Genomics

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Genomics

• MUPGRET Weekend Workshop

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Timeline Answers

• http//www.jgi.doe.gov/education/timeline_2.html
• Another timeline at http//www.dnai.org/index.htm
  .

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Reviewing the basics

• Cells are the basic working unit of an organism.
• DNA (deoxyribonucleic acid) contains all of the
  instruction needed to direct the activities in
  the cell.
• DNA is arranged into chromosomes.

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More reviewing

• Chromosomes are visible with high powered
  microscopes.

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Chromosomes are Dynamic Structures
Human Chromosomes
Metaphase Chromosome
CONDENSED EXTENDED
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More review

• Chromosomes contain hundreds of genes encoded
  within their DNA.
• Genes compromise a very small percentage of the
  DNA that makes up the chromosome, lt5 generally.
• DNA containing genes is called euchromatin.

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Heterochromatin

• Non-genic DNA is called heterochromatin.
• Heterochromatin and euchromatin stain
  differently.
• This difference causes the bands we see in a
  karyotype.

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Human karyotype
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Genome composition

• Euchromatin (genes) usually contains a higher
  proportion of GC.
• Euchromatin has more unique DNA sequences.
• Heterochromatin (non-coding) usually contains a
  higher proportion of AT.
• Heterochromatin contains more repetitive
  sequence.s

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DNA Content

• The amount of heterochromatin varies dramatically
  between organisms.
• Much of the difference in DNA content among
  closely related organisms is often due to changes
  in heterochromatin amount.
• Maize 2500 Mb
• Wheat 16,000 Mb
• Rice 430 Mb
• MbMega base pairs

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A NOVA look into DNA.

• http//www.pbs.org/wgbh/nova/photo51/jour-nf.html

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PCR

• Polymerase Chain Reaction
• A way to xerox a DNA fragment.

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Electrophoresis

• A way to separate DNA molecules.
• http//gslc.genetics.utah.edu/units/biotech/gel/

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What is genomics?

• The study of the entire DNA complement of an
  individual.
• The term genome refers to all of the DNA
  contained in one copy of the chromosomes of an
  organism.
• It contains both coding (genes) and non-coding
  DNA sequences.

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The Genome

• Nearly every cell in an organims contains a full
  copy of the genome.
• Most mammal cells contain two complete copies of
  the genome.
• Skin
• Lung
• Heart

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The Genome II

• Gametic cells like sperm, ovules, or pollen
  contain one copy of the genome.
• Some special cell types contain more than two
  copies of the genome.
• Human bone marrow
• Regenerating liver cells

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Plant Genome

• Corn plants contain two copies of the genome in
  their cells except for pollen, ovules, and
  endosperm (the fleshy part of the corn kernel).
• Pollen and ovules have one copy of the genome.
• Endosperm has three copies.

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Plant Genome

• Other plants like corn include
• Arabidopsis
• Barley
• Beans
• Tomato
• Pepper
• Rice

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Multicopy Plant Genomes

• Some plants normally have more than two copies of
  the genome in their cells.
• Wheat six copies
• Potato four copies
• Sugarcane gttwelve copies
• Strawberry gteight copies
• Banana three copies
• Watermelon three copies

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Chromosome number

• The term haploid refers to the base number of
  chromosomes in an organism.
• Diploid cells have two copies of all the
  chromosomes.

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How Many Chromosomes Are There?

• Bacteria usually have one circular
• chromosome and no nucleus
• Organisms with nuclei have variable numbers of
  chromosomes
• depending on the species
• Mosquito 6
• Chimpanzees 48
• Goldfish 94

 
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How Many Chromosomes Are There?
Some plants have few chromosomes like
Arabidopsis. Others, like sugarcane, have many.
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Wheat
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Rice
 
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Arabidopsis
Sugarcane
100
20
Maize
Potato
48
Tomato
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Cabbage
20
Carrot
18
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Ploidy vs. chromosome number
Organism Ploidy Chromosome number
Corn Diploid (2X) 20
Tomato Diploid (2X) 24
Arabidopsis Diploid (2X) 10
Potato Tetraploid (4X) 48
Wheat Hexaploid (6X) 42
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How many genes?

• The number of genes varies between organisms.
• Humans 30,000 to 40,000
• Maize 55,000
• Most genes between closely related species are
  conserved.
• Many genes between less closely related species
  are conserved.

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The human genome project

• Complete DNA sequence
• Understand the sequence variation between
  individuals.
• Understand the function of genes.
• Compare the sequences to other related organisms.
• Study the ethical, legal and social implications.

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The human genome project

• http//www.genome.gov/Pages/EducationKit/download.
  html
• Exploring our molecular selves video.
• Ethical legal and social implications video.

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Insight from the human genome draft sequence

• Protein coding region lt2.
• Repetitive DNA minimum of 50.
• Genes are randomly distributed.
• 3X as many proteins as Drosophila or C. elegans
  because of post-transcriptional modifications.

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Insight from the human genome draft sequence II

• Humans, C. elegans, Drosophila, and plants have
  most of the same proteins.
• There are 2X as many germline mutations in males
  vs. females.
• DNA sequence between two individuals is almost
  identical.
• Only 0.1 of sequence is different.

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Where do we go from here?

• Gene Expression
• Proteomics
• Structural genomics
• Mutagenesis
• Comparative genomics

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Medicine and the New Genomics

• Gene Testing
• Gene Therapy
• Pharmacogenomics

Anticipated Benefits

• improved diagnosis of disease
• earlier detection of genetic predispositions to
  disease
• rational drug design
• gene therapy and control systems for drugs
• personalized, custom drugs

Human Genome Program, U.S. Department of Energy,
Genomics and Its Impact on Medicine and Society
A 2001 Primer, 2001
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Ethical Considerations

• Privacy/confidentiality
• Reproductive issues
• Accuracy of genetic testing
• Access to technology
• Genetically modified foods and microbes
• Commercialization/Patents

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Benefits of Genomics

• Improved diagnostic tools.
• Rational drug design.
• Rapid identification of pathogens.
• Better understanding of mutagenesis.
• DNA forensics
• Improved agricultural products

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Plant Genome Projects

• Initiative began in 1998.
• Arabidopsis was the first model plant.
• Small genome size.
• Little repetitive DNA.
• Short life cycle.

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Arabidopsis 2010 Project

• Complete sequence of Arabidopsis in 2000.
• 2010 Project started in 2001.
• Goal was to determine the function of the 25,000
  genes in Arabidopsis by the year 2010 (ie.
  functional genomics of Arabidopsis).

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Tools for genomics

• Sequencing video from human genome project.
• Downloadable from http//www.genome.gov/Pages/Hype
  rion/educationkit/download.html