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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

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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A Regional Symposium Near You

We are delighted that more and more SEA schools are coming together to host regional SEA symposia. These meetings offer many benefits, including more opportunities for students and faculty to network, collaborate, and present their research. In 2017-2018, at least one fifth of SEA schools participated in a regional symposium.

Attending a Regional Symposium
This academic year, there are already 6 regional symposia that are being planned. These meetings will be posted at https://seaphages.org/meetings/. If you are interested in attending one of these meetings with your students, please contact the hosting faculty members. Space can be a limiting factor for some venues.

Hosting a Regional Symposium
If you would like to host a regional symposium in the 2018-2019 academic year, HHMI is able to provide up to $1,000 of support for the meeting. We recommend that you begin by contacting SEA faculty from institutions close to you to begin planning a meeting. Remember, especially for our colleagues out West, a regional meeting can be as small as 2 SEA institutions coming together. A map of all SEA schools is available here, and a list of SEA institutions is available at our program website: https://seaphages.org/institutions/. As you begin planning, please contact us (Vic Sivanathan & Billy Biederman) at sea@hhmi.org for additional information about the financial support. When possible, the SEA Team would be delighted to join your meeting. A list of recommendations for hosting a regional symposia is below, compiled from the experiences of SEA faculty.

Below is a list of considerations and recommendations as you plan for your regional symposium.

  • Participants: Identify SEA faculty from nearby SEA institutions that may be interested in hosting and/or participating in a regional symposium. A list of SEA institutions, sortable by location, is available at www.seaphages.org/institutions. The hosting institution should determine the number of participants that can be accommodated for the meeting, reserving appropriate space for talks, posters, meals, and other planned activities.

  • Date and Time: Begin planning early. Set a date for the meeting, taking into consideration when students will have gathered sufficient data to present or to work on collaboratively, as well as end of year events, including final exams, the Annual SEA Symposium, and the summer break. Start and end times for the symposium should accommodate travel time to and from the meeting.

  • Agenda: Past regional meetings have included a keynote presentation by an invited speaker, talks by SEA faculty, talks and posters by individual and/or teams of students, poster sessions, and activities such as a Genome Annotation Hackathon. Poster sessions and breaks are great opportunities for students to interact and network.

  • Collaboration: Early symposium planning provides opportunities for regional schools to collaborate. For examples, participating schools may choose to work of different Actinobacterial hosts followed by a collaborative host-range project, or working collaboratively on a common Actinobacterial host and varying isolation strategies.

  • Costs: Meeting costs include travel expenses, poster printing, meals, and keynote honorarium.

Sequencing Information 2018-19

This post contains some information on sending your SEA-PHAGES phage DNA samples to the University of Pittsburgh for sequencing.

Sample Submission Form: NEW!

New this year! We are now requiring you to 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 16.

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 interferes 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. The shipment should be sent with cold packs and overnight shipping for delivery to Pittsburgh on Tuesday-Friday.

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

Address

Dan Russell
344 Crawford 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.

Current Events

Order Phage Discovery Lab Supplies

March 1, 2019 to March 31, 2019

Upcoming Events

Receive, Prepare, and Test Biologicals for Phage Discovery **

April 1, 2019 to May 31, 2019

Midwest Regional SEA-PHAGES Symposium - 2019

April 5, 2019 to April 6, 2019

Phage Phest 2019

April 11, 2019

Recent Events

Submit Completed PITS Assessment IRB Approval Letter

March 15, 2019

Identify 2019 Symposium & Phage Discovery Workshop Trainees: for Cohort 12 only

March 15, 2019

Forum Activity

Welkin Pope posted in two integrases

GregFrederick@letu.edu posted in Mycolicibacterium rename...

Welkin Pope posted in Is pham 23434 a DNA recombinase or a helicase?

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