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Genomics. MUPGRET Weekend Workshop. Timeline Answers. Another timeline at . Reviewing the basics. Cells are the basic working unit of an organism.
GenomicsMUPGRET Weekend WorkshopTimeline Answers
  • Another timeline at .
  • 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
  • Chromosomes are visible with high powered microscopes.
  • Chromosomes are Dynamic StructuresFruit FlyHuman ChromosomesMetaphase ChromosomeCONDENSED EXTENDEDMore 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
  • Non-genic DNA is called heterochromatin.
  • Heterochromatin and euchromatin stain differently.
  • This difference causes the bands we see in a karyotype.
  • Human karyotypeGenome 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
  • 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.
  • PCR
  • Polymerase Chain Reaction
  • A way to “xerox” a DNA fragment.
  • Electrophoresis
  • A way to separate DNA molecules.
  • 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
  • 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
  • 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
  • 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 Genome
  • Other plants like corn include:
  • Arabidopsis
  • Barley
  • Beans
  • Tomato
  • Pepper
  • Rice
  • 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
  • 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?
  • 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 There?Some plants have few chromosomes like Arabidopsis.Others, like sugarcane, have many.42Wheat24Rice10ArabidopsisSugarcane+10020MaizePotato48Tomato24Cabbage20Carrot18Ploidy vs. chromosome numberHow 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
  • 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 project
  • Exploring our molecular selves video.
  • Ethical legal and social implications video.
  • 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
  • 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?
  • Gene Expression
  • Proteomics
  • Structural genomics
  • Mutagenesis
  • Comparative 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, 2001Ethical Considerations
  • Privacy/confidentiality
  • Reproductive issues
  • Accuracy of genetic testing
  • Access to technology
  • Genetically modified foods and microbes
  • Commercialization/Patents
  • 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
  • Initiative began in 1998.
  • Arabidopsis was the first model plant.
  • Small genome size.
  • Little repetitive DNA.
  • Short life cycle.
  • 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
  • Sequencing video from human genome project.
  • Downloadable from
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