CMB 551 Modules

 

Module 1

Section A: Controlling the Cell Cycle

Instructor: Danny Lew

The accurate copying of a cell's contents and their distribution to produce two daughter cells is a stunning feat requiring exquisite coordination.  The set of carefully orchestrated steps by which proliferating cells make copies of themselves constitutes the cell cycle.  In this module, we will discuss landmark papers that established the conserved mechanisms underlying cell cycle control, as well as recent papers dissecting the control circuitry.

In addition to learning about a fundamental process, this module will explicitly deal with strategies for reading primary Journal articles to critically assess the validity of their conclusions.  We will also discuss how to turn cartoon diagrams of regulatory pathways into equations and graphs producing quantitative predictions of pathway behavior, and address the importance of feedback pathways and bistable systems in generating sharp transitions in cell behavior.

Reading:

  1. Molecular Biology of the Cell, Alberts, et al., - Chapter 17 (First part: The Cell Cycle)

Section B: Mechanisms of Early Development

Instructor: David McClay

This module will cover the maternal to zygotic transition, initial asymmetries that launch cellular diversity, onset of signaling, mechanisms of specification, and control mechanisms necessary for morphogenesis. It will emphasize the means by which genomic information is used to drive development. Each class period will be a combination of primary literature review, lecture and discussion. Animal examples will be drawn from across the animal kingdom.

Reading:

  1. Molecular Biology of the Cell, Alberts, et al., 6th edition - Chapter 21
  2. Developmental Biology, Gilbert, 10th edition - Chapters 1-3

Section C: Quantitative Cell & Developmental Biology

Instructor: Stefano Di Talia

It is a common belief that biology is the least quantitative and theoretical of the natural sciences. However, many fundamental discoveries in biology (e.g. membrane excitability, spikes, proofreading) have come from the use of modeling and theoretical ideas. The goal of this module is to show how theoretical and mathematical ideas can contribute to develop deeper insights on biological problems. Focusing on primary literature, we will discuss how recent advancements in imaging technologies are improving our understanding of cell and developmental biology. Ideally by the end of this module, students will be able to distinguish good informative mathematical models from less informative models.

 

Reading: 

  1. Nurse, P and Hayles, J (2011) The Cell in an Era of Systems Biology. Cell, 144 (6), 850-854
  2. Oates, AC, Gorfinkiel, N, Gonzalez-Gaitan, M, Heisenberg, CP (2009) Quantitative approaches in developmental Biology. Nature Reviews Genetics, 10, 517-530.

Section D: Animal Models of Cancer

Instructor: James Alvarez

Animal models have provided important insights into the development, progression, and treatment of cancer. This module will cover the fundamentals of animal models of cancer, with a particular focus on mice. We will describe methodological approaches to generating mouse models of cancer, and discuss the advantages and limitations of different approaches. We will then focus on specific areas across tumor types in which mouse models have provided critical mechanistic insights into tumor biology. Each class will involve a discussion of primary research articles from the literature.

Reading:

  1. Hanahan D, Weinberg RA: Hallmarks of cancer: the next generation. Cell 2011, 144(5):646-674.
  2. Kersten K, de Visser KE, van Miltenburg MH, Jonkers J: Genetically engineered mouse models in oncology research and cancer medicine. EMBO Molecular Medicine 2017, 9(2):137-153.

 

Module 2

Section A: Cellular Mechanisms Controlling Animal Patterning

​Instructor: Michel Bagnat

In this module, we will examine basic cellular processes that underlie patterning events in metazoans including the formation of boundaries, body segments and specific cell arrangements within tissues. We will discuss how specific programs such as segmentation are executed in different taxa and how key genetic pathways are deployed in various contexts to produce diverse patterning outcomes. To do this we will go over the common themes in patterning illustrated by classic experiments and discuss how these apply to specific examples from recent literature. Students will then take one process of their interest and identify conserved or re-purposed cellular mechanisms and how they relate to its ancestral origin.

