilli, and Dr. Tea Glonti, offering theoretical sessions and hands-on lab experiences on techniques for isolating, characterizing, and producing therapeutically relevant phages. Register here.

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WorkshopPersonalized Phage Therapy

Atif Khan has created a Whatsapp channel for phage updates, providing researchers with the latest news and information about phages.

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WhatsAppNews

Jan Zheng is chairing a series of AI and infectious diseases talks at Westmead Health Precinct, Sydney, Australia Nov 6-7, as part of the The Short Course in Critical Infection.

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CourseInfectious DiseaseAI

C&T Round Up for October 2023!

Profile Image
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.

Hey everyone,

I’m writing this from the Melbourne Docklands library, as Jessica is presenting her work on systematizing Phage Australia’s phage production pipeline — with systems like AKTA — over at the Bioprocessing Network Conference. We’ll do a writeup (on the very cool results) in Capsid soon!

You might have noticed a slight redesign breezing through Capsid & Tail! We’re trying out a light refresh to Capsid, and I’m slowly rebuilding some data services which will support an (eventually) updated website. We’ve been building a lot of data tools for managing phages, bacteria, and biobank assets for Phage Australia, and I’ve been wanting to roll those updates back through Phage Directory’s website. I’m excited to update the way we list labs and phages, and completely revamp the sign up process to actually have accounts. But as you know, Phage Directory’s become a sort of hobby project at this point, as we’re spending most of our time working on Phage Australia’s process trial — I’m spending most of my time thinking about the “data stuff” and Jess is doing the “wet lab stuff.”

Recently there’s also been a lot more “AI stuff” in the mix, and we’re going to roll out more articles about how AI is shifting how we’re thinking about things: both from the “using ChatGPT for lab work” side to using OpenAI and other “foundation models” to do NLP and generative work. There’s a lot of experimentation going on right now, and some are more… experimental than others, but most of it’s not very polished. A lot of it is about rewriting the boring, backend, server-y code to be more flexible and support more tools and applications.

We’ll write more about that in the coming month!

Southeast Asia Hands-on Phage Workshop, by Phages for Global Health

by Donna May Papa

In this article Donna writes about her experiences with the Hands-on Phage Workshop by Tobi’s Phages for Global Health, which usually runs in Africa. This time they made a detour to Southeast Asia! I was surprised to learn how much nitty-gritty bioinformatics they learned, including setting up their own Linux environments. Honestly, I’d love to take the Phage Workshop (as a non-microbiologist) myself, to get my hands wet in the wet lab.

Evergreen 2023: Looking Back

by Jan Zheng

We were going to post about the highlights, photos, and learning from Evergreen right after Evergreen happened, but we had too many guest posts that needed to go out! We finally got around to posting the Evergreen recap this month. Evergreen was such a treat, with so many mini-fires burning in the background… but eventually turned out great! Take a look at just a few of the many pictures we took (and read about how we got stuck at Mt. Rainier until midnight…).

ChatGPT tips for lab work

by Jan Zheng and Jessica Sacher

In this article, Jessica and I wrote about experiences using ChatGPT for lab work and data work. This served mostly as an introduction / overview for all the articles we wanted to write, and we wrote it as a baseline. We got some emails saying “our use cases were pretty obvious” but you’d be surprised how few people turn to ChatGPT for help. When we’re used to doing math by hand, it can be sometimes be hard to remember to pull up the calculator — and ChatGPT is merely a calculator for words!

C&T Throwback!

I wanted to highlight our Slack Channel this time, which Sayde Perry wrote about in Issue 166 from the C&T archive! I’m calling it out because Jess has been asking a lot of production and “what machine to get” kind of questions — and getting a ton of helpful responses from other phage folks. Check out how you can make the best out of our Slack Channel! Also, don’t forget to actually Join our Slack!

Capsid & Tail

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Leona M. and Harry B. Helmsley Charitable Trust

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