BIOPHYS 440 001 FA 2023

Biophysics of disease

BIOPHYS440 / CHEM440

Instructor: Magdalena Ivanova           

Email: mivanova@umich.edu

Graduate Student Instructor (GSI): Trevor (Trev) Yeh

Email: tyeh@umich.edu 

 

Description 

This course focuses on biophysical methods for studying the molecular mechanism of complex diseases and the most common applications of these techniques for therapy development and disease diagnosis. Although the emphasis is on protein aggregation diseases (Parkinson's, Alzheimer's, and prion), the course will also cover diseases like cancer, viral (HIV, influenza, and SARS-CoV-2), and bacterial infections. Recently emerging cutting-edge techniques, along with classical biophysical methods such as X-ray crystallography and NMR, will be the subject of the class. Invited speakers will present some lectures about their studies of disease mechanisms allowing the students to learn from leaders in the field. 

 

Reading and Materials

The Instructor utilizes multiple sources (papers, textbooks, and online posts) to keep up with the most recent advancement in the area of disease mechanisms, and each lecture has information about the resources used. Additionally, students can find descriptions of some biophysical techniques in the textbooks listed below. All materials used for the class should be available free of charge through UM library database. 

1. Methods in Molecular Biophysics: Structure, Dynamics, Function (Cambridge University Press, 2007), by Serdyuk, Igor N.; Zaccai, Nathan R.; Zaccai, Joseph ISBN-10:052181524X

2. Biophysics: tools and techniques (CRC Press, 2016) Mark Leake Experimental

3. Biophysics: Biological Methods for Physical Scientists, (CRC Press, 2017, by Jay L. Nadeau

4. Protein NMR spectroscopy: principles and practice. (Academic Press, 2006), by Cavanagh, J., Fairbrother, W.J., Palmer III, A.G., Rance, M., and Skelton, N.J. ISBN-10:012164491X

5. NMR for Physical and Biological Scientists1st Edition (2006, Garland Science) by Pochapsky, Thomas; Pochapsky, Susan Sondej) ISBN-10: 0815341032

6. Crystallography made crystal clear. A guide for users of macromolecular models (Academic Press, 2006) by Gale Rhodes ISBN-10:0125870736

7. Three-Dimensional Electron Microscopy of Macromolecular Assemblies: Visualization of Biological Molecules in Their Native State2nd Edition (Oxford University Press, 2006) by Joachim Frank, ISBN-10: 0195182189

Class Schedule                     M and W 8:30am-10:00am

Class location                       Lec Room 1 MLB

Zoom connection                https://zoom.us/my/amyloid password: 430440

Lecture files (pdf format) will be posted in Files/Lectures

 

Office hours

Magdalena Ivanova            Time: 6pm-7pm Monday

      Location: 4027 BSRB or via zoom https://zoom.us/my/amyloid password: 430440

Trevor Yeh                            Time: 6pm-7pm Thursday

      Location: BSB 3150  or via zoom

https://umich.zoom.us/j/9900228482 

 

 

This class will be in-person.If you have any concerns about in-person attendance, don't hesitate to get in touch with us.

Accommodations for Students with Disabilities

Please let me know if you need accommodation for a disability at your earliest convenience. You may also need to contact the Services for Students with Disabilities (SSD) office (phone 734-763-3000), which typically recommends accommodations through a Verified Individualized Services and Accommodations (VISA) form. Please be aware that exams must be scheduled at least two weeks before the exam date. Any information you provide is private and confidential and will be treated as such.

Religious holidays

Please let us know if you have conflicts with the examination dates.

Use of ChatGPT and other AI Tools

It’s your responsibility to assess every source’s reliability. AI tools like ChatGPT are a source that may inform your writing, just as books, papers, lecture notes, websites, and the results of Google searches.

You should be aware that the output of AI tools is constructed to sound plausible and not checked by any expert. These results are often completely invented.

Some assignments will be written papers. The writing you submit must be of your creation. Your papers will naturally be informed by other written work. When it is, you must acknowledge this through appropriate citation.

AI tools can generate text, code, and images in response to a prompt. Such automatically generated text is not your work and cannot be submitted as if it is. Exceptions are assignments that specifically ask for the use of AI.

Course requirements and grading roster. 

We will deduct 25% of the exam grade for late submissions.

Make-up exams are to be approved only by the Instructor.

Graded assignment/exam	Grades
Assignment #1 Talk	10 pts
Assignment #2 Talk	10 pts
Discussion #1	6 pts
Discussion #2	6 pts
Discussion #3	6 pts
Discussion #4	6 pts
Participation	6 pts
Guest lectures attendance	5 pts
Quiz #1	5 pts
Quiz #2	5 pts
Quiz #3	5 pts
Mid-term Exam	12 pts
Synopsis of Final Project	3 pts
Final Project Write-up	15 pts
Total	100 pts

 

Participation (6 pts)

Participation credit will be earned as follows

            Attend 5 student presentations                                                          2 pts (5x0.4pts)

            Ask at least one question at the students' presentations.               2pts

            Active class participation                                                                    2 pts

Guest Lectures Attendance (5 pts total)

Attendance will be taken for all guest lectures. To earn credit, students must attend the classes in person. If you are unable to attend, please get in touch with us.

Presentation talks (10 pts each)

Students will present in person twice over the semester and teamed in groups of 3-4 for each presentation. All team members will share the same grade. For the presentations, it is helpful to have a systematic approach to discussing the material, including an appropriate background reading, using the correct references, and an in-depth understanding of the presented material. Students should be able to explain/comment on the methodology/theory necessary for the presentation.

If you are unable to attend due to sickness, please let your group members AND the instructor know as soon as possible. Group members will share the same grade.

The length of the talks should be between 15 min + 5 min Q&A

For teaching purposes, we will record the students' presentations. Please get in touch with the GSI or instructor during the first week of class if you do not want to be recorded.

Discussion (6 pts each)

Students can find the Discussion topics posted in the Canvas/Discussions. This assignment will require students to watch talks by biophysicists posted online, and answer the posted questions. Although this assignment will be remote and asynchronous, students will have the possibility to discuss it in class and provide feedback on the assignment's contents.

Quizzes (5 pts each)

Quizzes will be 20 min and the list of the lectures covered by the quizzes is below. Typically there will be 2-4 questions per lecture.

Quiz #1 - lectures 1-5

Quiz #2 - lectures 13-17

Quiz #3 - lectures 18, and 22-25

Mid-term exam (12 pts)

The mid-term exam can be taken as specified in the syllabus. The mid-term exam will cover lectures 1-9 with ~2-4 questions for each lecture.

Synopsis of the Final Project (3 pts)

Students must submit a synopsis summarizing their final exam by the specified date.

Final Project Write-Up (15 pts)

The final Project will be a write-up of 3 pages with 1-3 figures. Pages should be made with a 1-inch margin using 11 pts Arial font with single line spacing.

Final grades will be calculated using a standard scale

Grade	Range
A	100 %	to 93.0%
A-	< 93.0 %	to 90.0%
B+	< 90.0 %	to 87.0%
B	< 87.0 %	to 83.0%
B-	< 83.0 %	to 80.0%
C+	< 80.0 %	to 77.0%
C	< 77.0 %	to 74.0%
C-	< 74.0 %	to 70.0%
D+	< 70.0 %	to 67.0%
D	< 67.0 %	to 64.0%
D-	< 64.0 %	to 61.0%
F	< 61.0 %	to 0.0%

Calendar with the lectures and assignment/exam dates