Reading: 

  1. Chapters 2, 4, 9 and 17 of Developmental Biology, 11th edition, Gilbert and Barresi. http://11e.devbio.com/index.html

 

Section B: Glycobiology

Instructor: Mike Boyce

Glycosylation is found in all kingdoms of life and underlies every aspect of cell biology. In addition, glycobiology has major implications for an enormous range of fields, from human health to renewable energy to materials science. Recently, new technologies and experimental approaches have triggered explosive progress in the modern glycosciences. This module will sample some very recent papers – all published in 2017 – on a range of glycobiology topics, with an emphasis on protein glycosylation in mammalian health and disease. Our goals will be to get an overview perspective on current research in glycobiology, and to hone our critical reading skills. 

Reading: 

  1. Chapter 1 of Varki et al., Essentials of Glycobiology, available at http://www.ncbi.nlm.nih.gov/books/NBK1931/

Section C: Microscopy in Cell Biology

Instructor: Lisa Cameron and Benjamin Carlson

Microscopy has been revolutionized by fluorescence and now provides a vast array of tools with which to investigate biology. This module will cover the principles and possibilities of microscopy – how microscopes and photon‐based imaging systems work and what you can do with them. How do you visualize the morphology of microscopic objects using light and fluorescence? Which imaging modality is best for a particular sample? How do you gain information on the dynamics of systems such as the spatial and temporal patterns of signaling events? How do you extract quantitative information from images? We will discuss a range of techniques with a heavy emphasis on imaging living samples from microbes to vertebrate animals ‐ widefield imaging, optical sectioning by confocals, multi‐photon excitation and TIRF, protein dynamics, choosing and exploiting fluorescent proteins/probes and super‐resolution microscopy. The theory and physical principles of the imaging systems will be explained in the first half of the module to a level giving understanding of how they work and guidance for optimal use. The second part of the module will be a mixture of theory and exercises in FIJI/ImageJ covering the processing, visualization and quantification of microscopy data.

See: http://microscopy.duke.edu/learn/CMB551.html  

Reading: 

  1. Molecular Biology of the Cell, Alberts, et al., - Chapter 9 (focus on the sections discussing light/fluorescence microscopy)  

Section D: The Cytoskeleton – Dynamics and Function

Instructor: Terry Lechler

This is a primary literature reading intensive course that will cover aspects of cytoskeletal dynamics and functions in reconstituted systems, cultured cells and intact organisms. Diverse topics will be discussed, which may include: the role of cytoskeleton in mitosis/cytokinesis, cell migration, cell adhesion, cell signaling, cell shape control and mechanotransduction. Preparation and active participation required.

Reading: 

  1. Molecular Biology of the Cell, Alberts et al. Chapter 16 (Cytoskeleton)

 

Module 3

Section A: Understanding and Manipulating Protein-Protein Interactions

Instructor: Harold P. Erickson

Proteins are the machines of the cells. A few enzymes operate alone, but most proteins interact with others to form more complex machines. In this unit we will learn the basic principles of protein-protein interaction and bonding, and address the following questions.

How big is a protein molecule; how do you determine if it is a monomer or tetramer; how do you determine its shape? What is the structure of a protein-protein bond?  How many amino acids are in contact?  How does the dissociation constant relate to the strength of the bond?  How fast do two proteins form a bond, and once formed how long does the complex last before it dissociates?  If you want to eliminate or reduce a protein-protein bond by mutagenesis, how many amino acids to you need to change?  How do you decide which ones?

Reading: 

  1. Molecular Biology of the Cell", Alberts et al. Chapter 3 - Proteins. 
  2. Molecular Biology of the Cell", Alberts et al. Chapter 2 (to review basic biochemistry. Most important is to know the amino acids, which ones are hydrophobic, hydrophilic, charged)

Section B: Cell Migration / Invasion in Development and Cancer

​Instructor: David Sherwood

Cell migration/invasion through extracellular matrix and tissues play crucial roles in the development, maintenance and regeneration of multicellular organisms. Inappropriate and defective cell migration also underlies numerous diseases, including inflammatory diseases (i.e. asthma, rheumatoid arthritis, multiple sclerosis, psoriasis and Crohn′s disease), developmental disorders, and tumor spread. Understanding cell migration is also important for regenerative therapies, including stem-cell grafting, where defective migration/invasion is a major limitation. Cell migration takes on a variety of forms, and this course covers how cells migrate and invade as individuals, in groups as well as the plasticity of migration modes in development and cancer.

