Gene Regulation and Genomics

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Gene Regulation and Genomics
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Differentiation

• As development progresses, cells becomes more
  specialized and restricted in the expression of
  their genetic content. This leads to many types
  of cells in a complex organism.
• However, differentiated cell may retain all their
  genetic potential.
• Salamanders can regenerate a lost limb.
• Tissue culture has allowed many plants to
  beproduced from a single plant.

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Plant Tissue Culture

• This is BIG business, and is very important in
  the horticultural industry.
• Thirty years ago if an orchid breeder had a
  spectacular plant it might produce two or three
  asexual off-shoots per year. Each of these could
  be sold for, perhaps, 150-200. Sounds good?
• Today that same plant can be placed in tissue
  culture and the grower can produce 20,000
  identical plants, sell them for 10 each.
• 200,000 vs. 300-400?? You choose.
• The center for plant tissue culture in Florida is
  the area around Apopka.
• The process is simple in theory, but more
  complicated in practice. What growth medium is
  required? What part of the plant yields the best
  cells for tissue culture? At what rate and how
  long are cells shaken in solution? Etc.

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Theres a lot of information in that cell! How
can we regulate its use?

• In eukaryotes the cells genes are located on
  chromosomes.
• A chromosome consists of DNA and histones.
  Histone proteins are a framework around which the
  DNA can be tightly coiled. The term for the
  bead-like DNA-histone complex that can be seen in
  electron micrographs is termed a nucleosome.
• The tight packing of the DNA in the chromosome
  helps to regulate gene expression by preventing
  transcription proteins from contacting the DNA.
  Only when portions of the DNA uncoil can
  transcription of information occur.

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Alternative RNA splicing

• Remember the DNA message that is copied contain
  both introns and exons.
• The introns are removed to produce a functional
  mRNA.
• If splicing occurs in different ways, different
  mRNAs are produced and their products will also
  be different.
• This means that alternative RNA splicing can
  allow a gene to code for several different
  peptide chains, depending upon how the
  information is spliced together.

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A Cell is not a Simple Strucuture!

• After mRNA is produced other events will happen.
• mRNA must be broken down. When this happens is
  regulated by the cell.
• When translation actually occurs can be
  controlled by the cell.
• The peptide that is formed during translation may
  need to be bent, folded, or chemically altered
  before it becomes functional.
• Proteins may be destroyed by the cell after a set
  period of time.
• These mechanisms enable the cell to control the
  amount and the type of protein that is active in
  the cell at any given point in time.

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Reproductive Cloning

• Reproductive cloning adds a nucleus from a donor
  cell to an egg cell, whose nucleus has bee
  removed.
• The result is a new animal exactly like the
  parent (i.e. Dolly , the sheep)
• The technique is not without problems , and its
  usefulness is still to be proven.
• There are great ethical concerns about human
  cloning, and most researchers are strongly
  opposed to it. (Would you really want another
  you, and would you be you if you did get
  cloned??) Thats a lot of you!

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Therapeutic cloning

• Unlike reproductive cloning, therapeutic cloning
  has great medical potential.
• In this procedure stem cells (adult and/or
  embryonic) are cultured in the lab, and then
  induced to transform into specialized tissues.
• The use of embryonic stem cells has much promise,
  but much of this has been lost in the current
  moral and ethical debates.
• If one is truly opposed to embryonic stem cell
  research, one should also be ethically boound to
  forgo the use of any therapies or cures that
  result from it.

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Signal Transduction Pathway

• How do cell know when to differentiate?
• How are cellular activities regulated within an
  organism?
• The processes is relatively straightforward
• A signal molecule, produced elsewhere, attaches
  to a receptor protein on the cell membrane.
• This causes a cascade of reactions between relay
  proteins in the cells interior.
• The last relay molecule activates a transcription
  factor that causes the transcription of a
  specific gene in the DNA of the nucleus.
• This leads to the production of a protein that
  may act as an enzyme or structural element needed
  to effect a change in the cell.

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Oncogenes

• Oncogenes are cancer causing genes, and usually
  trigger increased production of cell growth
  factors.
• Active oncogenes, along with defective
  tumor-supressor genes, can lead to the
  development of cancerous tumors.
• Usually cancer is the result of multiple
  mutations in a somatic cell.
• Many cells probably develop these mutations, but
  are detected by cells of the immune system and
  eliminated before that can give rise to a tumor.
  
• The next slides has two illustrations of steps in
  tumor development.

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Tumor suppressor gene

• If a gene that inhibits cell division is
  defective, it can lead to the uncontrolled
  replication of cells and the development of a
  tumor.
• This is seen in the illustration below.

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Carcinogens

• Many factors can cause DNA mutations that lead to
  tumor development. These factors are called
  carcinogens.
• Carcinogens can be physical factors, such as,
  X-rays, UV radiation, and radiation from radon
  (naturally occurring) or nuclear weapons
  (man-made).
• They can be chemical factors, like the chemicals
  in tobacco, or cleaning agents, such as benzene.
• Even some viruses can lead to cancer. Cervical
  cancer is one example. This is the reason for
  the development of a vaccine against sexually
  transmitted viruses.
• Avoidance of risk factors is one way to decrease
  the chance of developing cancer.

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Genomics, the study of whole sets of genes

• DNA technology has lead to the development of the
  field of genomic research. This research has
  many potential applications in the areas of
  medicine, agriculture, forensic science, and
  production of products for industrial and
  pharmacological uses.
• With the development of these lines of research,
  a host of legal, ethical, social, and
  environmental issues have arisen. It may take
  years, if not decades, to resolve many of the
  concerns that individuals are voicing today.
• None the less, DNA technology and genomics is one
  of the most exciting areas of modern biology.

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Recombinant DNA Technology

• Plasmids are circular DNA molecules found in
  bacteria which can be used to insert genes into
  bacterial cells.
• The genes that are inserted can come from many
  sources other than bacteria.
• This technology has allowed the insertion of
  genes into bacteria, which can then be grown in
  great quantity, yield large amounts of the
  product for which that gene codes.
• This procedure can also yield large quantities of
  cells that carry gene that chaanges something
  aboutr the cell in which it is found.
• A diagram of this process can be seen in the next
  slide.

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Using plasmids to copy genes and make proteins
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Restriction enzymes

• To get a piece of DNA containing the gene to be
  studied, the DNA is cut into pieces using
  restriction enzymes.
• These enzymes recognize short segments of DNA and
  cut the DNA at those points.
• Because the cuts are staggered, there are
  unattached bases at the ends (sticky ends)
• New DNA pieces can attach to the sticky ends, and
  then DNA ligase covalently bonds the pieces
  together.

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• The process of inserting and cloning a gene can
  be seen in the illustration to the right.
• Note that once the plastid has a gene inserted
  into its DNA, and the plastid is put into a
  bacterium, tremendous numbers of bacteria
  containing the gene can be produced in a short
  period of time.

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How to make a clean gene!

• Remember, when you copy a DNA gene it consists of
  introns and exons. You need to remove the
  introns to get a clean piece of mRNA.
• To get a gene to clone, one must isolate the
  clean mRNA, and then use reverse transcriptase
  to make a DNA copy of the mRNA.
• After the RNA is removed, a complementary stand
  of DNA is formed. The result is double-stranded
  cDNA.

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Uses of Recombinant DNA Technology

• Both bacterial cells and mammalian cells have
  been used to generate useful products. Mammalian
  cells can be genetically engineered so that the
  desired protein is secreted in the animals milk.
  The product can then be isolated from the milk
  and used.

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Gel Electrophoresis

• One technique for studying DNA uses a thin gel to
  separate DNA based on size and electrical charge.
  A DNA sample is introduced into a well in the
  gel, and a high voltage current causes the
  molecule to migrate through the gel. The
  finished gels can be stained and photographed.
  Samples can be compared using the migration
  patterns that are present.

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DNA Fingerprints

• The use of DNA evidence in forensic science has
  become very widespread.
• The chance of two individuals having the same DNA
  pattern is extremely small if enough markers are
  used.
• DNA matches have enabled the identification of
  the victims of tragedies such as, plane crashes,
  9-11, ethnic cleansing.
• Innocent persons on death row have been freed due
  to DNA evidence which proved their innocence.

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Gene Therapy

• There has been much hope for effective gene
  therapy. It could allow the body to compensate
  for genes that are defective or non-functional.
• At present success has been very limited, and
  some clinical trials have been discontinued due
  to unforeseen problems.
• Will gene therapy place a significant role in the
  future of medicine? Only time will tell.

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Polymerase Chain Reaction (PCR)

• This technique has allowed researchers to take a
  minute amount of DNA and, from it, produce a
  large quantity of DNA for analysis.
• Using a series of enzymes and cycles of heating
  and cooling, new copies of DNA are created. A
  complete cycle only takes a few minutes,
  therefore in a few hours the number of DNA
  molecules produced is tremendous. (calculate how
  many you would have after 20 cycles)

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Human Genome Project

• No one in todays world should leave a basic
  biology course and not be aware of the Human
  Genome Project, its purpose and its potential for
  mankind.
• Purpose map out the entire nucleotide sequence
  of the DNA of the human chromosome.
• This was completed years ahead of schedule due to
  the rapid development of techniques in
  sequencing.
• Potential insight into human development
  insight into evolutionary relationships and .
• better diagnosis and treatment of many of our
  commonest and most debilitating diseases.
• Go to the links provided in this lesson to
  explore the Human Genome Project and the whole
  field of genomics.

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Pros and Cons of Genetically Modified Organisms

• Since the advent of the first genetically
  modified crops, questions of environmental impact
  and risks to health have surfaced repeatedly.
• The EU (European Union) has a very strong bias
  against GM crops. There is the concern that
  transgenic crops could endanger individuals with
  food allergies. You could consume a food not
  knowing that it contained an allergen that could
  trigger a severe and dangerous reaction.
• China has made wide use of GM crops. If you need
  to feed 1,300,000,000 people, high yield may be
  more important than the slight chance of
  mortality due to food allergy.
• There are many other concerns and benefits that
  we as a society will have to carefully weight as
  we move into this uncharted era GM plants and
  animals.

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This represents the information known to be
located on chromosomes 9 and 4. The graphics
are courtesy of the U.S. Dept. of Energy, Genome
Management Information System of the Oak Ridge
National Lab