SEA-PHAGES Logo

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

Considerations for Implementing SEA-PHAGES in 2020 - 2021

Considerations for Implementing PHAGES in 2020 - 2021

Faculty Discussions Summary:

SEA Faculty met virtually, in groups of 5 – 10, to discuss ideas for implementing SEA-PHAGES this coming academic year, focusing on strategies for maintaining safe distancing, preparing for the possibility of being fully online, and maintaining high student engagement. Below is a summary of suggested considerations, the majority of which are written in the context of Phage Discovery, though many are also applicable for Phage Genomics.

  1. Maintaining Safe Distancing.
  2. Preparing for Reversal to Fully Online Classes.
  3. Developing Students as Scientists

 

1. To Maintain Safe Distancing:
This will require modifying scheduling, space, and/or enrollment.

  • Request for increased/adequate space to avoid altering scheduling and enrollment.
  • Enroll fewer students to avoid altering scheduling and space.
  • Have students attend in-person labs in shifts, to avoid changes in enrollment or space. For example, with a 2 x 3 hrs weekly setup, students can attend in-person a fraction of the time, either 1 x 3 hrs or 2 x 1.5 hrs per week. This can be facilitated by having students work in teams of 2 or 4, so that the project can progress even if a given student can only be present for half of lab meeting times.
  • All reagents placed on benches to minimize students needing to move around lab.
  • Instructor responsible for moving items to and from incubators and lab.
  • Minimize sharing, by preparing individual aliquots (bacteria, plates, buffer, top agar) and pipettes.
  • Establish decontaminating procedures for student to perform on their bench and pipettes pre and post lab.
  • Consider providing print copies of the PDG that are laminated/covered in plastic sheet at the bench so that they can be disinfected.

 

2. Preparing for Reversal to Fully Online Classes.

  • Start early. For example: If you have students watch videos and read protocols for sample collection and enrichment, enrichments can begin within first week.
  • Have student watch as many pre-recorded materials before attending in-person, so that time in class can be focused on mentored lab work. Overview and/or demo videos are available for all steps of Phage Discovery, and many instructional videos are also available for Phage Genomics. The videos can be found under the resources tab of this website, and many can be downdloaded for edititng from QUBES.
  • Shorten the amount of time spent on the “isolation” phase:
    • Have students enrich many samples at once,
    • Set the goal for each team to collaboratively find one phage or for the entire class to isolate enough phages for each team (i.e. promote adoption).
    • Use hosts that have higher isolation rates, such as M. smegmatis.
    • May be worthwhile having some back-up phage isolated during the summer, though only to be used if students are unable to isolate ANY phage.
  • Normalize online activities:
    Should classes be forced to return online and instructors/TAs are the only ones allowed in lab, then instructors/TAs could possibly continue Phage Discovery by being the “hands-on” person. It may therefore be worthwhile normalizing they ways in which this will have to be structured, including:
      • Instructors/TAs integrating themselves as collaborators/team members, and occasionally being the hands-on person for a team.
      • Instructors/TAs regularly providing sample data for analyses.
        *this requires a bank of sample data, which all SEA faculty can contribute to.
      • Instructor/TAs joining in on weekly virtual discussions with small groups/teams of students.
  • Run PHAGES with at least 2 instructors or 1 instructors with well-prepared TAs. The goal here is to ensure that if one instructor much self-isolate, the class may continue to meet.
  • Begin introducing students to genome annotation early in the semester, so that they can continue with genome annotation is all access to lab (including for instructors) are restricted. For example, discuss the genomic sequence of SARS-CoV2.
  • Be mindful of barriers that some students may have with regard to technology (hardware and software) and connectivity. If students cannot maintain stable connection to a video-conferencing call/webinar, it may be helpful to ensure that all video calls/webinars are recorded and made available to students. If DNAMaster cannot be reliably run by some students, they may be allowed to use PECAAN while being partnered with a student that runs DNAMaster.

 

Developing Students as Scientists
Given the necessary modifications to the fall semester, and possible the need to revert to online-only classes, the following strategies may facilitate maintaining high student engagement:

  • Promote Collaborations within members of a team:
    • Use online collaborative tools like Trello for team members to communicate what they’ve completed, what needs to be done, data sharing. This will allow each student to work collaboratively while also maintaining their own e-notebook (or a shared e-notebook).
    • Use online tools like CATME (Comprehensive Assessment of Team Member Effectiveness) to promote smarter teamwork.
    • to promote teamwork
    • If possible, support live-streaming via Facetime, WhatsApp, Google Hangout, etc., during lab sessions.
    • Have students rotate roles, e.g. taking turns to be the note-taker, protocol verifier, hands-on person, data analyzer.
    • Have teams meet virtually once a week to review progress and discuss strategies for the following week.
      *If possible, ask SEA-PHAGES alum to “buddy” with a team and join in their weekly meetings and/or host separate virtual office hours. This may encourage peer discussions about their data and general research expectations).
       
  • Promote Individual Responsibility/Ownership in a Team:
    • Give students the responsibility to prepare for their teammates by requesting reagents for the next session.
    • While each team member will participate/support all aspects of Phage Discovery, it may be helpful to have each team member serve as the lead person for particular stages of Phage Discovery (e.g. Isolation, or Purification, or DNA Extraction).
    • Each student can take turns reporting out for the team. This can be a summary to the instructor/TA, or the instructor/TA can join their weekly meeting for a short period.
    • Find ways to recognize each student throughout the semester for group progress.
       
  • Community Building & Maintaining Engagement
    • Entire class meets regularly for
      • Fun (e.g. Trivia, via the Kahoot app or Flipgrid)
      • Report outs by students on team progress
      • Report out by faculty about class progress
    • Connect classmates via social media (Facebook group, Instagram) and provide introductory material (e.g. Perfect Predator video assignments) before the semester starts.
       
  • Science Identity
    • Connect the skills they are learning to the current pandemic in a way that encourages students to speak knowledgably about with their friends and family. This can include the importance of working aseptically and the utility of wearing a mask, as well as the concept of host range and transmission from wildlife to humans.
    • Have teams of students co-develop an elevator pitch about their work.

Microbacterium Phage Paper

Microbacterium Phage Paper

Thanks to everyone who participated in the 2019 Microbacterium Genomics Workshop. The paper we collectively worked on and wrote has now been published and is available at PLOS ONE. A must-read for anyone phage hunting using a Microbacterium host!

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0234636

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

Upcoming Events

Recent Events

Cohort 13 Phage Genomics Workshop

June 15, 2020 to June 26, 2020

12th Annual SEA Symposium CANCELLED

June 5, 2020 to June 7, 2020

Forum Activity

c.sunnen posted in softberry for terminators?

Debbie Jacobs-Sera posted in queuine tRNA ribosyltransferase

Debbie Jacobs-Sera posted in GTP cyclohydrolase I

FORUMS HOME PAGE