Course Syllabus
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.
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Methods in Molecular Biophysics: Structure, Dynamics, Function (Cambridge University Press, 2007), by Serdyuk, Igor N.; Zaccai, Nathan R.; Zaccai, Joseph ISBN-10:052181524X
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Biophysics: tools and techniques (CRC Press, 2016) Mark Leake Experimental
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Biophysics: Biological Methods for Physical Scientists, (CRC Press, 2017, by Jay L. Nadeau
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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
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NMR for Physical and Biological Scientists1st Edition (2006, Garland Science) by Pochapsky, Thomas; Pochapsky, Susan Sondej) ISBN-10: 0815341032
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Crystallography made crystal clear. A guide for users of macromolecular models (Academic Press, 2006) by Gale Rhodes ISBN-10:0125870736
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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 |
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1 |
August 30 Lecture 1 |
September 3 Lecture 2Discussion #1 |
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Speaker:Ivanova |
Topic:Class overviewQ&A |
Speaker:Ivanova |
Topic:ProteionopathiesQ&A |
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2 |
September 6 |
September 8 Lecture 3 |
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Labor day |
Speaker:Ivanova |
Topic:ProteinopathiesQ&A |
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3 |
September 13 Lecture 4Discussion 1 is dueDiscussion 2 |
September 15 Lecture 5Assignment #1 |
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Speaker:Ivanova |
Topic:ProteinopathiesQ&A |
Speaker:Ivanova |
Topic:X-ray diffraction Part IQ&A |
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4 |
September 20 Lecture 6Guidelines Assignment#1 and 2 |
September 22 Lecture 7Quiz #1 |
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Speaker:Ivanova |
Topic:X-ray diffraction Part IIQ&A |
Speaker:Ivanova |
Topic:X-ray diffraction Part IIIQ&A |
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5 |
September 27 Lecture 8 |
September 29 Lecture 9Discussion 2 is due |
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Speaker:Ramamoorthy |
Topic:NMRQ&A |
Speaker:Ivanova |
Topic:NMR techniques for studying diseaseQ&A |
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6 |
October 4 Lecture 10 |
October 6 Lecture 11 |
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|
Presentation #1 |
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Presentation #1 |
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7 |
October 11 Lecture 12Write-up #1 is due on Oct 16 |
October 13 Lecture 13Assignment#2Discussion#3 |
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Presentation #1 |
Speaker:Ivanova |
Topic:CryoEM Microscopy Part I
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8 |
October 18 |
October 20Mid-term exam |
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Study break |
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9 |
October 25 Lecture 14Final paper |
October 27 Lecture 15Discussion 3 is due |
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Speaker:Ivanova |
Topic:CryoEM Microscopy Part IQ&A |
Speaker:Min Su |
Topic:CryoEM Methods and data processingQ&A |
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10 |
November 1 Lecture 16 |
November 3 Lecture 17Quiz #2 |
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Speaker:Ivanova |
Topic:CryoEM part IIQ&A |
Speaker:Ivanova |
Topic:Viruses generalViruses/SARS-CoV2Q&A |
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11 |
November 8 Lecture 18Discussion #4 |
November 10 Lecture 19 |
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Speaker:Ivanova |
Topic:Viruses part IIQ&A |
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Presentation #2 |
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12 |
November 15 Lecture 20 |
November 17 Lecture 21Write-up #2 is due on Nov 21 |
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Presentation #2 |
Presentation #2 |
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13 |
November 22 Lecture 22Discussion #4 is due |
November 24Thanksgiving holidays |
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Speaker:Prof. Stefanie Galban |
Topic:Cancer DiseasesQ&A |
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14 |
November 29 Lecture 23 |
December 1 Lecture 24Paper selection for the final exam is due December 5 (replaces Discussion #5) |
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Speaker:Ivanova |
Topic:Liquid-liquid phase separationFluorescenceQ&A |
Speakers:Prof. Nils Walter |
Topics:Single molecule fluorescence for studying biological processesQ&A |
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15 |
December 6 Lecture 25 |
December 8 Lecture 26Quiz #3 |
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Speaker:Ivanova |
Topic:Biophysics techniques for drug developmentQ&A |
Speaker:Ivanova |
Topic:Drug developmentQ&A |
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16 |
Final exam by the Office of Registrar Dec 16 (1:30pm-3:30pm)Final paper due by 3:30pm |
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Course Summary:
Date | Details | Due |
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