Fall 2020

Cell Biology. BioS 367 Dr. Cassimeris

Office D227 Iacocca Hall

Tuesday/Thursday 7:55 - 9:10 am lc07@lehigh.edu

Zoom sessions: 8:50 - 9:10 am on class days, except as noted.

Textbook: Molecular Biology of the Cell 6th Edition. by Alberts et al.

Garland Scientific publisher.

The purpose of this course is to introduce you to modern molecular cell biology. We will explore the molecular
mechanisms underlying cell structure and function as outlined on the syllabus and link these processes to
disease.

The course will include 3 exams, a short presentation, and answers to questions posed by student
presenters. (presentation and questions/answers equals one exam grade)

Course Format:
We are all stuck in an unusual situation and we have to make the best of it. The first class will be live via Zoom.
After that, lectures will be pre-recorded and posted to Course Site. The final 20 min of our scheduled time (8:50
- 9:10 AM) will be live Zoom sessions for questions and answers. I will pose questions that ask you to apply
what you just learned through lecture and text readings. These sessions should help you learn, and help to you
anticipate the sort of questions I could ask on exams.

Student presentations: most likely recorded powerpoint presenations. You need to be brief - find the most
important points and focus on those. Plan on about 5 slides plus 1 question for your peers. Each student will
be assigned a cell function that is linked to disease and provided a review paper to focus the presentation.
Each presenter will summarize what we know so far concerning the disease, explaining the underlying cellular
basis of the disease and/or treatment for the disease. Depending on topic, an extremely short description of
the disease at the organ or tissue level will be useful. A list of topics and a review or two covering the topic are
listed and will be updated and completed by the time of Exam 2. Students will be assigned topics.

Learning objectives:
Understand major functions of biological molecules; integrate functions of these molecules in cells and how
macromolecular complexes function in cellular processes.

Understand the functions of cellular organelles; explain pathways of organelle biogenesis, evaluate how
abnormalities in cell structure/organelles impacts cell homeostasis.

Understand how disruption of individual cell function leads to disease in a the context of a multicellular
organism. Likewise, understand how loss or gain of function mutations impact cell functions well-beyond the
specific mutation.

Appreciate the common components and mechanisms controlling cellular processes of single-celled and
multicellular organisms.

Lehigh Policy for Accommodations for Students with Disabilities:

If you have a disability for which you are or may be requesting accommodations, please contact both
your instructor and the Office of Academic Support Services, University Center 212 (610-758-4152) as early as
possible in the semester. You must have documentation from the Academic Support Services office before
accommodations can be granted.

Lehigh University endorses The Principles of Our Equitable Community:

(http://www4.lehigh.edu/diversity/principles). I expect each member of this class to acknowledge and practice
these Principles. Respect for each other and for differing viewpoints is a vital component of the learning
environment inside and outside the classroom.
Aug 25 Introduction to course and cells; Review basics
Aug 27 How cells are studied (Chapters 8,9)

Sept 01 Membranes. (Chapter 10)

Sept 03 Nuclear structure and transport; Membrane protein synthesis, traffic Part I (Chapter 12)

Sept 08 Membrane Traffic Part II (Chapter 12,13)

Sept 10 Membrane Traffic continued (Chapter 12)

Sept 15 Exam 1
Sept 17 Signaling (Chapter 15)

Sept 22 Signaling (Chapter 15)

Sept 24 Cytoskeleton, Actin-based motility (Chapter 16)

Sept 29 Actin/Microtubules (Chapter 16)

Oct 01 Microtubules & motors (Chapter 16)

Oct 06 Intermediate filaments (Chapter 16)

Oct 08 Cell Cycle (Chapter 17)

Oct 13 Exam #2
Oct 15 Mitosis (Chapter 17)

Oct 20 Apoptosis (Chapter 18)

Oct 22 Extracellular matrix and cell adhesions (Chapter 19)

Oct 27 Extracellular matrix and cell adhesions (Chapter 19)

Oct 29 Cancer (Chapter 20)

Nov 03 Cancer (Chapter 20)

Nov 05 Exam #3

Nov 10 Stem cells and tissue maintenance (Chapter 22) OR COVID UPDATE
Nov 12 Student presentations 1-6

Nov 17 Student presentations 7-12

Nov 19 Student presentations 13-19

Nov 24 no class
Nov 26 THANKSGIVING

Dec 01 Student presentations 20-25

Dec 03 Student presentations 26-32

Answers to all questions posed by student presenters are due by Dec 7.

