Transcript Comprehensive Research Programs for the early Undergraduate

Construction and Deconstruction:
Comprehensive Research Programs for
the early Undergraduate
IRACDA, Baylor Houston. 06/20/11
Utpal Banerjee
Depts of Mol. Cell & Devl. Biol.; Biological
Chemistry;
Broad Stem Cell Research Center
UCLA
with
Construction: Large numbers of small observations
Construction
Deconstruction
A comprehensive inquiry-based teaching program for
Undergraduates at UCLA
Ira Clark, John Olson, Rafael Romero & Utpal Banerjee
How can we best prepare our students
for careers in science?
Can we make research a core part of the
science curriculum?
Our Motto
You don’t
need to be
a physicist
to know
how to ride a bike
Start research early.
1st and 2nd years
URCFG –
“hands-on”
research
(75 students/yr)
Research
Deconstruction
(300 students/yr)
UCLA Minor in
Biomedical Research
Our programs have provided research
instruction to over 1200 students
We now instruct over 300 new
students each year.
UCLA Undergraduate
Research Consortium
for Functional
Genomics
Sponsored by a grant from the Howard Hughes
Medical Institute Professors Program
560 students have participated in the Introductory Program so far.
Multifaceted Approach
•Didactic
–Ethics, career options, grant
and manuscript writing,
bioinformatics, record keeping
•Laboratory
–“Fly pushing” techniques,
time management, lab
notebook
•Computer
–Bioinformatics tools
•Writing
–Grant proposal, Final
paper
One Central Difficult Concept
Mitotic recombination as a
functional genomics tool
Genome-wide expressionbased lineage analysis
Post-transcriptional gene
silencing as a tool for
functional genomics
Discipline at the Bench
•5-generation
crossing scheme
•Each student
performs for 10
stocks
•Documents eye
phenotype
Real Data Generated
Introductory Program Details
• 2650 Separate introductory experiments
performed
• >120,000 Drosophila crosses performed
• 2159 Mutant stocks used
• 1375 Published stocks
• 379 X-Chromosome stocks used
• 1576 Verified phenotypes
• 1523 Verification experiments performed
• 642 Excision experiments performed
The Great Ball of Toil
Our First
Publication
134 undergraduate authors
Our Publication in the October 2007 issue of Genetics
With 264 undergraduate authors
Lineage Tracing Project
Genome-wide expression-based
lineage analysis
The G-TRACE System: Developed and
Characterized by a number of undergraduates
in our advanced program
Nature Methods
http://mcdb.ucla.edu/Research/Banerjee/LineageTracing
Summary of lineage tracing project
• 700 gal4 lines analyzed and documented for
expression patterns and cell lineage
• Over 30,000 digital images recorded
• An annotated Online database is being
developed
• Student that participate in the introductory
program are eligible to apply for the Minor in
Biomedical Research
Classroom Undergraduate Research
Experience Survey (CURE)
Dave Lopatto – Grinnell University
1st and 2nd years
URCFG –
“hands-on”
research
(75 students/yr)
Research
Deconstruction
(300 students/yr)
UCLA Minor in
Biomedical Research
How can we scale up our efforts to immerse
early-stage undergraduates in research?
“Deconstructing” scientific research – a practical and
scalable pedagogical tool to provide evidence-based science
instruction
Ira E. Clark1,4, Rafael Romero-Calderón1,4, John M. Olson1, Leslie Jaworski2, David
Lopatto2 and Utpal Banerjee1.3,5
PLoS Biology (Dec. 2009)
Science instruction through
research deconstruction
Teaching science through the scientific story
Up to 90 students / class – mostly 1st and 2nd-years
Full-scale research seminars by invited UCLA faculty
Seminars videotaped and placed on website with copy of
slides for students to review
“Deconstruction” classes use segments of seminar to teach
fundamental concepts and experimental approaches.
Q&A session with speaker at end of series
Multiple layers of instruction from
deconstruction
Seminar
Tim Lane – Wnt signaling and breast cancer
In this example of enhanced deconstruction, a research
paper was deconstructed along with the seminar.
Students follow the scientific story as it
unfolds.
Wnt10b overexpression causes mammary tumors
(mouse model)
Wnt10b causes decrease in cell cycle inhibitor p27
(protein, not RNA)
proteasome-dependent
non-canonical E3 ubiquitin ligase (i.e. not SCFSkp2)
candidate E3 ligase components ID’d among Wnt10b
transcriptional targets
Along the way, we discuss fundamental
scientific concepts.
cancer biology
signal transduction
- Wnt pathway
cell cycle
- Cyclins, Cdks and Cdk inhibitors
ubiquitin-mediated proteolysis
They also learn important techniques and
how to design experiments properly.
transgenic mice
Immunostaining
(genetic controls)
tissue culture
RT-PCR
(reference RNAs)
Western blots
RNAi
(loading controls)
(controls for off-target effects)
microarrays
coimmunoprecipitation
And they learn how to interpret experimental data.
