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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 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

  • ‘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 Special UNLV class takes a hands-on approach to discovering viruses

    Special UNLV class takes a hands-on approach to discovering viruses

    Denise Rosch

    KSNV NBC Las Vegas | Sept. 28, 2017

    Say the word "virus" and most people think of disease -- something to be avoided at all costs. However, at UNLV, students are getting their hands dirty to discover something that could keep us healthy. read more

    Related institution: University of Nevada Las Vegas

  • 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 Students in interactive course look to discover, name phages

    Students in interactive course look to discover, name phages

    Marlon Morgan

    Western Carolina News | Sept. 30, 2015

    Western Carolina University student Sean Kent didn’t pick the course, but when he saw he was registered for it, the name “Phage Hunters” immediately got his attention. Brooke Burns also found she was placed in the course. After hearing so many other freshmen at orientation say they were excited about WCU’s newest biology/chemistry course, she, too, decided to keep it. Now she says it’s by far her favorite....read more

    Related institution: Western Carolina University

  • 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

  • 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 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 Ibadan Bacteriophage Research Team: A SEA-PHAGES team with a difference

    Ibadan Bacteriophage Research Team: A SEA-PHAGES team with a difference

    Tolulope Oduselu and Olubusuyi Adewumi

    Capsid Tail | Nov. 20, 2020

    A team of 8 biomedical science researchers at the University of Ibadan, led by Prof. O. G. Ademowo, envisioned new opportunities to foster early career research participation for young undergraduate students. To achieve this goal, the University of Ibadan was enlisted as a cohort institution in the SEA-PHAGES project, an early-career research initiative of the Howard Hughes Medical Institute and the Graham Hatfull Research group at the University of Pittsburgh.read more

    Related institution: University of Ibadan

  • 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 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 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 Freshmen participate in huge research study on tiny viruses

    Freshmen participate in huge research study on tiny viruses

    CU Boulder Today | May 1, 2015

    A new study appearing this week in the scientific journal eLIFE about the rapid evolution of small viruses that infect bacteria includes 59 University of Colorado Boulder co-authors, all of whom conducted research for the paper as freshmen....read more

    Related institution: University of Colorado at Boulder

  • Research paper with 2,863 authors expands knowledge of bacteriophages

    Science Daily | May 11, 2015

    We know that bacteriophages are viruses that infect and replicate within bacteria. We know that they are the most abundant organisms on Earth. But we don't know much about their genetic architecture....read more

    Related institution: University of Pittsburgh

  • 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

Archiving Information 2020-21

The procedure for sending archiving samples to the University of Pittsburgh is largely similar this year, with two important changes.

  1. Our shipping address has changed—see below for the new address.
  2. We are asking you to fill out a quick form to let us know what you're sending and help us track your package.

Contact Us/Questions

Please send any questions about the information below to Debbie (djs@pitt.edu) and Becky (rag4@pitt.edu).

Please read the latest Archiving Instructions at the link below.

https://phagesdb.org/protocols/96/

Archiving Sample Submission Form

Please submit the information about the samples you are sending using this Google Form. This will help us keep track of samples, correct any spelling errors, and make sure your samples are accounted for.

We are asking that you add a tracking number in the appropriate place on the form. We have rotating lab staff, and want to make sure all packages are accounted for.

https://forms.gle/pHq9LHyYiuSJPCHF7

Timeline

You should send archiving samples for phages found in 2020 for arrival no later than December 16.

Shipping

Please be sure to include an up-to-date Archiving Report in the package. You can print one from your institution's page on seaphages.org.

Shipping Address (NEW THIS YEAR)

Attn: Becky Garlena
University of Pittsburgh
Langley Garage 120F
Langley Hall
Fifth and Ruskin Avenues
Pittsburgh, PA 15260
(412) 624 6976

DNA Samples

Just a note that DNA samples should be sent to the same address as above, and so if it's convenient to you, you can send DNA samples and archiving samples together in a single box.

Sequencing Information 2020-21

Sequencing Information 2020-21

It's been a weird year, but through many trials and adjustments we have still arrived at phage DNA sequencing season! This post contains information about sending your SEA-PHAGES phage DNA samples to the University of Pittsburgh for sequencing. Because of the pandemic and other issues, several things have changed since previous years, so please read carefully.

Contact Us/Questions

Please send any questions about the information below to Dan (dar78@pitt.edu) and Becky (rag4@pitt.edu).

