BIOPHYS 440 001 FA 2021

Biophysics of Disease

BIOPHYS440 / CHEM440

Instructor Magdalena Ivanova

Email: mivanova@umich.edu

Graduate Student Instructor (GSI): Nirupama Sumangala

Email: nirusuma@umich.edu

Description

The course will introduce the most commonly used biophysical methods for studying complex diseases and the application of these techniques for developing therapies. The emphasis will be on protein aggregation diseases (Parkinson’s, Alzheimer’s and prion), but diseases like cancer, viral (HIV, influenza, and SARS-CoV-2) and bacterial infections will be also discussed. Classical biophysical methods like x-ray crystallography, NMR and cryoEM will be covered, as well as, recently emerging cutting-edge techniques. Some lectures will be presented by invited speakers who will talk about their studies of disease mechanisms for which they apply a combination of biophysical, biochemical and molecular techniques.

 

Reading and Materials

Multiple sources will be used for the class, and each lecture will have a list of specific materials covered in class. Information about the covered techniques can be found in the textbooks listed below. These materials are recommended, but not required.

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                       Room 1449 Mason Hall

Remote Lectures                   Zoom link: https://zoom.us/my/amyloid password:440440

Lectures will be recorded synchronously and uploaded on Pages/Lecture Videos

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

All class assignments, exams, and quizzes will be posted on Canvas and can be taken synchronously within the specified times.

Office hours

Magdalena Ivanova                Time: Tuesday 4:00 - 5:00 PM

Location: zoom https://zoom.us/my/amyloid  password:440440

Nirupama Sumangala             Time: Friday  3:00 - 4:00 PM

Location: zoom  https://umich.zoom.us/j/98066209834

Please note that office hours won’t be recorded.

This is in-person class and all attendees should follow the required safety measures and guidelines of the State of Michigan and the University of Michigan. This includes wearing a face covering that covers the mouth and nose in all public spaces, and not coming to class when ill or in quarantine. Please make sure that all of you are familiarized with the most current guidelines for in-person communication. If you have any concerns about in-person attendance, please contact us.

It is critical that all of you keep up with the lectures and the assignments. If you were not able to attend the class, please make sure to view the class materials and answer the questions that accompany the lectures.

Course recording

All lectures will be recorded synchronously and posted on Canvas for asynchronous viewing. As part of your participation in this course, you may be recorded. If you do not wish to be recorded, please contact me or Nirupama  the first week of class to discuss alternative arrangements.

Lecture recording won’t be posted in case of technical difficulties with recovering video files.

Students are prohibited from recording/distributing any class activity without written permission from the instructor, except as necessary as part of approved accommodations for students with disabilities. Any approved recordings may only be used for the student’s own private use.

Accommodations for Students with Disabilities

If you need an accommodation for a disability, please let me know at your earliest convenience. You may also need to contact the Services for Students with Disabilities (SSD) office (734-763-3000; http://ssd.umich.edu ) which typically recommends accommodations through a Verified Individualized Services and Accommodations (VISA) form. Please be aware that exams need to be scheduled at least 2 weeks in advance. 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

Course requirements and grading roster

25% will be deducted 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 Write up	5 pts
Assignment #3 Talk	10 pts
Assignment #4 Write up	5 pts
Discussion #1	4 pts
Discussion #2	4 pts
Discussion #3	4 pts
Discussion #4	4 pts
Discussion #5 (Paper selection of final exam)	4 pts
Class Q&A	5 pts
Guest lectures attendance	5 pts
Quiz #1	5 pts
Quiz #2	5 pts
Quiz #3	5 pts
Mid-term Exam	10 pts
Final Project Write-up	15 pts
Total	100 pts

Lecture format (35/35)

Each lecture will consist of two instruction sessions each 35min long. In between each instruction session will be one 5-10min Q&A sessions posted on Canvas Discussion.

Participation in Class Q&As (20 x 0.25 pt each for 5 pts total)

This participation credit will be earned by answering the questions that accompany every lecture. Students can participate synchronously or asynchronously. Q&A will be posted on Canvas/Discussion prior each lecture and closed 48 hours after the end of the lecture. Credit will be given for submitting answers to Q&As. Incorrect answers won’t be penalized.

Guest Lectures Attendance (5 pts total)

Attendance will be taken for all guest lectures and everybody is expected to attend in-person or remote (zoom) all guest lectures. 

Presentation talks (10 pts each)

Students will present twice over the course of the semester. Students will be teamed in groups of 3-4 for each presentation. The partners will be different for each presentation. All team members will share the same grade. For the presentations, it is useful to have a systematic approach to discussing the material. This includes an appropriate background reading, and including critical references. Students should be able to explain/comment on methodology/theory necessary for the presentation.

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

Please note that your presentations will be recorded.

Write-ups (5 pts each)

Each student will write a paper summarizing the most important points of her/his oral presentation. All write-ups will be graded individually. The write-up should be written in a clear and concise manner to cover the material presented in class. Like with the presentation talks, students should do appropriate background reading and provide adequate citation used to prepare for the assignment. Please refer to the instructions provided in class on how to do the write-up.