Invited speakers for deconstruction courses
stem cell biology
Utpal Banerjee
Hanna Mikkola
Kathrin Plath
Volker Hartenstein
Amander Clark
April Pyle
Yi Sun
cell biology
Greg Payne
Rachelle Crosbie
Margot Quinlan
David Walker
Alex van der Bliek
James Wohlschlegel
cancer biology
Tim Lane
Paul Mischel
Heather Christofk
development
Eddy De Robertis
Luisa Iruela-Arispe
Alvaro Sagasti
Karen Lyons
Cory Evans
neurobiology
Larry Zipursky
Kelsey Martin
Art Arnold
Stephanie White
David Krantz
Patricia Phelps
Ellen Carpenter
Debora Farber
Fernando Gomez-Pinilla
gene regulation
Arnie Berk
Doug Black
Susan Krum immunology
Owen Witte
Steve Smale
Linda Demer
signaling
Gerry Weinmaster
Fuyu Tamanoi
John Colicelli
microbiology
Benhur Lee
Patricia Johnson
Beth Lazazzera
Students learn important concepts such as the role
of supporting evidence and the process of research
Clark et al. (2009)
PLoS Biology
Data collected by David Lopatto
(Grinnell College)
Learning gains from research deconstruction
Clark et al. (2009)
PLoS Biology
Advantages to research deconstruction
Easily exported – limited resource requirements
Scalable – can accommodate large class sizes
Adaptable to multiple research disciplines
“Works in Hebrew!” Benny Shilo, Weizmann Inst.
New approach for general education?
1st and 2nd years
URCFG –
Research
Construction
(75 students/yr)
Research
Deconstruction
(300 students/yr)
UCLA Minor in
Biomedical Research
The UCLA Minor in Biomedical
Research
1. Early recruitment and training.
2. Lab placement for extensive research
commitment (at least 4 quarters).
3. Research training courses.
4. Integration of social sciences and
humanities.
A Faculty Advisory Committee helps to set policy,
evaluate applicants and suggest lab placement.
Utpal Banerjee (Director) – Molecular, Cell and Developmental Biology
Michael Carey
– Biological Chemistry
Ellen Carpenter – Psychiatry and Biobehavioral Sciences
John Colicelli
– Biological Chemistry
Albert Courey
– Chemistry and Biochemistry
Soraya de Chadarevian – History
Center for Society and Genetics
Frank Laski
– Molecular, Cell and Developmental Biology
Aldons J. Lusis – Human Genetics
Kelsey Martin
– Biological Chemistry/ Psych. and Biobehavioral Sci.
Co-Director of UCLA Medical Science Training Program
Jeffery F. Miller – Microbiology, Immunology and Molecular Genetics
Dwayne Simmons – Physiological Science, Director of MARC
Stephen Smale – Microbiology, Immunology and Molecular Genetics
Co-Director of UCLA Medical Science Training Program
Yi Sun
– Mol. and Med. Pharmacology/ Psych. and Biobehavioral Sci.
Hong Wu
– Molecular and Medical Pharmacology
The Minor in Biomedical was
launched in Spring 2007.
It has now provided research training to over
190 students in over 100 laboratories at
UCLA.
www.biomedresearchminor.ucla.edu
Publication-quality research
32 publications by students in the Minor in first
four years of program
- 26 student authors
- 3 first-author papers
- top journals, including:
Developmental Cell
Cell Stem Cell
Nature Methods
Current Biology
J. Neuroscience
J. Bacteriology
J. Biol. Chemistry
Developmental Biology
Blood
Early returns from the Minor show that
graduates continue in top programs in basic
or health sciences.
MD-PhD
UCLA
Harvard/MIT
Northwestern
U. Iowa
U. Penn
UNC
Case Western
PhD
U. Wash.
UCLA
Harvard U. Mich.
Cornell U. Wisc.
Yale
USC
UC Irvine
UC Berkeley
MD
PharmD
UCSF
UCLA
UCSD
Stanford
UC Irvine
MS
UCSD
KAUST
Dartmouth
Georgetown
UT Houston
UCLA
Cleveland Clinic
Wash. U.
Research assistants (16) - UCLA, Cedar Sinai, NIH,
Harvard, Stanford, Northwestern
1 Gilliam Fellow
1 Fulbright Award
Challenges and advantages of building a
program at UCLA
Large public university – over 36,000 students
Large research community – 400 life science labs
Medical school adjacent to college campus;
faculty active in undergraduate education.
Synopsis
Freshmen or Sophomores (mostly)
“Deconstructing
Research” Class
Self directed
Undergraduate Consortium
in Functional Genomics
UCLA Minor in
Biomedical Research
At capacity expect 200 students
Self directed
Acknowledgements
Ira Clark; John Olson; Rafael Romero
Jiong Chen
Gerald Call
Allison Yabroff
TA: Nikki Villarasa;
Francie Diep;
Dan Huynh
Advisory Council for Minor
Cory Evans
Raghavendra Nagaraj
Admin: Nancy Purtill
Hillary Howard
Deans Reisler, Eiserling
Provost Smith
HHMI Professors Award and HHMI Institutional Grant
For more information, visit
www.biomedresearchminor.ucla.edu
and
www.bruinfly.ucla.edu