Topics with at least one review for each:

1. Disrupting the nuclear envelope during interphase.

Review: Hatch and Hetzer. 2014. Breaching the nuclear envelope in development and disease. J. Cell Biol.
205: 133-141.

2. Nuclear lamins and laminopathies.

Review: Osmanagic-Myers and Foisner. 2019. The structural and gene expression hypotheses in laminopathic
diseases - not so different after all. Mol. Biol. Cell. 30: 1786-1790.

3. Aneuploidy.
Review: Ricke and van Deursen. 2013. Aneuploidy in health, disease, and aging.

4. Mitotic inhibitors as anti-cancer agents. Example of Taxol.

Review: Weaver. 2014. How Taxol/paclitaxel kills cancer cells. Mol. Biol. Cell. 25:2677-2681.

5. Proteostasis and ageing.

Review: Hipp et al. 2019. The proteostasis network and its decline in ageing. Nature Rev Mol Cell Biol. 20:
421-435.

6. ER Stress/Unfolded Protein response in disease

Review: Wang and Kaufman. 2016. Protein misfolding in the endoplasmic reticulum as a conduit to human
disease. Nature. 529:326-335.

Review: Hetz et al. 2020. Mechanisms, regulation and functions of the unfolded protein response. Nat. Rev.
Mol. Cell Biol. 21:421-438.

7. Adaptor Proteins/Vesicles
Review: Sanger et al. 2019. Adaptor protein complexes and disease at a glance. J Cell Sci. 132: doi:
10.1242/jcs.222992.

8. Cystic Fibrosis
Review: Veit et al. 2015. From CFTR biology toward combinatorial pharmacotherapy: expanded classification
of cystic fibrosis mutations. Mol. Biol. Cell. 27:424-433.

Cystic Fibrosis treatments

Review: Hanrahan et al. 2019. Cystic fibrosis: Proteostatic correctors of CFTR trafficking and alternative
therapeutic targets. Expert Opinion on Therapeutic Targets. 23: 711-724.

9. Mechanosensing and diseases.

Review: Panciera et al. 2017. Mechanobiology of YAP and TAZ in physiology and disease. Nature Rev Mol
Cell Biol. 18:758-770.

10. Integrin adhesions and signaling pathways

Review: McCarty. 2020. alphaV beta8 integrin adhesion and signaling pathways in development, physiology
and disease. J Cell Sc. 133. doi:10.1242/jcs.239434

11. "Efferoctyosis"
Review: Boada-Romero et al. 2020. The clearance of dead cells by efferocytosis. Nature Rev Mol Cell Biol. 21:
398-414.

12. Autophagy
Review: Zhao and Zhang. 2019. Core autophagy genes and human disease. Curr Opin. Cell Biol. 61:117-125.

13. Mitochondria and cell death

Review: Bock and Tait. Mitochondria as multifaceted regulators of cell death. Nature Rev Mol Cell Biol. 21: 85-
100.

14. Hypoxia: role in skeletal muscle and fibrosis

start here: https://www.nobelprize.org/prizes/medicine/2019/advanced-information/
and here: https://www.sciencemag.org/news/2019/10/medicine-nobel-honors-work-cellular-system-sense-
oxygen-levels

Review: Valle-Tenny et al. 202. HIF-hypoxia signaling in skeletal muscle physiology and fibrosis. J Cell
Commun and Signaling. 14: 147-158.

15. Proteasome assembly.

Review: Rousseau and Bertolotti. 2018. Regulation of the proteasome assembly and activity in health and
disease. Nature Rev Mol Cell Biol. 19:697-712.

16. Inflammation
Review: Weavers and Martin. 2020. The cell biology of inflammation: from common traits to remarkable
immunological adaptations. J Cell Biol. 219: e202004003.

