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BIO403: Biotechnology

Unit 3: Genomics and Gene Expression Technology   This unit looks at how genome projects are performed and how systemic studies approach the complexity of organisms.  In 2003, biologists reached a milestone in biotechnology when sequencing a human genome was completed.  
           
We will look at the types of information contained in the genome map.  Next, we will examine high throughput comparative techniques, namely microarrays and bioinformatics.  Lastly, we will look at the impact of genomics in medicine and evolution.

Unit 3 Time Advisory
This unit should take you approximately 24 hours to complete.

☐    Subunit 3.1: 1.0 hour

☐    Subunit 3.2: 2.5 hours

☐    Subunit 3.3: 2.0 hours

☐    Subunit 3.4: 5.0 hours

☐    Subunit 3.4.1: 1.0 hour

☐    Subunit 3.4.2: 1.0 hour

☐    Subunit 3.4.3: 0.5 hour

☐    Subunit 3.4.4: 0.5 hour

☐    Subunit 3.4.5: 1.0 hour

☐    Subunit 3.4.6: 1.0 hour

☐    Subunit 3.5: 3.0hours

☐    Subunit 3.6: 2.5 hours

☐    Subunit 3.7: 2.0 hours

☐    Subunit 3.8: 2.0 hours

☐    Subunit 3.9: 4.0 hours

☐    Subunit 3.9.1: 1.0 hour

☐    Subunit 3.9.2: 1.0 hour

☐    Subunit 3.9.3: 1.0 hour

☐    Subunit 3.9.4: 1.0 hour

Unit3 Learning Outcomes
Upon successful completion of this unit, the student will be able to:

  • Compare genetic and physical genome maps.
  • Describe the design of genome projects.
  • Compare and contrast systemic studies.
  • Describe the significance of genetic makeup in personalized medical treatment.
  • Discuss the link between gene families and genetic evolution

3.1 Genome Maps   3.1.1 Genetic Maps   - Reading: Nature Education’s Scitable: Ingrid Lobo and Kenna Shaw’s “Thomas Hunt Morgan, Genetic Recombination, and Gene Mapping” Link: Nature Education’s Scitable:  Ingrid Lobo and Kenna Shaw’s “Thomas Hunt Morgan, Genetic Recombination, and Gene Mapping” (HTML)
 
Instructions: Please recall crossing over events during meiosis while you are studying this publication.  Crossing over causes genetic recombination, and it contributes to offspring diversity.  Crossing over events can be utilized to construct genetic linkage maps. Genetic linkage maps place genes at a certain distance on a chromosome.  The placement of the genes is relative to each other; their absolute distance stays unknown.
 
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3.1.2 Physical Maps   - Reading: John W. Kimball’s Biology Pages: “ Genetic Linkage and Genetic Maps” Link: John W. Kimball’s Biology Pages: “Genetic Linkage and Genetic Maps” (HTML)
 
Instructions: Please study the “Genetic versus Physical Maps” section on the page.  Please note that physical maps provide the absolute distance of the genes on the chromosome.  In situ hybridization of genes on a chromosome is a technique that results in a physical map.  The best physical maps derive from genome sequencing projects.
 
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3.2 Genetic Markers for Mapping   3.2.1 RFLPs (Restriction Fragment Length Polymorphisms)   - Reading: National Center for Biotechnology Information’s “Restriction Fragment Length Polymorphism (RFLP)” Link:  National Center for Biotechnology Information’s  “Restriction Fragment Length Polymorphism (RFLP)” (HTML)
 
Instructions: Please study this page.  Restriction fragment length polymorphism has been instrumental in mapping genes and in medical diagnosis.  RFLP was the first DNA technique employed in forensic laboratories for the identification of individuals.
 
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3.2.2 SNPs (Single Nucleotide Polymorphisms)   - Reading: National Center for Biotechnology Information’s “SNPs: Variations on a Theme” Link:  National Center for Biotechnology Information’s “SNPs: Variations on a Theme” (HTML)
 
Instructions: Please study this page.  Single nucleotide polymorphism results from point mutations in a certain position of the DNA sequence.  Point mutations may or may not have biological consequences, depending on whether they change the function of the gene product.  SNPs have been used in medical diagnosis.  A combination of SNPs can be used for identifying individuals and species.  
 
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3.2.3 VNTRs (Variable Number Tandem Repeats)   - Reading: Nature Education’s Scitable: P. Z. Myers’ “Tandem Repeats and Morphological Variation” Link:   Nature Education’s Scitable:  P. Z. Myers’ “Tandem Repeats and Morphological Variation” (HTML)
 
Instructions: Please study this page to learn about how repeat number variations can identify individuals in a population.  Robust change in the number of repeats in certain genetic positions is also linked to phenotypic changes.  Author Dr. Myers works at the University of Minnesota.
 
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3.2.4 Microsatellite Polymorphisms   - Reading: Davidson College’s: Department of Biology’s “Microsatellite DNA Methodology” Link: Davidson College’s: Department of Biology’s  “Microsatellite DNA Methodology” (HTML)
 
Instructions: Please study this page.  Note that microsatellite polymorphism is similar to VNTRs, but the size of the repeats is shorter.  Many applications refer to it as short tandem repeats (STRs).
 
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3.3 Physical Sequence Data   3.3.1 Sequence Tagged Sites (STSs)   - Reading: National Human Genome Research Institute’s “Sequence-Tagged Sites, Another Marker” Link:  National Human Genome Research Institute’s  “Sequence-Tagged Sites, Another Marker” (HTML)
 
Instructions: Please study this page.  Please note that sequence tagged sites are fundamental in recent genome project techniques.  STS sequences have no particular biological significance.  STS is a term used when we refer to a method.
 
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3.3.2 ESTs (Expressed Sequence Tags)   - Reading: National Center for Biotechnology Information’s “ESTs: Gene Discovery Made Easier” Link: National Center for Biotechnology Information’s “ESTs: Gene Discovery Made Easier” (HTML)
 
Instructions: Please study this page. ESTs serve us well in genome projects and gene expression studies.
 
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3.3.3 Contigs   - Reading: JGI Genome Portal’s “What Is a Scaffold?” Link:  JGI Genome Portal’s  “What Is a Scaffold?” (HTML)
 
Instructions: Please study this page.  Please note that a contig is a set of aligned, overlapping, nucleic acid sequences.
 
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3.3.4 Radiation Hybrid Mapping   - Reading: Biology Reference’s: Christine Klein’s “Radiation Hybrid Mapping” Link: Biology Reference’s: Christine Klein’s  “Radiation Hybrid Mapping” (HTML)
 
Instructions: Please study this page.  Please note the similarities to mapping with genetic recombination (BIO403 Subunit 3.1.1 Genetic Maps).  Radiation mapping is used to determine the relative distance between chromosomal markers.
 
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3.3.5 Cytogenetic Mapping   - Reading: Blackwell Publishing Ltd: Animal Genetics: G. P. Di Meo et al.’s “An Advanced Sheep (Ovis aries, 2n = 54) Cytogenetic Map and Assignment of 88 New Autosomal Loci by Fluorescence In Situ Hybridization and R-Banding” Link: Blackwell Publishing Ltd:Animal Genetics:  G. P. Di Meo et al.’s “An Advanced Sheep (Ovis aries, 2n = 54) Cytogenetic Map and Assignment of 88 New Autosomal Loci by Fluorescence In Situ Hybridization and R-Banding” (HTML or PDF)
 
Instructions: Please study the “Introduction” section on this page.  Cytogenetic mapping generates a physical map of genes on a chromosome.  You can access the PDF form from the top right corner of the page.
 
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3.4 Human Genome and Human Genome Project   3.4.1 Chromosome Walking   - Reading: Davidson College’s: Department of Biology’s “Chromosomal Walking to Clone the Cystic Fibrosis Gene” Link: Davidson College’s: Department of Biology’s  “Chromosomal Walking to Clone the Cystic Fibrosis Gene” (HTML)
 
Instructions: Please study this page.  Chromosomal walking can be used to determine the position of a gene in the genome.  It is employed only if the genome of the species is not sequenced.
 
