Synthetic Biology & Regulation of Genes Undergrad Course

BIOS 21410. Syntheic Biology and Regulation of Genes. 100 Units.

This lecture and lab course will take an empirical approach to understanding gene regulation during development in Drosophila. Topics include synthetic biology, Drosophila embryonic development, gene regulation, and enhancer evolution. 

Enhancers are short regions of the genome composed of clusters of transcription factor binding sites. Using the even‐skipped stripe 2 enhancer as a model system, the class will explore what is currently known about enhancer molecular organization and how it controls gene expression during development. Using modeling software, students will design their own enhancers. They will then construct these novel sequences using cutting‐edge DNA synthesis methods. Finally, students will clone their synthetic enhancers into an expression vector, and send the constructs for injection into Drosophila embryos. Reporter patterns generated by the students’ enhancers will be uploaded onto the course website after conclusion of the course. Students who produce usable data may be involved in co-authoring a resulting publication. 

Instructor(s): J. Moran, J. Reinitz, U. Schmidt‐OR, M. Kreitman. 
Quarter Offered: Spring.
Prerequisite(s): BIOS 20182, 20192, 20235, 20187 AA, or 20187 BB. Third or fourth year standing. Consent of Instructor.

IGSB/CBC Fellows Program

The Center seeks highly qualified, postdoctoral scientists for fellowships. Fellowships will be available to support research about the principles that transcriptional regulatory networks share as they respond to different types of environmental and genetic variation. Successful candidates will have a Ph.D. and/or M.D. with a strong publication record in genomics and molecular biology. Fellows will be required to identify a primary mentor among Center core leaders. In addition, they will be encouraged to identify a second mentor who is affiliated with the Center at another site in Chicago. In this way, fellows will serve as effective bridges between different laboratories and will help further the Center’s interdisciplinary goal.

Learn more about the CBC Fellows Program [pdf]

Systems Biology & Disease Course

The goal of the Systems Biology & Disease Journal Club Course ISTP 30440 is to introduce students to well designed systems biology experiments published in high quality journals. Systems biology investigators characterize biological networks at multiple levels of molecular and cellular complexity. Research focuses on how complex systems induce and sustain homeostasis, preserve health, develop/evolve life, and initiate/modulate disease states.

View 2010 Course Syllabus [pdf]

Committee on Genetics, Genomics & Systems Biology (GGSB)

GGSB is the new name of the Interdepartmental Committee previously known as the Committee on Genetics. GGSB is a partner of the Institute for Genomics and Systems Biology (IGSB). The program is aimed at training PhD scholars for careers as independent scientists in basic and applied biomedical research and education. The Graduate Program in Genetics, Genomics, & Systems Biology offers a program of basic study leading to Doctor of Philosophy in Genetics.

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Research Experiences for Undergraduates

The goal of the ten-week Summer Research Experiences for Undergraduates (REU) program is to provide hands-on scientific research activities in Center laboratories. Stipends are awarded on the basis of academic excellence, motivation, scientific potential and compatibility of personal interests and long-term career goals with current Center research interests. If selected, the student will be matched with a faculty research mentor. REU participants are selected from a nationwide pool of undergraduates, including University of Chicago students. Applicants with computational science backgrounds are especially encouraged to apply. At the conclusion of their projects, students will produce a written summary report and present findings at a symposium.

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High School STEM Education

High school students are guided by mentors and participate in
research projects in labs. At the end of the program they write
a final report about their experimental results and conclusions.

2011
Adrienne Chung, Whitney Young Magnet High School
Mentor: Zifeng Jiang, IGSB, University of Chicago
Title of Project: Emerging Pathogens: DNA Study at the Field Museum of Natural History

Hannah Koo, Illinois Mathematics and Science Academy
Mentor: Adam Hammond, Biophysical Sciences, University of Chicago
Title of Project: The Effects of Cholesterol Level Manipulations in Model Lipid Bilayers

2012
Noah Hamlish, Whitney Young Magnet High School
Mentor: Jennier Moran, IGSB, University of Chicago
Title of Project: New Applications of Synthetic DNA Technology

Teaching Systems Biology & Genetics Through Inquiry

CCSB, in collaboration with the IGSB and the Field Museum, offers a high school teacher professional development course every other summer:
Teaching Systems Biology & Genetics Through Inquiry.

