Woolford Laboratory  

 
 
Department of Biological Sciences l Carnegie Mellon University


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)

Download the Syllabus (PDF)


I.       Structure and expression of eukaryotic genomes

  • What are the model eukaryotic organisms and why are they model organisms?
  • What exactly are all of the steps required for a gene to be expressed?
  • B.C. …Before cloning:  Different populations of genes are expressed in different cell types at different times. How was this determined 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 high throughput RNA sequencing
  • Proteomics: study of all proteins present under different conditions
  • Functional genomics and proteomics: investigating gene function by constructing gene knockouts, knockdowns (RNAi) and knock-ins; CRISPR technology; constructing conditionally expressed genes by PCR, transformation and homologous recombination, epitope-tagging, purification of multi-molecular complexes, and identification of constituents by mass spectrometry, protein chips.
  • What does the future hold?

 

  • FIRST HOUR EXAM  (~Monday, October 3)

IV.    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)
  • Regulation of transcription initiation
  • Polymerase pausing and regulation of transcription elongation
  • Unraveling the three dimensional genome

 

V.      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 complex (spliceosome)
  • 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?

       SHOW AND TELL DAY: THE ART PROJECT  (~Monday, October 17)

  • SECOND HOUR EXAM (~Friday, October 28)

 

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

  • Coupling of export with transcription and splicing

 

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

  • Role of 5' caps and 3' poly(A): revisiting an old hypothesis
  • Trans-acting factors
  • Localized translation
  • Specialized ribosomes

 

VIII. Storage and turnover of nuclear and cytoplasmic RNA

  • Nobodies, P-bodies, Cajal bodies, stress granules, and others

 

  • THIRD HOUR EXAM (~Friday, December 2)
  • RESEARCH PROPOSAL  (TERM PAPER)
    • (Outline due Friday, November 18)
    • (Paper due Friday, December 9)
                         MOLECULAR BIOLOGY OF EUKARYOTES 2016

 

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:                             ~Monday, October 3                                         100 points
           
Art Project                                          ~Monday, October 17                                       50 points

Second hour exam                         ~Friday, October 28                                          100 points

Research proposal outline               ~ Friday, November 18                                 50 points

Third hour exam                             ~Friday, December 2                                        100 points

Research proposal                        ~ Friday, December 9                                       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 Blackboard 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, available in the bookstore.


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 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.
 
 

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