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Biotechnology

Purpose of Course  showclose

Course Information  showclose

Learning Outcomes  showclose

Course Requirements  showclose

• Unit 1
• Unit 2
• Unit 3
• Unit 4
• Unit 5
• Unit 6
• Unit 7
• Unit 8
• Unit 9
• Unit 10
• Final Exam
• All Units

Unit Outline show close

Unit 1: Introduction to Biotechnology  

In this unit, you will analyze DNA structure, practice Mendelian genetics problems, and familiarize yourself with gene expression studies and with biological systems in biotechnology.

Unit 1 Time Advisory   show close


Unit 1 Learning Outcomes   show close


1.1 DNA Structure  

• Reading: PBS: Lexi Krock's “Anatomy of Photo 51”

  Link: PBS: Lexi Krock's “Anatomy of Photo 51” (HTML)
   
  Instructions: Please investigate the critical evidence that led to the model of the DNA double helix.  Rosalind Franklin’s X-ray diffraction image #51 is shown here.  Click on the “Launch interactive” button and advance step by step from image #51 to the double helix model of DNA.  Please note that all structural parameters of the double helix are provided by image #51.
   
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1.2 Mendelian Inheritance  

• Web Media: Khanacademy’s “Introduction to Heredity”

  Link: Khanacademy’s “Introduction to Heredity” (Adobe Flash)
   
  Also available in:
  YouTube
   
  Instructions: Please watch the video (18 minutes) for a step-by-step tutorial on using Punnett squares to determine how alleles of one gene segregate.
   
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• Web Media: Khanacademy’s “Punnett Square Fun”

  Link: Khanacademy’s “Punnett Square Fun” (Adobe Flash)
   
  Also available in:
  YouTube
   
  Instructions: Please watch the video (26 minutes) for a step-by-step tutorial on using Punnett squares to determine how alleles of more than one gene assort independently.  During sexual reproduction, both parents pass on some of their traits to their offspring(s).  Mendel's law of segregation describes how different versions of one trait are combined in the offspring.  Mendel's law of independent assortment describes how different versions of different traits are combined in the offspring.  Please make sure that you can predict the genotype and phenotype of the F1 generation using Punnett squares.  You may need to follow this video several times.  Be patient; it may take some time to get used to the Punnett squares.  This is a great tool, used every day in genetic counseling.
   
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• Assessment: The Saylor Foundation: "BIO403 Unit 1.2 Assessments"

  Link: The Saylor Foundation: "BIO403 Unit 1.2 Assessments" (HTML)
   
  Instructions: You will find links to the following three assessments on this page: “Mendelian Inheritance of Traits,” “Codominance – an Extension of the Mendelian Inheritance of Traits,” and “Independent Assortment – Dihybrid Cross.” These are multiple choice assessments with one correct answer. Clicking on an answer will bring you to another page. If your answer is correct, then it is acknowledged with a short explanation. Please read the explanation carefully and proceed to the next assessment as prompted at the bottom of the page. If you clicked on the wrong answer, then the click will bring you to a tutorial page. Please study the tutorial page carefully. At the end of the tutorial page, you will be prompted to return to the assessment and complete it again. You can also move between multiple choice pages using the links at the top of the page. Please complete the three assessments in order, because the assessments are listed in increasing complexity.   
   
  

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1.3 Biotechnology Fields  

• Reading: Access Excellence: Pamela Peters' “What Is Biotechnology?”

  Link: Access Excellence: Pamela Peters' “What Is Biotechnology?” (HTML)
   
  Instructions: Please read this page carefully.  When you finish it, please continue your reading: Open the “Where Did Biotechnology Begin?” link at the bottom of the page. Please note that making bread, cheese, beer, or wine are all historical biotechnology applications.
   
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• Reading: BioBasics’ “Full Article: Traditional vs. Modern Biotechnology”

  Link: BioBasics’ “Full Article: Traditional vs. Modern Biotechnology” (HTML)
   
  Instructions: Please read this page, focusing on the differences between traditional and modern biotechnology application.  Please note that modern biotechnology is able to genetically engineer living organisms, and it often does so.
   
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Unit 2: Advanced Nucleic Acid Technologies  

This unit will discuss advanced nucleic acid technologies.  For example, methods to visualize DNA and cloning vectors are used in everything from creating gene therapies for disease to cleaning toxic oil spills.  While DNA techniques have been established much longer than RNA methods, RNA methods are exciting new and upcoming fields, especially in ribozymes and RNA interference.  Both have far-reaching implications in biotechnology that could lead to cures for disease and entire new biomedical industries.

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2.1 Fluorescence in Situ Hybridization (FISH)  

• Reading: Nature Education's Scitable: Clare O’Connor’s “Fluorescence In Situ Hybridization”

  Link: Nature Education's Scitable: Clare O’Connor’s “Fluorescence In Situ Hybridization” (HTML) 
   
  Instructions: Please study the “In Situ Hybridization Is Used to Localize DNA Sequences on Chromosomes,” “Fluorescent Probes Are Introduced,” and “Using FISH to Identify the Positions of Genes” sections on this page.  Author Clare O’Connor works in the Department of Biology at Boston College.
   
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2.2 Nucleic Acid Amplification  

2.2.1 Modifications of PCR  

• Reading: Dr. Kary Banks Mullis’s “Polymerase Chain Reaction”

  Link: Dr. Kary Banks Mullis’s “Polymerase Chain Reaction” (HTML)
   
  Instructions: Please read about Dr. Kary Bank Mullis.  It is rare that technological inventions receive a Nobel Prize, but Mullis was awarded the Nobel Prize in Chemistry in 1993 for his invention of the polymerase chain reaction (PCR) method.  Please study the main column and click on the “Questions About PCR” (PDF) link on the right and study that section as well.
   
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• Reading: University of South Carolina's School of Medicine: Margaret Hunt’s “Real Time PCR”

  Link: University of South Carolina's School of Medicine: Margaret Hunt’s “Real Time PCR” (HTML)
   
  Instructions: Please study this page carefully.  You can learn about an advanced PCR application, which is essential in tissue specific gene expression applications.  Please note that the first step is to reverse translate RNA to DNA, because we can amplify only DNA in the test tube.  Because of the reverse transcriptase step, this method is also called RT-PCR.  Here, it gets little confusing since the method is in real time as well, because it follows the PCR product production in real time.  The best way to keep all of these aspects in mind is to remember this method as “real time RT-PCR.”  Please make sure that you click on the thumbprints to enlarge all the images embedded in the left maroon-colored panel of this site.  
  
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2.2.2 Subtractive Hybridization  

• Reading: Evrogen’s “Suppression Subtractive Hybridization (SSH)”

  Link: Evrogen’s “Suppression Subtractive Hybridization (SSH)” (HTML)
   
  Instructions: Please learn the content of this page.  Please note that subtractive hybridization is a technique that compares the differences between two nucleic acid pools and exponentially amplifies the differences in these pools by PCR.  The nucleic acid pools are commonly mRNA pools, thus such experiments generate subtraction cDNA libraries.
   
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• Assessment: The Saylor Foundation: "BIO403 Unit 2.2 Assessments"

  Link: The Saylor Foundation: "BIO403 Unit 2.2 Assessments"
   
  Instructions: You will find links to the following four assessments on this page: "PCR," "RT-PCR," "Subtractive Hybridization," and "Differential Screening."  These are multiple choice assessments with one correct answer.  Clicking on an answer will bring you to another page.  If your answer is correct, then it is acknowledged with a short explanation.  Please read the explanation carefully and proceed to the next assessment as prompted at the bottom of the page.  If you clicked on the wrong answer, then the click will bring you to a tutorial page.  Please study the tutorial page carefully.  At the end of the tutorial page, you will be prompted to return to the assessment and complete it again. You can also move between multiple choice pages using the links at the top of the page. Please complete the four assessments in order as the assessments are listed in increasing complexity.

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2.3 Chemical Synthesis of Genes  

• Reading: Wiley Online Library: Markus Fuhrmann, et al.’s “A Synthetic Gene Coding For the Green Fluorescent Protein (GFP) Is a Versatile Reporter in Chlamydomonas reinhardtii”

  Link: Wiley Online Library: Markus Fuhrmann, et al.’s “A Synthetic Gene Coding For the Green Fluorescent Protein (GFP) Is a Versatile Reporter in Chlamydomonas reinhardtii” (HTML or PDF)
   
  Instructions:  You may read this as HTML or a PDF.  To access the PDF, go to “Article Tools” on the right side of the page and click on “Get PDF.”  This is a peer-reviewed publication.  Please study the last paragraph of the “Introduction,” the entire “Synthesis of a C. Reinhardtii-Adapted GFP” in the “Results” section, and the entire “Discussion” section on this page.  The aim of this project is to exchange the codons in the jellyfish GFP gene to codons that are more frequent in a unicellular alga.  Please note that the codon preference varies in different organisms. 
   
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• Assessment: The Saylor Foundation: "BIO403 Unit 2.3 Assessments"

  Link: The Saylor Foundation: "BIO403 Unit 2.3 Assessments"
  
  Instructions: You will find the following "Codon Preference" assessment here. This is a multiple choice assessment with one correct answer.  Clicking on an answer will bring you to another page.  If your answer is correct, then it is acknowledged with a short explanation.  Please read the explanation carefully.  If you clicked on a wrong answer, then the click will bring you to a tutorial page.  Please study the tutorial page carefully.  On the tutorial page, you will be prompted to return to the assessment and complete it again. You can also move back to the assessment main page using the link at the top of the page.

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2.4 RNA Methods  

2.4.1 Regulatory RNAs  

• Reading: Nature Education’s Scitable: Suzanne Clancy’s “RNA Functions”

  Link:  Nature Education’s Scitable:  Suzanne Clancy’s “RNA Functions” (HTML)
   
  Instructions: Please study this summary on the regulatory RNAs.  Here you will learn that besides the familiar mRNA, tRNA, and rRNA, other RNA functions are abundant in the cell.  The following sections will introduce you to several RNA techniques that are designed to modulate gene expression in the cell.
   
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2.4.2 RNAi (RNA Interference)  

• Reading: Macalester College: Mary Montgomery’s “RNAi”

  Link: Macalester College: Mary Montgomery’s “RNAi” (HTML)
   
  Instructions: Please study this page.  Please note that RNA interference is an experimental technique.
   
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2.4.3 Natural Ribozymes  

• Reading: John W. Kimball’s Biology Pages: “Ribozymes”

  Link: John W. Kimball’s Biology Pages:  “Ribozymes” (HTML)
   
  Instructions: Please study this page.
   
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2.4.4 Synthetic Ribozymes  

• Reading: National Center for Biotechnology Information’s PubMed: American Society for Clinical Investigation: Nassim Usman and Lawrence M. Blatt’s “Nuclease-Resistant Synthetic Ribozymes: Developing a New Class of Therapeutics”

  Link: National Center for Biotechnology Information’s PubMed:American Society for Clinical Investigation:  Nassim Usman and Lawrence M. Blatt’s “Nuclease-Resistant Synthetic Ribozymes: Developing a New Class of Therapeutics” (HTML or PDF)
   
  Instructions: Please study this publication on making synthesized ribozymes. This material is also available in PDF form from the top right corner of the page.
   
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2.4.5 Riboswitches  

• Reading: National Center for Biotechnology Information’s PubMed: Journal ACS Chemical Biology: Shana Topp and Justin P. Gallivan’s “Emerging Applications of Riboswitches in Chemical Biology”

  Link:  National Center for Biotechnology Information’s PubMed: Journal ACS Chemical Biology:  Shana Topp and Justin P. Gallivan’s “Emerging Applications of Riboswitches in Chemical Biology” (HTML or PDF)
   
  Instructions: Please study this page carefully.  This publication is challenging, but it helps you appreciate the regulatory roles of RNA in the cell.  Please rely heavily on the illustrations. It is not essential to memorize the names of the metabolites.  This material can also be viewed in PDF form from the top right corner of the page.  The authors work at Emory University.  This is a peer-reviewed publication.
   
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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   show close


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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.

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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.

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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, 4^th 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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Unit 4: Protein Engineering and Proteomics  

A proteome is the collection of all proteins expressed by a genome, and proteomics analyzes the proteome.  Proteins serve almost every purpose imaginable, from catalyzing reactions to providing structural support.  Research into proteomics can be more complex than genomics, as they are inherently much more versatile biomolecules.  
           
This unit will summarize the current state of proteomics and protein engineering.  We will first look at how a protein is currently studied, such as isolating and characterizing a protein.  We will then look at engineering novel proteins based on current techniques and knowledge.

