1. Challenges in Bioinformatics Part I
Vasileios Hatzivassiloglou
University of Texas at Dallas

2. Evolution timeline Earth forms (4.5 billion years ago)
Earth acquires solid crust (4.1 by)
First life form, self-replicating RNA (4 by); no oxygen in the atmosphere
First bacteria and archaea (3.9 by)
Photosynthesis in bacteria (3.5 by)
First eukaryotes (2.1 by)
Sexual reproduction (1.2 by)

3. Evolution timeline, part II
First multicellular organisms (algae and seaweeds, 1 by)
Sponges, jellyfish, worms (600 my)
First fish (500 my)
First plants on land (475 my)
Arthropods on land (450 my)
First insects (400 my)
Seeds in plants, amphibians (350 my)
Pangaea, First reptiles (300 my)

4. Evolution timeline, part III
Crocodiles, first dinosaurs (250 my)
Giant dinosaurs (150 my)
First flowers (130 my)
First ancenstor of mice and humans (100 my)
Dinosaurs extinct, mammals dominate (65 my)
First primates (55 my)

5. Evolution timeline, part IV
Earliest humans (homo habilis, erectus; 2 my)
Homo sapiens (140,000 years ago)
population reaches 5 million 11,000 years ago
150 million 2,000 years ago
6 billion 6 years ago
6.7 billion as of July 2008

6. Interactive evolution timeline
Online at

7. A familiar organism Kingdom: Animalia Phylum: Chordata
Subphylum: Vertebrata
Class: Mammalia
Order: Primates
Suborder: Anthropoidea
Superfamily: Hominoidea
Family: Hominidae
Genus: Homo
Species: Homo sapiens
Subspecies: Homo sapiens sapiens

8. Hominid species

9. What kind of biology? Biochemistry Molecular biology
lowest level, studies chemical substances and interactions
Molecular biology
gene/protein interactions, structure, and function
molecular genetics
proteomics

10. What kind of biology? Cellular biology
Histology / physiology / anatomy
studies multi-cell groups
Developmental biology
cell growth, morphogenesis
Genetics
mechanisms of heredity and variation
Evolutionary biology

11. Human migration Based on fossil record
study of mtDNA (mitochondrial DNA)
mtDNA better suited to tracking generations
more mutations
more copies
inherited only through the mother

12. Identification through mtDNA
Stone AC, Starrs JE, Stoneking, M. Mitochondrial DNA analysis of the presumptive remains of Jesse James. J of Forensic Sci 2001; 46(1):173–176.
Jesse James ( )
Notorious outlaw in Missouri

13. Human migration animation
Online animation at

14. Problems in Bioinformatics
Overview of major topics in bioinformatics
What the problem is
Elements of the solution
Computational issues

15. Sequencing Find the sequence of nucleotides
A genome must be sequenced in small parts (~1000 bp)
For each part, given fragments of a DNA sequence (e.g., matches via a DNA chip), assemble the entire fragment in the correct order
Reassemble the parts
an NP-hard problem

16. Polymerase chain reaction (PCR)
A general method for amplifying DNA (or RNA via reverse transcription)
In vitro technique (as opposed to in vivo)
Uses DNA polymerase to simulate replication, and primers (10-45 bp) as start and end markers
Proceeds in cycles; can amplify fragments up to 10kb long (sometimes 50kb)
Invented in 1983, Nobel prize in 1993

17. Applications of PCR Chain reaction (Sanger) sequencing
Genetic fingerprinting
Forensics
Paternity tests
Detection of hereditary diseases
Cloning of genes
Gene modification (mutagenesis)
directed versus random
production of recombinant DNA (rDNA)

18. Sample DNA fingerprint
Father
Child
Mother

19. Zebra fish

20. Recombinant DNA on zebra fish
Insert an additional gene that changes color and causes fluorescence
Added gene comes from jellyfish (green, yellow) or sea coral (red)
Developed in 1999 in Singapore / Taiwan
Purpose: Detect pollution by making fluorescence activated by toxins
Group of Texas entrepreneurs markets the fish for aquariums (2002)

21. GloFishTM