Kaplinsky lab at Swarthmore College

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In the upcoming semester, you will be using some materials supplied by GCAT. GCAT is interested in assessing the effectiveness of these materials for promoting learning. To that end, they have created a brief survey that should take no more than 15 minutes to complete. The first part of the survey asks for some demographic information to get a better idea of who uses GCAT materials. The second part of the survey consists of a short quiz to assess what you know about the subject before the semester begins. This quiz will not be graded but it will help GCAT determine the usefulness of the materials after the semester has ended. Thank you in advance for your participation.

Course description

Fundamental questions in biology are being answered using revolutionary new technologies including genomics, proteomics, metabolomics, systems biology, modeling, and large scale protein and genetic interaction screens. These approaches have fundamentally changed how scientists investigate biological problems and allow us to ask questions about cells, organisms and evolution that were impossible to address even five years ago. We will explore these modern approaches by reading primary literature. While many of the papers we read will focus on model organisms, next generation sequencing technologies are quickly turning all organisms into model organisms.

Expectations

The course consists of a classroom seminar (on Monday afternoons) as well as a independent laboratory projects (on Wednesday afternoons). Bio119 is a 2 credit course which means that it represents half of your academic work load. You are expected to come to seminar prepared to contribute to a discussion of the assigned readings. This means reading each assignment carefully and critically.

Just as you will spend time reading and preparing for presentations outside of the classroom, you are also expected to work on your independent laboratory project outside of the Wednesday afternoon. We will be performing microarray experiments in lab this semester, and many of the steps involved in the experiment will not fall neatly on Wednesday afternoons.

Presentations

Nick will provide an overview of the course during the first week and will present papers during week two. For the remainder of the semester the course will consist of student presentations. Each week two students will choose and present three papers which address a single biological question or theme. The papers will consist of two 'omics papers and one related background paper. Each week one student will present a paired classical and 'omics paper, the other student will just present an 'omic paper. The classic paper should be an example of how biologists approached the biological question in the 'omics paper without genome sequences. Each student will present twice during the semester - one of each type of presentation. Papers will be chosen by students with input and advice from Nick, and will be supplemented with selected sections of the textbook.

Textbook

Most of the reading in the course will consist of primary literature. Since many of the concepts and techniques in the reading will be new to you I have selected A Primer of Genome Science (3rd ed.) by Greg Gibson and Spencer V. Muse. It provides an excellent overview of the fields of genomics and systems biology.

Assignments

Apart from participation in the seminar and laboratory components of the course, there will be two assignments. For the seminar portion of the course you will make a significant contribution to Wikipedia by writing content that increases the breadth and quality of information about one of the topics covered in this course. For example, as of September 2009, there is very limited information about next generation or high throughput sequencing on Wikipedia. This assignment will involve presenting a proposal of the topic you will contribute to and a group evaluation of your contributions.

The assignment for the lab portion of the course will be a writeup and/or aposter describing what you did during the course of the semester. We will decide on a format as we get closer to the end of the semester.

Genome Consortium for Active Teaching
Microarray protocols
Arabidopsis microarray information
Maize microarray information
E. Coli microarray information

Plant RNA and reverse transcription protocol
Genisphere 350 protocol for labeling Arabidopsis and Maize arrays
Genisphere 900MPX protocol for labeling E. Coli arrays

One of the central questions we will investigate this semester is what is a sequenced genome good for? It turns out that nearly all of the approaches for asking biological questions which we will discuss depend on the availability of genome sequences. To get the semester started, I would like you to read a genome paper and come to the first class with short written answers to the questions below. You can choose any published genome paper.

A list of the 10 most cited genome papers can be found here. The list includes the first sequenced genome of a live organism (Haemophilus influenzae), the human genome (twice - a public and a private effort), and my favorite, Arabidopsis. Bacterial genomes are well represented in this list because they were the first genomes sequenced and have had time to rack up citations. You can access any of these papers that are not freely available using EZProxy from off campus.

