A Research Institute for Biomedical Sciences? This
is a topic which is exercising the minds of several research groups
and the following are some observations from the meeting held November
24th, entitled: Getting the Environment for Biomedical Research
Right. The main speakers from outside the University were: Dick
Bellamy (SBS, Auckland), John Mattick (IMB, Brisbane), Jim Watson
(Genesis R&D Corp). There were three models presented. One of them
is to go private like Jim Watson of Genesis said: "put your gonads
on the line". Genesis was probably unique in that the Vice-Chancellor
of Auckland University allowed the movement of Jim Watson's HRC
funding, equipment, and his group to move outside the University
to form Genesis. In a sense they were up and running without a lengthy
start-up period. Having a functional group carrying out high quality
research helped to attract investors and made the offers of stock
options to its members a possibility. Jim claims the book value
of Genesis is $200 M with $63 M in the bank.
John Mattick's development in Brisbane was interesting
in that from a modest sum of $400,000 which was 'top-sliced' from
departments he was able to turn that into a large research centre
with funding of about $110 M. This required the dedication by John
for about 12 years -- he said that he had to sometimes work till
dawn to achieve this. He was able to attract good people to the
Centre. To put it into context, there was a growth spurt in Queensland.
Growth is able to fund innovation and new developments. He was also
able to make good use of the rivalry between the Queensland and
Victoria (Walter Eliza Hall group) state governments for research
funding -- each vying to out do the other. The results of this ping
pong activity was to raise the research ante to $110 M.
The third model presented was by Dick Bellamy,
School of Biological Sciences at Auckland University. He took a
group of departments working in the biological sciences area, put
up a barb wire fence around them and said: you can not get out unless
you agree to work together and disassemble the feudalistic departmental
structures. In the process Dick was able to release some resources
which were previously duplicated and capture the benefits of operations
of scale. It is interesting to note that he advocated the most cost
effective way of teaching was to put a person in front of 1000 students
and deliver the lecture.
In all of this there was a take home message --
recruiting good people was the key to success -- recruit good, successful
people, they attract other good people. Give them adequate resources
and they will generate research funds. More good people will come
and they will establish networks and collaborations. Soon you have
a thriving research centre which has the critical mass and can spin
off commercial companies.
Otago has some unique problems; the University
is an old institution and there are many feudal structures which
are not easily breached. Some departments are still able to pull
up the drawbridge and man the battlements. It will take someone
with a great deal of dedication and energy and mania to overcome
The other message I got was that there was venture
capital money out there. The problem is that the venture capitalists
know that there is no point in parttime funding an of academic.
They know that academics are overworked -- academics try to be supermen
(sic super persons). Before venture capitalists will put their hands
into their pockets, you (as an academic) will need to step outside
the academic institution. There is the option as offered by Ian
Smith, of taking two years off, without pay, to move to the Centre
for Innovation and give your venture a go. It will be interesting
to see what the uptake of that option will be and how some of the
biotech ventures like BLIS Technologies will fare in the Centre.
To update you on some of behind the scenes activities
of the CGR, the following are notes from a recent CGR Committee
Updating of DNA sequencer -- There was
discussion about the replacement of the model 377 DNA sequencer
The current 377 model is no longer being manufactured and although
it has about 2-3 years of usable life left, we will have to face
replacement. A model which is being promoted to replace the Model
337 is the 16-capillary sequencer, the Model ABI 3100. It can run
up to 96 samples in a 24-hour period. A similar discussion was made
about the Real-Time Model 7700 PCR machine which is currently heavily
utilised. We do not charge depreciation on the use of the equipment.
There are service contracts of $4,000 and $16,000 for the PCR machine
and sequencer respectively. These costs are paid for from the CGR
Redesign of the CGR Website -- The University's
website is currently being redesigned and there will be an obligation
to have the CGR website conform to the new style guidelines and
'branding'. Apart from the changes in the look of the website, I
would appreciate any comments on what features the new website should
incorporate. The CGR website receives about 1,000 'hits' (files
served) a day and the Real-Time PCR html pages receive most of them
-- obviously keywords on the search engines. There is usually some
follow-on browsing of the rest of the site by the overseas visitors.
The current CGR database contains 312 members and this gets some
traffic as well.
CGR Activities for 2001 -- post-Theme era?
There was some soul-searching discussion about what we can contribute
and a reaffirming of our grass-roots origins. The themes are a fact
of life and where possible we can work in with them and provide
the infrastructure for member-initiated projects. We will continue
to run workshops and poster nights --- with a focus on bioinformatics
and microarrays in the coming year?
Finally this being the last Newsletter of the
year, I would like to wish you all the best for the holiday season
and may it be festive and merry one. Make a point of actually taking
a break, away from your lab and academic pursuits and from your
emails. Soak in some of that leisure time (I was going to say sun,
but that as we know is now a no-no) and come back next year, refreshed
and ready to do battle with the challenges in the New Year.
