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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 Faculty Meeting FAQ

As we gear up for the upcoming Faculty Meeting, below are some guidelines to help you prepare. Included are guidelines for the following:

REGISTRATION

Who should register?
All SEA faculty are invited to register and attend to 2021 SEA Faculty Meeting.

How do I register?
All SEA faculty members will receive instructions to register for the Faculty Meeting by email on May 10, 2021. If you are a SEA faculty member and need these instructions, please contact us at info@seaphages.org. Registration closes on May 14, 2021.
 

POSTERS

Who should submit posters?
SEA Faculty Members who are attending the Faculty Meeting are invited to submit an abstract and present a poster. Poster abstracts will be submitted via the seaphages.org program website by May 19, 2021, whereas the final posters will be uploaded to the Faculty Meeting website by June 6, 2021. Instructions for abstract and poster submissions are provided below.

How many posters should be submitted?
Faculty can submit as many posters as they have data or information to present. Posters can describe SEA-related course implementation, pedagogy, or research, the scope of which can go beyond the PHAGES and GENES courses. For example, faculty members who developed and published teaching resources on QUBES are all invited to present a poster.

What is the format for each poster?
Posters to be submitted as short video recordings of ~ 5 minutes. This will allow attendees to view poster presentations asynchronously before, throughout, and after the meeting. Minimally, the video must include a visual representation of your data and an accompanying narration. For example, your video poster can be prepared as a recorded PowerPoint presentation. We encourage you to add closed captioning for your video. The University of Washington's recommendations for doing so using free online tools can be viewed here.


What should I include in my abstract(s) and poster(s)?
We encourage you to include the following items in your poster, adding or subtracting from this list as you see fit.
i. goal(s) of your project(s),
ii. methodology, especially if it includes techniques that are not core to the SEA projects,
iii. findings, whether they be complete data figures or early observations,
iv. research or questions that will be explored next,
v. questions related to your project that the SEA community (i.e., poster attendees) might be able to provide insight.
vi. and of course, the usual poster items such as your school logo, poster title, and author information.
Your abstract will represent a summary of what will be included in your poster and can primarily focus on items i, iii, iv from the list below. There is a 3,000 character-limit for abstracts.

What is the format for the poster session?

While posters will be available for asynchronous viewing throughout the meeting, we will host a dedicated poster session for synchronous viewing. The poster session will be hosted as breakout rooms (on Zoom), with each poster presenter hosting a breakout room for ~15 minutes. During the 15 minutes, the poster presenter will provide a 5-minute live runthrough of their poster, and will then take questions from the audience for the remaining 10 minutes. After the 15 minutes are up, the breakout room will close. We expect to host multiple breakout rooms concurrently, and several consecutive 15-minute breakout sessions, depending on the number of posters submitted.

How do I submit my abstract(s)?
Once you are signed in at seaphages.org, links to add, modify, or view an abstract are provided at the top of your institution page. Abstracts should be submitted by May 14, 2021.

How do I submit my poster(s)?
Once you have submitted your abstracts, SEA staff will send you a unique link for each poster. With this unique link, you will be able to upload your video poster to the Faculty Meeting website, either by submitting a hyperlink to the poster-video or by uploading the poster-video file. There are 4 steps to uploading your video-poster. A Step-by-Step guide can be downloaded here. Video-posters should be submitted by May 31, 2021.
 

TALKS  

If you would like your abstract to be considered for a talk, you can indicate so during abstract submission. If your abstract is selected for a talk, you will be notified by May 21, 2021.

What is the format for talks?
We will host a session with several slots set aside for 12-minute faculty talks (+3 minutes for Q&A). Talks will be presented live.
There will also be several longer-format featured talks, including a keynote presentation by Professor of Psychology Judith Harackiewicz. The meeting agenda lists the dates and times for talks.

 

WORKING GROUPS & TOPICS

As with previous years, we invite SEA Faculty to submit topics that they would like discussed at the faculty meeting. Often, concurrent breakout/working groups are organized for these topics, and SEA faculty are invited to attend those of interest to them.

How do I propose a topic?
At the end of the registration process, a link will be provided to the seaphages.org forums where you can propose topics. You can also access the forums directly HERE.

What topics can I propose?
We welcome all topics, and encourage you to propose topics that will benefit from communty input or that will benefit the community. In the past, topics have included those on phage biology, collaborative research projects and tools, pedagogical tools, hackathons, and course implementation tips.
 

OTHER

How will symposium attendees be able to interact?
To provide many opportunities for you and your students to connect with the SEA community, there will be multiple ways for symposium attendees to interact, suited to particular sessions. We encourage all to participate in these interactions.

  • All talks and poster sessions will be hosted as a regular Zoom meeting. As such, members of the audience have the option to ask questions verbally, or using the Q&A feature provided by Zoom.
  • We will also host events on the virtual yacht, where you can see other attendees, wander up to each other to automatically launch a video-session, and interact with objects throughout the yacht.
     

What are important dates?
May 14, 2021:           Deadline to register for the Faculty Meeting.
May 19, 2021:           Deadline for abstract submission.
May 21, 2021:           Those selected to give talks will be notified.
June 6, 2021:             Deadline to upload Poster-videos to the symposium website.
June 7 - 9, 2021:       Attend the symposium [scheduled from 1 - 6 pm ET]. The meeting agenda is provided on the meeting site, accessible once you have registered for the meeting.

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.

Upcoming Events

2021 SEA Faculty Meeting

June 7, 2021 to June 9, 2021

Recent Events

2021 SEA Symposium

April 9, 2021 to April 11, 2021

Cohort 13 Phage Genomics Workshop (Dec 2020)

December 7, 2020 to December 18, 2020

Forum Activity

Debbie Jacobs-Sera posted in lysin A gene split with an intron?

Andrea Panagakis posted in lysin A gene split with an intron?

Debbie Jacobs-Sera posted in lysin A gene split with an intron?

FORUMS HOME PAGE