| From your Director
||"May you live in interesting times"
was a curse that Chinese in the Middle Kingdom used for impending
social and political changes. Today it seems more appropriate to quote
Bob Dylan: "the times they are a changing..." It could be
that time of the academic year but I am mentally exhausted with all
the proposed changes, restructuring and being Foresighted to death.
One of the changes that will directly affect the CGR is the move of
the DNA sequencing facilities and ancillary activities to a new laboratory
on the 8th floor of the Microbiology Building. This is likely to be
completed by the end of October. This should provide for a more coordinated
DNA sequencing service along with the recommissioning of the ABI 373
for GeneScan capabilities and a proper home for the quantitative PCR
(Taqman) equipment. And who knows maybe the new CGR Website and the
on-line DNA submission forms and accounting system will be ready by
then as well (promises, promises..).
Some of you will be aware that we have gone through an exercise
in strategic research planning for the University in regard to the
purchasing of major pieces of equipment. As a follow up to the CGR
Emerging Technologies Workshop held in August, there was a ground
swell of support for some kind of "Bioinformatics, Genomics,
Proteomics" initiative. A meeting was held in the Biochemistry
Department attended by interested parties and a 'shopping list'
(which totalled about $3 million) was produced and put forward to
the 'higher authorities'. Rumour has it that this list has received
a favourable response and we are now awaiting some kind of announcement.
Hopefully this will happen before Christmas!!!
In another arena, the CGR responded to Diana Twigden's document:
Foresight Gene Technologies Submission. Briefly, Diana proposed
the establishment of a National Gene Technology Centre (presumably
in Auckland) where the cutting edge genomic research would be carried
out. The view of the CGR Committee was that we did not favour a
'bricks and mortar' institute but preferred a National Genomic Network
and that the money was better spent supporting 'working scientists'
rather than buildings. An excerpt follows:
We agree that technologies associated with gene analysis are
important to have and develop in New Zealand. There is no doubt
that being part of such development is essential if NZ scientists
are going to be internationally competitive in the coming years.
NZ is a small country and its expertise is widely spread over
the main academic centres. For this reason, we favour the establishment
of a National Genome Network rather than a single Gene Technology
Centre. The different components of this network (nodes) could be
located strategically throughout the country. Thus, different expertises
would reside in different centres but linked in name and some notional
coordinating administration. Obviously, each facility would also
be linked by an electronic network.
[The CGR] has 213 members from within the University of Otago
in Dunedin and the Christchurch and Wellington campuses. This membership
represents some of the most creative and energetic scientists in
New Zealand (the world?). In 1997 the members received about $20
million from external competitive granting agencies. One of strengths
of the Centre [CGR] is its "grassroots" origins and the
fact that it represents active research scientists.
The Centre [CGR] would clearly then be a useful member of any
National Genome Network. Its already established network of scientists
would clearly aid in the development of such a Network.
If anyone wants the full reply to Diana Twigden, I can email you
Finally, next year's Queenstown Molecular Biology Meeting is being
organised by the CGR. It will be held August 15-20th. The planning
committee consists of the 'A' team: Anthony (Reeve), Andy (Mercer),
Antony (Braithwaite) and myself. We will be co-opting other people
and are asking for suggestions of speakers and themes and sponsors
and local participants. Contact any of the above members or me if
you want to be part of the organising committee or have any suggestions.
||The recent CGR workshop on emerging
technologies was a great success, bringing together over one hundred
researchers from around the University to discuss the latest developments
in gene research technologies. The original mandate from James Kalmakoff
was to host a meeting that would bring us up to date on quantitative
PCR, microarray technologies, proteomics and bioinformatics. In addition
to hearing about our own members' experiences and aspirations of these
new developments currently taking the world of molecular biology by
storm, we were also able to invite several leading scientists from
Australia to give insights into their own particular fields of expertise.
The meeting kicked off on the Friday evening with a social gathering
at the Staff Club where Professor George Petersen, in an after dinner
speech, modestly re-lived some of his early years as a molecular
biologist. His anecdotes of driving north from Oxford to attend
the Edinburgh Festival only to be thwarted by a dodgy car engine
and of his culinary skills when left alone for only a few days by
his wife were delivered with alacrity. George's enthusiasm in visiting
virtually every molecular biologist during a brief visit through
the States in the 60s, combined with his unstinting commitment in
setting up and leading a world-class biochemistry department back
in Dunedin, are lessons for us all to take inspiration from.
Saturday dawned calm and sunny, but with the threat of an approaching
southerly front to remind us that winter hadn't completely forsaken
us this year. Our first speaker was Professor Tony Reeve who, with
only three days' notice, had kindly agreed to step in following
the unavoidable withdrawal of Professor John Mattick from Brisbane.
Tony's remit was to enthuse everyone about new genomic technologies.
His introductory talk on the power of advanced molecular methods,
particularly gene microarrays, to push back the frontiers of medical
research ably demonstrated just what we wanted to achieve in hosting
The next two speakers, separated by commercial rivalry as well
as by morning tea, were both representatives from companies heavily
involved in the development of PCR. Brant Bassam, from PE Applied
Biosystems, gave an incisive talk on real-time PCR and its applications
based on the TaqMan and SYBR Green chemistries, including quantitative
PCR and allelic discrimination. This was particularly relevant and
welcome in light of the CGR's recent acquisition of a GeneAmp 5700
system - the platform for these applications. Not to be outdone,
John Mackay of Roche Diagnostics (formerly Boehringer Mannheim),
followed up with a full and technical presentation of an alternative
PCR platform on which to perform similar and additional applications
- the Light Cycler.