Reading: 

  1. Plasticity of cell migration: a multiscale tuning model. Friedl P, Wolf K. J., Cell Biol. 2010 Jan 11;188(1):11-9. doi: 10.1083/jcb.200909003. Epub 2009 Dec 1.

Section C: Germ Cells and Sex Determination

Instructor: Blanche Capel

This module will cover the formation, pluripotent characteristics, and male vs. female development of primordial germ cells in multiple species including Drosophila, C. elegans, fish and mammals. It will also cover sex determination and cell fate commitment in somatic cells of the gonad, including genetic and temperature/hormone-dependent mechanisms. We will likely also consider how sex chromosomes evolve and how species transition between sex determining mechanisms.

Reading: 

  1. Developmental Biology, Gilbert: Chapter 15 - Sex Determination
  2. Developmental Biology, Gilbert: Chapter 17 - The Saga of the Germ Line

Section D: Signaling: How Activation Leads to Specificity

Instructor: Bernard Mathey-Prevot

Detection of external cues at the cell membrane sets in motion a cascade of events that culminates in the deployment of a nuclear program, ensuring the appropriate response of that cell to an external ligand. Signal propagation is carried by a series of effector proteins that have been identified through genetic and biochemical approaches and shown to belong to distinct signal transduction pathways. The dominant view until recently had been to consider each of these pathway as a separate cassette consisting of tens of core proteins, being highly compartmentalized, hierarchical, and independent from the rest of the proteome. Recent high-throughput genetic and biochemical data suggest two major revisions to this traditional, canonical view: (1) a massive increase in the number of components linked to a particular pathway and (2) extensive crosstalk between these pathways. This new understanding, however, raises the important question of how specificity can be achieved in such a highly interconnected network.

This module will concentrate on general principles of signaling pathways. It will not dwell on an enumeration of the various components for each pathway. Rather, through students’ presentations of primary research articles, we will focus on how experimental strategies and technical innovations have changed our ability to measure and follow pathway activation. We will discuss various strategies used by the cell to insure specificity, and look into the increasing role that systems biology and quantitative approaches have had on current views of signaling networks under normal and disease conditions.

Reading: 

  1. Domains, Motifs, and Scaffolds: The Role of Modular Interactions in the Evolution and Wiring of Cell Signaling Circuits. Roby P. Bhattacharyya et al., Annu. Rev. Biochem. 75:655–80 (2006)
  2. Assembly of Cell Regulatory Systems Through Protein Interaction Domains. Pawson and Nash, Science 300:445-452 (2003)
  3. Scaffold Proteins: Hubs for Controlling the Flow of Cellular Information. Matt C. Good et al., Science 332:680-686 (2011)

 

Module 4

Section A: The Eye as a Digital Camera

Instructor: Vadim Arshavsky

We are well familiar with the metaphor comparing the eye with a photographic camera. Indeed, both rely on refraction and lenses to form images. What is perhaps less appreciated is that the eye functions as a digital camera. Information about the surrounding world reaches the back of the eye in the form of photons of variable wavelength, which are absorbed by rod and cone photoreceptor cells of the retina. The light-evoked electrical signals produced by photoreceptors are next processed by a network of retinal neurons, so that information about each point in visual space becomes digitized and reaches the brain through multiple channels, each reporting a different feature of the visual world (brightness, contrast, color, motion, etc.).

In this module, we will follow each step of this analog-to-digital transition by discussing critical experimental papers in three areas: phototransduction (the transformation of a light signal into an electrical signal); the functioning of the first synapse in the retina; and the split of visual information into multiple channels each carried by a highly-specialized type of the retinal ganglion cells. Our goal would be to integrate the findings of molecular, cellular and electrophysiological studies into a single big picture of how the retina works.

Reading: 

  1. Burns, M.E., Arshavsky, V.Y.  Beyond counting photons: trials and trends in vertebrate visual transduction. Neuron (2005) 48, 387–401.
  2. Masland, R.H. Cell populations of the retina: The Proctor Lecture. Inverst. Ophthalmol. Vis. Sci. (2011) 52, 4581-4591.

