Teaching

The following undergraduate classes are taught by Dr. Woolford. Teaching Assistants for these courses are typically graduate students from the Woolford Lab.

Molecular Biology of Eukaryotes (03-442, 03-742)

I.     Structure and expression of eukaryotic genomes…what are the emerging principles of gene expression?

  • What exactly are all of the steps required for a gene to be expressed?
  • What are the 3-4 “BIGGEST QUESTIONS” in molecular biology?
  • What are the “model” eukaryotic organisms used by biologists, and why are they model organisms?
  • B.C. …Before cloning: Different populations of genes are expressed in different cell types at different times. How was this initially discovered, and why was it of interest?

II.     B.S. Before sequencing: Recombinant DNA techniques: how to clone your favorite gene (Weaver, Chapters 4&5) What motivated the development of cloning tools? From where did these tools come?

  • Construction and use of recombinant DNA molecules: cDNA and genomic DNA clones

III.    A.S. After sequencing: Genomics, Transcriptomics, Proteomics and other ‘omics – High throughput analysis once your favorite genome is sequenced (Weaver, Ch. 24). What motivated development of these approaches? How were they developed?

  • Genomics: What have we learned from sequencing genomes of model organisms?
  • The transcriptome: assaying amounts of all transcripts under different conditions using gene chips, microarrays, and now, high throughput RNA sequencing
  • Proteomics: study of all proteins present under different conditions, using mass spectrometry
  • Functional genomics and proteomics: (1) investigating gene function by constructing gene knockouts, knockdowns (RNAi) and knock-ins; CRISPR technology; (2) constructing conditionally expressed genes or mutant alleles by PCR, transformation and homologous recombination; (3) epitope-tagging, purification of multi-molecular complexes, and identification of constituents by mass spectrometry.
  • How does gene expression vary among individual cells in a sample, e.g., one organ or tissue …the emergence of single cell ‘omics
  • What does the future hold?
  • FIRST HOUR EXAM  (~Friday, September 27)

IV.    Translation of mRNA (Weaver, Chs. 17-19)

  • Role of 5′ caps and 3′ poly(A): revisiting an old hypothesis
  • Cis-regulation of translation by upstream open reading frames or IRES elements
  • Trans-acting factors
  • Specialized ribosomes
  • Localized translation

V.      Transcription of eukaryotic genes (Weaver, Chapters 10-13)

  • Overview of transcription
  • Temporal and spatial-specific gene expression
  • Cis-acting elements (Weaver, Chapter 10)
    – Promoters, enhancers and silencers
    – Defining the eukaryotic promoter by mutating it in vitro, introducing it into living cells, and assaying expression in vivo
  • Trans-acting factors (Weaver, Chs. 10-12)
    – Basal transcriptional machinery: identification by genetic and biochemical methods
    – Regulatory proteins: enhancer binding proteins and adaptor proteins
    – DNA-protein as well as protein-protein interactions
  • Role of chromatin/chromosome structure in transcription: histones, nucleosomes, structural and posttranslational modification of nucleosomes, and the histone code (Weaver, Ch. 13)
  • Unraveling the three-dimensional genome …how is the genome organized in 3D space within the nucleus, and how does this affect gene expression?
  • Regulation of transcription initiation
  • Polymerase pausing and regulation of transcription elongation

SHOW AND TELL DAY: THE ART PROJECT  (~Wednesday, October 16)

    MID SEMESTER BREAK (Friday, October 18)

    COMMUNITY ENGAGEMENT DAY NO CLASS FRIDAY, OCTOBER 25

  • SECOND HOUR EXAM (~Friday, November 1)

VI.    Pre-mRNA processing (Weaver, Chs. 14 and 15)

  • Comparing and contrasting the structure of RNA vs. DNA; High throughput assays of RNA folding
  • There are several different classes of processed RNAs and RNA processing reactions.
  • Mechanism of pre-messenger RNA splicing in vivo and in vitro: essential cis-elements
  • Trans-acting factors: Splicing factors and the splicing complexes (spliceosome)
  • What have we learned from recent near-atomic resolution cryo-EM structures of splicing complexes?
  • Regulation of splicing and alternative splicing — another means to generate diversity in gene expression. Example: Regulation of sex determination in Drosophila
  • Coupling of transcription and splicing – one large machine?

VII.   mRNA localization: export of RNA from the nucleus to the cytoplasm and intracellular transport

  • Methods to detect intracellular localization of RNA molecules
  • Molecular machines that enable intracellular transport of RNA
  • Coupling of nuclear export of mRNA with its transcription and splicing

VIII. Storage and turnover of nuclear and cytoplasmic RNA

  • Nobodies, P-bodies, Cajal bodies, stress granules, and others
  • RESEARCH PROPOSAL OUTLINE DUE (Friday, November 22)
  • THIRD HOUR EXAM (~Friday, December 6)
  • RESEARCH PROPOSAL DUE (Friday, December 13)

Your grade in this course will be determined by the following:

Oral and written summaries of journal articles:  20 points each                           200 points

First hour exam:                             ~Friday, September 27                            100 points

Art Project                                         ~Wednesday, October 16                      50 points

Second hour exam                         ~Friday, November 1                                100 points

Research proposal outline               ~ Friday, November 22                              50 points

Third hour exam                            ~Friday, December 6                                100 points

Research proposal                        ~ Friday, December 13                               200 points
800 points

Research articles from scientific journals are the focus of this course. These are required reading, will be available on the class Canvas online, and each will be discussed in subsequent lectures. The exams will be based on the lectures, including information discussed from the articles. The textbook is Molecular Biology, Fifth Edition, (2011) by Robert Weaver, can be made available in the bookstore. Also, you can borrow a copy from me for a day.

 

Advanced Genetics (03-730)

This is a graduate level seminar course. Each week the class meets for three hours to discuss classic and recent papers focusing on one topic in genetics. We discuss how problems are chosen and framed, choosing or developing classical and molecular genetic tools to solve the problems, and building testable models based on the experimental data. Recent topics have included using yeast and fruit flies to understand the molecular basis of neurodegenerative diseases in humans, cell cycle checkpoint controls, mRNA turnover and P-bodies, nuclear import/export pathways, role of cohesins in chromosome segregation during mitosis and meiosis, and revisiting the original literature of cell cycle genetics.