Gene Expression & Proteomics
The first meeting of the Functional Genomics, Gene
Expression & Proteomics research theme was held in the Biochemistry
Department this week. The meeting opened with an excellent overview
of the present state of play in Proteomics from Stuart Cordwell
from the Australian Proteomics Analysis Foundation (APAF) in Sydney.
This facility has some of the world's best facilities for doing
proteomics work. Stuart described what is and isn't possible, outlining
each of the limitations of 2D analysis and how they try to get around
them. Stuart's own work has been mainly on bacteria and he explained
that it has been possible to identify 20% of the total proteome
of a bacteria on one gel.
"The essential thing is that the question you
ask has to be good enough for you to be able to make sense of the
answer", he said. At APAF their initial approach is to make theoretical
arrays from the goenome information before they start and then to
overlap the found data with these. Also, a cell fractionation approach
is seen as beneficial in helping to identify protein function.
After that they employ a three level analysis,
increasingly narrowing the pH gradients, until on the third pass
they span about one pH unit. In reality 32% of proteins are outside
the scope of 2D analysis, either because thay are too basic (15%),
too hydrophobic (14%) or too low in abundance (3%). How do they
overcome this? The narrow Ph gradient 2D analysis and pre-fractionation
allows a greater number of low abundance proteins to be seen as
more can be loaded. Basicity is a big problem. Work shows that even
on a 11-12 range gel everything above a PI of 9.77 is washed out
of the gel. They are working on new buffering reagents and new equipment
to try and overcome this.
Other speakers at the meeting discussed the Yeast
two hybrid system and x-ray crystallography and their usefullness
as high throughput protein analysis tools.
If DNA is Life, What
About the Details?
The last year has seen the official announcement
of the completion (although a little premature) of the human genome,
as well as the release of further prokaryote genomes. The number
of completed genomes is now quite impressive and new genome projects
are announced every day. At the same time, a second sequel to the
film Jurassic Park (titled, with some originality, Jurassic Park
3) is being made in Hollywood starring Sam Neil among others. I
never saw anything except fragments of Jurassic Park (and I've never
seen the Simpson's either) but I gather the story involves the recreation
of a number of dinosaur species from DNA recovered from the intestinal
tract of Jurassic mosquitoes preserved in amber. Quite apart from
the question of whether Jurassic mosquitoes existed and whether
they bit dinosaurs, it seems unlikely that fragmentary DNA could
be used to recreate a whole living creature. But what about whole
genomes? Could we recreate a creature by synthesizing its genome
and putting it into a suitable cellular container? Can we create
virus or a bacterium by simply knowing its genome? What about a
yeast, a lily or a hippopotamus?
Although this is rather a trivial question at
first sight, it hides a much more interesting question. Is the genome
of an organism sufficient to completely and explicitly describe
that organism? If we were synthesize a piece of DNA corresponding
to a simple virus, would this virus be viable? What other information
would be required to make this simple organism animate? If it is
possible to make a live virus, what extra things would be necessary
to make a bacterium viable: a cell membrane, some ribosomes, a complete
set of cytosolic enzymes?
It seems pretty clear that more than just the
genome would be necessary to make something even as simple as a
bacterium. Somehow it would be necessary to provide a minimal set
of cellular machinery to interact with the DNA so as to interpret
the instructions and to build the appropriate structures they encode.
If this is true, then it seems pretty clear that an organism is
not just a construct of its DNA but that a mechanism for translating
that genetic information is essential as well. All of this is neither
terribly surprising nor original but it does focus attention on
the old questions of where and how did life originate.
Before Darwin it was widely considered that there
must be underlying physical laws and principles which accounted
for both the similarity and diversity of living things. The discovery
of the laws of heredity and of genes diverted attention away from
these kinds of studies for it seemed clear that essential information
about an organism was transmitted from generation to generation
and that no underlying physical laws were necessary to explain the
way things were. Although this view is true as far as it goes, it
overlooks the fact that underlying physical laws are essential to
the expression of the information in the genome. In fact, many of
the really interesting questions are all about how the instructions
in the genome are translated into structures within organisms. Careful
consideration of the underlying physical laws is likely to greatly
assist in understanding how genetic information is translated into
a living thing.
Real-time PCR News
Due to the success of the first workshop on real
time technology in February this year a second workshop was held
recently in the Microbiology department. Already a waiting list
has started for third. The open seminars updated us all on the recent
and future developments in real time technology, there are many
exciting advances due out in the new year. The participants in the
"hands-on" workshop carried successful amplifications of their own
targets. Thus the numbers of people using the machine has greatly
increased and booking is essential, its now time to plan well ahead
to ensure a space on the machine. The diversity of uses of the Taqman
technology again was evident in the workshop.