Section B: Intersection of Signaling and Therapeutics 

​Instructor: Kris Wood

It is now possible to comprehensively map the numerous genomic alterations present in individual human tumors.  As a result of this stunning technological advance, we can now begin to design therapeutic strategies that function by “targeting” these alterations.  However, identifying the optimal therapeutic targets for a given tumor is challenging, and this challenge is further exacerbated by the problem of drug resistance, which commonly emerges as tumors evolve under pharmacological selection pressures.  In this module, we will construct a framework for understanding the related topics of pharmacogenomics and drug resistance in cancer, discussing landmark papers that established the guiding principles in each field.

Reading: 

  1. McLeod, Cancer pharmacogenomics: Early promise, but concerted effort needed. Science 339, 1563 (2013).
  2. Glickman and Sawyers, Converting cancer therapies into cures: Lessons from infectious diseases. Cell 148, 1089 (2012).

Section C: Stem Cells in Tissue Homeostasis and Disease

Instructor: Purushothama Rao Tata

Most tissues rely on specialized cells called stem/progenitor cells for their day-to-day turn over. Stem cells in some tissues directly differentiate into mature cells, whereas in other cases they undergo replication and generate intermediate cells which then differentiate into mature cell types. Both systemic and micro-environmental factors dynamically control the behavior of stem cells in a context dependent manner. In this module, we will be discussing how different factors such as microenvironment, cell-cell communication and cell plasticity influence stem cell behavior to control tissue homeostasis, regeneration and tumorigenesis. We will also discuss some of the new tools developed to unravel emerging concepts that are put forward in the recent years in stem cell biology.

Reading: 

  1. Developmental Biology by Scott F. Gilbert; 9th or 10th or 11th edition; Chapters- 2, 4 and 5.

Section D: The Biology of Cilia and Flagella

Instructor: Sarah Goetz

Cilia and flagella are microtubule-based cellular projections that perform a variety of important functions in eukaryotes including motility, generating fluid flow, and sensory perception. Non-motile primary cilia also play a critical role in modulating key developmental signaling pathways. Through critical reading of the primary literature, this module will examine the structure, function, and evolution of these important organelles. We will focus in particular on the relationship between cilia and cellular functions linked to human diseases including genetic syndromes, neurological disorders, and cancer.

Reading: 

  1. Molecular Biology of the Cell, Alberts, et al., 6th edition, Chapter 16 (Section on microtubules, pages 925-944).
  2. Bangs, F. and Anderson, KV. (2017) Primary Cilia and Mammalian Hedgehog Signaling. Cold Spring Harb Perspect Biol.  9(5). doi: 10.1101/cshperspect.a028175.
  3. Spassky, N. and Meunier, A. (2017) The Development and Function of Multiciliated Epithelia. Nature Reviews Molecular Cell Biology.  doi:10.1038/nrm.2017.21

 

 

Module 5

Section A: Organogenesis

Instructor: Brigid Hogan

Many organs of the body – for example the kidney, pancreas, lungs, ear and limbs – are composed of epithelial and mesenchymal cell populations organized into complex three-dimensional tissues with a dedicated blood and nerve supply. How are these adult organs built during development? They originate in the embryo from small collections of cells known as “primordia” that contain progenitors that will give rise to all the different mature epithelial and mesenchymal cell types. In order to understand how the process of organ development - or organogenesis - is controlled we must address many important questions. For example, we need to know how the epithelial and mesenchymal populations communicate with each other so that their proliferation and differentiation are co-ordinated, how they acquire specific 3D shapes specific to each organ and its physiological function, how blood vessels, nerves and lymphatics develop alongside the epithelial and mesenchymal components, and how adult stem cells are sequestered within the adult organ and maintain it throughout life. Answering these questions is important for many reasons: defects in organogenesis underlie many congenital abnormalities; understanding how organs develop in vivo can help us to bioengineer replacement tissues from embryonic stem cells in the lab; deciphering how different cell types cross talk during development can provide clues to processes such as tumor-stromal interactions, wound repair and aging. 

In this module we will read and discuss primary research papers relevant to core processes common to the development of many organ systems: (1) Branching morphogenesis – the process by which a simple bud of epithelial and mesenchymal cells gives rise to a branched, tree-like structure with region-specific differentiation of cell types; (2) Self organization of tissues in 3D organoid cultures; (3) Tissue vascularization and innervation during development; and (4) making stem cell niches.

