Issue 169
The latest on Instill: the peer-to-peer feedback platform
With feedback from users, the Instill platform is evolving. This week Katharine Muscat, phage PhD student and volunteer Instill coordinator, shares how members have benefited from and contributed to Instill, and what they've learned from testing it out!
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This year is the 130th anniversary of the birth year of George Eliava, who founded the Eliava Research Institute in Tbilisi, Georgia.
PHAGE Journal will celebrate this event with a focused issue of phage therapy then and now!
If you would like to include your phage therapy work in this June Issue, please submit by May 1st to be considered!
Community digest1alert5updates4jobs3posts
Phage alert
Urgent need for Aerococcus urinae, Corynebacterium sp. CDC group F-1, Proteus mirabilis, and Mycobacterium abscessus phages for patients in Canada
We are urgently seeking Aerococcus urinae, Corynebacterium sp. CDC group F-1, Proteus mirabilis, and Mycobacterium abscessus phages for patients in Canada.
Ways to help at this stage:
- By sending your phages for testing on the patient's strain
- By receiving the strain and testing your phages
- By receiving the strain and using it to search for new phages against the organism
- By offering to prepare phages supplied by others to clinical grade
- 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
Paper: A Phage Foundry framework to systematically develop viral countermeasures to combat antibiotic resistant bacterial pathogens
Paper: A mobile restriction–modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease
Paper: Development of an anti-Acinetobacter baumannii biofilm phage cocktail: genomic adaptation to the host
Paper: A Novel Method to Create Efficient Phage Cocktails via Use of Phage-Resistant Bacteria
Amazing undergraduates!: Lindsey Shimoda, Satvik Kethireddy, Yingyi Zhu and seven other Ohio State iGem students were awarded gold for their work on creating an engineered phage therapy to combat sepsis – more specifically, the buildup of lipid A.
Jobs
Postdoctoral Research Fellow: We are focusing our curricular revisions, initially, on developing course-based undergraduate research experiences (CUREs) in introductory courses in STEM. While we have already begun this effort by implementing the SEA-PHAGES program in biology laboratory courses, we intend to expand to other disciplines and to help faculty develop their own CUREs.
Research Technician in Bacterial Evolution/Antimicrobial Resistance: we will use molecular microbiology methods and genome sequencing to determine the genetic bases of phage resistance in evolved bacteria.
Assistant Professor: Join a 15-member programme at Yong Loo Lin School of Medicine, National University of Singapore, consisting of basic scientists and clinician scientists with strong expertise in multidrug resistance, emerging viruses, phage biology and more.
The Fountain Group is hiring a Scientist II (R&D) with experience in bacteriophage biology techniques such as phage overlay assay, phage infection kinetics to perform microbiology studies and methods to support development of bacteriophage therapeutics. Experience with analytical molecular biology assays such as nucleic acid purification and qPCR analysis required. Please contact Josue Nunez or apply online.
Community board
PHAGE GENOME ANNOTATION TWO-DAY VIRTUAL WORKSHOP A two-day course that will cover the processes of phage genome assembly, annotation and introduction to comparative phage genome analysis. Solutions to common phage genome assembly problems will be presented, through worked examples. Attendees can bring their own phage genomes or raw reads to assemble. When: 25-26 April 2022, time TBA Where: Zoom Instructor: Dr Andy Millard, University of Leicester
14th Euro-Global Conference on Infectious Diseases June 24-25, 2022 Berlin, Germany.
Greetings from Euro Infectious Diseases 2022! We would like to solicit your gracious presence as a speaker/delegate at the upcoming "14th Euro-Global Conference on Infectious Diseases" which is a CME accredited conference.
Ethan Lucas, Program Manager, Euro Infectious Diseases 2022.
