Tuesday, December 25, 2012

Designer genes - How the forces of natural selection are about to be replaced by the forces of human selection - Stephen Potter

Designer genes - How the forces of natural selection are about to be replaced by the forces of human selection - Stephen Potter, 2010


This book surveys developments in genetics over the last fifty years, in particular developments which have lead towards the possibility of genetic engineering of humans. These include:
  • The double helix model of the DNA (Watson/Crick, Nobel prize 1962)
  • The sequencing of the human genome (DNA sequencing, Sanger/Maxam/Gilbert (Nobel prize 1980), Protein sequencing (Sanger (Nobel prize 1958 )), Human Genome Project (Collins/Venter)
  • PCR: Creation of a large number of copies of a DNA sequence (Mullins, Nobel prize 1993)
  • Stem cells: Conversion of adult cells to stem cells (Yamanaka, Nobel prize 2010), allowing creation of multiple embryos by turning stem cells into gametes
  • Modification of the genes of a cell (Capecchi, Evans, Smithies, Nobel prize 2007)
The book then discusses the ethical implications of technology that commercializes and combines this research to allow human genetic engineering.

The current state of genetic engineering and what might be possible in the next few years:

The following technologies have been demonstrated in research. Commercialization of these technologies to reduce cost and increase speed is underway and advances are expected in the next few years:
  • Preimplantation Genetic Diagnosis (PGD): Identifying the presence or absence of a particular gene in an embryo at an early stage (8 cell blastocyte), by extracting a single cell from an 8 cell embryo from IVF.
  • Complete DNA sequencing on an embryo cell in a short time (order of hours)
  • Creation of thousands of embryos simultaneously through stem cells
  • Screening of multiple embryos in parallel
  • Modification of the genes of an embryo cell followed by implantation

Which genes do what

  • DNA: A long molecule consisting of sequences of bases (A, G, C, T)
  • Codon: A triplet of bases that codes for an amino acid. 4 bases =>4^3 = 64 possible codons
  • Amino acids: Building blocks of proteins:
    • 20 possible amino acids (out of 64 possible codons => 44 codons either do not specify amino acids or more than 1 codon maps to the same amino acid.)
  • Gene: Sequences of codons that code for protein generation
  • RNA: Long molecule consisting of bases ( A, G, C, U)
    • RNA can act as genetic material as well as a proteins. Might explain origin of life (Altman, Cech (Nobel prize 1989))
  • Proteins: Chain of amino acids (few hundred)  =>  >100^20 possible proteins
  • Generation of proteins from DNA:
    • Transcription: DNA used to generate mRNA, aided by protein RNA polymerase
      • RNA polymerase is a protein that takes one strand of DNA and transcribes a RNA copy (only the genes)
    • Translation: mRNA to Protein, happens in the ribosomes of the cell
  • Gene differences
    • Mutations: Deletion of block in DNA sequence-> Deletion of block in protein
    • Frame shift: Deletion of single base
    • Single base difference: Single nucleotide polymorphism (SNPs):
      • Can be in codons or non coding part
    • An individual has 2 copies of each gene: One from each parent

Sequencing the human genome

  • Genome: 3 billion bases
  • DNA per protein: 3 bases per amino acid, 100 -1000 amino acids per protein
    • => 3 billion/3000 = 1 million potential protein or genes per genome
  • Turns out there are only 30K genes in the human genome
    • => Approx 2.5%
    • Determined by transcription analysis of RNA
  • Differences in people = 0.1% of the genome i.e 3 million bases out of 3 billion

Sequencing revolution

  • Objective: Identify gene combinations (from the millions of SNPs in a single DNA sequence), that contribute to variation/disease
  • Map disease/traits to SNPs
  • 3 million differences between individuals
    • => Needs huge amount of data (samples from large population, mapped to diseases), computational power
  • As complexity of the genetic variation cause increases (more SNPs), the number of samples needed to identify it increase

Time scales

  • Genetic evolution can be rapid: Order of 1000s of years: Rapid, directed
  • E.g. Evolution of dogs from wolves directed by man

Gene expression

  • Transcription factors: Proteins that regulate transcription i.e expression of genes
    • Like all proteins, their generation is impacted by the genome
    • Can cause genetic cascades: Hundreds of genes altered in expression level
  • Introns: Interrupting codons: Sequence between codons that interrupt codons
    • Increased flexibility of gene expression
    • Transcription removes the introns, a process called RNA splicing
    • Exons: Expressed sequences
    • 2% of sequence are introns that regulate gene expression
  • Genetic regulatory network: Interwoven connection of genes, with some regulating
    • 3% of the genome is regulatory