You are not limited to these papers - there are hundreds of other sequenced and published genomes. Among these are the mouse, chimpanzee, dog, pufferfish, parts of a neanderthal genome, rice, maize, papaya, grape, c. elegans (the first multicellular sequenced genome), yeast, drosophila, and hundreds of bacterial and fungal genomes. Feel free to pick any genome paper that "describe the DNA sequence as well as relevant sequencing methods and biological discoveries revealed by the initial sequencing of the genome." (quote taken from the top 10 list web site).

Read the paper keeping in mind that there will be sections that do not make sense to you - this is new stuff for most of you! The Gibson and Muse book should help you understand some aspects of the paper you choose, others will become clear over the course of the semester. Each genome paper will be different. Early papers will not contain much comparative genomics, later papers will focus on comparisons with previously sequenced genomes. The quality of sequenced genomes varies wildly - finished can mean single contigs (contiguous DNA sequences) for each chromosome or 40,000 contigs which are not precisely ordered onto chromosome backbones.

Please come to the first class with a copy of the paper that you read and written answers to the following questions:

1) Why was this organism chosen for a genome sequence?
2) How was the genome sequenced and assembled?
3) What biological insights resulted from the genome sequence?
4) Which three findings in the paper surprised you?
5) List three things in the paper that you do not understand.

Nick will present the following papers and use them to illustrate how to read and present a scientific paper.

'Omics paper:
Collins et al., Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446:806-810, 2007.

An overview and comparison of global approaches for identifying protein interactions:
Yu et al., High-quality binary protein interaction map of the yeast interactome network. Science 322:104-110, 2008.

Gibson and Muse: pages 220-222 and 259-286.

Optional reading for those of you unclear what epistasis means:
Roth et al., Q&A: Epistasis. Journal of Biology 8:35, 2009.

Jennifer and Natasha will present the following papers which look at how the output of circadian clocks can be analyzed.

Classic paper:
Konopka and Benzer, Clock mutants of Drosophila melanogaster. PNAS68:2112-2116, 1971.

Circadian regulation of genes in Arabidopsis:
Harmer et al., Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290:2110-2113, 2000.

Circadian regulation of metabolites in mammals:
Minami et al., Measurement of internal body time by blood metabolomics. PNAS 106:9890-9895, 2009.

Gibson and Muse: pages 325-333 and Chapter 4.

Lorenzo and James will present the following papers which use whole genome and systems approaches for understanding development.

Root patterning in Arabidopsis:
Levesque et al., Whole-Genome Analysis of the SHORT-ROOT Developmental Pathway in Arabidopsis. PLOS Biology 4(5)e143, 2006.

Cell ablation - a classic way to understand patterning:
van den Berg et al., Short-range control of cell differentiation in the Arabidopsis root meristem. Nature 390:287-289, 1997.

A review of conservation of gene regulatory network architecture in development:
Oliveri and Davidson, Built to Run, Not Fail. Science 315:1510-1511, 2007.

A look gene regulatory network architecture in sea urchin development:
Davidson et al, A Genomic Regulatory Network for Development. Science 295:1669-1678, 2002.

Gibson and Muse: pages 338-341.

Frances and Julia will present the following papers which investigate the C value paradox, transposons, and how regulatory sequences might sculpt genome organization.

Cot curves:
Britten and Kohne, Repeated sequences in DNA. Science 161:529-540, 1968.

Do regulatory elements shape genome architecture:
Nelson et al., The regulatory content of intergenic DNA shapes genome architecture. Genome Biology 5:R25, 2004.

A review of transposons:
Capy and Deragon, Transposons. Encyclopedia if Life Sciences. 10.1038/npg.els.0005064, 2005.

Regulation of transposon activity to keep them silenced across generations:
Slotkin et al, Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136:461-472, 2009.

Cathy and Andrew will present the following papers which investigate the use of expression profiling for tumor typing and the identification and characterization of genes involved in cancer and metastisis .

