Instructor

Instructor

Dr. Gregory Underhill
gunderhi@illinois.edu
Office: 2112 Everitt Lab
217-244-2169
Office Hours: Email Appointment

Description

Description

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

Class meets Tuesdays/Thursdays 3:30 - 4:50 pm in 2233 Everitt Lab.

Required Textbook

Textbook

None.

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

Grading

Grading

Exams

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

Project

Students will organize into groups of approximately 3 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 presentation will be during normal class meeting 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 (3-4 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.

 

487:

Homeworks/Paper Presentation   27%

Midterm Exam #1  26%

Midterm Exam #2  26%

Project (Oral Presentation)  10%

Project (Written Paper)  11%

598:

Homeworks/Paper Presentation   25%

Midterm Exam #1  25%

Midterm Exam #2  25%

Project (Oral Presentation)  10%

Project (Written Paper)  10%

Additional 598-only Assignments 5%

Letter grade determination:

>97% = A+; >93% = A; >89.5% = A-; >87% B+; >83% = B; >79.5% = B-; >77% = C+; >73% = C; >67% = C-

 

Link to Gradebook- 487

Link to Gradebok- 598 

 

** Guidelines for Paper Presentation- Discussion Sections

** Project Introduction and Details

Week

Tuesday

Thursday

Homework Due

1/21, 1/23

Introduction: Types of stem cells, & course overview

Stem Cell Basics: 

Identifying and isolating stem cells

 

1/28, 1/30

Discussion: Primary paper, group presentation

(Example: Prof. Underhill)

Paper: Erikkson, Nature Med

Stem Cell Basics:

Population dynamics

- Additional Reading

 

2/4, 2/6

Discussion: Primary paper, group presentation

(David Johnson, Hannah Kimmel, Lauren Ladehoff)

Paper: Leushacke, Cell Reports

- Additional Discussion Slides

- Additional Review Reading

Stem Cell Genetics:

Reprogramming

Homework #1 Due 

In Class Thursday 2/6

2/11, 2/13

Discussion: Primary paper, group presentation

(Helena Bjereus, Alexandra Blanco, Hannah Choi)

Paper: Abad, Nature

- Additional Discussion Slides

Stem Cell Genetics:

Epigenetics & Karyotype

598 Students:

Additional Assignment #1

Due In Class Thursday 2/13

 

2/18, 2/20

Discussion: Primary paper, group presentation

(Garn Masathienvong, Tristan McCallister, Angelo Miskalis)

Paper: Lister, Nature

- Additional Discussion Slides

Stem Cell Genetics:

Genomic Scale & Single Cell Analyses

Homework #2 Due 

In Class Thursday 2/20

2/25, 2/27

Discussion: Primary paper, group presentation

(Luie Siegel, Brendan Sullivan, Anna Ulanova)

Paper: White, PNAS

- Additional Discussion Slides

 

Review Session

 

 

3/3, 3/5

Midterm Exam #1

Stem Cell Microenvironments:

Niche-Mediated Regulation

 

3/10, 3/12

Discussion: Primary paper, group presentation

(Qian Xu, Daniel Xun, Yu-Tung Yen)

Paper: Hartwell, Nat Chem Biol

- Additional Discussion Slides

Stem Cell Microenvironments:

Signals (Soluble, ECM)

Homework #3 Due 

In Class Thursday 3/12

3/17, 3,19

Spring Break

Spring Break

 

3/24, 3/26

Discussion: Primary paper, group presentation

(Ananthan Nambiar, Tej Patel, Claire Penrose)

Paper: Soen, Mol Syst Biol

- Additional Discussion Slides

Discussion: Primary paper, group presentation

(Leopold Pinot, Vamsikrishna Pisipati, Thomas Romanchek)

Paper: Toh, Integr Biol

- Additional Discussion Slides

 

3/31, 4/2

Stem Cell Microenvironments:

Mechanical Forces

- Additional Reading

Discussion: Primary paper, group presentation

(Imu Lin, James Liu, Tian Liu, Suyue Lyu)

Paper: Gilbert, Science

- Additional Discussion Slides

Homework #4 (Project)

Due In Class Tuesday 3/31

4/7, 4/9

Stem Cell Applications:

Scale-Up Biomanufacturing

Discussion: Primary paper, group presentation

(Sai Ganugapati, Apurva Godbole, Frida Hallberg, Lu Jiang)

Paper Cutler, Blood

- Additional Discussion Slides

598 Students:

Additional Assignment #2

Due In Class Tuesday 4/7

 

4/14, 4/16

Stem Cell Applications:

Drug Screening

Review Session

Homework #5 Due 

In Class Thursday 4/16

4/21, 4/23

Midterm Exam #2

No Lecture

Project Discussion Meetings

 

4/28, 4/30

Project Presentations

Project Presentations

 

5/5

Project Presentations

No classes

 

Exam Week

Written Proposal Due: 

5pm Wednesday 5/13 (1 copy per group, emailed to Prof. Underhill)