Obtaining and Using Computer Based Tools for the Freshman and Sophomore Biology Laboratory

1. Obtaining and Using Computer Based Tools for the Freshman and Sophomore Biology Laboratory 12th Annual Technology Conference October 6, 2006 Christopher Harendza, Professor of Biology

2. Abstract Biology has experienced an explosion of DNA sequence data and the human genome and those of several model organisms are complete. There are numerous free web based tools available to analyze this data. In addition, many laboratory exercises have been adapted to computer programs; some are traditional laboratories but many are mathematical models of complex processes that could not be studied in the lab. MCCC is in the third year of an NSF grant to implement the aforementioned approaches to the teaching of bioscience majors. The forum will discuss the grant process and current status of the project.

3. Today’s Discussion • Project Goals • National Science Foundation – CCLI A&I Program • Examples of What is Being Done • A Critique • Future Plans

4. P R O J E C T G O A L Traditional Science Education Model Inquiry & Project Based Labs Curriculum evolution “Cook Book Labs”

5. Curriculum Change • Evolution vs. “reform” • Keep the best of the old and bring in a fresh approach • Maintain standards

6. Primary focus: undergraduate research and education • Focus on educational reform • Numerous programs http://www.nsf.gov/

7. Project Based Activities Inquiry Based Labs Data Analysis Bioinformatics Modeling Collaboratories

8. Course, Curriculum &Laboratory Improvement (CCLI) Areas of Support Biological Sciences Chemistry Computer Science Engineering Geological Sciences Interdisciplinary Mathematics Physics/Astronomy Research/Assessment Social Sciences

9. Goal of NSF CCLI • “to promote excellent science, technology, engineering, and mathematics (STEM) education for all undergraduate students”

10. CCLI Tracks • Educational Materials Development (EMD) • Adaptation and Implementation (A&I) • National Dissemination (ND) • Assessment of Student Achievement (ASA)

11. Adaptation and Implementation (A&I) • Adapt and implement • find existing funded projects and modify (adapt) them to your situation • Carry out project • Disseminate what you have done to encourage change (“reform”)

12. A&I areas • “incorporation of laboratory experiments or field experiences that engage students in scientific processes and exploration of scientific concepts” • “adaptation and testing of exemplary materials for use by a student population significantly different from the one for which they were originally developed”

13. A&I Areas, con’t • “enhancement of teaching and learning through the use of resources, particularly instructional and information technologies, demonstrated to be of high quality” • “development and use of collaborative learning, learning communities, peer-led teaching, etc. that aim to improve pedagogy in courses” • “integration of significant advances or techniques from research fields into the undergraduate curriculum”

14. Finding ideas: • Search awards for thing (s) you like • Get help from your grants office • Write proposal

15. Adapt & Implement past funded projects: PCs for laboratory work Grant: Laptops for a Combined lab/ lecture/discussion setting computer modeling of complex labs bioinformatics

16. NSF Grant

17. Specifics • 13 student laptops with wireless internet connections • Wireless hub • Bioquest™, MicrobesCount™ & Virtual Fly software, etc. • Digital electrophoresis documentation system • Labor for IT and development

18. BioQUEST packages • BIRDD • DNA Electrophoresis • Fly a Cell • Lateblight • Metabolic Pathways • PEACH • Resistan • Winter Twig Key

19. Problems w/ BQ • Many of the better modules, e.g. Genetics Construction Kit, are Mac only • Not updated – a bit unsophisticated • Some things too advanced for freshman biology • Sometimes not easy to use

20. MicrobesCount! • ASM / BQ venture • Newer, nicer • Good mathematical modeling

21. Some MicrobesCount! Labs • The Scale of the Microbial World • Modeling Wine Fermentation ** • Biosphere2: Unexpected Interactions ** • Modeling Microbial Growth: TB and Antibiotic Resistance • Conjugation and Genetic Mapping • Tree of Life: Intro to Microbial Phylogeny **

22. Combined and adapted to Protein Explorer • Searching for Amylase • Proteins: Historians of Life on Earth • Visualizing Microbial Proteins • (see below)

23. Virtual Fly • Flexible and powerful model for use in genetic crosses using the classic model Drosophila

24. CLUSTAL Applications • Exploring HIV Evolution: An Opportunity for Research • Tree of Life: Introduction to Microbial Phylogeny • Tracking the West Nile Virus ***

25. Open access bioinformatics tools designed for student use

26. Definitions of Bioinformatics • any use of computers to handle biological information • computational molecular biology • the use of computers to characterize the molecular components of living things

27. Bioinformatics & the HGP

28. Biology Workbench Tools • BLAST • Amino acid • Nucleic acid • CLUSTAL • Amino Acid • Nucleic Acid Many variations and special applications

29. Some Specific Examples • Protein Explorer • Winemox fermentation to model alcohol production in a winery • SIMBIO@ ecosystem model • CLUSTAL W to study the spread of West Nile virus • BLAST to study orthology • Virtual fly

30. Protein Explorer • Molecular visualization program • Allows study of proteins in 3 dimensions

31. Uses Go to PE You will need a plugin called “chime” • Modeling of insulin (PDB code = 1APH) • Simple and important protein • Only 51 amino acids, DM • Hemoglobin (PDB code 1HGA; HbS/HbS PDB code = 2HbS) • Well studied • Common thread throughout course • Applications to sickle cell: evolution, multiculturalism, etc.

32. PE Outcome: positives • Excellent Flash Tutorial on use • Better appreciation for protein structure • Student exposure to authentic research data and models for protein structure

33. PE Outcomes: Negatives • Can be complicated for students who are ill prepared • Descriptive, not very experimental • Time consuming

34. Wine.mox • Mathematical model based on Extend software • Used as a “part II” to augment an existing wet lab on fermentation • Fermentation vs. time • Fermentation vs. time + O2 (Pasteur effect) • Both use MS Excel graphing

35. Standard Wet Lab assay

36. Students use the laptops & MS Excel in lab to generate data

37. Use of Wine.mox • Students hypothesize on how to increase ethanol production • Increase glucose concentration • Increase stress factors of yeast (wild yeasts ferment <<< 12% alcohol) • Possible to make other models

38. Wine.mox interface

39. Wine.mox output

40. Ecosystem modeling • Ecologists use mathematical models extensivley and field work is often not possible Biosphere II, Tuscon, AZ

41. SimBio 2 Model: Ran in lab & went to Blackboard Wiki Collaboratory

42. Default Results; N=8, Soil Biomass = 3000

43. Questions from the results above: • What is the relationship between CO­2 concentration and O2 concentration? • Why is there a cyclical fluctuation between CO2 and O2 concentration?

44. Next question • What is the maximum number of people Bio2 can support? • If O2 levels drop below 12% it seriously impairs human physiology

45. N = 16

46. N = 32

47. N=256

48. Conclusion • 3 acres of land does not support very many people! • O2 levels still decline to dangerously low levels – Why? • It turns out it was the biomass and the ants using the O2 to decompose it!

49. Effect of the soil • Biosphere2 was built using soil that was with unusually heavy in organic matter; hence the soil had fairly high rates of respiration • What affect does simulating a sandy soil (with less organic material) have?

50. WEST NILE VIRUS MIGRATION • Use CLUSTAL site at Biology Workbench • multiple sequence alignment program: aligns sequences & depicts the differences • examines relatedness, based on mutation rate