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The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

The SEA-PHAGES Program

SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) is a two-semester, discovery-based undergraduate research course that begins with simple digging in the soil to find new viruses, but progresses through a variety of microbiology techniques and eventually to complex genome annotation and bioinformatic analyses.

The program aims to increase undergraduate interest and retention in the biological sciences through immediate immersion in authentic, valuable, yet accessible research. By finding and naming their own bacteriophages, students develop a sense of project ownership and have a ready-made personal research project at a fraction of the cost of traditional apprentice-based research programs. Some of the positive effects of the SEA-PHAGES program have been reported here.

SEA-PHAGES is jointly administered by Graham Hatfull's group at the University of Pittsburgh and the Howard Hughes Medical Institute's Science Education division.

SEA-PHAGES IN THE NEWS

  • Thumbnail for Invisible Friends

    Invisible Friends

    Story by Joel Smith; photos by Rajah Bose

    Gonzaga—The Magazine of Gonzaga University | Aug. 15, 2016

    They may have goofy names, but these students’ microscopic pets are serious science. A junior in college, Vina Tran already has a bona fide scientific discovery to her name. Go ahead and look her up on the Actino-bacteriophage Database, a compendium of biological findings maintained by the University of Pittsburgh....read more

    Related institution: Gonzaga University

  • Thumbnail for Queens University student discovers a virus strain

    Queens University student discovers a virus strain

    Reid Creager

    The Charlotte Observer | April 16, 2016

    Sydney Dishman’s new pet isn’t cute and certainly isn’t something you’d want to cuddle with. But she feels good just thinking about it. Her “pet” is named Rex16, after the Queens University of Charlotte mascot and her year of graduation. Rex16 is a bacteriophage species she discovered while completing her honors research thesis, investigating bacteriophages in local soil samples....read more

    Related institution: Queens University of Charlotte

  • Thumbnail for Round Rock Cedar Ridge grad earns scientific honor

    Round Rock Cedar Ridge grad earns scientific honor

    Mike Schoeffel

    Austin American-Statesman | Feb. 28, 2017

    Isabel Delwel, a junior at the University of North Texas, was chosen to participate in the 2017 Howard Hughes Medical Institute Exceptional Research Opportunities Program. One of Delwel’s professor’s, Dr. Lee Hughes, encouraged Delwel to apply for a spot in the program.read more

    Related institution: University of North Texas

  • Thumbnail for WKU 2012 Goldwater Scholarship Recipient Charles Coomer

    WKU 2012 Goldwater Scholarship Recipient Charles Coomer

    innovateKY/YouTube | April 24, 2012

    Charles Coomer, a junior in the Honors College at WKU and the son of Evell and Don Coomer, has been involved in microbiological research for two years. In the lab of Dr. Rodney King, associate professor of biology, Coomer is characterizing viruses that infect bacterial cells...read more

    Related institution: Western Kentucky University

  • Thumbnail for Young Māori scientist discovers virus

    Young Māori scientist discovers virus

    Rukuwai Tipene-Allen

    Māori Television | April 22, 2018

    Young, Māori scientist Anezka Hoskins has discovered a new virus and is hopeful that it will spark curiosity amongst Māori to push boundaries of knowledge.read more

    Related institution: Massey University

  • Thumbnail for Biology 2.0

    Biology 2.0

    Andrea Gaul

    Baylor Arts & Sciences Magazine | May 9, 2017

    Baylor University has implemented a new kind of introductory biology lab that has proven successful in keeping students excited and engaged through hands-on research.read more

    Related institution: Baylor University

  • Thumbnail for Students isolate potentially novel soil-dwelling viruses

    Students isolate potentially novel soil-dwelling viruses

    WPI News

    Phys.org | June 8, 2016

    After sifting through soil samples collected from across Massachusetts, then drilling down to analyze the DNA of viruses they found, a team of undergraduates at Worcester Polytechnic Institute (WPI) hit pay dirt—three potentially novel viruses.... read more

    Related institution: Worcester Polytechnic Institute

  • Thumbnail for A summer of sequencing

    A summer of sequencing

    Joseph McClain

    Ideation | Sept. 6, 2013

    It was the summer that the freshmen ruled the sequencer. Technically, the six William & Mary students who logged heavy lab time with a state-of-the-art Ion Torrent gene sequencer had finished their freshman year and therefore did their summer work as rising sophomores....read more

    Related institution: College of William & Mary

  • Thumbnail for One student gets to name lab discovery

    One student gets to name lab discovery

    Oscar Santiago Torres

    Eagle News | Aug. 27, 2014

    An agar plate lies still. Omnicron has destroyed the layer of bacteria inside the plate, leaving plaques or dark holes 2 mm in diameter. Omnicron is a virus replicating itself inside the plate. The discovery of this virus belongs to Tasha Baer, a Florida Gulf Coast University student from the 2013-14 Virus Hunters course....read more

    Related institution: Florida Gulf Coast University

  • ‘Virus Hunters’ get hands dirty in UConn class

    Brett Donovan

    the Chronicle | Nov. 30, 2018

    University of Connecticut students involved in a unique learning experience are getting their hands dirty — literally.read more

