Professors
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Mr. Paul Rainey
Mr. Peter
Mr. Wayne Patrick
Dr. Austen Canley
Mr. J. M. O’ Sullivan( not much)
Mr. Paul Rainey
He was camera shy.
Science is……
1) Playing
a) We are all scientists, making sense of the world.
b) Questioning, playing.
2) Done by ordinary people
a) Scientists are ordinary people who look at the world through
different lens.
3) “Learning science is dull, but doing science is interesting”.
a) Doing science
- Find a problem by fascinating questions.
4) Some people who got the ‘science bug’…..
a) Charles Darwin
- Begin asking questions that didn’t include God.
- Sent to study questions
- Came from liberal free family
- Collected organisms went on journey onboard the Beagle for
5 years.
- Produced book “Origin of Species”
- “Common divine ancestors….”
b) Gregor Mendel
- Austrian Monk
- Model for inheritance
- “We do not get half of dad, half of mum. If we did, the world
would be grey.”
c) Edward Jenner (asked questions then hypothesis)
- Discovered vaccination for small pox
- Lived in England as a doctor without anesthetic
- “Milkmaids did not have small pox but had cow pox. Did not
have small pox because they had a dose of cow pox which
protected them.”
- Hypothesis: Milkmaids were vaccinated by small pox.
- Injected the gardener’s son with cow pox, then was given
small pox.
d) Francis Clark and James Wilson
- James Wilson was a Nobel Prize winner.
- Found out the means of hereditary
e) Maurice Wilikins and Rosalind Franklin
-
Rosalind Franklin
Maurice Wilkins
- Found precise matches between the humans and other
organisms.
f) Alan Wilson
- To be one of the first to say something about evolution
- Where they first evolve, when.
- Africa-the place of origin.
5) Obtaining DNA sequence
a) Paul (a subject)
- Obtained DNA nucleotide sequence from Paul.
- Compared to other organisms.
- Common ancestors with chimp
monkey
hippo
Whale
6) Conclusion
a) “Science is important, relevant and fun.”
Mr. Peter
1) Microgenomics
a) Specializes in microbes
- Microbes are by far the most abundant life, responsible for
converting key elements of life such as carbon, nitrogen,
oxygen and sulfur.
- Plant and animal with different diversity.
b) Carbon and Nitrogen Cycle
- Aquatic and terrestrial environment
c) Antonie van Leeuwenhoek(1676- 1723)
- Created microscope and observed microbes
d) Microbial Diversity
- Variety of microbial diversity in water and sponge
e) Morphological Diversity
- Bacteria is flexible
- plate and grow colonies
- Plating, “The great plate count anomaly.”
- Cultivating, “Hard to cultivate and only able to cultivate in
small amounts.”
f) Tools of molecular microbiology
I. DNA (nucleotides)
- barcode for bacteria.
- encyclopedia of bacteria.
II. Genomics
- ‘Meta’ means transcendent.
- The science of microbial communities using power
of genomics analysis.
- Selecting sample then extracting DNA. Then
determine what genes are and what they do.
g) What can be DISCOVERED?
What are
they doing?
How they
are doing it?
What they
are?
h) Applications of metagenomics
1) The genomes of the microbial communities living on
and within the human body contain many more genes
than the human genome.
a) Find information on obesity (in mice) on aspects like gut
flow.
b) Harnessing microbial power e.g. cellulose for ‘waste’?
c) Microbes for help on crops, and the “mystery on suppressive
soil phenomenon.
d) Environmental contamination clean up using microbes to
transform many deadly chemicals into harmless chemicals to
the environment
e) Microbes responsible for oxygen and GLOBAL impacts.
Summary: Reveal secrets of our microbial planet.
Mr. Wayne Patrick
A) Polymerase Chain Reaction and Ligase
 Amplify a piece of DNA that we are interested in
 Watson and Crick’s famous DNA structure
 Proposed double helix strand in 1953 on ANZAC day (model
not drawn by them but by the wife)
 Complementary base pairing
 PCR is based on the ability of the enzyme called DNA
polymerase to copy DNA
B) 1st step: Denaturation
 Separate the two DNA strands for the polymerase to copy
them by heating them up to 95°C.
-Target sequence (100 or 1000 of base pairs).
 Add short, single stranded primers, drop temperature to
58°C, for the primers to work at the optimum level.
C) 2nd Step: Annealing
 Primers are designed to bind at either end of the target
sequence.
D) 3rd step: extension
 Now the polymerase can make new DNA.
 It works best at 72° C and it needs building blocks (Dntp’s
which are free nucleotides).
 Polymerase can make 1000 bases of DNA per minute.
 Now you have more DNA strands.
 You can make copies of copies.
- 1 cycle=2 copies.
- 2 cycles=4 copies.
- 30 cycles= 230 copies.
E) My target.
 My target is 16s RNA gene.
 This gene is present in all bacteria.
 My primers are “universal” primers that bind to any 16 rRNA
genes.
F) Ligation(downstream step)
 Molecular bar codes need to be added to your amplified to
your 16 rRNA genes as part of sequencing protocol.
 Ligase(DNA) can join together the ends of the linear DNA
molecules.
Summary: 1) PCR, a reaction for amplifying pieces of DNA
2) Three steps: Denaturation, Annealing, Extension.
3) Ligation.
Dr. Austen Canley
1) DNA sequence
 $1000 genome project
- In 2004, the USA placed 1 million dollars in
companies to enable a person in the public to be
able to get their DNA genome sequenced for
$1000 in 2004 used for crime, cancer cell research,
metagenomics etc.
- The price $1000 in 2013 and the price of
$10000000 in previous years. This meant that the
price decreased by 4 orders of magnitude.
2) DNA sequencing
 DNA polymerase will tell you that a nucleotide has been
added.
 So place a nucleotide into a test tube one at a time and if
the DNA polymerase tells you something, the nucleotide
has been used.
3) Pyro-Sequencing
Plus dATP, dTTP, dGTP, dCTP.
 How to tell whether DNA polymerase tells.
 DNA polymerase will cause pyrophosphate to be released
which will then be converted to light energy. It will then
be detected by a CTD camera.
4) How do we do thousands?
 “Well technology.”
 Beads are covered in millions of identical DNA
molecules(but each head is different) are put onto slides.
 These slides have micro wells(44 nanometers in
diameter).
 Only one bead can fit in each well. This will allow up to a
million beads per slide.
 CTD tracks all wells.
5) Why do we have to use millions of identical DNA molecules on
each bead?
 Not enough flash of light created with one DNA and
therefore millions will create a large enough flash of light.
6) Bead Emulsion-PCR
 Another PCR reaction is created.
 Add primers, DNA, beads, polymerase, emulsion, we get
single bead with a single DNA molecule.
 The ROCHE machine called GS junior uses a day to carry
out bead emulsion.
J.M. Sullivan
 Title: “Discovering microflora at Hot Water Beach:Taking next
generation to the next generation.”
 Organisms are specialized in a specific environment.
1) Characteristics of different environments:
 Sample of sand into the joesterizer which spins at an
incredible rate and will leave nothing but DNA.