Unit 4 Time Advisory   show close


Unit 4 Learning Outcomes   show close


4.1 Protein Visualization and Identification  

4.1.1 SDS-PAGE (Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis)  

• Reading: Davidson College: Department of Biology’s “SDS-PAGE (PolyAcrylamide Gel Electrophoresis)”

  Links: Davidson College: Department of Biology’s  “SDS-PAGE (PolyAcrylamide Gel Electrophoresis)” (HTML)
   
  Instructions: Please study this page.  Please note that electrophoresis can be used to separate substances, which have electrical charge.  In the SDS-PAGE technique, proteins are associated with SDS, thus they become negatively charged.  Furthermore, the smaller SDS-associated proteins will travel faster in the electric field than the larger ones.   
   
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4.1.2 Western Blot  

• Reading: Davidson College: Department of Biology’s “Western Blot Procedure”

  Links: Davidson College: Department of Biology’s “Western Blot Procedure” (HTML)
   
  Instructions: Please study the outline of the Western blot analysis.  This procedure is also called immunoblot technique, because it is utilizing antibodies to detect specific proteins in a mixture.  In reality, antibodies are not absolutely specific, thus this method may produce a false positive or negative signal.
   
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• Lecture: Journal of Visualized Experiments: Gallagher and Chakavarti’ s “Immunoblot Analysis”

  Link: Journal of Visualized Experiments:  Gallagher and Chakavarti’ s “Immunoblot Analysis” (Adobe Flash)
   
  Instructions: Please watch the video (16 minutes) for a step-by-step tutorial on the immunoblot technique.
   
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• Assessment: The University of Arizona: The Biology Project’s “Introduction to Western Blot Activity”

  Link: The University of Arizona:  The Biology Project’s “Introduction to Western Blot Activity” (HTML)
   
  Instructions:  In order to assess your knowledge, follow the instructions and complete the four problems at the end of this activity.  Answer key is provided.  You can progress page by page by clicking on the “Next” bottom toward the bottom of the page.
   
  Note: One animation requires a QuickTime plugin.
   
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4.2 Protein Isolation and Purification  

4.2.1 HPLC (High-Performance Liquid Chromatography)  

• Reading: Jim Clark’s ChemGuide: “High-Performance Liquid Chromatography—HPLC”

  Link: Jim Clark’s ChemGuide: “High-Performance Liquid Chromatography—HPLC” (HTML)
   
  Instructions: Please study this page.  Please note that HPLC is used to purify peptides; it is not a typical protein purification method.
   
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4.2.2 Affinity Chromatography  

• Reading: John W. Kimball's Biology Pages: “Affinity Chromatography”

  Link: John W. Kimball's Biology Pages:  “Affinity Chromatography” (HTML)
   
  Instructions: Please study this page.  Please note that affinity chromatography is a very efficient purification technique as long as the immobilized molecule binds strongly and specifically to the protein of interest.  Antibody-antigen interaction is an example of strong and specific binding.
   
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• Reading: Davidson College: Department of Biology’s “Affinity Chromatography Method”

  Link: Davidson College: Department of Biology’s “Affinity Chromatography Method” (HTML)
   
  Instructions: Please study the outline of the Affinity Chromatography Method.
   
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4.2.3 Ion Exchange Chromatography  

• Reading: Florida State University: Michael Blaber’s “Protein Purification: Column Chromatography—Ion Exchange; Dialysis and Concentration”

  Link: Florida State University:  Michael Blaber’s “Protein Purification: Column Chromatography—Ion Exchange; Dialysis and Concentration” (HTML)
   
  Instructions: Please study this page.  Please note that proteins are typically purified from a biological sample.  Ion exchange chromatography is a low efficiency, but inexpensive purification technique.  It is oftentimes employed to remove substances from a complex mixture, which would otherwise interfere with the following specific purification step.
   
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4.3 Protein Sequencing  

4.3.1 Edman Degradation  

• Reading: Wikibooks’ “Protein Primary Structure”

  Link: Wikibooks’ “Protein Primary Structure” (PDF)
   
  Instructions: Please learn the “Edman Degradation” section on this page.
   
  Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0 (HTML).  You can find the original Wikibooks version of this article here (HTML).

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• Lecture: YouTube: Lamechivanes’ “Sequence Determination One Terminal Unit at a Time”

  Link: Video Lecture: YouTube: Lamechivanes’ “Sequence Determination One Terminal Unit at a Time” (YouTube)
   
  Instructions: Please watch the video (3 minutes) for a step-by-step tutorial on Edman degradation.
   
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4.3.2 Mass Spectrometry  

• Reading: The University of Leeds: Alison Ashcroft’s “An Introduction to Mass Spectrometry”

  Link: The University of Leeds:  Alison Ashcroft’s “An Introduction to Mass Spectrometry” (HTML)
   
  Instructions: Please study sections “1. What Is Mass Spectrometry (MS)? What Information Does Mass Spectrometry Provide?” and the content of subsections “4.1 Introduction,” “8.1 Tandem Mass Spectrometry,” “8.2 Tandem Mass Spectrometry Analyses,” and “8.3 Peptide Sequencing by Tandem Mass Spectrometry “ on this page.
   
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• Assessment: The Saylor Foundation: "BIO403 Unit 4.3 Assessment"

  Link: The Saylor Foundation: "BIO403 Unit 4.3 Assessment" (HTML)
   
  Instructions: You will find link to the "Mass Spectrometry" assessment on this page. This is a multiple choice assessment with one correct answer. Clicking on an answer will bring you to another page. If your answer is correct, then it is acknowledged with a short explanation. Please read the explanation carefully. If you clicked on the wrong answer, then the click will bring you to a tutorial page. Please study the tutorial page carefully. You will be prompted to return to the assessment and complete it again. Please note that mass spectrometry is a widely accepted confirmatory technique for the identification of organic molecules.

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4.4 Protein Interaction Methods  

4.4.1 Yeast Two-Hybrid System  

• Reading: John W. Kimball’s Biology Pages: “Proteomics”

  Link: John W. Kimball’s Biology Pages:  “Proteomics” (HTML)
   
  Instructions: Please study “The Yeast Two-Hybrid System” section on this page.
   
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4.4.2 Co-Immunoprecipitation  

• Reading: National Center for Biotechnology Information’s Bookshelf: Garland Science: Alberts, et al.’s Molecular Biology of the Cell, 4th edition: “Analyzing Protein Structure and Function”

  Link:  National Center for Biotechnology Information’s Bookshelf: Garland Science: Alberts, et al.’s Molecular Biology of the Cell, 4^th edition:  “Analyzing Protein Structure and Function” (HTML)
   
  Instructions: Please study "Affinity Chromatography and Immunoprecipitation Allow Identification of Associated Proteins" section on this page.
   
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4.4.3 Protein Arrays  

• Reading: Functional Genomics: Mike Taussig and Oda Stoevesandt’s “Protein Arrays Resource Page”

  Link: Functional Genomics:  Mike Taussig and Oda Stoevesandt’s “Protein Arrays Resource Page” (HTML)
   
  Instructions: Please study this page.  Please note that there are different types of protein arrays.  Protein arrays represent a more recent development of high throughput screening compared to DNA microarrays. 
   
   
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4.5 Recombinant Proteins  

4.5.1 Expression by Bacteria  

• Reading: European Molecular Biology Laboratory’s “Protein Expression and Purification Core Facility: Protein Expression E. coli”

  Link: European Molecular Biology Laboratory’s "Protein Expression and Purification Core Facility: Protein Expression E. coli” (HTML)
   
  Instructions: Please study this page.  Please note that E. coli can be employed to express a functional protein only if the biological function of the protein does not require posttranslational modification.
   
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4.5.2 Expression by Yeast  

• Reading: John W. Kimball’s Biology Pages: “Gene Regulation in Eukaryotes”

  Link: John W. Kimball’s Biology Pages: “Gene Regulation in Eukaryotes” (HTML)
   
  Instruction: Please study this page.  Focus on the differences between eukaryotic and prokaryotic genes expression, including posttranslational modifications.
   
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• Reading: BioPharm International: Rudolph et al.’s “Expression of Recombinant Proteins in Yeast”

  Links: BioPharm International: Rudolph et al.’s “Expression of Recombinant Proteins in Yeast” (HTML)
   
  Instructions: Please study this page.  Please note that Pichia pastoris and other yeast hosts have the capability to modify recombinant proteins posttranslationally.  Posttranslational modification is an essential feature of biologically active proteins.
   
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4.5.3 Expression by Mammalian Cells  

• Reading: BioMed Central: BMC Biotechnology: Nehlsen et al.’s “Recombinant Protein Expression by Targeting Pre-Selected Chromosomal Loci”

  Link: BioMed Central: BMC Biotechnology:  Nehlsen et al.’s “Recombinant Protein Expression by Targeting Pre-Selected Chromosomal Loci”  (HTML or PDF)
   
  Instructions: Please read the “Background” section found under “Abstract” on this page.  You can access the PDF version from the righthand side of the page, under "viewing options."  This is a peer-reviewed publication.
   
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4.5.4 Protein Glycosylation  

• Reading: National Center for Biotechnology Information's Bookshelf: Lodish, Berk, Zipursky, et al.’s Molecular Cell Biology, 4th edition: “Protein Glycosylation in the ER and in Golgi Complex”

  Link: National Center for Biotechnology Information's Bookshelf:  Lodish, Berk, Zipursky, et al.’s Molecular Cell Biology, 4^th edition:  “Protein Glycosylation in the ER and in Golgi Complex” (HTML)
   
  Instructions: Please study this entire section from Lodish, Berk, Zipurksy, et al.’s Molecular Cell Biology textbook.  Please note that protein glycosylation is very important for certain proteins to function properly in eukaryotes.  Proteins that are expressed in prokaryotic cell, for example, in E. coli, cannot be glycosylated, because these cells lack membrane-bound subcellular organelles.
  
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4.6 Protein Engineering  

4.6.1 Protein Folding in Biotechnology  

• Reading: Scientific Electronic Library Online Brazil: Brazilian Journal of Medical and Biological Research: J.M. Yon’s “Protein Folding: A Perspective for Biology, Medicine and Biotechnology”

  Link: Scientific Electronic Library Online Brazil: Brazilian Journal of Medical and Biological Research: J.M. Yon’s “Protein Folding: A Perspective for Biology, Medicine and Biotechnology” (HTML or PDF)
   
  Instructions: Please study the content of “Protein Folding in Biotechnology: Protein Engineering and Design” on this page.  You can access the PDF version from the right hand side of the page.  Author Yon works at the Institut de Biochimie, Biophysique Moléculaire et Cellulaire, UMR CNRS, Université de Paris-Sud, Orsay, France.
   
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4.6.2 Enzyme Binding Site Specificity  

• Reading: Oxford University Press’s Journal of Experimental Biology: Jeanneau, et al.’s “Manipulating PEPC Levels in Plants”

  Links: Oxford University Press’s Journal of Experimental Biology: Jeanneau, et al.’s “Manipulating PEPC Levels in Plants” (HTML or PDF)
   
  Instructions: Please study this article.  Review what you have learned about RiBisCo, and focus on the “Transgenic Plants” section on this page.  You can access the PDF version by clicking the “Full Text (PDF)” button on the right-hand side of the page.  This is a peer-reviewed publication.
   
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4.6.3 Structural Scaffolds and Domain Recombination  

• Reading: Oxford University Press’s Nucleic Acids Research: Sleight et al.’s “In-Fusion BioBrick Assembly and Re-Engineering”

  Links: Oxford University Press’s Nucleic Acids Research:  Sleight et al.’s “In-Fusion BioBrick Assembly and Re-Engineering” (HTML or PDF)
   
  Instructions: Please study this entire article. Focus on the “Introduction,” “Results,” and “Discussion” sections.  You can access the PDF from the right-hand side of the page.  This is a peer-reviewed publication. The authors work at the Department of Bioengineering, University of Washington, Seattle.
   
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4.6.4 Nonnatural Amino Acids  

• Reading: The FASEB Journal: Budisa, et al.’s “Toward the Experimental Codon Reassignment In Vivo: Protein Building With an Expanded Amino Acid Repertoire”

  Link: The FASEB Journal:  Budisa, et al.’s “Toward the Experimental Codon Reassignment In Vivo: Protein Building With an Expanded Amino Acid Repertoire” (HTML or PDF)
   
  Instructions: Please focus on the " 'Restricted' vs. 'Relaxed' Genetic Code" and "Codon Reassignment In Living Cell" sections.  You can access the PDF from the right-hand side of the page.  The authors work at the Max Planck Institut für Biochemie, Germany.  This is a peer-reviewed publication.
   