Currently it is used for Allelic determination,
quantitative PCR/RT-PCR and now quantitation of bacteria from biological
samples. I have used the ABI Real Time PCR machine for quantitative
detection of Bifidobacteria in pure cultures and in faecal samples.
The method has been rapid, sensitive and highly correlated with
standard plate counts of the same samples. These comments are from
Teresa Requena who attended the workshop.
The software for SYBR green analysis (melting
temperatures) has at long last been made available. The Cancer group
in Biochemistry has tested this system and if you have any questions
regarding this technology please contact Tumi Toro ext. 7868. As
many of you will know the Primer design software is now located
on the CGR server, at the PCR 7700 site. This has allowed easy access
for any one wishing to design primers/probes. Unfortunately with
the weak NZ dollar the prices have had to increase for reagents.
I have received the latest price list. We still have our discount
& a special offer to people setting up for the first time.
Please feel free to contact me for any information
on the ABI 7700.
The Vascular Research Group was represented by
Dr. Eugenie L. Harris at two recent conferences: GEHH2000,
the Genetics of Experimental and Human Hypertension symposium held
in Toledo, Ohio August 17-18. ISH2000, the International Society
of Hypertension conference in Chicago August 21-24.
In a talk at the GEHH symposium, Jean Harris reported
the results of a collaboration with Ross Barnard of the University
of Queensland to determine whether the New Zealand genetically hypertensive
(GH) rat had a putative A1079T transversion in the a1 isoform of
the Na+, K+-ATPase gene (Atp1a1). This gene lies within hypertension
QTLs in a number of crosses between hypertensive and normotensive
rat strains. A paper published in Science in 1990 claimed that a
point mutation in the Atp1a1 gene found in the inbred salt-sensitive
strain (SS/Jr) would result in a Q276L substitution in the
ATPase protein. Such a substitution was posited to alter the membrane
confirmation of the Na+, K+-ATPase, resulting in a change in the
Na+: K+-pumping ratio and a concordant increase in Na+ reabsorption
in the kidney. The existence of the transversion was challenged,
but the challenge was apparently rebutted.
Atp1a1 lies with a hypertension QTL found in a
cross between the GH and Brown Norway (BN) strains. Therefore we
sought to determine whether the GH rat carried the controversial
A1079T transversion. Since the controversy over the transversion
centered on the possibility of PCR bias, we chose a method, first
nucleotide change analysis, that can detect point mutations in a
mixed population of PCR products, even in the presence of PCR bias.
We confirmed our analysis using direct sequencing and restriction
enzyme digestion of PCR products. To assure the validity of our
analyses, we used site-directed mutagenesis to create positive controls
containing the mutation. Surprisingly, we found that, not only does
the GH rat not have the A1079T transversion, the SS/Jr strain doesn't
either. Indeed, the transversion was not found in any strain tested.
As an incidental observation, we sequenced the intron preceding
the exon containing the putative A1079T transversion. Within this
intron, a single base, C/T polymorphism was observed at base 132.
Our results definitively eliminated the putative A1079T transversion
in Atp1a1 as a causative factor underlying hypertension in the GH,
SHR and SS/Jr strains and indicated alternative candidate genes
within the region defined by the chromosome 2 hypertension QTLs
should be examined.
The talk was of great interest and was very well
received since the Atp1a1 transversion is so well known in hypertension
circles and had many important implications. One delegate was overheard
remarking, "Imagine. They got 10 years of NIH funding for that!"
We have recently submitted a paper on our findings to Hypertension.
A poster on the mapping of a gene causing breaks
in the internal elastic lamina (IEL) of the abdominal aorta of the
BN strain was presented at ISH2000. The IEL lesion gene is independent
of hypertension, though at least one gene from the GH rat greatly
increases lesion severity in F1 and F2 rats from the BN X GH cross
made to map the lesion gene. Since it is more within the realm of
vascular research, this work was not of such great interest to hypertension
researchers as the ATPase results. However, the conference allowed
Dr. Harris to talk with all the relevant people, resolve some issues
concerning a paper on the lesion gene and set the stage for some
future collaborations. Submission of a paper on the lesion gene
is awaiting the signatures of our collaborators at the Medical College
of Wisconsin on the copyright transfer agreement. Meantime, anybody
wishing further information on the mapping of the lesion gene is
welcome to consult
The conference venues were excellent. Though the
huge Chicago conference was a bit disorganized and didn't allow
electronic slide presentations, the Navy Pier setting was outstanding.
The Toledo Art Museum made a wonderful venue for the GEHH banquet.
Likewise, the Field museum with Sue, the famous Tyrannosaurus rex
exhibit, was an imaginative setting for the ISH2000 banquet.