Hello from rainy San Francisco!
We moved here about a month ago and are slowly settling in. We lucked out and are actually house-sitting for Tobi Nagel, who runs Phages for Global Health. She’s currently in Africa as part of her Fulbright Fellowship program!
We’re meeting a ton of people who do biology, machine learning, biotech, and “techbio.” It’s exciting! And really fun! But it wears you out if you go to every single one of them. (I’m actually skipping a meetup to write this…).
As we’re settling into the SF-biotech lifestyle, we’re also settling back into our regular cadence of Capsid & Tail posts, and we’re ready to hear what you’re working on!
If you’d like to share a bit about your research on Capsid, consider writing for us!
Without further ado, here’s what we covered in March.
by Elisabet More
In this guest post, Elisabet provides an overview of phage-based diagnostics, highlighting their advantages such as rapid detection, specificity, and cost-effectiveness. She explains various methods like phage amplification assays, phage display technology, and phage-induced bacterial lysis. Elisabet also details the process of producing phages for diagnostics, including phage-induced lysate, purification, storage, and transport. She presents a case study on the use of Actiphage TB for detecting viable Mycobacterium tuberculosis and discusses advancements and future directions in this field, such as the potential for assessing antibiotic resistance in bacterial strains.
by Urmi Bajpai, Ankush Gupta, and Shivani Bharadwaj
In this blog post, Urmi Bajpai, Ankush Gupta, and Shivani Bharadwaj summarize a series of talks organized by the International Bacteriophage Research Consortium (IBRC) & Open Source Pharma Foundation (OSPF) in association with the Indian Society for Bacteriophage Research and Therapy (SBRT) during World Antibiotic Awareness Week 2023. The talks featured leading clinicians from the United States, Australia, India, and Georgia who shared their experiences and insights on phage therapy. The discussions covered various topics, including phage sourcing, preparation, delivery routes, dosing, patient response, genetically engineered phages, and clinical trials. The post highlights the importance of standardized protocols, phage banks, and carefully structured clinical trials for the advancement of phage therapy. Despite the challenges, the clinicians expressed optimism about phage therapy as a potential solution to the antibiotic resistance crisis.
by Jessica Sacher
In this blog post, Jessica Sacher discusses a recent paper by Rupinder Kaur and colleagues, which shows how a prophage controls fly reproduction. The researchers found that specific nucleases encoded by a prophage living within a symbiotic bacterium (Wolbachia) inside the fruit fly (Drosophila) act as a switch that determines whether a new fly embryo lives or dies. The prophage proteins, CifA and CifB, degrade Drosophila sperm DNA and RNA, impairing the histone-to-protamine transition essential for successful fertilization. This leads to DNA damage in embryos and altered sperm development, ultimately causing embryos to die. Jessica highlights the significance of this discovery, as it demonstrates that phage proteins can enter the eukaryotic nucleus and perform important life-or-death functions in animals. She also raises questions about the potential implications for phage therapy and applications, as well as the broader context of biocontrol and insect population control.
by Jessica Sacher and Jan Zheng
In the first post of the month, we introduced a new format. We wanted to try to surface some of our favorite, “stickiest” papers that we love to revisit, or have a copy lying around our hard drives for quick reference. If you have a paper you come back to time and time again, please share it with us, and tell us why you love it!
- “Rapid assessment of changes in phage bioactivity using dynamic light scattering” by Tejas Dharmaraj et al. (https://doi.org/10.1093/pnasnexus/pgad406). The authors demonstrate how Dynamic Light Scattering (DLS) can be used as a quick, reliable, and non-destructive method to measure phage stability, reducing the need for time-consuming plaque assays.
- “Large language models improve annotation of prokaryotic viral proteins” by Flamholz et al. (https://doi.org/10.1038/s41564-023-01584-8). This paper shows how protein language models (PLMs) can improve the annotation of proteins compared to traditional methods, potentially leading to the discovery of new integrases, capsid proteins, and research areas. The code and data are available on GitHub for reproducibility.
C&T Throwback!
We’ve been super fortunate to feature so many of you dear readers. We’ve covered a wide range of topics, from using phages for Covid-19 (1, 2, 3), to a three-part series on how to build sustainable ecosystems for phage therapy (shout out to Ruby! 1, 2, 3).
You are all so awesome for reading and contributing to Capsid & Tail, and we couldn’t do this every week without you!
(Also yes, this is a sappy effort to recruit some writers for Capsid this year… so please write for us ;)
~ Jan & Jessica