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4.6.5 Domain Recombination  

• Reading: BioMed Central: BMC Medicine: David Davis and David Stokoe’s “Zinc Finger Nucleases as Tools To Understand and Treat Human Diseases”

  Link: BioMed Central:  BMC Medicine:  David Davis and David Stokoe’s “Zinc Finger Nucleases as Tools To Understand and Treat Human Diseases” (HTML or PDF)
   
  Instructions: Please focus on the following sections: “Methods for Design, Testing and Implementation of Zinc Finger Proteins (ZFPs):” “Addition of Functional Domains Expands the Utility of ZFPs:” and “Addition of Eendonuclease Activities to ZFPs to Create Targeted DNA Scissors.”  Please note that domain recombination is the recombining of two known functional domains of proteins to create a new kind of protein.  You can access the PDF from the right-hand side of the page.  Authors work in the Department of Molecular Biology at Genentech Inc.  This is a peer-reviewed publication.
   
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4.6.6 DNA Shuffling  

• Reading: National Center for Biotechnology Information’s Bookshelf: Wiley-Liss: Strachan and Read’s Human Molecular Genetics, 2nd edition: “Chapter 14: Our Place in the Tree of Life”

  Link: National Center for Biotechnology Information’s Bookshelf:  Wiley-Liss: Strachan and Read’s Human Molecular Genetics, 2^nd edition:  “Chapter 14: Our Place in the Tree of Life” (HTML)
   
  Instructions: Please study the “14.5.2 Exon Shuffling Permits Diverse Combinations of Structure and Functional Modules, and May be Mediated by Transposable Elements” section on this page.
   
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4.6.7 Combinatory Protein Libraries  

• Reading: National Center for Biotechnology Information’s PubMed: PLoS Biology: David R. Halpin and Pehr B. Harbury’s “DNA Display II. Genetic Manipulation of Combinatorial Chemistry Libraries for Small-Molecule Evolution”

  Link: National Center for Biotechnology Information’s PubMed:  PLoS Biology:  David R. Halpin and Pehr B. Harbury’s “DNA Display II. Genetic Manipulation of Combinatorial Chemistry Libraries for Small-Molecule Evolution” (HTML or PDF)
   
  Instructions: Please study “Strategy” in the “Results” section.  You can access the PDF from the top right corner of the page.  The two authors, Halpin and Harbury, work in the Department of Biochemistry at Stanford University’s School of Medicine. This is a peer-reviewed publication.
   
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4.6.8 Biomaterials  

• Reading: National Center for Biotechnology Information’s Bookshelf: Harvard Stem Cell Institute: Stephanie M. Willerth and Shelly E. Sakiyama-Elbert’s StemBook: “Combining Stem Cells and Biomaterial Scaffolds for Constructing Tissues and Cell Delivery”

  Link:  National Center for Biotechnology Information’s Bookshelf: Harvard Stem Cell Institute: Stephanie M. Willerth and Shelly E. Sakiyama-Elbert’s StemBook: “Combining Stem Cells and Biomaterial Scaffolds for Constructing Tissues and Cell Delivery” (HTML or PDF)
   
  Instructions:  Please study this page.  You can access the PDF from the right-hand side of the page under the “Download” section. The two authors, Willerth and Sakiyama-Elbert, are affiliated with the Department of Biomedical Engineering at Washington University, St. Louis.
   
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Unit 5: Genetic Engineering of Plants  

Plants have long been engineered for human use ever since the earliest civilizations established agricultural-based societies.  Most of the cultivated crops that we eat as food have already been artificially selected for thousands of years for certain characteristics.  With modern biotechnology, we have turned this largely trial-and-error process into a major science as we understand the functions of more and more genes and develop more sophisticated methods for introducing exotic genes into plants.  The new feature of the modern technology is the ability to produce transgenic plants.  For example, the addition of certain vitamins into rice plants has the potential to solve endemic malnutrition for millions of people in third-world countries.  This unit will also examine the safety and health issues surrounding genetically engineered plants.

Unit 5 Time Advisory   show close


Unit 5 Learning Outcomes   show close


5.1 Plant Breeding  

5.1.1 Cross-Pollination  

• Reading: National Center for Biotechnology Information’s Bookshelf: Sinauer Associates: S.F. Gilbert’s Developmental Biology, 6th edition: “Pollination”

  Link: National Center for Biotechnology Information’s Bookshelf:  Sinauer Associates: S.F. Gilbert’s Developmental Biology, 6^th edition:  “Pollination” (HTML)
   
  Instructions: Please study this excerpt from Giblert’s textbook in its entirety.
   
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5.1.2 Selective Breeding  

• Reading: University of Notre Dame: Lauren Willoughby’s “Selective Breeding and Hybridization”

  Link: University of Notre Dame: Lauren Willoughby’s “Selective Breeding and Hybridization” (HTML)
   
  Instructions: Please study this page.  Please note that humans have modified living organisms historically.
   
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5.1.3 Mutation Breeding  

• Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Miller, Suzuki, et al.’s Introduction to Genetic Analysis, 7th edition: “Mutation Breeding”

  Link: National Center for Biotechnology Information’s Bookshelf:  W.H. Freeman: Griffiths, Miller, Suzuki, et al.’s Introduction to Genetic Analysis, 7^th edition:  “Mutation Breeding” (HTML)
   
  Instructions: Please study this section on mutation breeding from Griffiths, Miller, Suzuki, et al.’s textbook.
   
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5.2 Plant Cultures and Properties  

5.2.1 Totipotency  

• Reading: Dave’s Garden: LariAnn Garner’s “Totipotency—The Wonder of Stem Cells in Plants”

  Link: Dave’s Garden:  LariAnn Garner’s “Totipotency—The Wonder of Stem Cells in Plants” (HTML)
   
  Instructions: Please study this page.
   
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5.2.2 Callus Culture  

• Reading: University of Florida: Alba Myers’ “Somatic Embryogenesis Induction in Delonix Regia (Boger.) Raf (Royal Poinciana)”

  Link: University of Florida: Alba Myers’ “Somatic Embryogenesis Induction in Delonix Regia (Boger.) Raf (Royal Poinciana)” (HTML)
   
  Instructions: Please read this page, and identify examples of callus culture.  Plant tissues are sterilized and placed on tissue culture medium, which induces “callus,” that is, undifferentiated cell formation.
   
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5.2.3 Suspension Culture  

• Reading: The University of New South Wales’ Cell Biology Wiki: Dr. Mark Hill’s “Group 4 Project—Cell Culture”

  Link: The University of New South Wales’ Cell Biology Wiki: Dr. Mark Hill’s  “Group 4 Project—Cell Culture” (HTML)
   
  Instructions: Please study the “Harvesting and Isolating Cells” section on this page.
   
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5.3 Insertion of Genes  

5.3.1 Ti Plasmid  

• Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Gelbart, Miller, et al.’s Modern Genetic Analysis: NCBI Bookshelf: Griffiths et al.’s “Recombinant DNA Technology in Eukaryotes”

  Link: National Center for Biotechnology Information’s Bookshelf:  W.H. Freeman: Griffiths, Gelbart, Miller, et al.’s Modern Genetic Analysis: NCBI Bookshelf: Griffiths et al.’s “Recombinant DNA Technology in Eukaryotes” (HTML)
   
  Instructions: Please study “The Ti plasmid” section on this page.  The Ti plasmid is actually inserted by a bacteria species called Agrobacterium.  Thus, when we talk about the Ti plasmid, we are referring to the plasmid inside Agrobacterium. 
   
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5.3.2 Electroporation, Particle Bombardment, Microinjection  

• Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Berg, et al.’s Biochemistry, 5th edition: “Manipulating the Genes of Eukaryotes”

  Link: National Center for Biotechnology Information’s Bookshelf:  W.H. Freeman: Berg, et al.’s Biochemistry, 5^th edition: “Manipulating the Genes of Eukaryotes” (HTML)
   
  Instructions: Please read the third and fourth paragraphs (starting with “Foreign DNA can be introduced . . . “) in the “6.3.6 Tumor-Inducing Plasmids Can Be Used to Introduce New Genes into Plant Cells” section.
   
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• Reading: Saint John’s University: Stephen G. Saupe’s “Introduction to the Protoplast Lab”

  Link: Saint John’s University:  Stephen G. Saupe’s “Introduction to the Protoplast Lab” (HTML)
   
  Instructions: Please study the “A Protoplast Primer” section on this page.
   
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• Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Miller, Suzuki, et al.’s Introduction to Genetic Analysis, 7th edition: “Recombinant DNA Technology in Eukaryotes”

  Link: National Center for Biotechnology Information’s Bookshelf:  W.H. Freeman: Griffiths, Miller, Suzuki, et al.’s Introduction to Genetic Analysis, 7^th edition:  “Recombinant DNA Technology in Eukaryotes” (HTML)
   
  Instructions: Please study the “Transgenic Eukaryotes” section on this page.
   
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5.4 Detection of DNA Insertion  

5.4.1 Reporter Genes  

• Reading: University of Central Florida: Dheeraj Verma and Henry Daniell’s “Chloroplast Vector Systems for Biotechnology Applications”

  Link: University of Central Florida: Dheeraj Verma and Henry Daniell’s “Chloroplast Vector Systems for Biotechnology Applications” (HTML or PDF)
   
  Instructions: Please study the “Reporter Genes Used In Plastids” section on this page.  You can access the PDF from the top right corner of the page.
   
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• Reading: Wellesley College’s “?-Glucuronidase (GUS) Activity Assays of Transformed Plants”

  Link: Wellesley College’s “β-Glucuronidase (GUS) Activity Assays of Transformed Plants” (HTML)
   
  Instructions: Please study this page.  Please note that β-glucuronidase is a reporter gene, which can be used to assess the succes of  transformation.
   
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• Assessment: The Saylor Foundation's "BIO403 Unit 5.4 Assessment"

  Link: The Saylor Foundation's "BIO403 Unit 5.4 Assessment" (HTML)
   
  Instructions: You will find link to the "GM Plant Design" assessment on this page.  This is a multiple choice assessment with one correct answer.  Clicking on an answer will bring you to another page.  If your answer is correct, then it is acknowledged with a short explanation.  Please read the explanation carefully.  If you clicked on the wrong answer, then you will be directed to a tutorial page.  Please study the tutorial page carefully.  You will be prompted to return to the assessment and complete it again.  Please note that plastid modification is a more recent development in GM plant.design.

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5.4.2 Cre-loxP System  

• Reading: The Jackson Laboratory’s “Introduction to Cre-Lox Technology”

  Link: The Jackson Laboratory’s “Introduction to Cre-Lox Technology” (HTML)
   
  Instructions: Please study this page. Note that Cre-Lox Technology is used both on animals and plants.
   
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5.5 Common Transgenic Properties  

5.5.1 Herbicide Resistance  

• Reading: International Service for the Acquisition of Agri-Biotech Applications: “Pocket K No. 10: Herbicide Tolerance Technology: Glyphosate and Glufosinate”

  Link:  International Service for the Acquisition of Agri-Biotech Applications:  “Pocket K No. 10: Herbicide Tolerance Technology: Glyphosate and Glufosinate” (HTML or PDF)
   
  Instructions: Please study this page.  You can access the PDF in various languages from the left-hand side of the page.
   
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5.5.2 Insect Resistance  

• Reading: John W. Kimball’s “Bacillus thuringiensis (Bt)”

  Link: John W. Kimball’s “Bacillus thuringiensis (Bt)” (HTML)
   
  Instructions: Please study this page.
   
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• Reading: Nature Education’s Scitable: Losey et al.’s “Transgenic Pollen Harms Monarch Larvae”

  Link: Nature Education’s Scitable: Losey et al.’s “Transgenic Pollen Harms Monarch Larvae” (PDF)
   
  Instructions: Please study this publication in its entirety.
   
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5.5.3 Stress Tolerance  

• Reading: Virginia Tech: Information Systems for Biotechnology: Teresa Capell’s “Enhanced Drought Tolerance In Transgenic Rice”

  Link: Virginia Tech:  Information Systems for Biotechnology: Teresa Capell’s “Enhanced Drought Tolerance In Transgenic Rice” (HTML)
   
  Instructions: Please study this page.  Author Theresa Chapel is from Department of Crop Genetics and Biotechnology, Schmallenberg, Germany.
   
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5.5.4 Crop Yield  

• Reading: The NCAT Sustainable Agriculture Project’s “Transgenic Crops”

  Link: The NCAT Sustainable Agriculture Project’s “Transgenic Crops” (HTML)
   
  Instructions: Please study the “Crop Yield, Costs, and Profitability” section on this page.
   