    Related institution: University of Connecticut

  • Thumbnail for First-years discover viruses, analyze DNA

    First-years discover viruses, analyze DNA

    Kate Nussenbaum

    The Brown Daily Herald | Feb. 10, 2012

    Sixteen first-years watched with excitement as their screens loaded the sequence of 59,625 nucleic acids that comprise the DNA of “Job42,” the virus a student in their class had discovered, isolated and named during the fall semester. “Each of them codes for something,” said Jordan Rego...read more

    Related institution: Brown University

  • Thumbnail for Bio major considered dream come true for department

    Bio major considered dream come true for department

    Melanie Greenberg

    Loquitor—Cabrini College Student Media | March 5, 2011

    Surrounded by only her thoughts and glass beekers, one Cabrini student spends much of her time diligently working in the Iadarola Science Center. Katie Mageeney, senior biology major and math and chemistry minor, is anything but an average student. “Katie is definitely dedicated to her lab work,”...read more

    Related institutions: Cabrini University | Lehigh University

  • Thumbnail for This scientific paper has 2,863 authors. How?

    This scientific paper has 2,863 authors. How?

    Danielle Wiener-Bronner

    Fusion | May 12, 2015

    The scientific journal eLife published a paper on viruses last month—specifically, the genetics of bacteriophages: viruses that infect, and replicate within, bacteria. By sequencing the genomes of individual bacteriophages, or phages, the authors were able to glean information about the genetic makeup of the viruses more broadly.... read more

  • Thumbnail for Del Mar student takes home award for research on bacteriophages

    Del Mar student takes home award for research on bacteriophages

    Fares Sabawi

    Corpus Christi Caller Times | March 29, 2016

    Before John Ramirez, 29, decided to go back to school, he worked at Northwest Hospital in Calallen. There, he saw how tuberculosis affected people. "It's almost intensified when you see it," Ramirez said....read more

    Related institution: Del Mar College

  • Thumbnail for Students "Hunt" - and Discover - Bacteria-killing viruses

    Students "Hunt" - and Discover - Bacteria-killing viruses

    CSU CONNects | Nov. 15, 2016

    “The goal of the course, part of a national pedagogical program, is to get students doing research early, so they can see what it’s like and learn the scientific process,” explains Dr. Edgington, Associate Professor of Biology.read more

    Related institution: Southern Connecticut State University

2019 SEA-PHAGES Annual Letter

The 2019 SEA-PHAGES letter is available in pdf format by clicking here, or you can read the text below.

Dear SEA-PHAGES Community,

The 2019 SEA-PHAGES Annual Symposium marks yet another highly successful year with a plethora of exciting events. The program continues to expand with inclusion of a new cohort of schools and we are especially pleased to welcome the Cohort 12 faculty to the Symposium. We are delighted to share with you a few of the highlights from the past year.

2018-19 Program Highlights and Accomplishments

  • Program Growth and Milestones

This fall, we will welcome 18 new institutions into the SEA-PHAGES program as Cohort 12. Included among these are our first schools from Arizona, New Hampshire, and Canada, as well as a second institution in Puerto Rico. Geographical diversity is great, but phage diversity is even better, so Cohort 12 will be trained using Arthrobacter globiformis and Gordonia rubripertincta as hosts. And SEA-PHAGES schools now represent 43 different US states, as well as the District of Columbia and Puerto Rico. 

Because of our collective efforts, we will soon pass 3,000 sequenced Actinobacteriophage genomes, and nearly 2,500 of those genomes are published in GenBank. We reached 2,000 sequenced genomes in May 2017, so we are now finding and sequencing the genomes of nearly 500 novel phages per year, which is a tremendous accomplishment and rich collection and data set. And there are now five genera on which we’ve isolated and sequenced at least 200 genomes: Mycobacterium, Arthrobacter, Gordonia, Microbacterium, and Streptomyces. Thank you for all your work in making this happen!

  • Mycobacteriophage therapy

One of the most exciting scientific developments over the past year culminated in the publication of a paper in Nature Medicine this May describing the use of a phage cocktail to treat a disseminated drug-resistant Mycobacterial infection in Isabelle Holdaway, a British 15-year-old with cystic fibrosis who had received a lung transplant. After receiving the three-phage cocktail—which contained two BRED-engineered phages—Isabelle showed substantial health improvement, and the story received international media attention. One of the three phages used, ZoeJ, was found by a SEA-PHAGES student at Providence College, but many of your SEA-PHAGES phages were screened to find the few that were useful.

The primary scientific goals of SEA-PHAGES are to understand the basic principles of phage diversity, but this development illustrates a key point: that translational applications depend on and emerge from basic scientific exploration. It is hard to imagine how this life-saving intervention could have occurred without the SEA-PHAGES program.

  • Microbiology Resource Announcements

In June 2017, we held a Genome Announcement Workshop where we encouraged SEA-PHAGES faculty members to learn to write and submit papers describing the phage genomes they’d found. The seed planted at that workshop has begun to bloom, as the past year has seen at least 12 Microbiology Resource Announcements on which (non-Pitt) SEA-PHAGES faculty members are the corresponding authors. Congratulations!

