Using Bioinformatics to Make the Bio-Math Connection

1. Using Bioinformatics to Make the Bio-Math Connection The Confessions of a Biology Teacher

2. Math? In a Biology Classroom? I know what you are thinking, and I’ve just written an algorithm that proves it is very effective.

3. "Complex assemblies of interacting proteins carry out most of the interesting jobs in a cell, such as metabolism, DNA synthesis, movement and information processing. These physiological properties play out as a subtle molecular dance, choreographed by underlying regulatory networks. To understand this dance, a new breed of theoretical molecular biologists reproduces these networks in computers and in the mathematical language of dynamical systems." (From "Network dynamics and cell physiology", by Tyson, Chen, and Novak, Nature Reviews in Molecular Cell Biology, 2001.).

4. bi·o·in·for·mat·ics The use of mathematical and informational techniques to solve biological problems by using computer programs. One of the main applications of bioinformatics is the data mining in and analysis of the data gathered in genome projects. Other applications are amino acid and nucleic acid sequence alignment, protein structure prediction, and virtual evolution.

5. Biology Student Workbench • revolutionary web-based tool • allows biologists to search protein and DNA databases around the world • integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface.

6. Outcomes and Observations • Integration of bioinformatics into the high school classroom using inquiry methods was successful. • Students were able to use the tools to generate real data, but more importantly were able to apply these applications and independently problem solve. • Students showed a greatly increased ability to make connections between units of study: protein structure, protein function, nucleic acids, genetics, genetic disease, and evolution.

7. Student Interface to the Biology Workbench (BSW) alternative interface to the Biology Workbench orientated towards interactive teaching and learning

12. BLASTN & MATH • Aligns the original strand with other strands • Numerous possibilities exist, but which alignment is the best? • A scoring criterion must be devised to evaluate the quality of an alignment. • For example, the alignment may be scored based on the following criterion: • +2 for each alignment of matched letters • -1 for each alignment of mismatched letters • -2 for each alignment of a letter with a gap

18. Protein Tools • May also do protein searches…Ndjinn • May look for similar proteins…BLASTP • Protein tools are more reliable for looking at evolutionary relationships

24. Clustal Distance Matrix (1) (2) (3) (4) (5) (6) (1) 0.000 0.000 0.007 0.000 0.021 0.028 (2) 0.000 0.000 0.007 0.000 0.021 0.028 (3) 0.007 0.007 0.000 0.007 0.028 0.035 (4) 0.000 0.000 0.007 0.000 0.021 0.028 (5) 0.021 0.021 0.028 0.021 0.000 0.028 (6) 0.028 0.028 0.035 0.028 0.028 0.000

27. Rooted Tree

30. Unrooted Tree

31. Graph Theory • A connected graph without a cycle is a tree. http://people.hofstra.edu/geotrans/eng/ch2en/meth2en/ch2m1en.html

32. Biology Uses • Find & compare DNA sequences • Translate DNA into an amino acid sequence • Find & compare protein sequences • Look at evolutionary relationships • Draw trees

33. Math Uses • Alignments • Matrixes • Graphs • Combinatorics

34. "The slippery gooiness of biology is a consequence of its incredible complexity, consisting as it does of complex systems based upon chemistry. And chemistry obeys the rules of physics, which exists because of, and is consequently best described by, mathematics." (From the Mathematics in Biology page at Brandeis.)