1. “Jumping Genes” Lead The Way
Uwe Hilgert, UofA
iPlant, BIO5 Institute & CDTIS
A bioinformatics/biotech workshop
at the
AZCTE Conference 2015

2. Research & Teaching PCR Agarose gel electrophoresis Electronic PCR
Sleuth genetic relationships
Navigate NCBI
DNA Subway
Hardy-Weinberg
Population Genetics/Allele Server
Simulation Server

3. Biology Human migration Polymorphisms and alleles
Random genetic drift vs. selective pressure
DNA amplification
Mobile genetic elements

4. Bioinformatics Access sequence databases Conduct sequence searches
Perform electronic PCR
Explain the various types of sequence searches
Retrieve sequences
Align sequences
Analyze sequences
Determine sequence relationships
Interpret gene and genome maps
Identify Genetic variation

5. Workshop Goodies Stuff Agenda: https://goo.gl/Df1T6f
Repository:
Etherpad:
People
Lead:
First TA:
Second TA:
Organizer:

6. Human Genome Human genome: Other Animation 25% protein-coding genes
3% protein-coding sequence
50% repetitive DNA
25% Alu and Line (L1) retro-transposons
Other
Corn: 75% Transposons
Lily: 98% Transposons
Animation
Chr 11 Flyover
Iris brevicaulis

7. Transposons Mode of transposition Structure Level of independence
Excise and Insert (Transposons, Transposase protein)
Copy and Paste (Retroposons, Reverse Transcriptase protein)
Structure
Central: Genes for “mobility proteins”
Flanking: Mobility protein action sites (repeats)
Level of independence
Have genes & flanks  can jump by own volition (Line, Ac)
No genes; flanks ok  can be jumped (Alu, Ds)
Genes, flanks faulty  can jump others

8. How do organisms live with TEs?
Most TEs are broken (cannot tranpose; “fossils”).
Active TEs evolved to insert into “safe-havens.”
Host regulates TE movement.
“Stress” conditions may activate TEs.
TEs can provide advantages.
Transposable elements can shake up otherwise conservative genomes and generate new genetic diversity.

9. TEs can alter gene expression
Can this have phenotypic consequences?
Nipponbare
EG4
EG4 is salt tolerant

10. Whose Ancestor? Mom + Dad DNA “Blood” relatives share DNA
PV92 locus/site in human genome
Exists in different form/alleles
Alternative allele arose about 100,000 years ago
No selection
Simulation Server

11. Whose Ancestor? PV92 Wetlab PV92 eLab Cheek-cell DNA ePCR PCR
Agarose gel
Personal
PV92 eLab
ePCR
PV92 locus/site
PV92 in humans
Species (Specia-l)
“Blood” relatives share DNA
PV92 locus/site in human genome
Exists in different forms/alleles
Alternative allele arose about 100 kya
No selection

12. Workshop Goodies Stuff Agenda: https://goo.gl/Df1T6f
Repository:
Etherpad:
People
Lead:
First TA:
Second TA:
Organizer: