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Genomics. MUPGRET Weekend Workshop. Timeline Answers. http://www.jgi.doe.gov/education/timeline_2.html Another timeline at http://www.dnai.org/index.htm . Reviewing the basics. Cells are the basic working unit of an organism.

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genomics

Genomics

MUPGRET Weekend Workshop

timeline answers
Timeline Answers
  • http://www.jgi.doe.gov/education/timeline_2.html
  • Another timeline at http://www.dnai.org/index.htm .
reviewing the basics
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.
more reviewing
More reviewing
  • Chromosomes are visible with high powered microscopes.
chromosomes are dynamic structures
Chromosomes are Dynamic Structures

Fruit Fly

Human Chromosomes

Metaphase Chromosome

CONDENSED EXTENDED

more review
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, <5% generally.
  • DNA containing genes is called euchromatin.
heterochromatin
Heterochromatin
  • Non-genic DNA is called heterochromatin.
  • Heterochromatin and euchromatin stain differently.
  • This difference causes the bands we see in a karyotype.
genome composition
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
dna content
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
    • Mb=Mega base pairs
a nova look into dna
A NOVA look into DNA.
  • http://www.pbs.org/wgbh/nova/photo51/jour-nf.html
slide12
PCR
  • Polymerase Chain Reaction
  • A way to “xerox” a DNA fragment.
electrophoresis
Electrophoresis
  • A way to separate DNA molecules.
  • http://gslc.genetics.utah.edu/units/biotech/gel/
what is genomics
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.
the genome
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
the genome ii
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
plant genome
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.
plant genome18
Plant Genome
  • Other plants like corn include:
    • Arabidopsis
    • Barley
    • Beans
    • Tomato
    • Pepper
    • Rice
multicopy plant genomes
Multicopy Plant Genomes
  • Some plants normally have more than two copies of the genome in their cells.
    • Wheat – six copies
    • Potato – four copies
    • Sugarcane – >twelve copies
    • Strawberry – >eight copies
    • Banana – three copies
    • Watermelon – three copies
chromosome number
Chromosome number
  • The term haploid refers to the base number of chromosomes in an organism.
  • Diploid cells have two copies of all the chromosomes.
how many chromosomes are there
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
how many chromosomes are there22
How Many Chromosomes Are There?

Some plants have few chromosomes like Arabidopsis.

Others, like sugarcane, have many.

42

Wheat

24

Rice

10

Arabidopsis

Sugarcane

+100

20

Maize

Potato

48

Tomato

24

Cabbage

20

Carrot

18

how many genes
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.
the human genome project
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.
the human genome project26
The human genome project
  • http://www.genome.gov/Pages/EducationKit/download.html
  • Exploring our molecular selves video.
  • Ethical legal and social implications video.
insight from the human genome draft sequence
Insight from the human genome draft sequence
  • Protein coding region <2%.
  • Repetitive DNA minimum of 50%.
  • Genes are randomly distributed.
  • 3X as many proteins as Drosophila or C. elegans because of post-transcriptional modifications.
insight from the human genome draft sequence ii
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.
where do we go from here
Where do we go from here?
  • Gene Expression
  • Proteomics
  • Structural genomics
  • Mutagenesis
  • Comparative genomics
medicine and the new genomics
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

ethical considerations
Ethical Considerations
  • Privacy/confidentiality
  • Reproductive issues
  • Accuracy of genetic testing
  • Access to technology
  • Genetically modified foods and microbes
  • Commercialization/Patents
benefits of genomics
Benefits of Genomics
  • Improved diagnostic tools.
  • Rational drug design.
  • Rapid identification of pathogens.
  • Better understanding of mutagenesis.
  • DNA forensics
  • Improved agricultural products
plant genome projects
Plant Genome Projects
  • Initiative began in 1998.
  • Arabidopsis was the first model plant.
    • Small genome size.
    • Little repetitive DNA.
    • Short life cycle.
arabidopsis 2010 project
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).
tools for genomics
Tools for genomics
  • Sequencing video from human genome project.
  • Downloadable from http://www.genome.gov/Pages/Hyperion/educationkit/download.html
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