Instructor

Dr. Gregory Underhill
gunderhi@illinois.edu
3236 DCL
217-244-2169
Office Hours: Email appointment

Description

Application of engineering approaches for the quantitative analysis of stem cell biology, including stem cell genetics and stem cell microenvironments.  Design principles underlying stem cell-based therapies and diagnostics.  Stem cell biomanufacturing.

Class meets Tuesday, Thursday 11:00am-12:20pm in 218 Ceramics Building.

Course Objectives

Required Textbook

None.

Reading material will be assigned from a combination of book chapters, review articles, and primary research papers.

Grading

Exams

Two midterms (roughly 7th and 14th week of the semester).  Midterms are closed-book exams during the normal lecture period.

Project

Students will organize into groups of approximately 5 students, select a topic from a list provided, and complete a project (oral presentation and written paper) related to stem cells.  Detailed guidelines will be provided during the course.  Group oral presentations will be during assigned class periods.

Homeworks and Group paper presentation

- Approximately 4-5 short answer problem sets based on assigned reading material.

Note: Students may discuss homework problems, but students must complete their own work and write up solutions independently.

- Students will also lead a class discussion of an assigned primary research paper in the stem cell field.  This will be done in assigned groups (5 students, assigned by Prof. Underhill).  The assignment schedule will be provided during the first week, along with details of the format. 

Additional 598 assignments

Graduate students registered for the 598 version of the course will have 2 additional homework assignments during the semester.

 

Grading

Link to Gradebook- 498

Link to Gradebook- 598

498: 

Homeworks/Paper Presentation   27%

Midterm #1  26%

Midterm #2  26%

Project (Oral Presentation)  10%

Project (Paper)  11%

 

 

598:

Homeworks/Paper Presentation   25%

Midterm #1  24%

Midterm #2  24%

Project (Oral Presentation)  10%

Project (Paper)  10%

Additional 598-only Assignments 7%

 

**Guidelines for Paper Presentation-Discussion Sections

** Project Introduction and Details

Week

Tuesday

Thursday

Homework Due

1/17, 1/19

Introduction: Types of stem cells,

Course overview

Stem Cell Basics:

Identifying and isolating stem cells

 

1/24, 1/26

Discussion:

Primary paper, group presentation

(Example: Prof. Underhill)

Paper: Erikkson, Nature Med

Stem Cell Basics:

Population dynamics

- Additional Reading

 

1/31, 2/2

Discussion:

Primary paper, group presentation

(Kathryn Sullivan, Raul Sun Han Chang, Nathan Tague, Aleczandria Tiffany, Hanway Wang)

Paper: Leushacke, Cell Reports

- Additional Discussion Slides

- Additional Review Reading

Stem Cell Genetics: Reprogramming

2/7, 2/9

Discussion:

Primary paper, group presentation

(Ruibo Wang, Elizabeth Woodburn, Sherry Yu, Alana Joy Alfeche, Esra Altun)

Paper: Abad, Nature

- Additional Discussion Slides

Stem Cell Genetics:

Epigenetics & karyotype

HW #1 Due in class, Thursday 2/9

HW #1 Solutions

2/14, 2/16

Discussion:

Primary paper, group presentation

(Sairth Bandara, Aidan Brougham-Cook, Marley Dewey, Ryan Fizgerald, Aidan Gilchrist)

Paper: Lister, Nature

- Additional Discussion Slides

Stem Cell Genetics:

Genomic scale & single cell analyses

HW #2 Due in class, Thursday 2/16

HW#2 Solutions

2/21, 2/23

Discussion:

Primary paper, group presentation

(Audrey Gomez, Lauren Grant, James Hilton, Gabriela Hinner, Sameed Jamil)

Paper: White, PNAS

- Additional Discussion Slides

**No Lecture on Thursday

**Review Session: Wed 2/22, 6pm, 1265 DCL building

 

598 Students: Additional Assignment #1 Due in class, Tuesday 2/21

598 Additional #1 Solutions

2/28, 3/2

Midterm #1

Topics for Review- Sample Questions

Stem Cell Microenvironments:

Niche-mediated regulation

 

3/7, 3/9

Discussion:

Primary paper, group presentation

(Katherine Kiang, Erin Kim, Allison Lahood, Johannes Lee)

Paper: Hartwell, Nat Chem Biol

-Additional Discussion Slides

Stem Cell Microenvironments:

Signals (Soluble, ECM)

 

3/14, 3/16

Discussion:

Primary paper, group presentation

(Ravi Malpani, Anirudh Mittal, Jennifer Moy, Zafar Siddiqui)

Paper: Soen, Mol Syst Biol

-Additional Discussion Slides

Stem Cell Microenvironments:

Mechanical forces

- Additional Reading

HW #3 Due in class, Thurs 3/16
3/21, 3/23

Spring Break

Spring Break

 
3/28, 3/30

Discussion:

Primary paper, group presentation

(Harris Nisar, Rushi Patel, Christian Pressnall, Christine Promisel)

Paper: Gilbert, Science

-Additional Discussion Slides

Stem Cell Microenvironments:

Engineered in vitro platforms

598 Additional Assignment #2 Due in class, Thurs 3/30

4/4, 4/6

Discussion:

Primary paper, group presentation

(Zachary Quicksall, Ashley Roberts, Partha Ryali, Ellen Qin)

Paper: Toh, Integr Biol

-Additional Discussion Slides

Stem Cell Applications:

Scale-up biomanufacturing

 

4/11, 4/13

Discussion:

Primary paper, group presentation

(Nikhil Shiva, Jasleena Singh, Thomas Srnak)

Paper: Cutler, Blood

-Additional Discussion Slides

Stem Cell Applications:

Drug screening, transplantation

HW #4 (Project) Due in class, Tues. 4/11

HW #5 Due in class, Thurs. 4/13

4/18, 4/20

Midterm #2

No Lecture

Project Discussion Meetings

 

4/25, 4/27

Project presentations

Group 1: Cancer Stem Cells (James Hilton, Audrey Gomez, Jennifer Moy, Ashley Roberts, Tom Srnak)

Group 2: Reprogramming (Johannes Lee, Christian Pressnall, Esra Altun, Hanway Wang)

Group 3: Stem Cell Aging (Aidan Gilchrist, Sairth Bandara, Marley Dewey, Alec Tiffany, Raul Sun Han)

Project presentations

Group 4: Adult Cardiac Stem Cells (Sherry Yu, Jasleena Singh, Allison LaHood, Katherine Kiang, Erin Kim)

Group 5: Single Stem Cell Genomics (Nathan Taque, Sameed Jamil, Harris Nisar, Zafar Siddiqui)

Group 6: Adult Neural Stem Cells (Charistine Promisel, Gabby Hinner, Kathryn Sullivan, Ellen Qin)

 

5/2

Project presentations

Group 7: Adult Skeletal Muscle Stem Cells (Rushi Patel, Zach Quicksall, Lauren Grant, Aidan Brougham-Cook)

Group 8: Microfluidic Envrionments for Stem Cells (Alana Alfeche, Anirudh Mittal, Ruibo Wang)

Group 9: Adult Cardiac Stem Cells (Nikhil Shiva, Ravi Malpani, Partha Ryali, Ryan Fitzgerald)

No classes  

Exam Week

Project Paper Due: Thurs 5/11, 5pm