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3.4.2 Shotgun Sequencing   - Reading: Genome News Network: Bijal P. Trivedi’s “Sequencing the Genome” Link:  Genome News Network: Bijal P. Trivedi’s  “Sequencing the Genome” (HTML)
 
Instructions: Please study this page.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.  The shotgun genome sequencing method has been designed by Craig Venter.  This method skips physical mapping.

3.4.3 Heterochromatin Gaps   - Reading: Nature Education’s Scitable: “Chromosomes” Link: Nature Education’s Scitable: “Chromosomes” (HTML)
 
Instructions: Please study the “Why Is Complex Packing Critical for Eukaryotic Chromosomes?” section on this page.  Please note that heterochromatins are tightly packed regions of the genome at the centromer and telomer regions.
 
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  • Reading: National Human Genome Project Institute’s “Drosophila Heterochromatin Genome Project” Link:  National Human Genome Project Institute’s  “Drosophila Heterochromatin Genome Project” (HTML)
     
    Instructions: Please read the “Background” section on this page.
     
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3.4.4 Relative Components of Human Genome   - Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “About the Human Genome Project” Link:  U.S. Department of Energy, Office of Science’s Human Genome Project Information:  “About the Human Genome Project” (HTML)
 
Instructions: Please study this page.
 
Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.  Human genome sequencing has been greatly speeded up by the shotgun sequencing method.  The sequencing of genomic regions that are rich in repetitive sequences, such as telomeres and centromeres, are still in progress.

3.4.5 Estimated Gene Content   - Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “How Many Genes are in the Human Genome?” Link:  U.S. Department of Energy, Office of Science’s Human Genome Project Information:  “How Many Genes are in the Human Genome?” (HTML)
 
Instructions: Please study this page.  Please note that we have only estimations on the number of genes in the human genome.  These predictions are aided by bioinformatics but should be verified in the future by experiments.
 
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3.4.6 Pseudogenes   - Reading: Yale University’s Gerstein Lab: “Pseudogene.org: Genome Analysis” Link:  Yale University’s Gerstein Lab: “Pseudogene.org Genome Analysis” (HTML)
 
Instructions: Please study this page.  Follow the link in "What causes pseudogenes to arise?" box for a graphical illustration.  Please note that pseudogenes do not have a known biological function.
 
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3.4.7 Noncoding DNA Types, Including Junk DNA   - Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Lodish, et al.’s Molecular Cell Biology, 4th edition: “Chromosomal Organization of Genes and Noncoding DNA” Link:  National Center for Biotechnology Information’s Bookshelf:  W.H. Freeman: Lodish, et al.’s Molecular Cell Biology, 4th edition:  Chromosomal Organization of Genes and Noncoding DNA” (HTML)
 
Instructions: Please study the “Genomes of Higher Eukaryotes Contain Much Nonfunctional DNA” section on this page.  Please note that some DNA regions are genes coding proteins or functional RNA products, while other regions are noncoding.  Some of the noncoding regions, for example, repeat sequences and pseudogenes and have no known function.  These seemingly useless regions are referred as “junk DNA.”
 
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3.5 DNA Microarrays   3.5.1 Monitoring Gene Expression   - Reading: National Human Genome Research Institute’s “DNA Microarray Technology” Link:  National Human Genome Research Institute’s  “DNA Microarray Technology” (HTML)
 
Instructions: Please study this page.  Please note that microarray is an efficient and widely used high throughput technology of differential gene expression studies.
 
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  • Lecture: YouTube: Proneural’s “DNA Chips and Microarrays” Link: YouTube: Proneural’s “DNA Chips and Microarrays” (YouTube)
     
    Instructions: Please watch the brief, 2-minute video.
     