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• Reading: Nature Education’s Scitable: Leslie A. Pray’s “Quantitative Genetics: Growing Transgenic Tomatoes”

  Link: Nature Education’s Scitable:  Leslie A. Pray’s “Quantitative Genetics: Growing Transgenic Tomatoes” (HTML)
   
  Instructions: Please study the entire article. Please note the similarities and differences between complex quantitative traits and single gene determined traits.
   
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5.5.5 Nutrition  

• Reading: International Service for the Acquisition of Agri-Biotech Applications: “Biotechnology and Biofortification”

  Link:  International Service for the Acquisition of Agri-Biotech Applications: “ Biotechnology and Biofortification” (HTML or PDF)
   
  Instructions: Please read the content of this page.  You can access the PDF from the left-hand side of the page.
   
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• Reading: The American Society for Nutritional Sciences: The Journal of Nutrition: Bo Lönnerdal’s “Genetically Modified Plants for Improved Trace Element Nutrition”

  Link:  The American Society for Nutritional Sciences:  The Journal of Nutrition:  Bo Lönnerdal’s “Genetically Modified Plants for Improved Trace Element Nutrition” (HTML or PDF)
   
  Instructions: Please study the “Insertion of Genes for Novel Metal-Binding Proteins” section on this page. You can access the PDF form from the right side of the page.  Author Bo Lönnerdal works in the Department of Nutrition at the University of California.  This is a peer-reviewed publication.
   
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5.6 Functional Genomics of Plants  

5.6.1 Metabolic Pathways  

• Reading: Jim M. Dunwell’s “Transgenic Approaches to Crop Improvement”

  Link: Jim M. Dunwell’s “Transgenic Approaches to Crop Improvement” (HTML or PDF)
   
  Instructions: Please study the content of this page. You can access the PDF form on the righthand side of the page.
  
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• Reading: John W. Kimball’s Biology Pages: “Arabidopsis Thaliana: Another ‘Model Organism’”

  Links: John W. Kimball’s Biology Pages:  “Arabidopsis Thaliana: Another ‘Model Organism’” (HTML)
   
  Instructions: Please study this page.  Please note that A. thaliana is the most widely used model organism in research aiming to produce new genetically modified plants.
   
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5.6.2 Mutagenesis  

• Reading: Oxford University Press’s Journal of Experimental Botony: Parry et al.’s “Mutation Discovery for Crop Improvement”

  Link: Oxford University Press’s Journal of Experimental Botony:  Parry et al.’s “Mutation Discovery for Crop Improvement” (HTML or PDF)
   
  Instructions: Please study the “Introduction” and “Conclusions” sections on this page. You can access the PDF from the right side of the page.  This is a peer-reviewed publication.
   
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5.6.3 Gene Knockouts  

• Reading: Arizona Genomics Institute, Arizona Genomics Computational Laboratory, and Stanford University: “The Maize Full Length cDNA Project”

  Link: Arizona Genomics Institute, Arizona Genomics Computational Laboratory, and Stanford University: “The Maize Full Length cDNA Project” (HTML)
   
  Instructions: Please study the “Disrupt Gene Regulation: ‘Knockdown’ Technology” section on this page.
   
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5.7 Genetically Modified Plants  

5.7.1 Tomatoes  

• Reading: National Education’s Scitable: Leslie A. Pray’s “Quantitative Genetics: Growing Transgenic Tomatoes”

  Link: National Education’s Scitable:  Leslie A. Pray’s “Quantitative Genetics: Growing Transgenic Tomatoes” (HTML)
   
  Instructions: Please study the content of this page.  Longer shelf life, size, and taste are some of the traits that are targeted in transgenic tomatoes.  Please note the broad range of traits, which transgenic technology attempts to modify.
   
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5.7.2 Soybeans  

• Reading: National Center for Biotechnology Information: The Yonsei University’s College of Medicine: Yonsei Medical Journal: Sang-Ha Kim, et al.’s “Evaluating the Allergic Risk of Genetically Modified Soybean”

  Link: National Center for Biotechnology Information: The Yonsei University’s College of Medicine: Yonsei Medical Journal:  Sang-Ha Kim, et al.’s “Evaluating the Allergic Risk of Genetically Modified Soybean” (HTML or PDF)
   
  Instructions: Please study the “Introduction” and “Discussion” sections on this page. You can access the PDF form from the top left corner of the page.  This is a peer-reviewed publication.  Please note that possible allergic reaction to transgenic soybean is discussed.
   
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5.7.3 Corn  

• Reading: PLoS Biology: Virginia Gewin's “Genetically Modified Corn— Environmental Benefits and Risks”

  Link: PLoS Biology: Virginia Gewin's “Genetically Modified Corn— Environmental Benefits and Risks” (HTML or PDF)
   
  Instructions: Please study this page. You can download this material in PDF form from the top right corner of the page.  Protection from insect pests was a major driving force of transgenic corn development.  Please note the environmental risk of decreasing diversity. Author Gewin is a freelance science journalist.
   
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5.7.4 Hawaiian Papaya  

• Reading: Plant Management Network: Dennis Gonsalves and Steve Ferreira’s “Transgenic Papaya: A Case for Managing Risks of Papaya Ringspot Virus in Hawaii”

  Link: Plant Management Network:  Dennis Gonsalves and Steve Ferreira’s “Transgenic Papaya: A Case for Managing Risks of Papaya Ringspot Virus in Hawaii” (HTML)
   
  Instructions: Please study this page.  Protection from viral infection was the major driving force of transgenic papaya development.  Please note the impact of the transgenic plant on the cultivation of nontransgenic papaya in the virus infected area.
   
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5.7.5 Rice  

• Reading: GMO Compass: “Rice”

  Link: GMO Compass: “Rice” (HTML)
   
  Instructions: Please study this page.  Please note that golden rice is an example of improved nutritional value of a genetically modified plant.
   
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5.8 Safety Issues  

5.8.1 Human Health  

• Reading: Ohio State University: Dresbach et al.’s “The Impact of Genetically Modified Organisms on Human Health”

  Link: Ohio State University: Dresbach et al.’s “The Impact of Genetically Modified Organisms on Human Health” (HTML or PDF)
   
  Instructions: Please study this page.  You can access the PDF at the bottom of the page.
   
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5.8.2 Nontarget Organisms  

• Reading: Emory University’s “GMO and Environment: Once a Gene’s In, Where Does It Go?”

  Link: Emory University’s “GMO and Environment: Once a Gene’s In, Where Does It Go?” (HTML)
   
  Instructions: Please study this page.  Please note that a decreasing diversity makes species more vulnerable to environmental changes.
   
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Unit 6: Genetic Engineering of Animals  

Just as biotechnology has given rise to genetically engineered plants, it has also applied many of the same techniques and knowledge to animals.  This unit provides an overview of the current state of animal genetic engineering.  So far we have produced genetically modified mice, fish, flies, hydra, and pigs, just to name a few.  As you can imagine, the applications of modifying animals to suit our needs can have immense consequences and have raised significant concern.  This unit also examines some of the issues surrounding the production of “customized” animals, including the ethics of genetically altering humans.

Unit 6 Time Advisory   show close


Unit 6 Learning Outcomes   show close


6.1 Creating Transgenic Animals  

• Reading: Nature Education’s Scitable: Leslie Pray’s “Recombinant DNA Technology and Transgenic Animals”

  Link: Nature Education’s Scitable: Leslie Pray’s “Recombinant DNA Technology and Transgenic Animals” (HTML)
   
  Instructions: Please study this page.  Dr. Pray gives an overview on the making of transgenic animals. 
   
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• Reading: Wellcome Trust: Richard Twyman’s “Transgenic Mice”

  Link: Wellcome Trust:  Richard Twyman’s “Transgenic Mice” (HTML)
   
  Instructions: Please study this page including the slide show. 
  
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6.2 Engineering Design  

6.2.1 Chimeric Animal  

• Reading: John W. Kimball’s Biology Pages: “Genetic Mosaics”

  Link: John W. Kimball’s Biology Pages: “Genetic Mosaics” (HTML)
   
  Instructions: Please study this page.  Please note that chimeras can be considered as paternal twins living in one body.  Chimeric individuals may look and function perfectly normal and may stay unnoticed unless genetic testing is performed on their different body parts.
   
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6.2.2 Differential Gene Expression  

• Reading: Kenyon College: Dr. Wade Powell’s “Differential Gene Expression and Development”

  Link: Kenyon College: Dr. Wade Powell’s “Differential Gene Expression and Development” (HTML)
   
  Instructions: Please study this page.  Please note that differential gene expression may result in cell differentiation without the loss of genetic information in the differentiated cell.
    
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6.2.3 Site-Specific Recombination  

• Reading: Case Western Reserve University’s “Targeting Vector Design”

  Link: Case Western Reserve University’s “Targeting Vector Design” (HTML)
   
  Instructions: Please study the content of this page.
   
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6.2.4 Conditional Transgene Expression  

• Reading: National Center for Biotechnology Information’s PubMed: Society for Endocrinology's Journal of Endocrinology: Ryding, et al.’s “Conditional Transgenic Technologies”

  Link: National Center for Biotechnology Information’s PubMed: Society for Endocrinology's Journal of Endocrinology: Ryding, et al.’s  “Conditional Transgenic Technologies” (PDF)
   
  Instructions: Please click on “Society for Endocrinology Free Full Text” (in blue box, right top side of the page under PubMed.gov heading), and download the full publication as a PDF.  Study the entire publication.  The authors work at the University of Edinburgh, UK.  This is a peer-reviewed publication.
   
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6.3 Transgenic Mice  

6.3.1 Knockout and Knockin Mice  

• Reading: Nature Education’s Scitable: “Scientists Can Analyze Gene Function by Deleting Gene Sequences”

  Link: Nature Education’s Scitable: “Scientists Can Analyze Gene Function by Deleting Gene Sequences” (HTML)
   
  Instructions: Please study this page.  Knockout mice refer to mice that have a selected gene intentionally silenced or removed.
   
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• Reading: Nature Education’s Scitable: “Transgenic Animals Have Genomes That Have Been Permanently Altered Through Recombinant DNA Technology.”

  Link: Nature Education’s Scitable:  “Transgenic Animals Have Genomes That Have Been Permanently Altered Through Recombinant DNA Technology.” (HTML)
   
  Instructions: Please study the diagram.
   
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• Reading: Nature Education’s Scitable: John Sterling’s “Gene Therapy Restores Vision to Mice”

  Link: Nature Education’s Scitable: John Sterling’s “Gene Therapy Restores Vision to Mice” (Adobe Flash)
   
  Instructions: Please listen to the audio (10 minutes).  Knockin mice refer to mice that have a specific gene intentionally added.
   
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6.3.2 Phenotypic Studies  

• Reading: National Center for Biotechnology Information’s Bookshelf: CRC Press: Rodriguiz and Wetsel’s Animal Models of Cognitive Impairment: “Chapter 12: Assessments of Cognitive Deficits in Mutant Mice”

  Link:  National Center for Biotechnology Information’s Bookshelf: CRC Press: Rodriguiz and Wetsel’s Animal Models of Cognitive Impairment: “Chapter 12: Assessments of Cognitive Deficits in Mutant Mice” (HTML)
   
  Instructions: Please study this entire chapter from Levin and Buccafusco (ed.)’s Animal Models of Cognitive Impairment.  The authors are affiliated with Duke University’s Medical Center.
   
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6.4 Genetically Modified Animals  

6.4.1 Transgenic Fruit Flies  

• Reading: The Company of Biologists’ Development: Venken and Bellen’s “Transgenesis Upgrades for Drosophila melanogaster”

  Link: The Company of Biologists’ Development:  Venken and Bellen’s “Transgenesis Upgrades for Drosophila melanogaster” (HTML or PDF)
   
  Instructions: Please study the following sections: “Summary,” “Introduction,” “Fig.1 Drosophila Transgenesis,” “Box 4. Site-Specific Recombinases and Integrases,” and “Future Applications.”  You can access the PDF from the right-hand side of the page.
   
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6.4.2 Transgenic Mosquitoes  

• Reading: Wiley Online Library: Yamamoto, et al.’s “ Flying Vaccinator; a Transgenic Mosquito Delivers a Leishmania Vaccine via Blood Feeding”

  Link: Wiley Online Library: Yamamoto, et al.’s “Flying Vaccinator; a Transgenic Mosquito Delivers a Leishmania Vaccine via Blood Feeding” (HTML or PDF)
   
  Instructions: Please study the “Abstract,” “Introduction,” “Generation of Transgenic Lines,” and “Antibody Responses to mDsRed-SP15 in Mice Exposed to Transgenic Mosquitoes” sections on this page.  You can access the PDF for the right-hand side of the page under “Article Tools.”  The authors work in the Department of Infection and Immunity at the Jichi Medical University, Japan.  This is a peer-reviewed publication.
   
