1. Bioinformatics in the Dynamic Genome Course
Introducing Freshmen to computational biology
University of California, Riverside

2. Dynamic Genome Course Give Freshmen a taste of research: First Half
Core Biological Concepts
Key molecular biology skills
Basic Bioinformatics
Second Half
Open ended guided research project

3. Some history…DG at UGA
Research Project: Identify transposable elements in newly sequenced genomes by homology
Steps:
BLAST exemplar(s) against genome
Align top scoring “hits”
Build gene trees of newly identified elements

4. History con’t… >Copia_RT WVYRVKHKQDGSIDRYKARLVAKGYTQVEGLDYLDTFSP
VAKTTTLRLLLALAASQGWFLHQLDVDNAFLHGTLDEEI
YMRLPPGVSSPRPNQVCLLQKSLYGLK

5. Next design primers and verify location in genome.
POL
Next design primers and verify location in genome.
Simple, right…...?

6. Students hated it File Formats
BLAST
FASTA
Command Line
Clunky web based tools (2007)
It took several weeks to get to the gene tree
Solution…

7. TARGeT: Tree Analysis of Related Genes and TEs.
Graduate student wrote a scritp
First chapter in thesis
Yujun Han, James Burnette, and Susan Wessler (2009). TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences. Nucleic Acids Research
Hosted by CyVerse (a.k.a iPlant Collaborative)
target.iplantcollaborative.org

8. Quick TARGeT Demo

9. TARGeT Recap Removed tedium Results mostly within attention span
Spend more time on biology in class…

10. Ping protein query against Rice and Soybean

11. Ping Transposase query against Rice genome
Protein query
Nucleotide query
Ask students:
Why does the protein query find more putative homologs?

12. Gene Families: Actin
Rice
Maize
Query: Rice Actin

13. Actin compared with Ping Tpase

14. An aside: This summer 17 rising sophomores
Investigating genetic variation within gene families in Citrus and related genera

15. Transpose to Riverside
Quarter system
20 class meetings of three hours each
4-5 weeks for background
5-6 weeks for project
As of fall 2016, 6 sections per quarter
Neil A. Campbell Science Learning Laboratory
Most diverse R1 University
60% First to college
Must provide the technology
Be very careful with terminology

16. Module 1: Genetic Information Flow
Students review central dogma outside of class
Review in class with concept maps
Experiment: Amplify the Actin gene from gDNA and cDNA

17. Module 1: Locating Introns: Step 1
1. BLAST gDNA sequence vs cDNA sequence using BLAST2Sequences

18. Step 2: Find locations

19. Step 3: Draw gene structure
This analysis can be done on tablets!!

20. Module 2: DNA Sequence Polymorphism
Experiment: Amplify a locus from many strains of maize
Introduce idea of reference genome (B73)
Sometimes introduce genome browsers, PCR primer design

21. Sequence Analysis Multiple Sequence Alignment Burnette and Wessler
Genetics 2013

22. Electronic Laboratory Notebook
The Dynamic Genome Laboratory Notebook is completely electronic
We developed our own:
FERPA compliant
FREE
Allows combining bioinformatics and wet lab data
Allows collecting “big data”
Robb et al. Course Source

23. Demo eNotebook, data collection
Robb et al. Course Source

24. Example Research Projects
Verify predicted TE insertions in rice and maize
Phenotypes of transcription factor knock-outs in planaria and C. elegans. Verify knock out with PCR
Characterize Ruby alleles in Citrus
Polyembryony in Citrus and Poncirus (if time show data collection 3326)

25. Challenges
Students are not as computer literate as we are lead to believe.
Simple curosity – “Did you google it?” “Did you Pubmed it?”
Resistance to anything non-Facebook
Good interfaces: DNA Subway
Lots of support
Diversity of examples
TERMINOLOGY
Three vocabularies
Biological Words (transcription, translation) (gene, locus, ROI)
Laboratory Words (PCR, gel, mini-prep)
Computer Words (parameter, input, format, file type)

26. Acknowledgments Dr. Sofia Robb Dr. Matthew Collin Dr. Yujan Han
Alex Cortez
Rochelle Campbell