C&T Round Up for March 2023!

Issue 217 | March 31, 2023
6 min read
Capsid and Tail

This month we featured a new phage startup out of Shanghai, and massive write-ups on lab automation, working with tabular data, and using qPCR for phage therapy.


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What’s New

Akos Nyerges (Harvard Medical School) and colleagues published a new paper on developing a genetic firewall to prevent viral infections and gene transfer in organisms, which could be used to make any organism resistant to all natural viruses and prevent genetic information flow into and out of genetically modified organisms.

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Research paperGenetic Engineering

In a new preprint, Rebekah Silva and colleagues from New England Biolabs report the first in vitro reconstitution of phage Mu’s DNA hypermodification (glycine harvested from tRNA to hypermodify adenine) from purified components.

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DNA modificationPreprint

In a new paper in Scientific Reports, Nader Abdelhamied (Zewail City of Science and Technology, Egypt) and colleagues describe a new phage-based biosensor for the detection of Escherichia coli O157:H7.

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BiosensorResearch paper

In a new paper in PHAGE, Janet Nale (University of Leicester) and colleagues examine the activity of phages to control the growth of chicken and swine Salmonella strains in avian, porcine, and human cell cultures. They found that a six-phage cocktail was most effective in preventing bacterial growth.

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Phage for agricultureResearch paper

The Scottish Health Technologies Group has published advice on the use of phage therapy for the Scottish National Health Service. It recommends that phage therapy may be appropriate for patients with difficult to treat bacterial infections given it has been supported by a small number of randomized controlled trials.

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Phage therapyRecommendation

Latest Jobs

FacultyVirus-host Interactions
Dalhousie University is seeking applicants for an Assistant/Associate Professor position with a focus on Virus-Host Interactions, restricted to individuals who self-identify as women. The position is closing on April 1st and is open to phage researchers who are interested in increasing the representation of the phage community in Nova Scotia.
Temperate phagesResearcher
The University of Ljubljana’s Biotechnical Faculty (Slovenia) has an open position for a Researcher to work on a project focused on control of bacteria by temperate phages, considering phenotypic changes, molecular mechanisms and evolutionary dynamics.
Assistant professorStructural biology
The University of Connecticut seeks to fill a non-tenure track Research and Teaching Scholar position (Assistant Research Professor) beginning in August 2023 who is interested in studying biochemical and biophysical aspects of dsDNA virus assembly using phages as models.
Phage productsResearch Scientist
Intralytix is seeking an experienced Research Scientist to participate in various research projects focused on the development of bacteriophage-based products and the genetic characterization required for commercialization.

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!

Phage Phriday is back talking GMP & phages w/regulators & experts in the field. “Just say no to GMP?” with @Motherofphage, @AdriCaroHM, @PaulPirnay, Barbara Brenner @phages2patients, Patrick Druggan, and more! Friday, 31 Mar at 8:00 PM CEST on @clubhouse.

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ClubhouseVirtual Event

The 4th International Conference on #Bacteriophage Research and #AntimicrobialResistance is happening at the University of Madras, Guindy Campus, Chennai, India September 28-30, 2023.

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In this CIDRAP podcast episode, ‘Phage Against the Routine’, Steffanie Strathdee, Greg Merril, Patrick McGann, and Jason Bennett discuss how infections caused by resistant Acinetobacter impact patients and new treatments.

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Antimicrobial ResistancePodcast

C&T Round Up for March 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

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.

March was an action-packed month! We had a great post about a new phage startup out of Shanghai, and great tutorial-like topics this month involving lab coding and lab automation, working with tabular data, and doing qPCR for phage therapy. If you find these useful, and you are itching to write something in this vein: we’d love to hear from you. Just email me (Jan: [email protected]) any time!

CreatiPhage – The Pioneer in China

by Adam Yang

CreatiPhage is a new phage therapy startup in Shanghai, China, founded in 2021 to develop broad-spectrum phage cocktails and personalized phage therapies against different bacterial strains, including Enterococcus, Staphylococcus, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Escherichia coli. The company is working with Chinese medical institutions and provincial Municipal Health Commissions to provide phages through the Restrictive Medical Technology application pathway.

Learning to Code as a Lab Rat

by Thomas Hunt

Thomas talks through the experience of automating lab procedures by learning to code — and the challenges of using them to manipulate liquid handling robots and automating assays. He points out the importance of reliability and repeatability with automation tools, and talks about coding and calibrating robots for performance. There’s also a ton of cool guides and pictures in this one to geek out about!

Working with tabular data

by Jan Zheng

My article is all about manipulating and analyzing tabular data in Google Sheets. This is a mini overview of using Google Sheets to analyze some Phage Directory data, and covers tricks like using VLOOKUP to combine sheets, and stringing together confusing formulas to generate values that can be used in pivot tables. I cover the limitations of these methods, and compare spreadsheets to databases.

qPCR as a window into phage therapy

by Jessica Sacher

Jessica’s post is all about using qPCR to track phages and bacteria during phage therapy. She talks about using it as a way to quantify the amount of target DNA, and how it changes over time, while also addressing the limitations. She also goes deep into developing qPCR standards, and provides a step-by-step on how she’s preparing and running qPCR on patient serum samples.

C&T Throwback!

I’ve been digging through some of our really old posts, and we’ve had some great ones from the start. In issue number nine (!), from 2018, we had Q&A with BiomX about using phages to tweak the microbiome: Tweaking the microbiome with phages: Q&A with BiomX CBO Assaf Oron

Capsid & Tail

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Supported by

Leona M. and Harry B. Helmsley Charitable Trust

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