Sample Submission Form

Please submit the information about the samples you are sending using Google Form. This will help us keep track of samples, correct any spelling errors, and make sure your samples are accounted for. Please fill out a copy of this form for each sample you are submitting. The best time to fill it out is as you are getting your shipment packed, so that when your box arrives, we'll already have the information on your phages in our database.

NEW THIS YEAR: We are asking, if possible, that you add a tracking number in the appropriate place on the form. We have rotating lab staff, and want to make sure all packages are accounted for. Please note whether each sample is a "Priority" or "Backup" in the Notes field, along with any other info we should have.

https://docs.google.com/forms/d/e/1FAIpQLSfdhZpw1LHL42zxAotEVqhmrr8RBN9-kuPL_42ioYmuBU-4-Q/viewform

Quantity

Each SEA-PHAGES school may have two genomes sequenced per Bioinformatics section that it is teaching during the current academic year. Please indicate any order of preference, if you have one.

NEW THIS YEAR: Because many schools were not able to perform phage discovery as usual during the fall but still want to do bioinformatics in the spring, we will need some extra DNA samples to be donated to the Genome Exchange. If you have managed to extract more good quantity, high quality DNA samples than you need for your class, we would welcome those as well. Please indicate "Donate to Exchange" on the Notes field of the form. And thanks for helping out your fellow SEA-PHAGES institutions!

Deadlines

Semester Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Friday, November 20.

Quarter Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Friday, January 8.

If you will have trouble meeting these deadlines for any reason, please contact us.

Guidelines for DNA

Buffer

Samples that are resuspended in TE are problematic, since the EDTA may interfere with enzymatic shearing of the DNA. You can resuspend your DNA in Elution Buffer (Tris) or in purified water.

Amount

We need a minimum of 4 µg (micrograms) of genomic DNA. If you're in the ballpark of this number but not quite there, contact Dan and Becky to see if it's okay.

Concentration

At least 40 ng/µl. Ideal is 100-300 ng/µl. If you're above 300 ng/µl please consider diluting to a workable concentration and workable volume. Shipping volumes less than 20 µl is not recommended. Keep in mind that spec-based quantifications (like Nanodrop) count all absorbance at 260 nm, not just genomic DNA, so they often overestimate the real concentration. Err on the high side of the amount of DNA you send.

Gel Picture

Please submit—either via email or in the shipping box—an image of the gDNA being run on an agarose gel. We use these to look for sample integrity (not already sheared/degraded) and purity (no RNA).

Labeling

Please clearly label the tubes you are sending with the name of the phage as it appears on PhagesDB. Don't label tubes using student's initials only, or other ambiguous names like "Phage1" or "PittPhage". If possible, put a small circular sticker on the top of the tube and write the phage name only on it.

Shipping

Packaging

We prefer standard microcentrifuge tubes, and strongly recommend wrapping the caps with Parafilm to prevent spilling or evaporation. The tubes can be packed into a 50 ml conical tube with some KimWipes to stabilize them during shipment. If shipping overnight (preferred), you can actually just send the samples at room temperature, as the DNA should be fine for 24 hours in transit. If shipping on a slower schedule, you should use cold packs. Aim for delivery to Pittsburgh on Tuesday-Friday. If shipping near holidays, please check with us about when we'll be around to receive samples.

You can include a packing slip with any information you think we should have about the enclosed phages.

Address (NEW THIS YEAR)

Attn: Becky Garlena
University of Pittsburgh
Langley Garage 120F
Langley Hall
Fifth and Ruskin Avenues
Pittsburgh, PA 15260
(412) 624 6976

Additional Samples

For the past several years, the Genomics Sciences Laboratory at NC State has provided high-quality, for-cost sequencing services to schools in the SEA-PHAGES program who wish to sequence additional genomes beyond those allotted by the program. Contact Andy Baltzegar at dabaltze@ncsu.edu for pricing and details.

Archiving Samples

Just a note that archiving samples should be sent to the same address as above, and so if it's convenient to you, you can send DNA samples and archiving samples together in a single box.

tRNAScanSE is Offline due to California Wildfires

As of August 21, 2020, tRNAScanSE is offline because it is hosted at the University of California, Santa Cruz, and their campus is facing a mandatory evacuation due to the ongoing wildfires. In the meantime, you can still use Aragorn for tRNA purposes. We'll update when we have more information.

Upcoming Events

Recent Events

2021 GENES Faculty Workshop

June 15, 2021 to June 16, 2021

2021 SEA Faculty Meeting

June 7, 2021 to June 9, 2021

Forum Activity

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cdshaffer posted in PD-(D/E)XK endonuclease

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