Jumping genes

  • Transposable elements: Discrete parts of the chromosome, capable of moving form one chromosome position to the other (McClintock)
    • Enzymes allow the transposable elements to copy themselves, float around and attach to  a new place in the DNA sequence
    • Drosphilia Melanogaster: P elements detected in wild fruitfly DNA which was different from DNA extracted from fruitfly a few years previously/
  • Horizontal gene transfer: Viral DNA: Retroviruses can convert RNA to DNA using enzyme called reverse transcriptase (Temin/Baltimore, Nobel 1975)
    • Causes hybrid dysgenesis i.e. reduced fitness
    • Repressors
  • Transduction: Moving DNA material from one species to another
    • Balance between harmful effects (which are subject to survival of the fittest) and preferential replication). Can spread because of ability to outreplicate the competing genome sequences.
  • DNA: 2% coding, 3% gene expression, 30% parasitic transposable
    • Why is there >50% with no known purpose: Has evolution created this unused portion to mitigate the effects of transposable DNA?

Genetic disease

  • Every gene has two copies - one from each parent
  • A mutant gene in 2 parent => child has 25% chance of getting a bad genes
  • Nature vs. nurture: Minnesota Twins study: 70-80% of IQ is genetic
  • Genes have a surprising amount of contribution to psychological traits: love, faith

Embryo

  • Gametes: Have 23 chromosomes
  • Chromosome: Long DNA molecule
    • Individual has 23 pairs of chromosomes: one set from each parent
    • One copy of each chromosome goes into sperm/egg during meiosis => 2^23combinations from a pair of parents
    • Identical twins: Monzygotic (single egg, fertilized by single sperm, divides after blastocyst stage)
    • Fraternal twins: Dizygotic (two eggs fertilized by different sperm)
    • Chimera: Fusion of multiple eggs (fusion of two dizygotic embryos)
  • When number of cells < 32 (?), cells can develop into any type of cell

Stem cells

  • Origin: 
    • Embryo cells
    • Adult stem cells: Bone marrow cells
  • Programming adult cells to become stem cells
    • History of development:
      • Gene expression appears to be controlled by a master switch and a genetic pyramid of hierarchy.
      • Genes at the top of the hierarchy control those below them
      • Homeobox controls the master blueprint i.e type of the species, e.g. fruitfly vs. mouse
      • Single genes can initiate extensive development programs e.g. growth of a leg drive expression
    • Genes can make adult cells revert to stem cells
      • 4 genes activated in a mouse cell reverted it to a stem cell (Yamanaka, Nobel 2012)
    • Implication: Egg cells can be created, increasing the number of samples available for selection (over the 500 created)

Gene modification

  • Technology to modify genes (Capecchi, Evans and Smithies, Nobel 2007)
  • Procedure:
    • Desired version of the gene is created in a test tube
      • Generated using DNA synthesis machine or recombinant DNA strategies
    • Synthetic gene introduced into stem cells grown in an incubator
      • Modified gene introduced into stems cells by electroporation
      • Process of change is not clearly understood, happens by DNA recombination similar to meiosis
    • One of these correctly engineered stem cells is used
      • Only 1 in a million stem cells can be used, need screening to detect the stem cells which are good
      • Screening done by polymerase chain reaction (PCR), similar to preclude used in DNA matching
    • Create large number of copies of the DNA sequence (Mullins, Nobel prize 1993)
    • Genetically altered stem cells added to a blastocyte
  • Stem cell cloning: Dolly the sheep, 1997, nucleus of a mammary gland

Ethical questions

  • Ontogeny recapitulates phylogeny: Development of the individual copies evolutionary history
    • E.g. In embryos a primitive pair of kidneys is formed followed by a more advanced pair, and then the final pair
    • Is the early embryo truly human?
  • Optimal gene combinations
    • Sickle cell gene provides resistance to malaria: Genes are tradeoffs, not binary decisions
    • Connection between artistic genius and mental illness
  • Appearance of the Foxp2 gene responsible for speech (absent in chimpanzees), coincides with explosion in rate of progress.
  • Is genetic engineering any different from eugenics, improvement of the gene pool via human selection

No comments:

Post a Comment