Twenty high school teachers from the Chicago Public Schools (CPS) participate in systems biology related training activities linked to ISBE standards.

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Systems Biology Exploration Camp

In the summer, high school students participate in a systems biology program to explore topics in genomics, genetics and evolution through…. presentations, role-playing scenarios, and lab-based experiments. This collaborative project is led by the Field Museum’s Education Department and Pritzker Laboratory and Center scientists. The goal is to introduce fundamental concepts about genes, DNA, and genetics to students.

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Now Accepting Applications

Now accepting applications for high school students to attend the Systems Biology Exploration Camp, July 12-16, 2010.  Contact: Erica Zahnle, The Field Museum (312) 665-7691.

Research in the Biological Sciences (RIBS)

The goal of the Research in the Biological Sciences (RIBS) program at the University of Chicago is to provide a four-week training program for high school students. It surveys topics related to molecular, microbiological, and cell biological techniques currently used in research laboratories. Basic lab skills are taught. Some students will be invited back the following summer to carry out a research project in one of the faculty labs at the Center. A hands-on systems biology module will link students to Center projects. Modeling activities highlight links between environmental perturbations (such as osmotic stress) and complex system dynamics.

Students who are interested in applying must have completed 10th-grade and excelled in high school biology.

Learn more about RIBS

Collegiate Scholars Program

The goal of the Collegiate Scholars Program (CSP) at the University of Chicago is to provide Chicago Public School (CPS) students an opportunity to enjoy systems biology lab experiences in the summer. Ninth graders who have distinguished themselves through their academic achievements and contributions to school and community are invited to apply to CSP. In the summer there are opportunities for some Scholars to work in CCSB research labs. A summer stipend is provided. In 2009, four students worked in labs at the University of Chicago and Northwestern University.

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Faculty Career Development

The purpose of the faculty Career Development Program is to identify and train investigators. They must be interested in systems biology research and developing new Center projects about transcriptional dynamics and modeling programs using core resources. Pilot grants are available for support.
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Education (2)

Training the next generation of scientists in the art of interdisciplinary research is a critical focus of the Institute for Genomics and Systems Biology (IGSB) at the University of Chicago. The main goal of IGSB education programs is to foster scientific discovery in which biological questions are formulated and addressed in the context of complex systems. As a result, cutting-edge investigative skills emphasizing genome analysis, molecular systems modeling, and simulation are developed for professional applications. IGSB produces a variety of graduate, post-doctoral, and faculty training programs.

The IGSB education programs are in partnership with the Chicago Center for Systems Biology (CCSB). CCSB is composed of investigators working at the University of Chicago, Northwestern University and the University of Illinois at Chicago. It is one of ten National Centers for Systems Biology funded by the National Institute of General Medical Sciences (NIGMS). The IGSB and CCSB collaborate to generate education and outreach programs for K-12 students, K-12 teachers, undergraduate students, graduate students, post-docs, faculty, and the general public. IGSB is in alliance with the University of Chicago’s Committee on Genetics, Genomics & Systems Biology (GGSB) program.

Announcements & Events

2010 Research Experiences for Undergraduates (REU)

Now accepting applications for the 2010 Research Experiences for Undergraduates (REU) programDownload application

Resources for Teachers

Science, Technology, Engineering, and Mathematics (STEM) Teacher Resources

STEM Education Slides

Morimoto Slides (pdf)

Why We Vary: The Science of Genetic Variation (pdf)