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6.4.3 Transgenic Insects  

• Reading: Action BioScience: Thomas A. Miller’s “Designing Insects”

  Link:  Action BioScience:  Thomas A. Miller’s “Designing Insects” (HTML)
   
  Instructions: Please read this page.  Dr. Miller works as a professor of entomology at the University of California, Riverside.
   
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  The Saylor Foundation does not yet have materials for this portion of the course. If you are interested in contributing your content to fill this gap or aware of a resource that could be used here, please submit it here.

  Submit Materials

6.5 Cloning Animals  

6.5.1 Nuclear Transplantation and Dolly  

• Reading: National Center for Biotechnology Information’s Bookshelf: Wiley-Liss: Strachan and Read’s Human Molecular Genetics, 2nd edition: “Chapter 21: Genetic Manipulation of Animals”

  Link: National Center for Biotechnology Information’s Bookshelf: Wiley-Liss: Strachan and Read’s Human Molecular Genetics, 2^nd edition: “Chapter 21: Genetic Manipulation of Animals” (HTML)
   
  Instructions: Please study “Manipulating Animals by Somatic Cell Nuclear Transfer” on this page, including the “Principles and Practice of Animal Cloning” and “The Successful Cloning of an Adult Animal Has Major Implications for Research, Medicine and Society” sections.
   
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• Reading: National Center for Biotechnology Information’s PubMed: Canadian Medical Association Journal: Leigh Turner’s “A Sheep Named Dolly”

  Link:  National Center for Biotechnology Information’s PubMed: Canadian Medical Association Journal:  Leigh Turner’s “A Sheep Named Dolly” (PDF)
   
  Instructions: Please study this publication. Click on PDF under the title to download the full text.  Author Turner works at the Hastings Center.
  
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6.5.2 Livestock Improvement  

• Reading: Nature Education’s Scitable: Swanson et al.’s “Extraordinary Salmon Growth”

  Link: Nature Education’s Scitable:  Swanson et al.’s “Extraordinary Salmon Growth” (PDF)
   
  Instructions: Please study this entire paper.  The authors work at  Harvard Medical School.
   
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6.5.3 Premature Aging  

• Reading: National Center for Biotechnology Information’s PubMed: Reproductive Biology and Endocrinology: Jie Xu and Xiangzhong Yang’s “Will Cloned Animals Suffer Premature Aging—The Story at the End of Clones’ Chromosomes”

  Link:  National Center for Biotechnology Information’s PubMed: Reproductive Biology and Endocrinology:  Jie Xu and Xiangzhong Yang’s “Will Cloned Animals Suffer Premature Aging—The Story at the End of Clones’ Chromosomes” (HTML or PDF)
   
  Instructions: Please study the content of this page.  You can access the PDF from the top right corner of the page.  This is a peer-reviewed publication.
   
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• Assessment: The Saylor Foundation's "BIO403 Unit 6.5 Assessment"

  Link: The Saylor Foundation's "BIO403 Unit 6.5 Assessment" (HTML)
   
  Instructions: You will find link to the "Pet Cloning" assessment on this page.  This is a multiple choice assessment with one correct answer.  Clicking on an answer will bring you to another page.  If your answer is correct, then it is acknowledged with a short explanation.  Please read the explanation carefully.  If you clicked on the wrong answer, then the click will bring you to a tutorial page.  Please study the tutorial page carefully.  You will be prompted to return to the assessment and complete it again.  Please note that this assessment is focusing on animal cloning, which is very expensive, but commercially available.  The commercially available genetically engineered animals are not covered by this assessment.

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6.6 Applications  

6.6.1 “Pharm” Animals  

• Reading: John W. Kimball’s Biology Pages: “Transgenic Animals”

  Link:  John W. Kimball’s Biology Pages: “Transgenic Animals” (HTML)
   
  Instructions: Please read the “Transgenic Sheep and Goats”  and “Transgenic Chickens” sections on this page.
   
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• Reading: Iowa State University: David F. Betsch’s “Pharmaceutical Production from Transgenic Animals”

  Link:  Iowa State University:  David F. Betsch’s “Pharmaceutical Production from Transgenic Animals” (HTML)
   
  Instructions: Please study this page.
   
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6.6.2 Organ Transplantation  

• Reading: John W. Kimball’s Biology Pages: “Organ Transplants”

  Link:  John W. Kimball’s Biology Pages:  “Organ Transplants” (HTML)
   
  Instructions: Please read starting with “What are the future prospects for transplantation?” to the end this page.
   
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6.7 Bioethics  

6.7.1 Designer Children  

• Reading: Nature Education’s Scitable: Leslie A. Pray’s “Embryo Screening and the Ethics of Human Genetic Engineering”

  Link: Nature Education’s Scitable:  Leslie A. Pray’s “Embryo Screening and the Ethics of Human Genetic Engineering” (HTML)
   
  Instructions: Please study this page.  Dr. Pray reviews opposing opinions and recent practice on preimplantation genetic diagnosis.  She is challenging you by asking "What do you think?:" should we improve human genome, or should we focus on the danger of misuse?
   
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6.7.2 Loss of Biodiversity  

• Reading: Sierra Club’s “Genetic Engineering at a Historic Crossroads”

  Link: Sierra Club’s “Genetic Engineering at a Historic Crossroads” (HTML)
   
  Instructions: Please read “Historic turning point.” 
   
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6.7.3 Cloning Pets  

• Reading: MIT’s Technology Review: Emily Singer’s “The Dark Side of Pet Cloning”

  Link: MIT’s Technology Review:  Emily Singer’s “The Dark Side of Pet Cloning” (HTML)
   
  Instructions: Please study this page.  Please note that genetically identical animals have different personalities, just like identical twins.
   
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6.7.4 Transgenic Animals for Art  

• Reading: KAC’s version of Jeremy Manier’s “Art Takes a Genetic Engineering Leap”

  Link: KAC’s version of Jeremy Manier’s “Art Takes a Genetic Engineering Leap” (HTML)
   
  Instructions: Please read this page.  This article was originally published in the Chicago Tribune on September 19, 2000.
   
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6.7.5 Conflict with Religion  

• Reading: University of Hawaii, Honolulu: Professor Ronald C. Pine’s version of Bob Sullivan’s “Religious Views of Cloning Do Not Agree”

  Link:  University of Hawaii, Honolulu: Professor Ronald C. Pine’s version of Bob Sullivan’s “Religious Views of Cloning Do Not Agree” (HTML)          
   
  Instructions: Please read this page.
   
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Unit 7: Genetic Defects and Gene Therapy  

One of the great potentials of biotechnology is the ability to create cures for human genetic defects.  Because such a disease is directly caused by a dysfunctional or missing gene, in theory, by injecting patients with a product that replaces or adds the target gene, they will be cured forever.  Gene therapy efforts attack retroviral infections as well, for example, by modifying the host cell’s virus recognition site.  

Unit 7 Time Advisory   show close


Unit 7 Learning Outcomes   show close


7.1 Abnormal Chromosomes  

7.1.1 Altered Chromosome Number  

• Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Gelbart, Miller, et al.’s Modern Genetic Analysis: “Changes in Chromosome Number”

  Link: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman:Griffiths, Gelbart, Miller, et al.’s Modern Genetic Analysis:  “Changes in Chromosome Number” (HTML)
   
  Instructions: Please study the content of the “Aneuploidy” section, including the “Nondisjunction,” “Monosomics (2 - 1),” and “Trisomics (2n + 1)” subsections on this page.
   
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7.1.2 Chromosomal Rearrangement  

• Reading: National Center for Biotechnology Information’s Bookshelf: W.H. Freeman: Griffiths, Gelbart, Miller, et al.’s Modern Genetic Analysis: “Chromosomal Rearrangements”

  Link: National Center for Biotechnology Information’s Bookshelf:  W.H. Freeman:  Griffiths, Gelbart, Miller, et al.’s Modern Genetic Analysis:  “Chromosomal Rearrangements” (HTML)
   
  Instructions: Please study this page.
   
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7.1.3 Epigenetic Defects  

• Reading: Nature Education’s Scitable: Danielle Simmons’ “Epigenetic Influences and Disease”

  Link: Nature Education’s Scitable:  Danielle Simmons’ “Epigenetic Influences and Disease” (HTML)
   
  Instructions: Please study this page.  Epigenetics is "in addition to" genetics.  Please note that epigenetic changes result in gene expression changes without changing the sequence of the genomic DNA.  Identical twins may be susceptible to different diseases, if their epigenetics are different due to different life style.
   
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7.2 Genetic Disorders  

7.2.1 Sickle Cell Anemia  

• Reading: Nature Education’s Scitable: Abram Gabriel and Jennifer Przybylski’s “Sickle-Cell Anemia: A Look at Global Haplotype Distribution”

  Link:  Nature Education’s Scitable:  Abram Gabriel and Jennifer Przybylski’s “Sickle-Cell Anemia: A Look at Global Haplotype Distribution” (HTML)
   
  Instructions: Please study the content of this page.  Authors Gabriel and Przybylski work at the Rutgers University.  Please note the advantage, what the deadly sickle-cell anemia provides for heterozygous individuals.
   
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7.2.2 Cystic Fibrosis  

• Reading: National Human Genome Research Institute’s “Learning about Cystic Fibrosis”

  Link: National Human Genome Research Institute’s  “Learning about Cystic Fibrosis” (HTML)
   
  Instructions: Please study the content of this page.
   
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7.2.3 Hemophilia  

• Reading: National Center for Biotechnology Information’s PubMed: Blackwell Publishing Ltd.'s British Journal of Haematology: Samuel L. Murphy and Katherine A. High’s “Gene Therapy for Haemophilia”

  Link: National Center for Biotechnology Information’s PubMed: Blackwell Publishing Ltd.'s British Journal of Haematology:  Samuel L. Murphy and Katherine A. High’s “Gene Therapy for Haemophilia” (HTML or PDF)
   
  Instructions: Please study the content of this page. You can access the PDF from the top right corner of the page.  The authors work in the Department of Pediatrics at the Children's Hospital of Philadelphia. This is a peer-reviewed publication.
   
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• Web Media: Khanacademy’s “Sex-Linked Traits”

  Link: Khanacademy’s “Sex-Linked Traits” (Adobe Flash)
   
  Also available in:
  YouTube
   
  Instructions: Please watch the video (15 minutes) for a step by step tutorial on the inheritance of sex-linked traits.  You may need to review Punnett squares (see subunit 1.2 of this course) and to follow this video several times.
   
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7.2.4 Phenylketonuria  

• Reading: National Center for Biotechnology Information’s “Phenylketonuria”

  Link: National Center for Biotechnology Information’s  “Phenylketonuria” (HTML)
   
  Instructions: Please study the content of this page.  Please note that phenylalanine is an essential amino acid, thus it can not be omitted entirely from the diet.
   
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7.2.5 Duchenne muscular dystrophy  

• Reading: National Center for Biotechnology Information’s “Duchenne Muscular Dystrophy”

  Link: National Center for Biotechnology Information’s  “Duchenne Muscular Dystrophy” (HTML or PDF)
   
  Instructions: Please study the table on this page.  Please note that Duchenne muscular dystrophies are X-linked, thus the disease is more common in males.
   
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7.2.6 Repeat extensions  

• Reading: Nature Education’s Scitable: Heidi Chial’s “Huntington’s Disease: The Discovery of the Huntingtin Gene”

  Link: Nature Education’s Scitable:  Heidi Chial’s “Huntington’s Disease: The Discovery of the Huntingtin Gene” (HTML)
   
  Instructions: Please study this page.  More than 40 CAG nucleotide repeat in the HTT gene is linked to the onset of Huntington’s disease.
   
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• Reading: National Center for Biotechnology Information’s “Fragile X Syndrome

  Link: National Center for Biotechnology Information’s  “Fragile X Syndrome” (HTML or PDF)
   
  Instructions: Please study the content of this page.  Fragile X syndrome is the most common inherited mental retardation.  It is an X-linked condition.  Please note that the chromosome becomes fragile only during a staining procedure; it is not fragile in the cell.  More than 200 CGG nucleotide repeat in the fragile X gene causes the disease.
   
