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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

SEA-PHAGES and PHIRE Contributors to the Microbacterium sp. Paper

Genomic diversity of bacteriophages infecting Microbacterium spp.

SEA-PHAGES and PHIRE Contributors

PDF Version

SEA-PHAGES participants

HHMI at University of Maryland, Baltimore County

Ilzat Ali

Aleem Mohamed

Emily Davis

Acacia Eleri Jones (Keele University)

Indian River State College

Josh Moreno

Brandon Bryant

Ariana Burch

Rhode Dorissaint

Cayce Douthitt

Jeffrey Garafalo

Jaclyn Kuiack

Samuel Marcillon

Jordan Norus

Matthew Parks

Kelly Wilse

LaSierra University

Steven Tran

Gillian E. Miller

Rhiannon R Abrahams

Daniel C Bazan

Beglau C Bryceson

Ethan C Blaylock

Jessica D Choi

Shannon K Grewal

Elmira V Hernandez

Daniel J Kim

Kay K Kim

Yumin Lee

Michael K Linde

Meagan B Lopez

Emily Pangalila

Markell A Parker

Rachel C Specht

Ming Chung Teng

Benjamin Toledo

Houting Yu

Nancy Kalaj

Natasha S Dean

Lehigh University

Katie Volpe

Mount Saint Mary College

Kaitlyn A. Barber

Amanda Barnett

Destiny R. Bettica

Olivia Bracco

Erica C. Eack

Elizabeth Halpin

Camren Iorio

Nasayah S. Israel

Nicholas J. Mahoney

Jessica Musacchio

Chandlir M. Radcliffe

Andrew Velazquez

Sabina A. Zarod

Nebraska Wesleyan University

MacKenzie Batt

Cora Svoboda

Elijah Washburn

Morgan A. Shipley

Austin Reed

Maudie Melcher

Elaine Hart

Dayton D. Dolincheck

Johan Vizoso-Marino

Jordan Brozek

Dan Novinski

Laurel Heskett

Nyack College

Maria I. Paschalis

Mariana Moraes

Angela Bryanne DeJesus

Sucely Ponce Reyes

Maridalia Lillis

Seton Hill University

Nathan Baker

Jordan Barzensky

Jaret Beechy

Rachael Bowers

Kalen Brown

Keelyn Brown

Tiffany Burden

Sidney Chapman

Joseph Constantin

Lauren Cosey

Ashly DeFalco

Faith Dent

Viktoria Farian

Alyssa Ference

Taylor Fusco

Joseph Greico

Heather Haas

Donald Hamilton

Kayla Harris

Anna Heitzenrater

Caitlynn Hirak

Victoria Hrach

Ella Hudson

Urriah Huffine

Gabriella Jablonski

Danielle Jones

Daleitha Johnson

Hannah Judy

Kennedy Kehew

Kathryn Kingman

Harrison Klein

Lauren Kosslow

Elizabeth Kuniega

Matthew Laird

Paige Lamberson

Kyle Lovisone

Haley Lucas

Molly Lukacs

Brianna Marks

Alexandra Masocco

Sierra Megonnell

Rebecka Meyer

Saige Minear

Kylie Moffat

Samantha Moon

Taner Moore

Zoe Moran

Baylee Musser

Megan Nestor

Carson Offman

Natalie Opalka

Allison Pavlan

Geno Petrarca

Victoria Pickford

Elise Poll

Brittany Postma

Layna Reinhart

Chase Rucker

Matthew Sanchez

Whitney Sasso

Steven Semekoski

Kallie Shaffer

Abbey Sitko

Abigail Skatell

Maurisa Sloan

Nicole Susi

Tristan Tinney

Lauren Villone

Sarra Wiles

Hannah Woitkowiak

Jeffrey Yurek

Southern Connecticut State University

Dathan Stone

University of Central Oklahoma

Katie Chalifoux

Jessica Mejia

Carina Gutierrez

Micah Byrne

Zachary Stone

An Ngoc Nguyen (Oklahoma City Community College)

