Genomes and Genomics - Mississippi Genome Exploration Laboratory - MGEL - Daniel G. Peterson - Genomics, Cytogenetics, Molecular Genetics

GENOMES & GENOMICS

NOTE: Students enrolled in Genomes & Genomics can access class handouts, study tools, diagrams, their grades, test keys, etc., through MS State's WebCT.

1. CATALOG DESCRIPTION
PSS/BCH 8653. Genomes and Genomics. (3) Three hours lecture. (Prerequisites: BCH 4113/6113 or BCH 4713/6713 or BCH 8643 or consent of instructor). Overview of genome structure and evolution with emphasis on genomics, the use of molecular biology, robotics, and advanced computational methods to efficiently study genomes.

2. DETAILED COURSE OUTLINE
This course meets twice per week for 1 hours per lecture.

Unit 1. Fundamental Biological Concepts
    A. Genome and Genomics
        1. Definitions
        2. Things with genomes and things without genomes
    B. Editorial: "Failure of Scientific Education" and "The Balance of Nature"
    C. Fundamental biological concepts
        1. Central Dogma of Genetics
        2. Genetic Code
        3. Nucleic Acids
        4. Replication
        5. Transcription
        6. Translation
        7. Genes, alleles, and loci
        8. Recombination
Unit 2. Molecular Biology and Molecular Mapping
    A. Restriction enzymes
    B. Molecular cloning
        1. Constituents of a clone
        2. Plasmid features
            a. Antibiotic resistance genes
            b. Alpha-complementation
            c. Partitioning and replication
        3. Ordered libraries
        4. Robot clone picking
        5. Clone archival
    B. Plasmid preparation
        1. Manual
        2. Robotic
    C. Sequencing
        1. Sequencing centers
        2. ABI 3730
    D. Computers
        1. Bioinformatics
        2. Computational biology Unit
    C. DNA libraries
        1. cDNA
        2. Genomic
        3. Expression
    D. Gel electrophoresis
        1. Standard agarose
        2. Pulsed-field gel electrophoresis (PFGE)
    E. Molecular markers
        1. Restriction fragment length polymorphisms (RFLPs)
        2. Molecular mapping
    G. Blotting techniques
    H. Polymerase Chain Reaction (PCR)
    I. Fluorescence in situ hybridization (FISH)
Unit 3. DNA Sequencing
    A. Chemical sequencing (Maxam-Gilbert sequencing)
    B. Chain termination sequencing (Sanger sequencing)
        1. Original Sanger sequencing
        2. Dye terminators
        3. Cycle sequencing
        4. Capillary electrophoresis
        5. Modern Sanger sequencing
    B. Synthesis sequencing
        1. Pyrosequencing
            * 454/Roche sequencing
        2. Fluorescent in situ sequencing (FISSEQ)
            * Illumina sequencing
    C. Primer-based sequencing
            * ABI SOLiD sequencing
    D. Nanopore sequencing, etc.
Unit 4. Prokaryotic Genomes
    A. Introduction
    B. Prokaryotes
        1. Characteristics
        2. Monera
        3. Archaea
    C. The Prokaryotic Cell
    D. The Prokaryotic Genome
        1. Bacterial chromosome
        2. Archaeal chromosome
    E. Prokaryotic Genes Unit
Unit 5. Viral Genomes
    A. Definition of Virus
    B. Structure - Virion shapes
    C. Transfection
    D. Viroids
    E. Virus reproductive cycle
        1. Lytic reproductive cycle
        2. Lysogenic reproductive cycle
        3. Enveloped virus reproduction cycle
    F. Plant viruses
    G. Types of Viral genomes
        1. DNA viruses
        2. RNA viruses
        3. Retroviruses - Generic retrovirus genome
    H. Transduction
Unit 6. Organellar Genomes
    A. Introduction to chloroplasts & mitochondria
    B. Endosymbiont theory
    C. Secondary endosymbiosis
    D. Chloroplasts
    E. Mitochondria
    F. Reproduction of mitochondria and chloroplasts
    G. Maternal inheritance of mitochondria
Unit 7. Eukaryotic Genomes
    A. Eukaryotes Definition
    B. Ring of Life
    C. Characteristics of eukaryotes
    D. Eukaryotic genomes
        1. Ploidy, Polyploidy, and Aneuploidy
        2. C-value and the C-value paradox
        3. Gene duplication
        4. Repetitive DNA
    E. Eukaryotic genes
        1. Exons
        2. Introns
        3. Spliceosome and alternative RNA splicing
        4. Regulation of eukaryotic genes
        5. Induction
        6. Eukaryotic vs. prokaryotic gene regulation
        7. Other gene control mechanisms
        8. Promoter model
    F. Gene expression
        1. Enhancers
        2. Silencers
        3. Insulators and Insulators in imprinting
    G. Gene islands and interspersion
    H. Gene evolution and speciation
    I. Differential gene expression
Unit 8. Mobile Elements
    A. DNA elements
        1. Autonomous
            * Standard DNA transposons
            * Helitrons
            * Mavericks/Polintons
        2. Non-autonomous
            * MITEs
    B. Retroelements
        1. Autonomous
            * LTR retroelements
                - Gypsy elements
                - Copia elements
            * LINEs
            *SINEs
        2. Non-autonomous

