1. Understanding Drosophila Development at the Molecular Level Gene Myers EECS, UCal, Berkeley

2. On Systems Biology  The goal is to understand cells and organisms as molecular systems. An objective that can be reached in the next 10-25 years is the elucidation of the topology of the “circuit” diagram of a species’ cells.  Rationale drug design will become a reality.  We will be able to predictable modify systems at the cellular level.

3.  Accurately reconstruct 6-12 Drosophila genomes with a shotgun approach as cost-efficiently as possible.  Compare the Drosophila genomes to:  Understand evolution of whole genomes  Better predict the genes and regulatory signals within each My Drosophila Plan Sequence Parts List Mechanism

4. Based on sequence anchor blocks Courtesy Lisa Stubbs Oak Ridge National Laboratory Evolution as Genomic Rearrangements

5. Given a ladder of 5-10 Drosophila genomes we should be able to accurately discern most protein encoding genes, many RNA genes, and a host of regulatory signals Comparative Gene Finding sechellia mauritiana simulans melanogaster orena teissieri yakuba mimetica 0M10M20M30M40M pseudoobscura Find genes by requiring all HMM models (ab initio), trained for each genome on cDNA-discovered (homology) genes, to be highly probable subject to the constraint that the encoded proteins are consistent with the evolutionary relatedness of the species (comparative).

6.  Empirically validate all genes and their alternate splice forms.  Measure (e.g. ChIP-chip) or infer from spatio-temporal expression, the cis- regulatory control of all genes and their transcription factor binding sites.  Build a spatio-temporal model of Drosophila embryonic development and associated regulatory-control “circuit”.  Dissect cellular complexes (pull-downs + MS) and signal cascades (in vitro MS/MS) My Drosophila Plan Sequence Parts List Mechanism  Accurately reconstruct 6-12 Drosophila genomes with a shotgun approach as cost-efficiently as possible.  Compare the Drosophila genomes to:  Understand evolution of whole genomes  Better predict the genes and regulatory signals within each

7. Expression of Gene CG14897 Stage 1: Maternal Stage 4: Pole Plasm Stage 8: Neuroderm Anlage Stage 11: Protocerebrum Primordium Stage 14: Embryonic Central Nervous System Affy expr. profile: 1 st 12 hours

8. Sea Urchin Endo-Meso TF “Circuit” (Davidson Lab, Caltech)

9. Some possibilities  Intuitive systems for scientific analysis  Modeling of molecular processes in multi-cellular systems.  New paradigms for architecting software  Nano-exploration of the cell  Fully robotic molecular biology lab

10. DNA in the chromosomes of the genome contains all the information to develop an organism and operate all its cell types.DNA in the chromosomes of the genome contains all the information to develop an organism and operate all its cell types. RNA serves both short-term informational roles and structural roles.RNA serves both short-term informational roles and structural roles. Proteins execute the functions of a cell and provides its structural integrity.Proteins execute the functions of a cell and provides its structural integrity. Small metabolites (fats, sugars, etc.) provide energy, raw materials, and serve some limited structural roles.Small metabolites (fats, sugars, etc.) provide energy, raw materials, and serve some limited structural roles. The Elements of Molecular Biology A principal goal is to understand cells and organisms as molecular systems / machines. The basic classes of molecules are:

11. Cell Nucleus Cells As Molecular Machines Genome Transport TranslationProtein Metabolics: Synthesis Synthesis Degradation Degradation Energy EnergyActivation Receptor SignalCascade Gene mRNATranscription Splicing Secretion RibosomePolymerase TBF

12.  Determining the DNA sequences of the chromosomes of a species. Sequencing  An accurate parts list of all the proteins and RNAs in the cell. Annotation  A graph of all the interactions taking place between these agents. Pathways  What is happening during each interaction. Function  Where each interaction is taking place. Subcellular Localization Understanding Cells at the Molecular Level

13. Apoptosis: Programmed cell death

14. A Proposal based on Drosophila  Goal: Develop a comprehensive set of accurate genomics-based data and biological resources for the advancement of cellular biology. Make them openly and readily accessible and available to all. 1.Sequence 10-20 species of Drosophila, 3-5 to a nearly-finished state and 10-15 to an assembled state. 2.Understand the evolution of the genomes and accurately annotate the genes and regulatory signals using comparative informatics. 3.Develop a comprehensive, experimentally verified annotation of all possible transcripts of the nearly-finished species. Capture each in a gate-way clone library. 4.Build state of the art expression assays for these genomes and apply them in a number of surveys. 5.Utilize mass spec. technology to begin systematically exploring the pathways and function of Drosophila cells.

15. Why Drosophila?  Sufficiently interesting model: development, differentiation, behavior  Easy to stock lines and many experimental methods.  Compact genome: 20 Dros. Genomes = 1 mammalian genome  Excellent evolutionary and molecular model for humans  Large community: coordinated efforts are possible