Recommended Books

Biology Books

• Genetics: Analysis of Genes and Genomes, 7th Edition, Daniel Hartl and Elizabeth Jones, 2009
• DNA: The Secret of Life, James Watson, 2003
• Naturalist, Edward Wilson, 1994
• The Double Helix, James Watson, 1969
• A Feeling for the Organism: The Life and Work of Barbara McClintock, Evelyn Fox Keller, 1983
• Endless Forms Most Beautiful: The New Science of Evo Devo, Sean Carroll, 2005
• The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution, Sean Carroll, 2006
• Why Evolution is True, Jerry Coyne, 2009
• Molecular Biology of the Cell, Bruce Albert, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter, 2007
• Molecular Cell Biology, 6th Edition, Harvey Lodish, Arnold Berk, Chris Kaiser, Monty Krieger, Matthew Scott, Anthony Bretscher, Hidde Ploegh, Paul Matsudaira, 2007
• The Beak of the Finch: A Story of Evolution in Our Time, 1995
• Molecular Biology of the Gene, 6th Edition, James Watson, Tania Baker, Stephen Bell, Alexander Gann, Michael Levine, and Richard Losick, 2007
• Genes IX, Benjamin Lewin, 2008
• Time, Love, Memory: A Great Biologist and His Quest for the Origins of Behavior, Jonathan Weiner, 2000
• Lehninger Principles of Biochemistry, 5th Edition, Albert Lehninger, David Nelson, and Michael Cox, 2008
• The Selfish Gene, 3rd Edition, Richard Dawkins, 2006
• The Blind Watchmaker, Richard Dawkins, 1996
• Climbing Mount Improbable, Richard Dawkins, 1997
• River Out of Eden, Richard Dawkins, 1996
• Discovering Genomics, Proteomics, & Bioninformatics, 2nd Edition, A. Malcolm Camopbell & Laurie Heyer, 2007
• SYNC: The Emerging Science of Spontaneous Order, Steven Strogatz, 2003
• The Regulatory Genome: Gene Regulatory Networks in Development and Evolution, Eric Davidson, 2006
• EMERGENCE: The Connected Lives of Ants, Brains, Cities, and Software, Steven Johnson, 2001
• The Ghost Map: The Story of London’s Most Terrifying Epidemic—and How it Changed Science, Cities, and the Modern World, Steven Johnson, 2007.
• Microbe Hunters, Paul de Kruif, 1926

STEM Education Books

• Ready, Set, Science!: Putting Research to Work in K-8 Science Classrooms, Sarah Michaels, Andrew Shouse, and Heidi Schweingruber, 2008
• Taking Science to School: Learning and Teaching Science in Grades K-8, Richard Duschl, Heidi Schweingruber, and Andrew Shouse, 2007
• Smart Schools: Better Thinking and Learning for Every Child, David Perkins, 1992
• Outsmarting IQ: The Emerging Science of Learnable Intelligence, David Perkins, 1995
• Scientific Teaching, Jo Handelsman, Sarah Miller, and Christine Pfund, 2007
• Benchmarks for Science Literacy, AAAS, 1993
• How People Learn: Brain, Mind, Experience and School, Expanded Edition, NRC, 2000

Education

Training the next generation of scientists in the art of interdisciplinary research is a critical focus of the Institute for Genomics and Systems Biology (IGSB) at the University of Chicago. The main goal of IGSB education programs is to foster scientific discovery in which biological questions are formulated and addressed in the context of complex systems. As a result, cutting-edge investigative skills emphasizing genome analysis, molecular systems modeling, and simulation are developed for professional applications. IGSB produces a variety of graduate, post-doctoral, and faculty training programs.

The IGSB education programs are in partnership with the Chicago Center for Systems Biology (CCSB). CCSB is composed of investigators working at the University of Chicago, Northwestern University and the University of Illinois at Chicago. It is one of ten National Centers for Systems Biology funded by the National Institute of General Medical Sciences (NIGMS). The IGSB and CCSB collaborate to generate education and outreach programs for K-12 students, K-12 teachers, undergraduate students, graduate students, post-docs, faculty, and the general public. IGSB is in alliance with the University of Chicago’s Committee on Genetics, Genomics & Systems Biology (GGSB) program.

Announcements & Events

2012 Systems Biology Research Experiences for Undergraduates (REU)

Starts June 11, 2012
Download PDF

2012 Conte Center Research Experiences for Undergraduates (REU)

Starts June 13, 2012
Download PDF