Principles of Biotechnology & Genomics
Biotechnology: "The use of biological systems to create goods & services"
       Medical:          Diagnosis & Treatment of human genetic conditions
                                    CRISPR-cas9-based treatment for Sickle Cell Anemia (Dr Curtis French)
        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
                               GMO tomatoes, "Golden Rice"

Genomics: the study of complete gene sets (genomes) of organisms
        Proteomics: study of coordinated protein expression patterns across genomes
                                "Only one genome, but many proteomes"
                              Genome expression varies by tissue, life stage, medical condition, etc.
        Bioinformatics:  computational analysis of genomic & proteomic data
Restriction Fragment Length Polymorphism (RFLP) analysis

  Restriction maps vary among individuals & species according to DNA sequence
       SNPs alter restriction sites & produce Restriction Fragment Length Polymorphisms (RFLPs)
       RFLPs inherited as Mendelian co-dominant alleles

  Variation in the pattern of restriction digests identifies point mutations
   RFLP may indicate point mutation (SNP) directly
       Ex.: MstII RFLP test differentiates sickle-cell HbS versus HbA alleles
   RFLP can be genetic marker for allele of interest
       marker: restriction site shows presence / absence of genetically linked trait  [HOMEWORK]
            Phenotypic markers do not cause genetic traits!

Allele-Specific Oligonucleotides (ASOs)

   Allelic differences due to single SNPs
        ASOs used as SNP-specific probes
        "Southern Blot" without electrophoresis, probe "sticks" to only one allele:
            Genetic screen "positive / 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 counseling ....
       Ex.: Pre-implantation Genetic Diagnosis (PGD)

  Species-Specific Oligonucleotides (SSOs)

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

                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 [HOMEWORK] with high probability
              CODIS Multiplex Fingerprinting

DNA "Chips"
       Oligonucleotide probes ("oligos") immobilized on glass chip
              randomly-cut genomic DNA tagged & "probes" chip
                [Animation of DNA microarrays]

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

       "GeneChips" perform automated "Northern" analysis:
             specific mRNAs / cDNAs detected in proteome
            "Heat Map" indicate levels of gene expression by cool & hot colors

       DNA "re-sequencing (iterative) array" sequences ~500 Kbp in one experiment

Genomics: genetic analysis of entire genomes    
               The Human Genome Project  (sponsored by HuGO)
               A statement of genetic ethics (Lee et al. 2008)
     3.2 x 109 base pair (3,200 Mbp) genome sequence completed (2003)
               Genome projects underway in multiple species

  Insights: ~ 20,050 protein-coding "genes" in human genome
                  ~   6,000 have unknown functions
                  Function explored with Expressed Sequence Tags (ESTs)
                       partial sequences of 5' ends of cDNA reverse transcribed from mRNA
                           cDNA   DNA sequence expressed as mRNA  presumptive "gene"
                           Sequence of EST with unknown function found in "non-model" species
                               compared with genes of known function from "genome-enabled" species

             >60% of genome without typical genetic function
                       repetitive DNA arranged tandem or dispersed repeats
                       Alu repeat family constitutes 11% of human genome: affects splicing & transcription

              only  ~ 7,000 novel genes in Homo wrt Drosophila
               Homo & Pan (Chimpanzee) genomes  98.44% similar: What's the differences? 

      Bioinformatics: extracting biological information from (huge) data sets [e.g., NCBI GenBank resource]
           Example: Functional differences in Caspase-12 gene of Human versus Chimpanzee :                 
                          Go to NCBI data base: Search for " Pan + Caspase 12 "
                          Go to  Nucleotide database: Retrieve chimp CASP12 DNA sequence in FASTA format
                          Identify human homolog human CASP12 (variant 2) with BLAST [Basic Local Alignment and Search Tool]                        
                          Find ORFs in Chimp & Human sequences with ExPASy: What's up with that?

    Proteomics: pattern of protein expression in an organism
             Ex.: life-stage & tissue-specific patterns

All text material ©2025 by Steven M. Carr