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• Assessment: The Saylor Foundation: "BIO403 Unit 7.2 Assessment"

  Link: The Saylor Foundation: "BIO403 Unit 7.2 Assessment" (HTML)
   
  Instructions: You will find links to five pedigrees within the "Family Pedigree" assessment on this page. These are multiple choice assessments with one correct answer. You are asked to determine if the highlighted trait in the pedigree follows dominant, or recessive or sex-linked inheritance. Clicking on an answer will bring you to another page. If your answer is correct, then it is acknowledged with a short explanation. Please read the explanation carefully. If you clicked on the wrong answer, then the click will bring you to a tutorial page. Please study the tutorial page carefully. You will be prompted to return to the assessment and complete it again. Please note that family pedigrees are indispensable in medical counseling.

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7.3 Genetic Screening and Counseling  

• Reading: Nature Education’s Scitable: Karen E. Norrgard’s “Genetic Counseling: Genetic Testing, Family History and Psychosocial Evaluation”

  Link:  Nature Education’s Scitable:  Karen E. Norrgard’s “Genetic Counseling: Genetic Testing, Family History and Psychosocial Evaluation” (HTML)
   
  Instructions: Please study the three case studies on this page.
   
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• Web Media: Khanacademy’s “Hardy-Weinberg Principle”

  Link: Khanacademy’s “Hardy-Weinberg Principle” (Adobe Flash)
   
  Also available in:
  YouTube
   
  Instructions: Please watch the video (15 minutes) for a step by step tutorial on calculating probabilities of the expected traits of the offspring.  You may need to review Punnett squares (see subunit 1.2 of this course) and to follow this video several times.
   
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• Reading: Nature Education’s Scitable: Karen Norrgard’s “Diagnosing Down Syndrome, Cystic Fibrosis, Tay-Sachs Disease and Other Genetic Disorders”

  Link: Nature Education’s Scitable:  Karen Norrgard’s “Diagnosing Down Syndrome, Cystic Fibrosis, Tay-Sachs Disease and Other Genetic Disorders” (HTML)
   
  Instructions: Please study the content of this page.  Dr. Norrgard reviews genetic screening in the newborn, during pregnancy and before implantation.
   
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7.4 Gene Therapies  

7.4.1 Loss-of-Function Disease and Dominant Disease  

• Reading: Nature Education’s Scitable: Heidi Chial’s “Gene-Based Therapeutic Approaches”

  Link: Nature Education’s Scitable:  Heidi Chial’s “Gene-Based Therapeutic Approaches” (HTML)
   
  Instructions: Please learn content from the “Putting the Human Genome to Work: Using Genes to Treat Disease” section to the end of this page.
   
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7.4.2 Ex Vivo and In Vivo Gene Therapy  

• Reading: National Center for Biotechnology Information’s Bookshelf: Strachan and Read's "Human Molecular Genetics": "Chapter 22: Gene Therapy and Other Molecular Genetic-Based Therapeutic Approaches"

  Link: National Center for Biotechnology Information’s Bookshelf: Strachan and Read's "Human Molecular Genetics:” "Chapter 22: Gene Therapy and Other Molecular Genetic-Based Therapeutic Approaches" (HTML)
   
  Instructions: Please scroll down to and read section 22.2: “The Technology of Classical Gene Therapy.”
   
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7.4.3 Aggressive Gene Therapy: Prodrug Treatment  

• Reading: American Society for Clinical Investigation's The Journal of Clinical Investigation: Caroline J. Springer and Ion Niculescu-Duvaz’s “Prodrug-Activating Systems in Suicide Gene Therapy”

  Link: American Society for Clinical Investigation's The Journal of Clinical Investigation: Caroline J. Springer and Ion Niculescu-Duvaz’s  “Prodrug-Activating Systems in Suicide Gene Therapy” (HTML or PDF)
   
  Instructions: Please study the introduction, “Parameters that influence the success of GDEPT systems,” and “Future perspectives” sections.  You can access the PDF under “article tools” on the left-hand side of the page.  The authors work in the Cancer Research Campaign Centre for Cancer Therapeutics at the Institute of Cancer Research, Sutton, Surrey, UK.
   
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7.5 Gene Therapy Design  

7.5.1 Adenovirus Vectors  

• Reading: John W. Kimball’s Biology Pages: “Gene Therapy II”

  Link: John W. Kimball’s Biology Pages: “Gene Therapy II” (HTML)
   
  Instructions: Please study this page.
   
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7.5.2 Retrovirus Vectors  

• Reading: Genetherapynet.com’s “Retroviral Vectors”

  Link: Genetherapynet.com’s “Retroviral Vectors” (HTML or PDF)
   
  Instructions: Please study this page. You can access the PDF by clicking on the Adobe icon at the top of the page.
   
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7.5.3 Particle Bombardment  

• Reading: Davidson College: Megan McDonald’s “Gene Guns”

  Link: Davidson College: Megan McDonald’s “Gene Guns” (HTML)
   
  Instructions: Please study this page.
   
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7.5.4 Liposomes and Lipofection  

• Reading: University of Pennsylvania’s Diamond Lab: “Gene Therapy”

  Link: University of Pennsylvania’s Diamond Lab:  “Gene Therapy” (HTML)
   
  Instructions: Please study this page.
   
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7.5.5 Antisense Therapy  

• Reading: Thomas Jefferson University’s “Laboratory of Nucleic Acid Therapeutics”

  Link: Thomas Jefferson University’s “Laboratory of Nucleic Acid Therapeutics” (HTML)
   
  Instructions: Please read this page.
   
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7.6 Current Gene Therapy Models  

7.6.1 SCID (Severe Combined Immunodeficiency)  

• Reading: John W. Kimball’s Biology Pages: “Gene Therapy I”

  Link: John W. Kimball’s Biology Pages: “Gene Therapy I” (HTML)
   
  Instructions: Please study this page.
   
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7.6.2 Duchenne Muscular Dystrophy  

• Reading: Gene Therapy Review: Christophe Pichavant’s “Gene Therapy for Duchenne Muscular Dystrophy”

  Link: Gene Therapy Review:  Christophe Pichavant’s  “Gene Therapy for Duchenne Muscular Dystrophy” (HTML)
  
  Instructions: Please study the entire article.
   
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7.6.3 HIV (Human Immunodeficiency Virus)  

• Reading: PLOS Pathogens: Wilen et al’s “Engineering HIV-Resistant Human CD4+ T Cells with CXCR4-Specific Zinc-Finger Nucleases”

  Link: PLOS Pathogens:  Wilen et al’s “Engineering HIV-Resistant Human CD4+ T Cells with CXCR4-Specific Zinc-Finger Nucleases” (HTML or PDF)
   
  Instructions: Please study the “Abstract,” “Author Summary,” and “Introduction” sections.  You can download the PDF from the top right corner of the page.  This is a peer-reviewed publication.
   
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Unit 8: Forensic Biotechnology and Biometrics  

One of the practical applications of genomics and DNA technology has been its impact in security and the legal system.  Because every human being has a unique genome, scientists have used DNA visualization technology to identify individuals according to a particular genetic makeup.  Because the odds of someone else having the same sequence are extremely low, it is used as an error-proof test of identification or verification.  The most common application has been paternity testing in cases of doubt as to who is the parent.  The addition of DNA evidence into the legal system has also implicated and freed many people of crimes based on what was collected at the crime scene.  DNA fingerprinting is the most reliable biometrics technique that is used to identify an individual.  This unit briefly describes two non-DNA biometrics techniques as well, namely friction ridge pattern analysis and iris recognition.  The fingerprint reader and the iris scanner investigate developmental patterns, thus these techniques can distinguish identical twins.

Unit 8 Time Advisory   show close


Unit 8 Learning Outcomes   show close


8.1 DNA Fingerprinting  

8.1.1 Genetic Identity  

• Reading: Stanford University: Phillip Thurtle’s “The Creation of Genetic Identity”

  Link: Stanford University:  Phillip Thurtle’s “The Creation of Genetic Identity” (HTML)
   
  Instructions: Please study “Budding Concerns: The Creation of Genetic Identity” on this page.
   
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8.1.2 DNA Profiling  

• Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “DNA Forensics”

  Link: U.S. Department of Energy, Office of Science’s Human Genome Project Information:  “DNA Forensics” (HTML)
   
  Instructions: Please study this page.
   
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8.1.3 Short Tandem Repeats  

• Reading: Nature Education’s Scitable: Karen Norrgard’s “Forensics, DNA Fingerprinting, and CODIS”

  Link: Nature Education’s Scitable:  Karen Norrgard’s “Forensics, DNA Fingerprinting, and CODIS” (HTML)
   
  Instructions: Please study the content of this page.  Please note that FBI is using STR sequences from 13 noncoding regions for the identification of individuals; the amelogenin gene is used additionally for gender determination.
   
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• Reading: FBI’s “CODIS Core STR Loci”

  Link: FBI’s “CODIS Core STR Loci” (HTML)
   
  Instructions: Please study the content of this page.  Please note that the STR repeats are used from different chromosomes.  "AMEL" stands for the amelogenin gene, and it is used for sex-typing.
   
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8.2 DNA Evidence in Legal System  

• Reading: Nature Education’s Scitable: Leslie A. Pray’s “Legislative Landmarks of Forensics: California v. Greenwood and Shed DNA”

  Link: Nature Education’s Scitable:  Leslie A. Pray’s “Legislative Landmarks of Forensics: California v. Greenwood and Shed DNA” (HTML)
   
  Instructions: Please read the content of this page.  Please note that the 13 STRs that are currently used for DNA profiling do not reveal medical information.
   
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8.3 Paternity Testing with DNA Fingerprinting  

• Reading: Nature Education’s Scitable: Jill Adams’ “Paternity Testing: Blood Types and DNA”

  Link: Nature Education’s Scitable:  Jill Adams’ “Paternity Testing: Blood Types and DNA” (HTML)
   
  Instructions: Please study the content of this page.  Please note that blood typing is a good and inexpensive starting point in paternity cases.  DNA fingerprinting can be used for high accuracy result.  
   
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• Assessment: The University of Arizona: The Biology Project’s “Problem 10: Determining Paternity”

  Link: The University of Arizona:  The Biology Project’s “Problem 10: Determining Paternity” (HTML)
   
  Instructions: In order to assess your knowledge, complete the “Problem 10: Determining Paternity” activity.  Answer key is provided.
   
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8.4 Tracing Genealogy  

8.4.1 Mitochondrial DNA  

• Reading: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “DNA Forensics”

  Link: U.S. Department of Energy, Office of Science’s Human Genome Project Information: “DNA Forensics” (HTML)
   
  Instructions: Please study the “Mitochondrial DNA Analysis” section on this page.  Please note that mitochondrial DNA is maternally inherited; a mother and her children all have identical mitochondrial DNA.  Thus, mitochondrial DNA is not individual.  On the other hand, it is present in many copies in a cell, which offers higher sensitivity.  Higher sensitivity is crucial, when samples are decayed. Forensic mitochondrial DNA analysis is more elaborate, because it involves sequencing and sequence analysis of the samples.
   
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8.4.2 Y Chromosome  

• Reading: Science Spectra: Neil Bradman and Mark Thomas’ “Why Y?”

  Link: Science Spectra:  Neil Bradman and Mark Thomas’ “Why Y?” (HTML)
   
  Instructions: Please study this page.  Please note that human Y chromosome is paternally inherited.  Males in one paternal lineage have identical Y chromosomes.
   
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8.5 Non-DNA Biometrics  

8.5.1 Fingerprint Reading  

• Reading: Michigan State University: Salil Prabhakar and Anil Jain’s “Fingerprint Identification”

  Link: Michigan State University:  Salil Prabhakar and Anil Jain’s “Fingerprint Identification” (HTML)
   
  Instructions: Please study this page.  Please note that friction ridge pattern analysis is a pattern analysis that is not fully computerized.  Thus, it requires the opinion of experts.
   
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8.5.2 Iris Recognition  

• Reading: John Daugman’s “Iris Recognition”

  Link: John Daugman’s “Iris Recognition” (HTML)
   
  Instructions: Please study this page.
   
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• Assessment: The Saylor Foundation: "BIO403 Unit 8.5 Assessment"

  Link: The Saylor Foundation: "BIO403 Unit 8.5 Assessment" (HTML)
   
  Instructions: You will find link to the "Fingerprint Reading" assessment on this page. This is a multiple choice assessment with one correct answer. Clicking on an answer will bring you to another page. If your answer is correct, then it is acknowledged with a short explanation. Please read the explanation carefully. If you click on a wrong answer, then the click will bring you to a tutorial page. Please study the tutorial page carefully. You will be prompted to return to the assessment and complete it again. Please note that this assessment is a brief introduction to classical friction ridge pattern analysis. The modern high throughput fingerprint analysis is computerized; for example the FBI is using the Integrated Automated Fingerprint Identification system (IAFIS). IAFIS relies on minutia recognition rather than the identification of the basic loop-arch-whorl (LAW) friction ridge patterns. The results of the computerized fingerprint database analysis are further analyzed by several criminalist. This last manual step is once again relies on complex friction ridge pattern recognition, including LAW. Original prints are the courtesy of Frederick Ford.  