  • Future Symposia, Faculty Meetings, and Workshops

If you’re from one of the earlier SEA-PHAGES cohorts, you probably remember when you could bring a faculty member and two students to the Symposium each year.  But the growth of the program has bumped up against the capacity of Janelia Research Campus, and we’ve had to moderate the number of attendees per institution to fit everyone. In the interests of long-term sustainability, therefore, the 2020 Symposium will be held at a new location, the National Conference Center in nearby Leesburg, VA. This facility has been carefully vetted and should provide an excellent location and atmosphere to accommodate our ever-growing group of student researchers and faculty members.

Each year, immediately following the Symposium, we hold another meeting for faculty only. In even-numbered years, this is a full faculty meeting where one representative from each institution is invited, and in odd-numbered years it is a specialized workshop of some sort, where invitations are based on the topic covered in the workshop. This year we are hosting a Microbacterium Phage Genomics workshop, whereas next year will be a full faculty meeting.

  • Removing Annotation Bottlenecks

With nearly 500 genomes being sequenced each year, the task of getting high-quality annotations into GenBank in a timely fashion has grown. This past year saw a number of developments that aimed to remove some of the bottlenecks in the annotation pipeline.

First, the June 2018 full SEA-PHAGES faculty meeting focused on improving the quality of phage genome annotations and bringing everyone up to speed with the current best practices. There were lots of “aha” moments and many genomes were submitted directly to GenBank as a result of the meeting.

Second, the number of expedited submitters has grown to include 50 SEA-PHAGES faculty members representing 39 institutions. Expedited submitters use a streamlined submission form and their genomes go quickly into GenBank, easing the QC burden. We thank those of you who have worked to achieve this status and hope to add many more this coming year.

Third, a sustained effort from a dedicated team at Pitt allowed us to completely clear out the pile of genomes awaiting QC in early 2019. We have new plans in place to make sure your genomes are processed as expeditiously as possible in the future, and your adherence with the annotation deadlines will help to make this a reality!

We will continue to improve this pipeline in ways that it is helpful to you. This will include an online file-checker that will allow you to identify and fix any issue with your submission files before entering them in PhagesDB, and will avoid them being returned to you for common errors. Watch out for announcements soon!

  • Feedback

We are always interested in hearing your feedback, suggestions, concerns, and questions about the larger aspects of the SEA-PHAGES program’s direction. We’ve created a new forum called “Larger Program Questions” and encourage you to share items there.

Thanks for being part of this vibrant and productive community. Wishing all of you a successful and fun year, and we look forward to seeing you at the Symposium.

Sincerely,

David Asai and Graham Hatfull

Abstract Submission and Posters for the 2019 SEA-PHAGES Symposium

The 2019 SEA Symposium is approaching, and we want you to submit abstracts and prepare posters, because you've done amazing things and we want to know about it.

Students at the Symposium are expected to submit only one scientific abstract from the student's institution about actinobacteriophage work they accomplished this year. Abstracts will be presented as posters at the Symposium. Only one poster space will be set aside for each participating school's students. Each school may also submit up to one additional faculty abstract to be presented by the attending faculty. Some of the faculty abstracts will be selected for presentation at the poster session. Cohort 12 schools will not submit any abstracts for the 2019 SEA Symposium.

Abstract titles can be up to 200 characters long. Abstract body text can be up to 3,000 characters long. A photo (headshot) for each presenter is needed to submit an abstract.

Abstracts selected for talks will also present a poster. Posters can't be bigger than 4’ x 4’. Poster headings should include a title, names of authors, and the name of your institution. SEA-PHAGES and HHMI have LOGOS for your poster.

Faculty at schools that are participating in the Symposium should work together to ensure that one student abstract and no more than one faculty abstract are submitted from your institution. Users with faculty accounts on seaphages.org can submit abstracts from the faculty timeline page or the "My Institution" link on the seaphages.org homepage.

Abstracts are due on Thursday, May 2, 2019.

Keep in touch with the most up-to-date information on the upcoming Symposium. Email info@seaphages.org if you have any questions.

GenBank Submission Numbers

Below is a live spreadsheet showing the numbers assigned by GenBank to phage annotations that have been submitted and are soon to be (or have been) released.

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Current Events

Phage Discovery Workshop 12A

June 22, 2019 to June 28, 2019

Upcoming Events

Phage Discovery Workshop Option B

July 6, 2019 to July 12, 2019

Phage Discovery Workshop 12B

July 7, 2019 to July 13, 2019

Virtual Site-Visit with SEA Team

September 1, 2019 to October 31, 2019

Recent Events

2019 Faculty Workshop

June 9, 2019 to June 12, 2019

2019 SEA GENES Faculty Meeting

June 9, 2019 to June 11, 2019

Forum Activity

Mitchell Balish posted in Ro-like RNA binding protein

cellokiwi posted in A. globiformis aquisition

Steven Caruso posted in Aragorn Issue

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