    C. The origin of mobile elements
    D. Mobile elements and genome evolution
        1. Gene expression
        2. Generation of new genes
        3. Diversity
Unit 9. DNA Reassociation Kinetics
    A. Cot analysis
        1. Cot
        2. Cot point
        3. Cot curve
            a. Curve analysis
            b. Single component Cot curves
            c. Two Cot decade region
            d. DNA outside of the Cot curve
            e. Small genome eukaryotes
            f. Large genome eukaryotes
            g. What we learn from Cot curves
        4. Calculating genome size
        5. Reassociation rate
        6. Sequence complexity
        7. Kinetic complexity
    B. Fractionating genomes (Cot filtration)
Unit 10. Nucleus and Chromatin
    A. Nuclei
        1. Size and shape
        2. Nucleus structure
            a. Envelope
            b. Pores
            c. Lamina
            d. Matrix
    B. Chromatin
        1. Matrix attachment regions (MARs)
        2. Scaffold attachment regions (SARs)
        3. Eukaryotic nucleosomes
        4. 10 nm chromatin fiber
        5. 30 nm chromatin fiber
        6. Eukaryotic chromosome condensation
        7. Nucleosomes & transcription
    C. Euchromatin and heterochromatin
        1. Definitions
        2. CpG islands
        3. Types of heterochromatin
        4. Position-effect variegation (PEV)
        5. Nucleolus Unit
Unit 11. Chromosomes & Cell Cycle
    A. Chromosomes
        1. Homologous chromosomes
        2. Idiogram and karyotype
        3. Sister chromatids
        4. Nucleolus Organizer Regions (NORs)
    B. Cell cycle of eukaryotes
    C. Euploidy & aneuploidy
    D. Chromosome aberrations
Unit 12. Meiosis, Recombination, and Sex
    A. Meiosis and sex
        1. Fertilization
        2. Meiosis and ploidy
        3. Meiocytes
        4. Mixis and apomixes
        5. Amixis
    B. Evolution of meiosis
    C. Results of meiosis
    D. Stages and substages of meiosis
    E. Sex, meiosis, & diversity
Unit 13. Physical Mapping
    A. BACs
        1. BACs vs. YACs
        2. BAC vectors
        3. Ordered BAC libraries
        4. Genome coverage
    B. Macroarrays
    C. Probes
        1. ESTs
        2. Molecular markers
        3. Sequence tagged sites (STSs)
        4. Sequence tagged connectors & BAC end sequences
        5. Overgos
    D. Traditional Physical mapping
        1. Steps in traditional physical mapping
        2. Minimum tiling paths
        3. Insert sizes
    E. Sequencing BACs
    F. Cytomolecular mapping
Unit 14. Genome Sequencing
    A. Sequencing strategies
        1. Whole genome shotgun sequencing (WGSS)
        2. Clone-by-Clone Sequencing
        3. Gene enrichment
            a. EST sequencing
            b. Methylation Filtration (MF)
            c. Cot Filtration (CF)
            d. Gene enrichment combinations
        4. Bar Code-Based Physical Mapping/Sequencing
    B. Assembly
    C. Utilizing whole genome sequences
Unit 15. Gene Expression
    A. ORFs (open reading frames)
    B. Differential gene expression techniques
        1. Northern blotting
        2. EST sequencing
        3. Microarrays
        4. Gene microarrays
    C. Microarray methods
        1. Quantifying gene expression
        2. Changes in expression over time
        3. Large-scale expression analysis
        4. Unigene sets
        5. Limitations
Unit 16. Functional Genomics
    A. Transgene expression
        1. Principles and applications
        2. Limitations
    B. Gene knockout
        1. Principles and applications
        2. Limitations
    C. RNAi - gene knockdown
        1. Principles and applications
        2. Limitations
    D. Yeast two-hybrid system
        1. Principles and applications
        2. Limitations
Unit 17. Genomic Diversity
    A. A genome sequence?
    B. SNPs and indels
    C. SNPs as molecular markers
    D. Reference genomes
    E. Detecting SNPs and indels
    F. Resequencing techniques
        1. DNA resequencing techniques
        2. Oligonucleotide chips
        3. Array-based resequencing
        4. Detecting base mismatches
        5. DHPLC
        6. Flow cytometry

Last Lecture: Demonstration of Genomics Robots

Grading Scale: Students will be assigned grades using a traditional grading scale (A, B, C, D, and F).

