3- Developmental genetics

• Development


  • The irreversible process organisms undergo from single-celled zygote to multicellular organism
  • an interaction of the genome, cell cytoplasm and environment, and involves a programmed sequence of events
• Zygote


  Starts as a totipotent cell- has potential to be any cell in body
• Determination


  The process where genetics "programs" a cell to become specialized (fate), often done through induction, or chemical signaling
• Differentiation


  • The process in which determined cells undergo physical changes to become specific cell types- e.g., nerve cells, antibodies, etc.
  • controlled by gene expression- synthesis of specific proteins guide fate of the cell
• Morphogenesis


  "Generation of form," process or anatomical structure formation and cell shape and size changes
• Genetic programs regulate 3 Developmental processes

  • DETERMINATION - Individual cells are fated to become...
  • DIFFERENTIATION - Individual cells change to actually become...
  • MORPHOGENESIS - Structures form by changes in cell #, shape, position
• Developmental defects seen at birth (congenital) are caused by defects in the cellular processes of development
• ~50% of concepti do not implant (implantation 8-10 dpf, Heart beat at 21 dpf), a further ~30% die and abort after implantation

  • 3-4% of all live births possess a macroscopically visible congenital defect (120,000 babies/year in the USA).
  • 1% of all babies are born with a heart defect.
  • 20% of neonatal deaths are caused by congenital defects (the leading cause of neonatal death in the USA)
  • congenital disorders are the cause of 50% of pediatric admissions in the USA

  *Developmental defects seen at birth (congenital) are caused by defects in the cellular processes of development*
• Model organisms


  • Must have mutants that affect development, and involved genes must be mapped and cloned for study
  • Zebrafish (Danio rerio) is especially good for development because embryos are transparent- genetics heavily studied
• Development Controversy:

  In developing cells, is DNA lost to accommodate specific cell types, OR Are only certain genes expressed in a constant-sized genome?

  • Experiments with carrots in 1950’s: differentiated cells could be used to grow an entire new carrot so DNA is NOT lost during development
• • 1950’s carrot experiments didn’t convince everyone
  • 1975: nuclei from skin cells of frogs were injected into eggs to make tadpoles, but few survived to adults, those that did were sterile
  • 1996: scientists in Scotland (Ian Wilmut) cloned the first animal (a sheep) from an adult cell nucleus, meant adult cell nuclei could become totipotent again
  • Clearly shows differentiation is not from loss of DNA, but from gene expression
• Somatic Cell Nuclear Transfer (SCNT)


  • Remember: somatic cells are non-sex (gamete) cells
  • Suggests adult cell nuclei became totipotent again by being transplanted into a new cellular environment
  • All the info to make a new set of cells was in the DNA- just had to be turned on again
  • "Dolly" from Wilmut's sheep cloning experiment was a clone of a donor ewe and was born/grew normally; gave birth to Bonnie through sexual reproduction
• • Cats cloned at Texas A&M- complicated relationship between genotype/phenotype and environment means clone is not the same as donor "mother"
  • Most clones die before or soon after birth like with the sheep
  • Scientists used microarray analysis and found many abnormal gene expressions- explanation is differentiated nuclei must be reprogrammed
  • human/dinosaur cloning is still nowhere near possible
• • Jack Horner and colleagues have isolated blood vessels from Tyrannosaurus rex bones- iron in animal's body prevented decay of collagen and other proteins
  • Blood vessel structure nearly identical to modern ostrich- bolsters evidence that birds are direct descendants of dinosaurs
  • Over time, DNA degrades (half life is 521 years), and after 6.8 million years, all bonds would be broken
  • BUT, chemicals similar to DNA have been found with iron-preserved collagen & with dino sequence, it would be possible to clone with ostrich egg- Horner wants to do this!
• • In December 2022, scientists published environmental DNA (eDNA) data from plants and animals that are 2 million years old
  • Samples were obtained from permafrost in Greenland, and include 135 different species ranging from mastodons to ants
  • "The survival of such ancient eDNA probably relates to its binding to mineral surfaces.”
• Gene expression and hemoglobin development (1)

  • Humans have two α and two β chains, controlled by separate genes
  • Two genes are similar because one was duplicated from the other during our evolutionary history
• Gene expression and hemoglobin development (2)

  • During development, several genes code for different hemoglobin polypeptides
  • In embryos, two ζ (zeta) and two ε (epsilon) chains are made in yolk sac
  • After 3 months, fetal hemoglobin (Hb-F) is synthesized in liver and spleen, with 2 α and 2 γ (gamma) chains
  • Before birth, synthesis shifts to bone marrow, which makes Hb-A and some δ (delta) chains
  • Arrangement of hemoglobin chains on chromosomes matches order of gene expression in development
• Lymphocytes


  White blood cells involved in immune response
• B cells


  Develop in bone marrow, when activated by an antigen (e.g., foreign protein on virus or bacteria) they form plasma cells that make antibodies after a few days
• Antibodies


  Attach to antigens, and mount the body's defense system
• We develop immunity over time from clonal selection- cells with antibodies to an antigen are stimulated to proliferate and make more antibodies
• Antibodies


  Proteins called immunoglobins, with 2 identical short or light (L) chains and 2 identical long or heavy (H) chains
• Disulfide (S-S) bonds


  Hold antibody chains together
• Antigen-binding sites


  The two arms of the Y-shaped antibody contain the antigen-binding sites, which attach to antigens and stimulate clonal selection
• Hinge region


  Allows antibody arms to move independently, and bind to separate antigen sites to help disable infecting agents
• Antibody classes


  • IgA, IgD, IgE, IgG, and IgM
  • IgG is the most abundant class in blood, and IgM is the class that recognizes new antigens
  • Have 5 different H-chain polypeptides and 2 L-chain polypeptides
  • H chains have 4 domains (3 constant regions, 1 variable region), L chains have 2 domains (1 constant, 1 variable)
• Antibody domains


  Each polypeptide chain in an antibody is organized into domains of 110 amino acids each - part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain
• Somatic recombination


  Random DNA rearrangements during B cell development that join different gene segments and exclude others
• Light chain somatic recombination

  1. V (variable), J (joining) and C (constant) gene segments are widely separated on the chromosome at beginning of B cell development

  2. As B cell develops, certain V, J, and C segments become associated with each other to the exclusion of others

  Example: if mice have 350 V segments, 4 J segments and 1 C segment = 1400 possible variable regions
• Heavy-chain recombination


  • Includes V (variable), D (diversity), J (joining) and C (constant) gene regions that can be shuffled
  • Example:

  1. if mice have 350 V segments, 4 J segments and 1 C segment = 1400 possible variable regions for light chains
  2. if mice have 500 V regions, 12 D regions, 4 J regions, and 1 constant region = 500 X 12 X 4 X 1 = 24,000 rearrangements for heavy chains
  3. This means the combined probability of light (1400) and heavy (24,000) chains is 33,600,000 possible antibody molecules
• Sex determination in mammals


  In placental mammals, Y chromosome makes testes, whereas absence of Y chromosome defaults to ovaries
• Testis-determining factor (TDF)


  Genes on the Y chromosome (maybe SRY gene) code for this, which causes testis formation
• All other differences between sexes are a result of hormones or factors from the gonads, so TDF is most important event in development for sex determination