17. Inflammasomes:
Review: Sharma and Kanneganti. 2016. The cell biology of inflammasomes: mechanisms of inflammasome
activation and regulation. 213: 617-629.

18. Cilia and disease.

Review: Mitchicon and Valente. 2017. Motile and non-motile cilia in human pathology: from function to
phenotypes. J. Pathol. 241:294-309.

19. Fanconi Anemia pathway.

Review: Sumpter and Levine. Emerging functions of the Fanconi anemia pathway at a glance. J. Cell Sci. 130:
2657-2662.

20. Parkinson's disease

Review: Abeliovich and Gitler. Defects in trafficking bridge Parkinson's disease pathology and genetics.
Nature. 539:207-216.

21. ALS
Review: Taylor et al. 2016. Decoding ALS: from genes to mechanism. Nature. 539:197-206.

22. Atherosclerosis
Review: Tabas et al. 2015. Recent insights into the cellular biology of atherosclerosis. J. Cell Biol. 209: 13-22.

23. Muscular Dystrophies

Review: Rahimov and Kunkel. 2013. Cellular and molecular mechanisms underlying muscular dystrophy. J.
Cell Biol. 201:499-510.

24. Intermediate Filaments and Disease

Review: Jacob et al. 2018. Types I and II Keratin Intermediate filaments. Cold Spring Harb Perspect Biol.
10:a018275.
Review: Toivola et al. 2015. Keratins in health and disease. Curr Opin Cell Biol. 32:73-81.

25. Heart Regeneration

Review: Deshmukh et al. 2019. Leading progress in heart regeneration and repair. Curr. Opin. Cell Biol. 61:
79-85.

26. Virus Entry and/or escape from endosomes

Review: Staring et al. 2018. Viral escape from endosomes and host detection at a glance. J Cell Sci. 131:
doi:10.1242/jcs.216259.

27. Hepatocytes
Review: Schulze et al. 2019. The cell biology of the hepatocyte: A membrane trafficking machine. J Cell Biol.
218: 2096-2112.

28. Insulin
Review: Tokarz et al. 2018. The cell biology of systemic insulin function. J Cell Biol. 217: 2273-2289.

29. Osteoclasts and osteoporosis.

Review: Blangy et al. 2020. The osteoclast cytoskeleton - current understanding and therapeutic perspectives
for osteoporosis. J. Cell Sci. doi:10.1242/jcs.244798

30. Renal filtration

Review: Scott and Quaggin. 2015. The cell biology of renal filtration. J Cell Biol. 209: 199-210.

31. The cell biology of the blood brain barrier.

Review: Tietz and Engelhardt. 2015. Brain barriers: Crosstalk between complex tight junctions and adherens
junctions. J. Cell Biology. 209: 493-506.

32. Retinal Pigment Epithelial Cells

Review: Storm et al. 2020. Membrane trafficking in the retinal pigment epithelium at a glance. J. Cell Sci.
doi:10.1242/jcs.238279.

33. Microautophagy
Review: Microautophagy - Distinct molecular mechanisms handle cargoes of many sizes. J. Cell Sci.
doi:10.1242/jcs.246322.

34. O-linked sugars

Review: Bond and Hanover. 2015. A little sugar goes a long way: The cell biology of O-GlcNAc. J Cell Biol.
208: 869-880.

35. Clocks
Review: Gliech and Holland. 2020. Keeping track of time: the fundamentals of cellular clocks. J. Cell Biol. 219.
e202005136.

36. Mitophagy
Review: Killackey et al. 2020. Mitophagy pathways in health and disease. J Cell Biol. 219:e202004029.

37. Epithelium mechanical properties and tumors

Review: Fiore et al. 2020. Mechanics of a multilayer epithelium instruct tumour architecture and function.
Nature. doi.org/10.1038/s41586-020-2695-5.

38. mTOR: the integration hub of everything

Review: Liu and Sabatini. 2020. mTOR at the nexus of nutrition, growth, ageing and disease. Nat. Reviews
Mol. Cell Biol. 21: 183-203.

39. Hearing
Review: Schwander et al. 2020. The cell biology of hearing. J. Cell Biology. 190: 9-20.