Phage Lab Introductions SlidesSyllabus TA share experiences Phage

Phage Lab @ Introductions Slides/Syllabus TA share experiences

Phage Lab @ Allison Johnson Associate Professor

My Path BS in Biology Ph. D in Molecular Biology Postdoc in Biochemistry/pharmacology Faculty at VCU

Allison Johnson Associate Professor • Teach Phage Lab, and other • Research viruses, genomics, biochemistry • Service to Center, Bioinformatics Programs, • HHMI Inclusive Excellence in STEM Your TAs are: Nikhita Puthuveetil, grad TA 9 am (L 01) Ahmed Ismail Zainab Gbadamosi Prekshah Jerajani 11 am (L 02) Leila Alickovic Jacob Essig

HHMI’s Science Education Alliance SEA Goal: “To create a national course that will make it possible for undergraduates to have an authentic research experience” • • Administered through HHMI’s Precollege and Undergraduate Science Education Program Graham Hatfull, University of Pittsburgh, Lead Scientist A national network of like-minded science educators Annually >100 institutions participate, many in Virginia

“Phage Lab” at VCU Course Goals: 1) Target freshmen science majorsthe earlier, the better 2) Learn science by doing science 3) Do something really interesting! Started in 2009 Team-taught 2 yrs with Anneke Padolina, Biology For the Bioinformatics Program: A mechanism to introduce our freshmen students to genomics and bioinformatics For Bioinformatics, this is now our ‘preferred’ course series, substituting for BIOZ 151/152 SEA PHAGES program was recently cited as the primary opportunity nationwide for biology students to learn bioinformatics!

BNFO 251: Phage Discovery Lab From Dirt to a Genome Students: Isolate novel bacteriophage Characterize plaque morphology Predict lifestyle (lytic vs. temperate) Take a picture of their phage (TEM) Name it! Purify & characterize genomic DNA Submit DNA for sequencing (a few) Attend regional symposium Some are selected for genomic DNA sequencing

James River Rockpools

Bacterial infection by lytic virus

Characteristic Bacteria Viruses Size Small (1 -5 mm) Smaller (100 -200 nm) Independent growth? Yes No Susceptible to antibiotics Yes No Found everywhere? Yes More abundant? No Yes

1. Enrichment culture How we find a phage 1. Flood soil sample 2. filtration or 3. Serial dilution 3. Infect Bacillus cultures 4. Infect Bacillus cultures 5. Plate with top agar 4. Plate with top agar

Once you find a phage Enriched Isolation spot test Make sure you record soil collection/location information! 2 -3 rounds of plaque purification by serial dilution and plating

We’ve Found Lots of Phages

Spring Semester: Gene Annotation and Comparative Genomics Examine DNA sequencing data Find genes, predict function Compare against other phages Ask questions, dig into the biology Present work at regional symposium Present work at VCU undergraduate research festival Submit annotation to Genbank Submit Genome Announcement = publication!

We’ve Annotated 44 Genomes -each genbank file includes student coauthors!

We’re Publishing -each includes student coauthors!

We’re Publishing -each includes student coauthors! April 2015 paper included: 627 phages 2853 coauthors 24 VCU students

Syllabus/schedule Resources Seaphages. org- protocols Blackboard- assignment submission, grades VCU Wiki- lab notebook Lab safety- must get lab coat and safety goggles Math packet due 9/5 Pipetting and serial dilution

Grading! Requirement Grade Participation 20 Math packet Journal Club Question Sets (3) 30 Notebook 15 Archive 10 Lab quizzes (4) 10 Final presentation Total % 5 10 100

Please watch this video before August 27 th class! Accurate pipetting is essential to reproducible work in this class. https: //www. youtube. com/watch? v=QGX 490 ku. Kjg