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Unit 9: Environmental Biotechnology and Renewable Energy  

This unit focuses on the biotechnology to help clean our environment, with the help of microorganisms.  For a century, microbes have been used to clean our sewage; recently, scientists have begun to create new ways for microbes to aid our environmental cleanup efforts.  This unit focuses on how microbes are grown and cultured for environmental purposes.  We discuss the current state of bioremediation or the use of organisms to clean contaminants from the environment.  We will end with an overview of the current ways we use biotechnology to create renewable sources of energy, such as biodiesel and biogas.

Unit 9 Time Advisory   show close


Unit 9 Learning Outcomes   show close


9.1 Environment and Microbiology  

9.1.1 Environmental Niche of Microbes  

• Reading: Kenneth Todar’s Online Textbook of Bacteriology: “The Impact of Microbes on the Environment and Human Activities”

  Links: Kenneth Todar’s Online Textbook of Bacteriology:  “The Impact of Microbes on the Environment and Human Activities” (HTML)
                                  
  Instructions: Please study all four pages.  Use the “next page” or “chapter continued” buttons at the bottom of the page to access pgs 2-4.
   
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9.1.2 Microbial Growth and Energy  

• Reading: MIT’s Biological Energy Interest Group: Weigele’s “Biology of Hydrogen Production”

  Links:  MIT’s Biological Energy Interest Group: Weigele’s “Biology of Hydrogen Production” (HTML)
   
  Instructions: Please study the content of this page.
   
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9.1.3 Microbial Nutrition and Metabolism  

• Reading: University of South Carolina, School of Medicine’s Microbiology and Immunology Online: Alvin Fox’s “Bacteriology—Chapter Three: Nutrition, Growth and Energy Metabolism”

  Links:  University of South Carolina, School of Medicine’s Microbiology and Immunology Online:  Alvin Fox’s “Bacteriology—Chapter Three: Nutrition, Growth and Energy Metabolism” (HTML)
   
  Instructions: Please study this page.
   
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9.1.4 Chemostat Studies  

• Reading: National Center for Biotechnology Information’s Bookshelf: ASM Press: David R. Drake and Kim A. Brogden’s Polymicrobial Diseases: “Continuous-Culture Chemostat Systems and Flowcells as Methods to Investigate Microbial Interactions”

  Links:  National Center for Biotechnology Information’s Bookshelf:  ASM Press: David R. Drake and Kim A. Brogden’s Polymicrobial Diseases:  “Continuous-Culture Chemostat Systems and Flowcells as Methods to Investigate Microbial Interactions” (HTML)
   
  Instructions: Please study this page.
   
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9.2 Biofilm Reactors  

• Reading: BioMed Central: Microbial Cell Factories: Nasib Qureshi et al.’s “Biofilm Reactors for Industrial Bioconversion Processes: Employing Potential of Enhanced Reaction Rates”

  Link: BioMed Central: Microbial Cell Factories:  Nasib Qureshi et al.’s “Biofilm Reactors For Industrial Bioconversion Processes: Employing Potential of Enhanced Reaction Rates” (HTML or PDF)
   
  Instructions: Please study the content of this page.  You can access the PDF under “viewing options” on the right-hand side of the page.  This is a peer-reviewed publication.
   
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9.3 Bioremediation of Soil  

9.3.1 Soil Organic Matter Characteristics  

• Reading: The Samuel Roberts Noble Foundation’s “What Does Organic Matter Do In Soil?”

  Link: The Samuel Roberts Noble Foundation’s “What Does Organic Matter Do In Soil?” (HTML)
   
  Instructions: Please study the content of this page.
   
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9.3.2 Pesticides  

• Reading: Province of British Columbia: Ministry of Agriculture’s “Environmental Protection”

  Link: Province of British Columbia: Ministry of Agriculture’s “Environmental Protection” (HTML)
   
  Instructions: Please study this page.
  
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9.3.3 Hydrocarbons  

• Reading: National Center for Biotechnology Information’s PubMed: American Society for Microbiology: Microbiological Reviews: Leahy and Colwell’s “Microbial Degradation of Hydrocarbons in the Environment”

  Link: National Center for Biotechnology Information’s PubMed:  American Society for Microbiology: Microbiological Reviews: Leahy and Colwell’s “Microbial Degradation of Hydrocarbons in the Environment” (PDF)
   
  Instructions: In order to access the full manuscript, follow the directions under “Full Text” heading. Please study the full text.  The authors work in the Department of Microbiology at the University of Maryland.
   
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9.3.4 Industrial Chemicals  

• Reading: Green Footsteps’ “Industrial Pollution Causes Land Pollution”

  Link: Green Footsteps’ “Industrial Pollution Causes Land Pollution” (HTML)
   
  Instructions: Please study this page.
   
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9.3.5 In-Situ and Ex-Situ Bioremediation  

• Reading: Federal Remediation Technologies Roundtable’s “In Situ Biological Treatment for Soil, Sediment, Bedrock and Sludge”

  Link: Federal Remediation Technologies Roundtable’s “In Situ Biological Treatment for Soil, Sediment, Bedrock and Sludge” (HTML)
   
  Instructions: Please study this page.
   
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• Reading: Federal Remediation Technologies Roundtable’s “Ex Situ Biological Treatment for Soil, Sediment, Bedrock and Sludge”

  Link: Federal Remediation Technologies Roundtable’s “Ex Situ Biological Treatment for Soil, Sediment, Bedrock and Sludge” (HTML)
   
  Instructions: Please study this page.
  
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9.4 Bioremediation of Air  

9.4.1 Air Pollutants  

• Reading: United States Environmental Protection Agency’s “What Are the Six Common Air Pollutants?”

  Link: United States Environmental Protection Agency’s “What Are the Six Common Air Pollutants?” (HTML)
   
  Instructions: Please read this page, and follow these links to learn about common air pollutants: “Ozone,” “Particulate Matter,” “Carbon Monoxide,” “Nitrogen Oxide,” “Sulfur Dioxide,” “Lead,” “Latest Findings on National Air Quality: Status and Trends,” and within it the air pollutants link; furthermore, please follow all links under the “Health Effects Information” heading.
   
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9.4.2 Degradation of Air Contaminants  

• Reading: Green Solutions Magazine: Maggie Romuld’s “Using Bio-Oxidation to Prevent Air Pollution”

  Link: Green Solutions Magazine:  Maggie Romuld’s “Using Bio-Oxidation to Prevent Air Pollution” (HTML)
   
  Instructions: Please study the content of this page.
   
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9.4.3 Biological Filtration Processes  

• Reading: Rensselaer Polytechnic Institute: Selvi B. Anit and Robert J. Artuz’s “Biofiltration of Air”

  Link: Rensselaer Polytechnic Institute:  Selvi B. Anit and Robert J. Artuz’s “Biofiltration of Air” (HTML)
   
  Instructions: Please study this page.
   
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9.5 Bioremediation of Water  

9.5.1 Major Contaminants of Groundwater  

• Reading: Texas A & M University: Robert Stewards’s “Groundwater Contamination”

  Link: Texas A & M University: Robert Stewards’s “Groundwater Contamination” (HTML)
   
  Instructions: This page summarizes contaminants and it also outlines activities that lead to groundwater contamination.  Please study the entire page.
   
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• Reading: Texas A & M University: Robert Stewart’s “Environmental Science in the 21st Century - Ground Water Contamination”

  Link: Texas A & M University: Robert Stewart’s “Environmental Science in the 21st Century - Ground Water Contamination” (HTML)
   
  Instructions: Please study the content of this page for an overview on ground water contamination.
   
  Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

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9.5.2 Ex Situ Bioremediation  

• Reading: Federal Remediation Technologies Roundtable’s “Ex Situ Biological Treatment for Groundwater, Surface Water, and Leachate”

  Link: Federal Remediation Technologies Roundtable’s  “Ex Situ Biological Treatment for Groundwater, Surface Water, and Leachate” (HTML)
   
  Instructions: Please study the content of this page.
   
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9.5.3 In-situ Bioremediation  

• Reading: United States Environmental Protection Agency’s “In-Situ Groundwater Bioremediation”

  Link: United States Environmental Protection Agency’s  “In-Situ Groundwater Bioremediation” (HTML)
    
  Instructions: Please study the content of this page.
   
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9.5.4 Landfill Biotreatment  

• Reading: Center for Public Environmental Oversight’s “Bio-Reactors”

  Link: Center for Public Environmental Oversight’s “Bio-Reactors” (HTML)
   
  Instructions: Please study this page.
   
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9.6 Emerging Environmental Biotechnologies  

9.6.1 Phytoremediation  

• Reading: United States Department of Agriculture’s “Phytoremediation: Using Plants to Clean Up Soils”

  Link: United States Department of Agriculture’s “Phytoremediation: Using Plants to Clean Up Soils” (HTML)
   
  Instructions: Please study this page.
   
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9.6.2 Biomembrane Reactors  

• Reading: Environmental Thinking: Tony Kobilnyk’s “Energy Savings Using Membrane Bioreactor Technology"

  Link: Environmental Thinking: Tony Kobilnyk’s  “Energy Savings Using Membrane Bioreactor Technology” (HTML)
   
  Instructions: Please study this page.
   
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9.6.3 Sequestering Carbon Dioxide  

• Lecture: Stanford University: Brent Constantz’s “Sequestering Carbon Dioxide in the Built Environment: A Revolutionary Cement Technology”

  Link: Stanford University: Brent Constantz’s “Sequestering Carbon Dioxide in the Built Environment: A Revolutionary Cement Technology” (Adobe Flash)
   
  Also available in:
  iTunes U
  YouTube
   
  Instructions:  Please read the introduction on this page.  Please follow the lecture on YouTube or iTunes as the video box next to the introduction is very tiny.
   
  Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

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9.7 Biotreatment of Metals  

9.7.1 Bioaccumulation  

• Reading: Marietta College: Dave McShaffrey’s “Bioaccumulation & Biomagnification”

  Link:  Marietta College:  Dave McShaffrey’s “Bioaccumulation & Biomagnification” (HTML)
   
  Instructions: Please study the content of the “Heavy Metals and Other Substances” section on this page.
   
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9.7.2 Bioleaching  

• Reading: Universidad Católica de Valparaíso, Chile's Electronic Journal of Biotechnology: Fernando Acevedo’s “Present and Future of Bioleaching in Developing Countries”

  Link:  Universidad Católica de Valparaíso, Chile'sElectronic Journal of Biotechnology:  Fernando Acevedo’s “Present and Future of Bioleaching in Developing Countries” (HTML or PDF)
   
  Instructions: Please study this page. You can access the PDF by clicking the “Reprint (PDF) link above the Abstract.
   
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9.7.3 Biological Methylation  

• Reading: Microbiology: Geoffrey Michael Gadd’s “Metals, Minerals and Microbes: Geomicrobiology and Bioremediation”

  Link: Microbiology:  Geoffrey Michael Gadd’s “Metals, Minerals and Microbes: Geomicrobiology and Bioremediation” (HTML or PDF)
   
  Instructions: Please study the “Metal Mobilization” and “Metal Immobilization” sections on this page. You can access the PDF format in the right-hand side of the page.  Author Gadd works in the Division of Molecular Microbiology, College of Life Sciences at the University of Dundee, UK.  This is a peer-reviewed publication.
   
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9.7.4 Oxidation and Reduction  

• Reading: Society for General Microbiology's Microbiology: Geoffrey Michael Gadd’s “Metals, Minerals and Microbes: Geomicrobiology and Bioremediation”

  Link:  Society for General Microbiology's Microbiology: Geoffrey Michael Gadd’s “Metals, Minerals and Microbes: Geomicrobiology and Bioremediation” (HTML or PDF)
   
  Instructions: Please study the “Reductive Transformations, Nanoparticle Formation and Nano-Biotechnology” section on this page.  You can access the PDF format in the right-hand side of the page.  Author Gadd works in the Division of Molecular Microbiology, College of Life Sciences at the University of Dundee, UK.  This is a peer-reviewed publication.
   
