Applications of Biotechnology & Genomics
Biotechnology: “The use of biological systems to create goods & services" (Bio3950, Drs Marshall & Carr)
       Clinical :     Diagnosis & Treatment of human genetic diseases
       Forensic :  Data  Evidence in legal proceedings
                            Identification of unknown or questioned material
       Commercial : Production of transgenic products & organisms
                                 Improvement of production traits of agricultural species

Genomics: the study of complete gene sets (genomes) of organisms (Bio4251, Dr Rise)
        Proteomics: study of coordinate protein expression patterns across genomes (Bio4255, Dr Bykova)
                                "There is one genome, there are many proteomes."
        Bioinformatics:  computational analysis of genomic & proteomic data (Bio3951, Dr Peña-Castillo)
        Advanced Genetics: In-depth consideration of molecular & classical genetics (Bio4241, Dr Carr)
Restriction Fragment Length Polymorphism (RFLP) Analysis

  Restriction maps vary among  species &  individuals according to DNA sequence
       SNPs may produce Restriction Fragment Length Polymorphism (RFLPs)
       RFLPs are inherited in Mendelian co-dominant alleles

  Variation in the pattern of restriction digests identifies point mutations
   RFLPs may indicate point mutations (SNPs) directly
       Ex.: MstII RFLP test differentiates sickle-cell HbS versus HbA alleles [HOMEWORK]
   RFLPS can be genetic markers for specific alleles
       marker: restriction site shows presence / absence of genetically linked trait  [HOMEWORK]
            Markers do not cause the traits!
            Restriction fragment pattern indicates which trait alleles are present          

       Useful in combination with amniocentesis for in utero genetic diagnosis
            Cells, fluids, & DNA from at-risk fetus can be examined genetically

Allele-Specific Oligonucleotides (ASOs)

   Allelic differences are due to single SNPs
        ASOs are SNP-specific probes
             [Probe: instrument or method that measures something: e.g., thermometer]
    "Southern Blot" test without electrophoresis, probe "sticks" to only one allele:
            genetic screen is "positive or negative" result
            Ex.: 508-ASO Test for Cystic Fibrosis probes deletion mutation (OMIM219700)
       
    Pre-Natal Screening: the GATACCA model

       Ex.: Mr. & Ms. Mus seek genetic counselling ....
       Ex.: Pre-implantation Genetic Diagnosis (PGD) [NPR story]

   See also Species-Specific Oligonucleotides (SSOs)

DNA Fingerprinting
    Determination of an individual-specific genetic patterns
  
  Variable Number of Tandem Repeat (VNTR) loci

        Short DNA motifs repeated many times 
        Minisatellites - 15~100 nucleotide motifs repeated several times
        Microsatellites - di-, tri-, tetra-nucleotide motifs repeated 101s ~ 106s of times
                                      (CACACACACACA versus CACACACA)
         Origin by slipped-mismatch replication
         Copy number mutates rapidly, even between parents & children
             VNTR loci are highly polymorphic  [HOMEWORK]
                  good marker for within-population studies
                  [Animation of DNA Fingerprinting for forensics ]


        Forensics - use of DNA data as legal evidence
             Positive identification of individuals with high probability
                  [For an extended lecture on DNA Forensics, click here]

DNA "Chips"
       Oligonucleotide probes ("oligos") immobilized on a glass chip
              randomly-cut genomic DNA is tagged & used to "probe" the chip
              [click here for an animation of DNA microarrays]

      "Variant Detector Arrays (VDAs)" detect specific SNP alleles in genome                                                             

       "GeneChips" perform automated "Northern" analysis:
             specific mRNAs or cDNAs are detected in proteome
            "pseudo-colours" indicate levels of gene expression

       DNA "re-sequencing arrays" sequence of 30~500 Kbp in one experiment

Transgenic organisms
        transgenes: re-combination of genetic material from different species

             Recombinant DNA functions in a biological system
                   "Strong" bacterial promoter + eukaryotic gene of interest
                "reporter gene" for luciferase indicates presence of transgene expression
             Transgenic plants created via naturally-occuring Ti Plasmids

                     plants can be regenerated from calluses

              Ocean-farmed Transgenic Salmon - a debate

    Commercial production processes
           Diabetes formerly treated with Insulin extracted from cow pancreas
           Human Insulin can be cloned & expressed in bacteria
                "A" & "B" chains cloned separately / Proinsulin cloned & cleaved
                    [ cf. ordinary post-translational processing ]
 
     Gene Therapy
             Ex.: Growth-Hormone Therapy in  mice
                        transgene incorporated stably & inherited in Mendelian manner

Genomics: the genetic study of entire genomes

    The Human Genome Project  (sponsored by HuGO)
               A statement of genetic ethics (Lee et al. 2008)
     2.85 x 109 basepair (2,850 Mbp) genome sequence completed
                10-year project: first draft announced: March 2001 (Venter et al. 2001)
                     'Finished' draft of euchromatic sequence: October 2004
                     Personal Genome Sequence of James Watson: June 2007
                 Similar projects completed in Drosophila & Mouse
                    Genome projects underway in multiple species [Current list]

   'Top Down' Strategy: Move from large-scale  fine-scale map
            Large-scale mapping of chromosomes  provides "scaffold"
            Fine-scale mapping of individual genes
            Sequence contigs   complete genome

  Insights: < 25,000 protein-coding genes in human genome
              only 6,000 have known functions
                  ~ 7,000 novel genes in Homo wrt Drosophila
               Comparison of Homo wrt Chimpanzee (Pan) genome: ~ 98.44% similar
                   Differences? non-functional human caspase-12 gene implicated in Alzheimer’s

-------------------- Final Exam coverage stops HERE in 2011 -----------------------

           Expressed Sequence Tags) (ESTs)
                   partial sequences of 5' ends of cDNAs
                  cDNA "expressed" DNA sequence presumptive "gene"
                  Sequences of ESTs with unknown functions [from "non-model" species]
                       compared with genes of known function from "genome-enabled" species

          Single Nucleotide Polymorphisms (SNPs) occur at intervals of <1,000 bp:
                > 90% of genes have known SNPs
                 Hypothesis: almost everyone is heterozygous at every locus

     Proteomics: the total pattern of protein expression in an organism
            There is one genome, but many proteomes:
             DNA Chips to explore life-stage & tissue-specific patterns

     Bioinformatics: extracting biological information from (huge) data sets
          Species identification via mtDNA forensics: "How To Tell a Sea Monster"

            NADH2 sequence identified from GenBank


     Next-Generation Sequencing (NGS) - clinical applications


Local Genomics projects: Biodiversity applications
      Genetics & Hereditary Disease in Newfoundland
      Genomic variation in the founding population of Newfoundland
            Cod & Pollock: Multiple origins of Pacific species
            Atlantic Cod: the "Out of Newfoundland" Hypothesis
            Harp Seals: Differentiation of  breeding grounds

All text material ©2011 by Steven M. Carr