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3.5.2 Comparative Studies   - Reading: Nature Education’s Scitable: “Scientists Can Study an Organism’s Entire Genome with Microarray Analysis” Link: Nature Education’s Scitable:  “Scientists Can Study an Organism’s Entire Genome with Microarray Analysis” (HTML)
 
Instructions: Please study this page and watch the video.
 
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  • Web Media: Davidson College: Department of Biology’s “DNA Microarray Methodology” Link: Davidson College: Department of Biology’s “DNA Microarray Methodology” (Adobe Flash)
     
    Instructions: Please watch the animation.
     
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3.5.3 ChIP-Chip (Chromatin Immunoprecipitation)   - Reading: Brandeis University’s: Jim Haber’s “Chromatin Immunoprecipitation” Link: Brandeis University’s: Jim Haber’s  “Chromatin Immunoprecipitation” (HTML)
 
Instructions: Please study this page, and follow the “protocol” link on the bottom of the page.  Chromatin immunoprecipitation is used to identify interacting proteins and DNA segments.
 
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3.6 Bioinformatics and Genomics   3.6.1 Data Mining   - Reading: Bio Databases: Houle, et al.’s “Database Mining in the Human Genome Initiative” Link: Bio Databases: Houle, et al.’s “Database Mining in the Human Genome Initiative” (HTML)
 
Instructions: Please learn the content of the white paper, from the “Abstract” to the “Conclusion.”
 
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3.6.2 Comparative Genomics   - Reading: PLoS Biology: Ross C. Hardison’s “Comparative Genomics” Link:  PLoSBiology:  Ross C. Hardison's  “Comparative Genomics” (HTML or PDF)
 
Instructions: Please study this publication. You can access the PDF format from the top right corner of the page.  Genome sequence comparisons can be used to predict gene function between species and between the individuals of a species.  It is also used to determine phylogenetic distances among species.
 
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  • Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “Functional and Comparative Genomics Fact Sheet” Link:  U.S. Department of Energy, Office of Science’s Human Genome Project Information:  “Functional and Comparative Genomics Fact Sheet” (HTML)
     
    Instructions: Please study this page.
     
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3.7 Medicine and Genomics   3.7.1 Gene Testing   - Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “Gene Testing” Link:  U.S. Department of Energy, Office of Science’s Human Genome Project Information:  “Gene Testing” (HTML)
 
Instructions: Please study this page.  Gene testing is performed primarily in medical diagnosis. It is also a mostly historical forensic technique for the identification of individuals.
 
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  • Reading: National Health Museum’s “Understanding Gene Testing—What Does a Predictive Gene Test Tell You?” Link:  National Health Museum’s  “Understanding Gene Testing—What Does a Predictive Gene Test Tell You?” (HTML)
     
    Instructions: Please study this page.  Please note that gene testing can link the presence of a gene to the probability of developing a condition (disease) in an individual or in the offspring of an individual.  
     
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  • Reading: Nature Education’s Scitable: Leslie A. Pray’s “Questionable Prognostic Value of Genetic Testing” Link:  Nature Education’s Scitable:  Leslie A. Pray’s “Questionable Prognostic Value of Genetic Testing” (HTML)
     
    Instructions: Please study this page.  There is an increasing interest on the environmental factors on trait penetrance.  Research should unravel how to take advantage of a genetic prognosis.  Environmental factors such as nutrition and personal habits, seem to influence gene expression and the penetrance of traits.  Medications can also be developed to decrease the risk of undesired traits (disease).
     
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3.7.2 Pharmacogenetics and Pharmacogenomics   - Reading: The Royal Society’s “What Is Pharmacogenetics?” Link: The Royal Society’s “What Is Pharmacogenetics?” (HTML)
 
Instructions: Please study this page.  Please note that individual genetic makeup will influence the response to a medication.
 
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  • Reading: Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “Pharmacogenomics” Link:  U.S. Department of Energy, Office of Science’s Human Genome Project Information:  “Pharmacogenomics” (HTML)
     
    Instructions: Please study this page.  Pharmacogenomics is a way drugs can be designed in the future.  It requires knowing individuals' genetic makeup besides the risk factors what doctors use today.  It holds the promise of safer and more efficient medication.
     