Identifcation of p53 as a tumor supressor:
Baker et al., Chromosome 17 Deletions and p53 Gene Mutations in Colorectal Carcinomas. Science 244:217-221, 1989.

Tumor identification:
Alizadeh et al., Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403:503-511, 2000.

Identification and characterization of SATB1, a gene involved in metastasis:
Han et al., SATB1 reprogrammes gene expression to promote breast tumour growth and metastisis. Nature 452:187-193, 2008.

Youda and Charlie will present the following papers which investigate the use of proteomic techniques for identifying the structural features shared among chaperone substrates.

The crystal structure of GroEL:
Baig et al., The crystal structure of the bacterial chaperonin GroEL at 2.8 A. Nature 371:578-586, 1989.

X ray crystallography background:
X ray crystallography background.

An introduction to GroEL functions:
Tokuriki and Tawfik, Chaperonin overexpression promotes genetic variation and enzyme evolution. Nature 459:668-673, 2009.

Identification of GroEL substrates:
Houry et al., Identification of in vivo substrates of the chaperonin GroEL. Nature 402:147-154, 1999.

Identification of protein folds thath require GroEL:
Kerner et al., Proteome-wide Analysis of Chaperonin-Dependent Protein Folding in Escherichia coli. Cell 122:209-220, 2005.

Gibson and Muse: pages 259-276.

Frances and Andrew will present the following papers which use systems approaches for understanding evolution of anticipatory behavior in bacteria and prediction and testing of hypotheses about the metabolism of newly identified organisms.

Understanding the evolution of predictive behavior in bacteria:
Tagkopoulos et al., Predictive behavior within microbial genetic networks. Science 320:1313-1317, 2008.

Predicitive physiological models:
Bonneau et al., A predictive model for transcriptional control of physiology in a free living cell. Cell 131:1354-1365, 2007.
Bonneau et al. supplemental tables

Dissection of the function of a single archaeal regulon:
Baglia et al., Genomic and genetic dissection of an archaeal regulon. PNAS 98:2521-2525, 2001

Julia and Youda will present papers which use large scale RNAi screens to identify genes required for stem cell identity and for cancer cell viability

RNAi as a tool in C. elegans:
Fire et al., Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806-811, 1998.

Genes required for self renewal in stem cells:
Ivanova et al., Dissecting self-renewal in stem cells with RNA interference. Nature 442:533-538, 2006.

Identification of cellular pathways which may be good drug targets in cancers with activated Ras Oncogenes:
Luo et al., A Genome-wide RNAi screen identifies multiple synthetic lethal interactions with the RAs oncogene. Cell 137:835-848, 2009.

Jennifer and James will present papers in which genomic approaches are used to identify quantitative trait loci in C. elegans and in maize.

Mapping the genes involved in maize domestication:
Doebley and Stec, Genetic analysis of the morphological differences between maize and teosinte. Genetcis 129:285-295, 1991.

Mapping the genes that control flowering time in maize:
Buckler et al., The Genetic Architecture of Maize Flowering Time. Science 325:714-718, 2009.

Mapping the genes that control expression plasticity in response to environmental change in nematodes:
Li et al., Mapping Determinants of Gene Expression Plasticity by Genetical Genomics in C. elegans. PLoS Genetics 2:e222, 2006.

Also read Gibson and Muse: pages 155-164 and The FAQs at Panzea.org

This week Cathy and Lorenzo will present papers which investigate the regulation of the cell cycle using high-content screening and RNAi.

Cloning a S. pombe cyclin:
Hagan et al., Cloning and sequencing of the cyclin-related cdc13+ gene and a cytological study of its role in fission yeast mitosis. Journal of Cell Science 91:587-595, 1988.

An arrayed lentiviral RNAi high content screen:
Moffat et al., A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen. Cell 124:1283-1298, 2006.

Genome wide identification of mitotic regulators:
Mukherji et al., Genome-wide functional analysis of human cell-cycle regulators. PNAS 103:14819-14824, 2006.