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Yeast and Oxygen: Incorporating Functional Genomics Research into Three Integrated Undergraduate Laboratory
Classes
Clare O’Connor
Biology Department
Boston College
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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
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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
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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
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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.
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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
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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
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Course pages serve multiple functions
Syllabi
Lectures
Class data
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Protocols are available for student use as needed
A long list
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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
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MsrA
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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.
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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
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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
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Lab partners for life?
One unanticipated outcome
Teams
Students prefer groups of three
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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