University of Wisconsin River Falls

Sidique F. Bachelani

Alix Bookler

Byrgen Buetow

Courtney A. Carlson

Keisha H. Carlson

Beau D. Clemmensen

Emily M. Dailey

Dakota C-M. DeWindt

Kayla M. Doucette

Jonathan A. Duclos

Amanda R. Edstrom

Samantha Flandrick

Brenna Franke

Rachel B. Furey

Tinothy A. Gelatt

Cassie Glynn

Blake R. Hansen

Alyssa M. Hass

David H. Hensley

Eric W. Hoffstatter

Serena K.L. Jacob

Kiley K. Jones

Pamela J. Lisowski

Dawson P. Luttrell

Bailey K. Paulus

Morgan A. Pliszka

Hannah Preder

Cassandra Pugh

Jared M. Ricchio

Evan P. Ruesch

Karie S. Seif

Lizbeth A. Servin-Meza

Courtney E. Solberg

Paul H. Timm

Sam P. Wang

Michelle M. Weinberg

Ryan S. Wright

Madison A. Zobrist

University of Maine Honors College

Dakota Archambault

Katharynne Hebert

Alan Baez

Joshua Passarelli

Western Carolina University

Paige M. Robinson

Boman T. Wiseman

Graceanne E. Stanley

Joshua M. Radey

Celeste E. Smith

Winthrop University

Hallie V. Smith

PHIRE students

University of Pittsburgh

Alyssa Betsko

Gabrielle Gentile

Kerry Iles

Audrey Jonas

Emily Kukan

Alexandra McDonough

Patrick Rimple

Johnathan Schiebel

Ann-Catherine Stanton

Leah Szpak

Megan Ulbrich

Robin Tomczak

Sequencing Information 2019-20

It's sequencing season! This post contains some information on sending your SEA-PHAGES phage DNA samples to the University of Pittsburgh for sequencing. Most of the information is the same as last year, but please note that our lab has moved to a new building and the shipping address has changed.

Sample Submission Form

Please submit the information about the samples you are sending via a quick 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. 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. We recommend that you send at least one backup sample in case one of your samples fails our QC. Please indicate any order of preference, if you have one.

Deadlines

Semester Schools

Please send your genomic DNA so that it arrives in Pittsburgh by Friday, November 22.

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 Dan Russell at dar78@pitt.edu.

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 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 to dar78@pitt.edu 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

Dan Russell
303 Clapp Hall
Department of Biological Sciences
4249 Fifth Avenue
Pittsburgh, PA 15260

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.

Fall 2019 Faculty Hack-A-Thons

What is it?

 

The Fall Faculty Hack-A-Thons is a series of one-day annotation workshops for faculty that are hosted by our SEA-PHAGES SMART Team and expedited submitters. The goal of the Hack-A-Thons are to improve faculty annotation skills across the SEA and help everyone refresh their memories before they teach the bioinformatics component in the Spring. These small group, faculty-focused workshops will either work through the annotation of one genome from the genome exchange or will focus on a particular annotation topic. Along the way, faculty will be reoriented to SEA-PHAGES bioinformatics tools, the Online Guide, annotation submission guidelines, changes from previous years, and useful forums and resources on seaphages.org.

 

Who should attend?

 

We encourage all faculty that will be leading the bioinformatics course to attend at least one of these workshops. Teaching assistants are welcome if there is space. Cohort 12 faculty will soon attend a week-long in-depth bioinformatics training workshop. There will be some hack-a-thon sessions available as follow up for Cohort 12 trainees, but it’s not recommended to attend a Hack-A-Thon until after the workshop.

 

How to attend one?

 

These workshops will take place as in-person meetings, virtual meetings, or a combination of both. To attend one of these meetings, refer to the sign-up link below, which lists all the dates and locations for these meetings. Once all faculty have identified their top three choices, you will be contacted with additional details about the meetings. Food will be provided at in-person meetings, but travel to and from a meeting is at your own expense.

 

Please identify up to three workshops that you can attend, and rank your preference, by Sunday Oct 20, 2019.

 

Sign-up here: https://www.surveymonkey.com/r/2019FallHackathon

 

Happy Annotating!

 

The SEA-PHAGES Team

Current Events

12th Annual SEA Symposium CANCELLED

June 5, 2020 to June 7, 2020

Upcoming Events

Cohort 13 Phage Genomics Workshop

June 15, 2020 to June 26, 2020

Recent Events

Students Complete Spring Semester PITS Survey [Semester Schools]

May 8, 2020

Submit Genome Annotations for Quality Control

May 1, 2020