Each student is required to write an overview of his/her dissertation or thesis research project. The overview is limited to a 1 to 2 page Project Description and a References Cited page(s) (i.e., a page providing an alphabetized listing of publications cited in the Project Description). The Project Description should provide key background information, outline the main goals of the project, and provide an overview of the methods to be utilized. In addition, it should clearly discuss the value of the project (directly or indirectly) to humankind. Students can summarize preliminary research results if desired. The Project Description should be prepared so that it can be readily understood by someone with a moderate knowledge of biology (e.g., someone with a B.S. degree in biological sciences). References should be cited in the text and listed on the References Cited page using the format described below. Ask Dr. Peterson if you have questions about citation format and appropriateness.

References should be cited in the text using the Harvard (name−date) system. Where there are three or more authors, only the first author's name should appear, followed by et al. Where several references are cited at the same point in the text, these should be arranged in chronological order. In the References Cited list, citations should be arranged in alphabetical order. References should include: names and initials of all authors; year of publication; full title of the article; source using abbreviations for journals as shown in Index Medicus; volume number; and first and last page numbers. Abstracts should be identified as such. For citations from books, the chapter title should be followed by the names and initials of all editors, the title of the book, edition, place of publication, publisher and first and last page numbers.

Examples:

Bunge J, Epstein SS, Peterson DG (2006) Comment on "Computational Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil." Science 313: 918.

Lamoureux D, Peterson DG, Li W, Fellers JP, Gill BS (2005) The efficacy of Cot-based gene enrichment in wheat (Triticum aestivum L.). Genome 48: 1120-1126.

Peterson DG (2005) Reduced representation strategies and their application to plant genomes. In: The Handbook of Plant Genome Mapping: Genetic and Physical Mapping. Edited by: Meksem K, Kahl G. WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany. pp. 307-335.

Wicker T, Robertson JS, Schulze SR, Feltus FA, Magrini V, Morrison JA, Mardis ER, Wilson RK, Peterson DG, Paterson AH, Ivarie R (2005) The repetitive landscape of the chicken genome. Genome Res. 15: 126-136.

Only accepted papers should be referenced; all other material should be referred to in the text as 'in preparation', 'personal communication,' or 'unpublished observations' and should not be included in the reference list.

World Wide Web: All references should include the same information that would be provided for a printed source (or as much of that information as possible). The Web information is then placed at the end of the reference. It is important to use "Retrieved from" and the date because documents on the Web may change in content, move, or be removed from a site altogether. To cite a Web site in text (but not a specific document), it is sufficient to give the address (e.g., http://www.apa.org) there and no reference entry is needed. However, when citing a particular web page a citation in the text (e.g., Gaten 2000) and an entry in the reference list will be required.

For example:

Gaten E. (2000) Internet references. Retrieved from http://www.le.ac.uk/biology/teach/mod300/ecitations.html on 19-Sep-2000.

One of the most comprehensive guides to citing internet references is provided by the American Psychological Association: http://www.apastyle.org/elecref.html

4. JUSTIFICATION AND LEARNING OUTCOME
Justification
The DNA of an organism is referred to as its genome. An organisms genome contains it genes, i.e., those DNA sequences that underlie the heritable traits that are responsible for the appearance, structure, function, and ultimately the evolutionary success/failure of that organism. While genes are not the only sequences found in genomes, genes function and evolve within the context of genomes. Consequently, genome research represents a gateway through which we may be able to understand and manipulate genes in living organisms. The potential applications of such knowledge include curing human/animal/plant diseases, manufacturing patient-specific pharmaceuticals, improving crop plants and domesticated animals, development of cost effective biofuels, and more efficient protection of the planets biological diversity.

Genomics is a rapidly growing branch of genome research in which robotics, automated DNA sequencing, and advanced computational methods are used to rapidly and efficiently characterize the genes and numerous other DNA sequences found within genomes. Ultimately the goal of genomics is to understand genes and their relationships to each other, non-gene sequences, proteins, metabolic pathways, and morphological and physiological characteristics. Such an ambitious goal requires the participation of numerous scientists with diverse backgrounds including molecular biologists, computer scientists, engineers, plant/animal breeders, mathematicians, statisticians, physicists, chemists, etc. The multi-disciplinary nature of genomics and its potentially enormous benefits have made genomics a rapidly growing industry, employing a diverse group of hundreds-of-thousands of individuals worldwide.

It is to the advantage of Mississippi State University to provide its students with the background they need to participate in a workplace in which genomics is becoming more and more prevalent. However, at present there is no regular course taught at MS State that has genome biology/genomics as its central focus. Genomes and Genomics will remedy this deficiency in a way that engages students from multiple disciplines across campus and help prepare them for active roles in genomic research.

Learning Outcome
Students that take Genomes and Genomics will receive...

First Exam	25%	125 points
Second Exam	25%	125 points
Writing Assignment	20%	100 points
Final Exam	30%	150 points
Total	100%	500 points