Phages 2022 Oxford - 12th International Conference Dates: 05-06 September 2022 Email: PhageOxford@gmail.com Twitter: @PhageOxford; Hashtag: #PhgOx22
We warmly invite you to attend you to attend our 12th annual Oxford bacteriophage conference – the longest running phage conferences series in Europe. We are committed to holding this conference as a ‘virtual-in-person’ hybrid event at our traditional venue of St Hilda’s College, Oxford, UK (COVID-19 situation permitting).
Get involved in shaping the conference agenda: The conference agenda will include most aspects of bacteriophage research and application in medicine, food and biotechnology.
We welcome proposals for: • keynote and other speakers • agenda topics • an emerging ‘phage-ologist’ award
Registration will open soon. In the meantime, please send any queries to PhageOxford@gmail.com. We look forward to seeing you in Oxford in September!
What is Instill again?
Instill strives to improve research output and connectivity in the phage community by providing an open platform for peer-based reviews, recruitment of potential collaborators, and requests for expertise. The Phage Directory initiative is still in its infancy and will be subject to further development, particularly as its reach increases. An important objective for the Instill service is to provide an easy, useful and time-reasonable experience for researchers, as let’s face it, time is often not our friend! Thanks to the initial users of Instill, improvements to the platform are already underway.
Current developments to Instill
User feedback from the peer review and collaborator search channels has brought to light the value of online meetings for communication between peers in the Instill space. PhD student, Carmen, was able to receive advice on a concept via a zoom meeting after reaching out through an Instill request, and we are excited by her success!
We reached out to Carmen and her responder, Michael, about their Instill experience and here is what they had to say:
Carmen: “I love the experience. Michael is awesome and I enjoyed the fact that we can chat over Zoom and actually be able to go into the details.”
Michael: “It was a great experience overall! Carmen and I discussed her question, which then led into some other questions I had that related to the work she does, and vice-versa. Overall, I liked how the discussion evolved from a single question to forming a new connection with a fellow phage phan!”
We think the use of Instill to facilitate virtual meetings between peers far and wide will not only allow for discussion of researcher queries but could have other beneficial follow-on effects, such as the inspiration of new ideas or future networking opportunities.
The success of Carmen and Michael’s experience has inspired us to explore the option of using a zoom call to provide feedback for peer reviews as an alternative to the current online form. The peer review system has already been up and running on Instill and encouragers reviewers to devote no more than 30 minutes of their time to providing feedback.
As an Instill contributor myself, I also wanted to talk about my own reviewing experience.
My experience as a peer reviewer
Hearing about the Instill initiative and its aims to bring researchers together was both exciting and refreshing for me, knowing that the academic world can often be quite competitive. Providing a contribution was a fulfilling experience and a good opportunity to improve my own reviewing skills.
The Instill review process was straightforward, with a simple form to complete. The sections to rate on different aspects (e.g. Significance, Clarity, Originality) of the manuscript were a good summary of how the manuscript was coming across. Additionally, the form also allowed for specific feedback details to be provided.
Being a person that tends to get carried away with spending more time on others than I have to give, I appreciated having a time limit, which was not overly demanding to ask of a volunteer reviewer but also decent enough to provide a reasonable amount of feedback for the requester. I also appreciated the strict warnings that were made to reviewers to maintain confidentiality with respect to submitted manuscripts, as is the case with usual journal peer review processes.
Big thanks to the below members for their responses to Instill requests so far!
Atif Khan (x2) Katharine Muscat (x2) Archana L Shanmuga Sozhamannan Michael Shamash
Thanks so much to Atif Khan for digging up links for this week's issue!
Katharine Muscat
I am a late-stage PhD candidate working with bacteriophages of Rhodococcus equi. My project focuses mainly on characterisation of these phages for potential future use in biocontrol on farms and exploring genetic features that could be contributing to R. equi susceptibility/resistance to phage infection. I am interested in any opportunities to improve my knowledge and skills, particularly for bioinformatics work but also working with phage/bacteria in general. I am also interested in any potential future research (postdoctoral) or job opportunities in the field, preferably in animal health.