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3.8 Genetic Evolution   3.8.1 Molecular Phylogenetics   - Reading: National Center for Biotechnology Information’s “Systematics and Molecular Phylogenetics” Link:  National Center for Biotechnology Information’s  “Systematics and Molecular Phylogenetics” (HTML)
 
Instructions: Please study this page.  Molecular phylogenetics establishes relationship between species based on their genetic material.  Before the availability of molecular techniques, species were classified based on their phenotype and behavior.
 
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3.8.2 Gene Superfamilies   - Reading: Sandwalk: Larry A. Moran’s “The Evolution of Gene Families” Link:  Sandwalk:  Larry A. Moran’s “The Evolution of Gene Families” (HTML)
 
Instructions: Please study this page by Dr. Moran, Professor of Biochemistry at the University of Toronto.
 
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3.9 Other Systemic Studies   3.9.1 Transcriptome   - Reading: Nature Education’s Scitable: “Systems Biology Allows Us to Think Broadly” Link:  Nature Education’s Scitable: “Systems Biology Allows Us to Think Broadly” (HTML)
 
Instructions: Please study the diagram.  You may want to return to this diagram, as you are completing the remaining subunits in Unit 3.
 
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  • Reading: Nature Education’s Scitable: Jill U. Adams’ “Transcriptome: Connecting the Genome to Gene Function” Link:  Nature Education’s Scitable: Jill U. Adams’  “Transcriptome: Connecting the Genome to Gene Function” (HTML)
     
    Instructions: Please study this page by freelancer science writer Dr. Adams in its entirety. Please recall that the genetic material is identical in all somatic cells of a multicellular organism, but a different set of genes is expressed in different cells. The transcriptome is the collection of the expressed genes, and it is different in different cell types. 
     
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3.9.2 Proteome   - Reading: Nature Education’s Scitable: Jill Adams’ “The Proteome: Discovering the Structure and Function of Proteins” Link: Nature Education’s Scitable: Jill Adams’ “The Proteome: Discovering the Structure and Function of Proteins” (HTML)
 
Instructions: Please study this page by freelancer science writer Dr. Adams in its entirety. The proteome is the collection of proteins that are expressed.  Please note that the proteomes of different cell types are different.  Both proteome and transcriptome reflect gene activity.   
 
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3.9.3 Metabolome   - Reading: BioTechnique: Ute Roessner and Jairus Bowne’s “What Is Metabolomics All About?” Link: BioTechnique: Ute Roessner and Jairus Bowne’s “What Is Metabolomics All About?” (HTML or PDF)
 
Instructions: Please study all three pages of this publication.  You can switch to the next page by clicking a number on the bottom of the page.  To access the PDF format, click the Full Text (PDF) button on the linked page.
 
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  • Reading: Genome Alberta and Genome Canada’s “The Human Metabolome Project” Link: Genome Alberta and Genome Canada’s  “The Human Metabolome Project” (HTML)
     
    Instructions: Please study this page.  Please note that the metabolome consists of a variety of unrelated small molecular mass substances.  We usually know that these substances are present if they are above the detection limit of an employed analytical technique.
     
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3.9.4 Metagenome   - Reading: Nature Education’s Scitable: Lorenz and Eck’s “Metagenomics and Industrial Applications” Link: Nature Education’s Scitable:  Lorenz and Eck’s “Metagenomics and Industrial Applications” (PDF)
 
Instructions: Please study this publication carefully.  Metagenome is the genetic information, which is extracted from an environmental microbial population.  It contains genetic material from multiple living organisms.  
 
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  • Reading: Nature Education’s Scitable: Kira Zhaurova’s “Genomes of Other Organisms: DNA Barcoding and Metagenomics” Link: Nature Education’s Scitable: Kira Zhaurova’s “Genomes of Other Organisms: DNA Barcoding and Metagenomics” (HTML)
     
    Instructions: Please study this page.  Please compare the nature of full genome sequences and metagenomic data.
     
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