Yeast and Oxygen: Incorporating Functional Genomics Research into Three Integrated Undergraduate Laboratory

Classes

Clare O’Connor

Biology Department

Boston College

The problem: How can we provide large numbers of undergraduate students the opportunity to participate in original research in biology?

Too many undergraduate majors: ~700

Too few faculty research labs: 18

A solution: Reconfigure existing advanced laboratory classes (cell biology, molecular biology, biochemistry) to include original research activities

Genome projects with model organisms have provided a wealth of resources that can be used by undergraduate students

The science: Yeast and oxygen

Yeast are an excellent choice for undergraduate experiments

• rapid growth, simple culture and storage requirements

• wealth of information and resources availableOxidative damage is important and interesting to students

• students are aware of positive effects of antioxidants

• implications for human disease

• connections to chemistry

Year 3: Focus on yeast methionine sulfoxide reductases

Bovine MsrA

YER042W

N. gonorrhoeae

YCL033C

E. coli Frmsr

YKL069W

Orthologs of putative yeast Msrs are structurally divergent enzymes with related functions

High-throughput studies show different sets of interactors

YER042W is considered by SGD to be functionally characterized

YCL033C is an uncharacterized ORF with putative Msr function

YKL069W is listed as an ORF with unknown function

Course goals

Students will learn to construct scientific hypotheses based on existing knowledge.

Students will design experiments to test their hypotheses and critically evaluate the results.

Students will learn effective time management and cooperation skills by working in teams.

Students will communicate their results in scientific publications and oral presentations.

Students will appreciate the interdisciplinary aspects of modern science.

Typical course schedule

Course kick-off - classes meet together

First few weeks Students:

become familiar with basic techniques

are organized into teams

use databases and literature to formulate hypotheses~1 month Students submit and refine proposals

Remaining weeks Students work on projects

weekly “group meetings”

literature presentations

prepare reports in format of scientific publication

Coordination: class website with multiple components

Publicly available in early 2008

Provides student access 24/7

Easily updated as documents are revised

Room to grow

Course pages serve multiple functions

Syllabi

Lectures

Class data

Protocols are available for student use as needed

A long list

Tutorials are constructed with Adobe Captivate

Output as Flash movies (.swf)

Slides - computer screen shots, Power point slides, images

Sound - imports sound directly

also imports mp3 files constructed in Audacity

MsrA

Students present their results

Students from the courses meet several times per semester

Poster sessions

QuickTime™ and aTIFF (Uncompressed) decompressor

are needed to see this picture.

Evaluation: pre- and post-course surveyHow familiar are you with…..?

(1=not; 2=somewhat; 3=fairly; 4=very)

Pre- Post-Chang

e

Methods used by cell biologists to answer questions 2.52 3.27 +0.75

Methods used by biochemists to answer questions 2.13 3.05 +0.92

Online databases containing genetic information for humans or model organisms 2.09 3.00 +0.91

Evaluation: pre- and post-course survey

How confident are you that you can…..? (1=not; 2=somewhat; 3=fairly; 4=very)

Pre- Post- Change

Construct a testable hypothesis 3.22 3.57 +0.35

Design an experiment to test hypothesis 2.83 3.32 +0.49

Identify appropriate controls in an experiment 3.00 3.59 +0.59

Critically evaluate experimental results 2.87 3.23 +0.36

Write a scientific paper 2.78 3.00 +0.22

Organize scientific data into a figure or table for publication 3.30 3.45 +0.15

Schedule activities involved in an experiment 3.35 3.86 +0.51

Present results in an oral presentation 3.17 3.38 +0.21

Lab partners for life?

One unanticipated outcome

Teams

Students prefer groups of three

Thanks to:

Instructors

Arlene Wyman

John Wing

Michael Piatelli

Students!

BC Academic Technology

Sarah Castricum

Bill Porter

Beth Clarke

Lynch School of Education

Michael Barnett

Larry Ludlow

Katie TrongNational Science Foundation