​​Readings:

  1. Guillot, C., and Lecuit, T. (2013) Mechanics of epithelial tissue homeostasis and morphogenesis. Science 340: 1185-1189
  2. Lancaster, M.A. and Knoblich, J.A. (2014) Organogenesis in a dish: Modeling development and disease using organoid technologies. Science 345: DOI: 10.1126/science.1247125
  3. Hatch, J and Mukouyama Y.S. (2015) Spatiotemporal mapping of vascularization and innervation in the fetal murine intestine. Dev Dyn 244: 56-68
  4. Udan, R.S., Culver, J.C. and Dickinson, M.E. (2012) Understanding vascular development. Wiley Interdiscip. Rev. Dev Biol. 2
  5. Etzrodt, M., Endele, M. and Schroeder, T. (2014) Quantitative single-cell approaches to stem cell research. Cell Stem cell 15: 546-58

Optional:

  1. Keller, P.J. (2013) Imaging morphogenesis: technological advances and biological insights. Science 340, 1234168  DOI: 10.1126/science.1234168
  2. Costantini, F. (2012) Genetic controls and cellular behavior in branching morphogenesis of the renal collecting system. Wiley Interdiscip. Rev. Dev. Biol. 5: 693-713
  3. Heisenberg, C-P., and Bellaiche, Y. (2013) Forces in tissue morphogenesis and Patterning (2013) Cell 153: 948-962

Section B: Regulation of Mitochondrial Metabolism

Instructor: Matthew Hirschey

This workshop-style module will examine how post-translational modifications can modulate the structure and function of proteins.  Protein phosphorylation, ubiquitination, and acylation will be covered. As a working example, we will focus on protein acetylation, which has been shown to modify the majority of metabolic enzymes in the mitochondria.  Students will be exposed to basic mitochondrial biology, including functions and dynamics, and then choose an enzyme to perform a detailed analysis of acetylation sites.  Methods for identifying putative acetylation sites and performing basic structural analyses will be discussed.  Students will then generate novel predictions as to how acetylation might affect their enzyme of choice.  Strategies for assessing these hypotheses will also be covered.  Although the focus will be on acetylation of mitochondrial proteins, the skills acquired in this module will be broadly applicable.

Reading: 

  1. Mitochondrial protein acetylation regulates metabolism. Anderson, K.A., and M.D. Hirschey, 2012, Essays Biochem.  52, 23–35.
  2. Molecular Biology of the Cell, Alberts et al., - Chapter 14 (pages 813-840)

Section C: Regeneration

Instructor: Kenneth Poss

Questions of how and why tissue regeneration occurs have captured the attention of countless biologists, biomedical engineers, and clinicians. Regenerative capacity differs greatly across organs and organisms, and a range of model systems that use different regenerative strategies and that offer different technical advantages have been studied to understand regeneration. In this module, we will cover key concepts and mechanisms of tissue regeneration, focusing our attention on the cellular and molecular events that drive regeneration of skeletal muscle after trauma. 

Reading: 

  1. Brack, A. and Rando, T.  (2012).  Tissue-specific stem cells: lessons from the skeletal muscle satellite cell.  Cell Stem Cell 10, 504-514.  
  2. Poss, K. D.  (2010).  Advances in understanding tissue regenerative capacity and mechanisms in animals.  Nature Reviews Genetics 11, 710-722.

Section D: Cell Biology of the Synapse

Instructor: Scott Soderling

How the brain is wired during development and how these connections are modified by experience are fundamental questions of neural cell biology.  In this module we will cover examples of how axons navigate to properly innervate their targets.  We will also cover how the synapse is formed and how the strength of the synaptic connection is modified by experience.  Finally we will investigate how impairments to these processes are the basis to many neurological disorders.

Reading: 

  1. Molecular Biology of the Cell, Alberts et al. Chapter 11 - Ion Channels and the Electrical Properties of Membranes.
  2. Molecular Biology of the Cell, Alberts et al. Chapter 21 - Neural Development.