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9.8 Renewable Energy  

9.8.1 Bioalcohols  

• Reading: Wikipedia’s “Alcohol Fuel”

  Link: Wikipedia’s “Alcohol Fuel” (PDF)
   
  Instructions: Please study this page.  Please note that not all alternative fuels are produced without using microorganisms; for example, esterification, a chemical reaction, is used to make biodiesel, and fractional distillation, a physical method, is employed to make green diesel.  Methods that do not use living organisms for production are not covered in this course.
   
  Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0 (HTML).  You can find the original Wikipedia version of this article here (HTML).

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9.8.2 Biogas  

• Lecture: YouTube: Bioconstructer’s “How Does a Biogas Plant Work?”

  Link: YouTube: Bioconstructer’s “How Does a Biogas Plant Work?” (YouTube)
   
  Instructions: Please watch the video (10 minutes).  Note that this process uses fermentation.
   
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9.8.3 Biohydrogen  

• Reading: National Center for Biotechnology Information’s PubMed: Springer: Photosynthesis Research: Hemschemeier et al.’s “Analytical Approaches to Photobiological Hydrogen Production in Unicellular Green Algae”

  Link: National Center for Biotechnology Information’s PubMed: Springer: Photosynthesis Research: Hemschemeier et al.’s “Analytical Approaches to Photobiological Hydrogen Production in Unicellular Green Algae” (HTML)
   
  Instructions: Please study this publication, because it explains several approaches for biohydrogen production.  Please note that genetically engineered microorganisms are in the focus of biohydrogen production.  This is a peer-reviewed publication.
   
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• Assessment: The Saylor Foundation’s "BIO403 Unit 9.8 Assessment"

  Link: The Saylor Foundation’s "BIO403 Unit 9.8 Assessment" (HTML)
   
  Instructions: Please click on the link above to launch the "Biohydrogen" assessment.  This is a multiple choice assessment with one correct answer.  Clicking on an answer will bring you to another page.  If your answer is correct, then it is acknowledged with a short explanation.  Please read the explanation carefully.  If you clicked on a wrong answer, then the click will bring you to a tutorial page.  Please study the tutorial page carefully.  You will be prompted to return to the assessment and complete it again.  Please note that this assessment is focusing on the regulation of molecular hydrogen evolution in microbes.  Biohydrogen is a promising renewable energy source; it is novel and requires appropriate safety measures

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9.8.4 Algae Fuel  

• Reading: MIT’s Technology Review: Kevin Bullis’s “Fuel from Algae”

  Link: MIT’s Technology Review: Kevin Bullis’s “Fuel from Algae” (HTML)
   
  Instructions: Please study this page. Note that genetically engineered algae is used to make oil.
   
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Unit 10: Emerging Biotechnology Fields  

Our last unit looks at some emerging areas of biotechnology.  Immune-based biotechnology, for example, utilizes our highly sophisticated and potent immune system to do certain tasks like destroying tumor cells.  Another example, nanobiotechnology, looks at cellular processes not as microscopic things but as large-scale assemblers and builders.  Pathway engineering tries to create entire new sets of reaction pathways so that we might one day be able to convert toxic waste into something useful, such as table sugar! 

Unit 10 Time Advisory   show close


Unit 10 Learning Outcomes   show close


10.1 Nanobiotechnology  

10.1.1 The Nanometer Scale  

• Reading: Wikipedia’s “Nanobiotechnology”

  Link: Wikipedia’s “Nanobiotechnology” (PDF)
   
  Instructions: Please study the content of this page.
   
  Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0 (HTML).  You can find the original Wikipedia version of this article here (HTML).

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10.1.2 Atomic-Scale Visualization  

• Reading: Nanoscience’s “Atomic Force Microscopy”

  Link: Nanoscience’s “Atomic Force Microscopy” (HTML)
   
  Instructions: Please study this page.
   
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10.1.3 Nanoparticles for Drug Delivery  

• Reading: National Center for Biotechnology Information’s PubMed: Dove Medical Press Limited: Wim De Jong and Paul Borm’s “Drug Delivery and Nanoparticles: Applications and Hazards”

  Link: National Center for Biotechnology Information’s PubMed: Dove Medical Press Limited: Wim De Jong and Paul Borm’s “Drug Delivery and Nanoparticles: Applications and Hazards” (HTML or PDF)
   
  Instructions: Please study the content of this page.  You can access the PDF from the top right corner of the page.  This is a peer-reviewed publication.
   
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10.1.4 Biomolecular Motors  

• Reading: Nano Science and Technology Institute: Srinivas Iyer, et al.’s “Biomolecular Motors”

  Link: Nano Science and Technology Institute:  Srinivas Iyer, et al.’s “Biomolecular Motors” (HTML)
   
  Instructions: Please study the content of this page.
   
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10.1.5 Nanosensors  

• Reading: Oak Ridge National Laboratory’s “Nanosensor Probes Single Living Cells”

  Link: Oak Ridge National Laboratory’s “Nanosensor Probes Single Living Cells” (HTML)
   
  Instructions: Please study this page.
   
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10.2 Biowarfare  

• Reading: Federation of American Scientists’ “Introduction to Biological Weapons”

  Link: Federation of American Scientists’ “Introduction to Biological Weapons” (HTML)
   
  Instructions: Please study this page.
   
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10.3 Immunology Biotechnology  

10.3.1 Monoclonal Antibodies  

• Reading: Davidson College: Department of Biology’s “Monoclonal Antibodies”

  Link: Davidson College: Department of Biology’s  “Monoclonal Antibodies” (HTML)
   
  Instructions: Please study this page.
   
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10.3.2 Antibody Engineering and Constructs  

• Reading: National Center for Biotechnology Information’s PubMed: e-Century Publishing Corporation's American Journal of Translational Research: Peter D. Burbelo et al.’s “Synthetic Biology for Translational Research”

  Link: National Center for Biotechnology Information’s PubMed: e-Century Publishing Corporation's American Journal of Translational Research:  Peter D. Burbelo et al.’s “Synthetic Biology for Translational Research” (HTML or PDF)
   
  Instructions: Please study the “Synthetic Biology for Immunoassay Diagnostics” section on this page.  You can access the PDF from the top right corner of the page.  The authors work at the National Institute of Health, Bethesda.  This is a peer-reviewed publication.
   
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10.3.3 Antibody Therapies  

• Reading: Mayo Clinic’s “Monoclonal Antibody Drugs for Cancer Treatment: How They Work”

  Link: Mayo Clinic’s “Monoclonal Antibody Drugs for Cancer Treatment: How They Work” (HTML)
   
  Instructions: Please study this page.
   
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10.3.4 Edible Vaccines  

• Reading: Indian Journal of Medical Microbiology: Lal, et al.’s “Edible Vaccines: Current Status and Future”

  Link: Indian Journal of Medical Microbiology: Lal, et al.’s “Edible Vaccines: Current Status and Future” (HTML)
   
  Instructions: Please study the content of this page.  The authors work at the University College of Medical Sciences, Guru Teg Bahadur Hospital, New Delhi.  This is a peer-reviewed publication.
   
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10.3.5 Immune-Based Cancer Therapies  

• Reading: John W. Kimball’s Biology Pages: “Cancer Immunotherapy”

  Link: John W. Kimball’s Biology Pages: “Cancer Immunotherapy” (HTML)
   
  Instructions: Please study the content of this page.
   
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10.4 Stem Cells  

10.4.1 Embryonic and Adult Stem Cells  

• Reading: Nature Education’s Scitable: Sonia Y. Hunt’s “Controversies in Treatment Approaches: Gene Therapy, IVF, Stem Cells, and Pharmacogenomics”

  Link: Nature Education’s Scitable: Sonia Y. Hunt’s “Controversies in Treatment Approaches: Gene Therapy, IVF, Stem Cells, and Pharmacogenomics” (HTML)
   
  Instructions: Please study the “Gene Therapy” and “Stem Cell Therapy” sections on this page.  Totipotency means the ability to differentiate to any type of cell.  Other potencies are more limited in what the cells can transform into. 
   
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• Web Media: Khanacademy’s “Embryonic Stem Cells”

  Link: Khanacademy’s “Embryonic Stem Cells” (Adobe Flash)
   
  Also available in:
  YouTube
   
  Instructions: Please watch the video (20 minutes).
   
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10.4.2 New Paradigms for Therapy  

• Reading: National Center for Biotechnology Information’s PubMed: Journal of Experimental and Clinical Assisted Reproduction: Jason Hipp and Anthony Atala’s “Tissue Engineering, Stem Cells, Cloning, and Parthenogenesis: New Paradigms for Therapy”

  Link:  National Center for Biotechnology Information’s PubMed: Journal of Experimental and Clinical Assisted Reproduction: Jason Hipp and Anthony Atala’s “Tissue Engineering, Stem Cells, Cloning, and Parthenogenesis: New Paradigms for Therapy” (HTML or PDF)
    
  Instructions: Please study the content of this page. You can access the PDF from the top right corner of the page.  This is a peer-reviewed publication.
   
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10.5 Pathway Engineering  

10.5.1 Degradation of Starch and Cellulose  

• Reading: National Center for Biotechnology Information’s PubMed: Journal of Royal Society Interface: Christopher E. French's "Synthetic Biology and Biomass Conversion: a Match Made in Heaven?"

  Link: National Center for Biotechnology Information’s PubMed: Journal of Royal Society Interface: Christopher E. French's "Synthetic Biology and Biomass Conversion: a Match Made in Heaven?" (HTML)
   
  Instructions: Please study the “1. Introduction”, " 2.3. Commercial Biomass Conversion Processes", and " 2.4. Transfer of Cellulose Degradation Capability to Heterologous Hosts" sections on this page.
   
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• Reading: Society for General Microbiology's Microbiology: Rainer Kalscheuer, et al.’s “Microdiesel: Escherichia coli Engineered for Fuel Production”

  Link:  Society for General Microbiology's Microbiology:  Rainer Kalscheuer, et al.’s “Microdiesel: Escherichia coli Engineered for Fuel Production” (HTML or PDF)
   
  Instructions: Please study the content of “Introduction,” “Fig. 1. Pathway of FAEE Biosynthesis in Recombinant E. coli,” “Fig. 4. Map of Plasmid pMicrodiesel,” and “Discussion” on this page.  You can access the PDF from the right-hand side of the page.  Authors work in the Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Germany.  This is a peer-reviewed publication.
   
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10.5.2 Biorefining of Fossil Fuel  

• Reading: Biomass Magazine: Erin Voegele’s “ORNL Team Converts Cellulose into Isobutanol”

  Link: Biomass Magazine: Erin Voegele’s “ORNL Team Converts Cellulose into Isobutanol” (HTML)
   
  Instructions: Please study this page.
   
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10.5.3 Antibiotics Engineering  

• Reading: Stanford University: Dawn Levy’s “Genetic Engineering Speeds Development of New Antibiotics”

  Link: Stanford University: Dawn Levy’s “Genetic Engineering Speeds Development of New Antibiotics” (HTML)
    
  Instructions: Please read this page.
   
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10.5.4 Gene Doping  

• Reading: Nature Education’s Scitable: Leslie A. Pray’s “Sports, Gene Doping, and WADA”

  Link:  Nature Education’s Scitable:  Leslie A. Pray’s “Sports, Gene Doping, and WADA” (HTML)
   
  Instructions: Please study the content of this page.
   
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• Assessment: The Saylor Foundation: "BIO403 Unit 10.5 Assessment"

  Link: The Saylor Foundation: "BIO403 Unit 10.5 Assessment" (HTML)
   
  Instructions: You will find link to the "Pathway Engineering – Gene Therapy" assessment on this page. This is a multiple choice assessment with one correct answer. Clicking on an answer will bring you to another page. If your answer is correct, then it is acknowledged with a short explanation. Please read the explanation carefully. If you click on a wrong answer, then the click will bring you to a tutorial page. Please study the tutorial page carefully. You will be prompted to return to the assessment and complete it again. Please note thatmetabolic pathway engineering takes place during gene therapy.

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10.6 Synthetic Genomics  

• Reading: Wikipedia’s “Mycoplasma Laboratorium”

  Link: Wikipedia’s “Mycoplasma Laboratorium” (PDF)
   
  Instructions: Please study the content of this page.
   
  Terms of Use: The article above is released under a Creative Commons Attribution-Share-Alike License 3.0 (HTML).  You can find the original Wikipedia version of this article here (HTML).

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Final Exam  

• Final Exam: The Saylor Foundation's BIO403 Final Exam

  Link: The Saylor Foundation's BIO403 Final Exam
  
  Instructions: You must be logged into your Saylor Foundation School account in order to access this exam.  If you do not yet have an account, you will be able to create one, free of charge, after clicking the link.

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