Jeff Young, Botanist [e-mail] x3638 Office: BI412

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Jeff Young, Botanistyoung_at_biol.wwu.edux3638Offi
ce BI412
Office Hours M WF - 1 - 2 pm by appointment.
Genome-based, molecular study of plant physiology
and environmental responses.
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DNA Sequence Reagent for the 21st Century
Biology is in the midst of an intellectual and
experimental sea change.... ...essentially the
discipline is moving from being largely a
data-poor science to becoming a data-rich
science.
Vukmirovic and Tilghman, Nature 405, 820-822
(2000)
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Data Poor Era
Data Rich Era

• Great DATA, but you had to get it yourself,
• Collect data from previous day,
• Set-up experiment,
• Lunch,
• Analyze, discuss data,
• Repeat

• Free DATA, more than any one person could ever
  use.

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Course Goals

• Introduce Genome Scale Research,
• Develop and improve skills in reading, analyzing
  and understanding primary literature,
• Enjoy, responsibly, the enormous amount of
  creativity and genius that is being expended,
  right now, in the biological sciences.

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Class Evaluation
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Reading Assignments available online

• ? ?ll materials will be from the primary
  literature, and journal reviews.
• ? All materials may be downloaded (for free) for
  printing,
• however, sometimes figures are best viewed on a
  monitor.
• ? You are responsible for understanding these
  papers, including all figures and tables.
• ? You must read each assigned paper prior to
  lecture (if you want to do OK).
• Recommended (optional) background and supporting
  materials will be made available.

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Reading Recommendations

• Read before class,
• Follow references, (link)
• abstracts, if not entire papers are free on line
  (NCBI PubMed),
• may contain materials and methods,
• Look up words and concepts that arent familiar,
• Dont neglect Figures and Tables.

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Genomics

• the systematic study of genomes that begins with
  large scale DNA sequencing,

• Structural genomics the study of DNA sequence,
  chromatin structure, and DNA physical
  interactions,
• Functional genomics how particular DNA sequences
  facilitate biological functions,
• Bioinformatics computational discipline that has
  evolved to handle modern biological data...

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Genomics
Hieter P and Boguski M. Science 278, 601-02.

• ... Genomics... is characterized by high
  throughput or large-scale experimental
  methodologies combined with statistical and
  computational analysis of the results.
• ...the fundamental strategy in a functional
  genomics approach is to expand the scope of
  biological investigation from studying single
  genes or proteins, to studying all genes or
  proteins at once in a systematic fashion.

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DNA
mRNA
Protein
Genome
Transcriptome
Proteome

• Genome... the dynamic complement of heritable
  genetic material,

• Transcriptome... mRNA in a cell, tissue,
  organ or individual,
• complexity increases resulting from
  transcription control and post-transcription
  modification,

• Proteome... protein in a cell, tissue, organ
  or individual,
• complexity increases due to post-translational
  modification, protein-protein interactions, etc.

Modern research integrates data from all of these
sources.
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Course Contents

• Introduction to Functional Genomics
• Sequencing Complex Genomes
• Environmental Genome Sequencing
• NexGen Technology
• Bioinformatics I (Genetics, Mouse Knockouts)
  Bioinformatics II (Protein Biochemistry)
• Reverse Genetics I (RNAi)
• Reverse Genetics II (Target Genes)
• Transcriptome I (Expression Microarray)
• Transcriptome II (DNA Microarray)
• Proteomics I (Mass Spectrometry, Y2H)
• Student Presentations

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Student Presentations

• Environmental/Ecological Genomics
• Canine Genomics
• Malaria Genomics
• Comparative Genomics
• NexGen Results
• Evolutionary Genomics

• Bioinformatics
• Personal Genome Projects
• Sequencing Projects/Results,
• Mouse
• Chicken
• Chimpanzee,
• etc.
• Systems Biology
• Others, with approval.

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GENOMICSControversial From the Start

• Objection 1 Big Biology Is Bad Biology
• Objection 2 Why Sequence the Junk?
• Objection 3 Impossible to Do!
• Besides, whod want to do it?

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(No Transcript)
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Science 291 (5507), 1182-1188
In the 1980s
Sydney Brenner
... facetiously suggested that project leaders
parcel out the job to prisoners as
punishment--the more heinous the crime, the
bigger the chromosome they would have to decipher.
Who wanted to do it?
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It turns out a lot of people did....with the
help of lots of machines.

• This once-ludicrous proposal became one of most
  hotly contested--and contentious--races in recent
  scientific history.
• Although the race has been dominated in the past
  few years by the acrimonious feud between the
  public and private teams, tensions go way back

Science 291 (5507), 1182-1188
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Objection 1 Big Biology Is Bad Biology

• Researchers feared that a massive sequencing
  project would siphon precious dollars from
  investigator-initiated research, destroying the
  cottage industry culture of biology in the
  process.
• 1988, US Congress agreed to fund the HGP
  separately.
• ...just as bad, the project didn't even amount to
  hypothesis-driven science at all. Rather, critics
  charged, it was no more than a big fishing
  expedition, a mindless factory project that no
  scientists in their right minds would join.

Science 291 (5507), 1182
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Hypothesis vs. Discovery

• "Discovery science has absolutely revolutionized
  biology," says Leroy Hood, now director of the
  Institute for Systems Biology in Seattle,
  Washington...
• ...it's given us new tools for doing
  hypothesis-driven research," maintains Hood, and
  these tools help rather than hinder individual
  investigators."

Science 291 (5507), 1182
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Objection 2 Why Sequence the Junk?

• 2 of the human genome codes for polypeptides,
• why not sequence the 6o million bases that make
  something.
• besides, sequencing the rest, often called junk
  DNA,
• ...(it) would be a waste of time and money to
  include the repetitive, hard-to-sequence regions
  in the genome project.

Science 291 (5507), 1184
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Why Sequence the Junk?

• Promoters!
• control expression.
• Telomeres!
• prevent the ends of the chromosome from fraying
  during cell division and help determine a cell's
  life-span.
• Repetitive and non-protein coding sequences!
• plays a crucial role in X chromosome
  inactivation,
• plays a similar role in the regulation of other
  genes/genomic regions,
• plays a role in genome surveillance/protection,
• noncoding DNA (may) provide "a built-in
  plasticity that ... if an organism is going to
  evolve, may be a huge selective advantage.
• Other?

Science 291 (5507), 1184
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Objection 3 Impossible to Do

• State-of-the-art sequencing could produce about
  500 bases per 8 hours per rig, working day in and
  day out,
• and the computer technology that came to play
  such a vital role in the project wasn't even
  invented yet.
• "In the early days, it was believed that a
  radical new technology would be required to
  sequence the full human genome,
• ...but it didn't turn out that way.
• - Stanford University geneticist David
  Botstein.

Science 291 (5507), 1186
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Not Revolution, Evolution

• radioactive probes --gt fluorescent probes,
• allowed automated, laser-based detection,
• slab gels --gt capillary tubes,
• automation and computer technology.

"It was definitely evolution...but you can go a
long way with evolution. ...David Baltimore,
president of the California Institute of
Technology.
Science 291 (5507), 1186
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• gt 206 Gb (Dec. 2007)
• gt 165,000 organisms

Presently
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Reference, GOLD
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Nature Reviews Genetics
Friday pp. 302 - 307 (figs 1 -3)