 

Module 6

Section A: Bioinformatics and Genomics for the Biologist

Instructor: David MacAlpine

Computational biology and genomics are a mainstay of modern biology.  For example, sequence alignments, identification of gene orthologs and paralogs by blast searches, and motif identification are now routine practices in the laboratory.  In addition, the explosion of whole genome sequencing in the last decade has led to a variety of genomic approaches (many based on microarray technology and next-generation sequencing) to phenotype the cell at the level of gene expression and identify networks of co-regulated genes.  These computational tools and genomic approaches are likely to be integral components of many research projects.

In this module, we will explore the tools and approaches to analyze next-generation sequencing data.   We will make extensive use of Unix, bash scripting, and the R environment for statistical computing.  The student will not only learn to critically evaluate these complex genomic experiments, but will also gain first hand experience at analyzing primary data.

Reading: 

Unix Tutorial 
http://www.ee.surrey.ac.uk/Teaching/Unix/

R Tutorial
http://www.cyclismo.org/tutorial/R/

  1. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016. PubMed PMID: 22383036; PubMed Central PMCID: PMC3334321.

Section B: Nuclear Structure/Gene Regulation

Instructor: Eda Yildirim

Understanding how transcriptional status of genes are established, maintained, and regulated is crucial to answer the questions of how diverse cellular functions are orchestrated during development of multicellular organisms. During recent years, it has become evident that gene expression is controlled not only on the basis of DNA sequences at the promoter and enhancer elements, but at the epigenetic level by elements of nuclear structure. These include chromatin modifications of DNA and histones, noncoding RNA-mediated epigenetic regulation, higher-order chromatin arrangements and variable aspects of nuclear architecture. In this module, we will discuss key papers that reveal these levels of gene regulation. We will be learning to approach these exciting papers critically and design experimental ways to test and explore this new area of Cell Biology.

Reading: 

  1. Molecular Biology of the Cell, Alberts et al. Chapter 4 - Overall Chromatin Structure (limit to pp. 202-245, in 5th edition)
  2. Molecular Biology of the Cell, Alberts et al. Chapter 7 - Overview of Gene Control (limit to pp. 411-432, in 5th edition)
  3. Molecular Biology of the Cell, Alberts et al. Chapter 12 - Overview of Nuclear Structure (limit to pp. 704-712, in 5th edition)

Section C: Genome Instability

Instructor: Don Fox

Protection of the genome is key to maintaining normal cellular function.  Numerous safeguards exist to detect genome alterations and potential cell division errors, thus maintaining a stable genome.  Failure in such regulation leads to genome instability.  A variety of human diseases are derived from genome instability, including diseases of aneuploidy such as trisomies.  Genome instability is also present in cancer, and a current debate in the literature is whether genome instability is a major cause, rather than a consequence, of cancer. 

In this module, we will take a look at recent literature on causes and consequences of genome instability in various model systems and in human disease.  In the six papers we will discuss, the wide range of concepts discussed will include cell cycle checkpoints, aneuploidy, and cancer genomics.   Methods used in the papers will similarly cover a wide range of genetic, molecular, and cell biological assays.  Most importantly, this class is geared towards developing critical literature analysis skills.

Reading: 

  1. Gordon DJ, Reiso B, and Pellman, D.  (2012). Causes and consequences of aneuploidy in cancer.  Nature Reviews Genetics 13, 189-203
  2. Optional reading (if further background is needed): Alberts et al, Chapter 17 (The cell cycle). 

Section D: Humans as Model Organisms

Instructor: Vann Bennett

Translational research is frequently viewed as the application of established principles of basic science to promote human health.  This section will develop the theme that deciphering the molecular basis for human disease can be far from straightforward, and both require and contribute to elucidation of new fundamental biology.  We will focus this year on nervous system-related diseases, beginning with Creutzfeldt-Jacob and related neurodegenerative disorders where molecular breakthroughs have led to the prion concept.  We will then consider Alzheimer’s disease, where genetic mutations and risk factors are known, but the pathophysiology is still unresolved.  We will end with discussion of autism, which since 1980 has transitioned from a rare disorder to one affecting 1% of the population.  Autism is heritable and autism susceptibility genes are known.  However, autism still lacks a unifying concept and is an attractive target for future research.

Reading: 

  1. Pruisner’s Nobel Lecture (.pdf)