Length of the text for Write-ups #2 should be 1page (1,000 word count) with 0-1 figures. Pages should be made with 1 inch margin using 11 pts Arial font with single line spacing. Deposited files should be in both pdf and Microsoft word format.

Direct copying from the source materials will be penalized by losing the assignment credit. 

Five topic discussions (4 pts each)

Topics for discussions will be posted in the Discussion section on Canvas. Students are expected to engage in the discussions at a level indicating that they have read and thought about the topics that are presented during the assigned presentations. Examples of discussions are posting comments on the zoominar series, answering questions on posted papers and topics, annotating papers etc. The discussions can be done both synchronous and asynchronous participation.

Quizzes (5 pts each)

Quizzes will be posted on canvas and taken within 24 hours window synchronously or asynchronously. On the quiz day the class will end 20min earlier for those of you who want to take the quiz synchronously. Below is the list of the lectures that will be covered by each quiz. Typically there will be 2-4 questions per lecture.

Quiz #1 - lectures 1-5 
Quiz #2 - lectures 13-16 
Quiz #3 - lectures 17,18, and 22-25 

Mid-term exam (10 pts)

Mid-term exam can be taken remotely during the time and date specified in the syllabus. Mid-term exam will cover lectures 1-9. There will be ~2-4 questions for each lecture. The questions will based on the material and/or papers posted with each lecture.

Final Project Write-Up (15 pts)

Final Project will be a write-up of 2 pages (1,500-2,000 word count) with 1-3 figures. Pages should be made with 1 inch margin using 11 pts Arial font with single line spacing. You will need to submit a synopsis of your final exam at 11pm on December 5. Please notice that the synopsis will be not graded. If you do not submit the synopsis, 2 points will be taken from the grade of your final assignment. 

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%

Text in green – assignment posting

Text in red – exam dates or assignment due dates

W/k	Mon			Wed
1	August 30                                   Lecture 1			September 3                                           Lecture 2 Discussion #1
	Speaker: Ivanova		Topic: Class overview Q&A	Speaker: Ivanova				Topic: Proteionopathies Q&A
2	September 6			September 8                                         Lecture 3
	Labor day			Speaker: Ivanova				Topic: Proteinopathies Q&A
3	September 13                               Lecture  4 Discussion 1 is due Discussion 2			September 15                                       Lecture 5 Assignment #1
	Speaker: Ivanova	Topic: Proteinopathies Q&A		Speaker: Ivanova				Topic: X-ray diffraction  Part I Q&A
4	September 20                                Lecture 6 Guidelines Assignment#1 and 2			September 22                                       Lecture 7 Quiz #1
	Speaker: Ivanova	Topic: X-ray diffraction Part II Q&A		Speaker: Ivanova				Topic: X-ray diffraction Part III Q&A
5	September 27                              Lecture 8			September 29                                        Lecture 9 Discussion 2 is due
	Speaker: Ramamoorthy	Topic: NMR Q&A		Speaker: Ivanova				Topic: NMR techniques for studying disease Q&A
6	October 4                                    Lecture 10			October 6                                          Lecture 11
		Presentation #1						Presentation #1
7	October 11                                  Lecture 12 Write-up #1 is due on Oct 16			October 13                                         Lecture 13 Assignment#2 Discussion#3
		Presentation #1		Speaker: Ivanova				Topic: CryoEM Microscopy Part I Q&A  Q&A
8	October 18			October 20                                       Mid-term exam
	Study break
9	October 25                                  Lecture 14 Final paper			October 27                                     Lecture 15   Discussion 3 is due
	Speaker: Ivanova	Topic: CryoEM Microscopy Part I Q&A		Speaker: Min Su		Topic: CryoEM Methods and data processing Q&A
10	November 1                              Lecture 16			November 3                                    Lecture 17 Quiz #2
	Speaker: Ivanova	Topic: CryoEM part II Q&A		Speaker: Ivanova			Topic: Viruses general Viruses/SARS-CoV2 Q&A
11	November 8                              Lecture 18 Discussion #4			November 10                                    Lecture 19
	Speaker: Ivanova	Topic: Viruses part II Q&A				Presentation #2
12	November 15                             Lecture 20			November 17                                    Lecture 21 Write-up #2 is due on Nov 21
		Presentation #2			Presentation #2
13	November 22                             Lecture 22           Discussion #4 is due			November 24                                   Thanksgiving holidays
	Speaker: Prof. Stefanie Galban	Topic: Cancer Diseases Q&A
14	November 29                             Lecture 23			December 1                                    Lecture 24 Paper selection for the final exam is due December 5 (replaces Discussion #5)
	Speaker: Ivanova	Topic: Liquid-liquid phase separation Fluorescence Q&A		Speakers: Prof. Nils Walter		Topics: Single molecule fluorescence for studying biological processes Q&A
15	December 6                              Lecture 25			December 8                                    Lecture 26 Quiz #3
	Speaker: Ivanova	Topic: Biophysics techniques for drug development Q&A		Speaker: Ivanova		Topic: Drug development Q&A
16	Final exam by the Office of Registrar  Dec 16 (1:30pm-3:30pm)              Final paper due by 3:30pm