Our first overseas invited speaker was Dr Marc Wilkins, from the
Australian Proteome Analysis Facility at Macquarie University. Coining
the term 'Proteome' in 1994, as a response and complement to the
burgeoning interest in genomics and DNA, Dr Wilkins has been instrumental
in setting up an original and highly resourced centre for comprehensive
protein expression analysis. His talk, entitled "Proteomes
and Proteomics: tools and techniques for the high-throughput analysis
of proteins", was entertaining and not a little enlightening
for the 'gene jockeys' amongst us, giving a timely reminder that
genetic studies alone cannot be used to predict phenotypic outcomes
- the subtleties of proteomics are another layer of molecular control
altogether. Rest assured there'll still be lots to do once Venter
has finished sequencing DNA...
Breaking for lunch back at the Staff Club those of us not way-laid
by the media for comments on genetically modified food were given
the opportunity to eat, drink and watch microarraying robots strutting
their stuff. As well as trade displays from Roche and ABI, Stuart
Elmes from the Cambridge-based company BioRobotics was also attending
the workshop, showing a video of their MicroGrid instrument in action.
Suitably refreshed, it was time for the second of our overseas
speakers - Dr Tim Littlejohn, the head of the Australian National
Genomic Information Service. Speaking about "Integration, delivery
and access to bioinformatics resources", Dr Littlejohn gave
an excellent presentation on the downstream implications of all
this genomic and proteomic data, namely how the hell do we set about
analyzing it. Well, it seems the Australians have stolen the march
and have developed a whole host of integrated tools for "database
inter-operation, high performance methods for phylogenetic analysis
and efficient methodologies for the delivery of biocomputing services".
We must ensure that funding will be forthcoming to enable us to
subscribe to these essential bioinformatics tools.
Afternoon tea was accompanied by the predicted southerly, heralding
the final part of the workshop programme - microarray technology.
This session was planned as an informal discussion, to briefly cover
just what microarrays are being used for, dispel some of the hype
and myths associated with the much vaunted "DNA chips"
and to talk a little about what kinds of array experiments researchers
at Otago might like to carry out. Introducing the session, I explained
the highs and lows of expectation I'd experienced in talking to
scientists in America and Europe who are developing microarray technology,
more specifically for mutation detection. Dr Mike Sullivan, senior
lecturer in paediatrics and a principal investigator in the Cancer
Genetics Laboratory at the University of Otago, then eloquently
described several experiments he could undertake immediately in
order to answer questions about the coordinate expression of genes
involved in childhood tumours, if only he could have access to microarray
technology. Bren Collinson (from the company Molecular Dynamics,
which manufactures some of the microarray-analysis equipment) gave
us some insights into the pitfalls of this technology, though some
of us thought he was being overly pessimistic (or perhaps just politic?).
Watch this space.....
In summary, I think the workshop was both informative and very
timely. It is clear that the University of Otago needs to embrace
many of these new technologies if it is to compete successfully
in the rapidly changing world of molecular biology. To take a leaf
out of Professor Petersen's book, it wouldn't do us any harm if
we were to actually take a lead in some of them too.
No workshop is successful without the input of many people. In
addition to all the speakers, I would especially like to thank the
rest of the organising committee: Chris Brown, Glen Buchan, Bronwyn
Carlisle, Mark Dalphin, James Kalmakoff, Mike Hubbard and Craig
Marshall. Thanks too to the graduate students who worked the projectors
and to the University who subsidised the meeting through the CGRs
'Gene Structure and Function' theme.
||On Monday 2nd November, Jan Luton from
Genomic Solutions will be in Dunedin to talk about her company's products,
including microarraying robotics and all downstream analysis tools.
Genomic Solutions also has products in development relating to 'Proteomics'.
A Special Seminar will be advertised closer to the date, but if anyone
would like to meet with Jan, please contact Scott Tebbutt (email@example.com).
The new ABI 7700 Sequence Detection System (Real
||In May this year the Center for Gene
Research purchased the ABI 7700 sequence detection system. It has
been installed on the 8th floor of the Microbiology department. This
system enables fully-automated real-time detection of specific PCR
products possible. The system integrates four major elements : 1.
fluorogenic chemistry for target-specific oligonucleotide probes 2.
exploitation of the polymerisation-dependant 5" nuclease activity
of the DNA polymerase 3. instrumentation to measure fluorescence signal
within a closed PCR reaction tube 4. software to process and analyse
the data. The 96 well format allows high-throughput particularly important
in genetic screening studies. There are several applications for this
technology : pathogen detection (several kits are available from the
company), allelic discrimination and quantitative PCR. This technology
has specific guidelines for PCR primer and probe design and dedicated
software has been supplied. The latest updated version has now been
installed and a manual is available. The company is looking at producing
a start up kit in order to reduce initial costs. This will include
a Taqman core kit (enzyme, reagents, Rox dye for standardising the
background & one probe) and specialised tubes.
To date it has successfully been used to genotype over 200 animals
and RT-PCR quanitative analysis. Below are comments from the two
I was looking forward to the arrival of this system as for the
past two years I have done semi-quantitative RT-PCR the "old
way" ie blotting, probing & scanning. The advantage of
the ABI system is that it is quantitative & fast with no further
manipulations after the PCR run. After an initial change in my thinking
for optimisation, things fell into place. Both primer & probe
concentrations need to be optimised, in order to save money finding
the lowest concentration of probe required is beneficial. The results
from my first run looked nothing like the test run we did with the
technician during the installation. Fortunately they have an 0800
help number to their technician, the number has been well used.
At last I could run some "real" samples. It was great
to finally be able to put a quantitative value on the amount of
message I had previously been seeing. I did a run with the ABI machine
& a run the traditional way (gel & scanning). The ABI results
were completed by the end of the morning while it took the rest
of the day to complete the other, & considerably more "hands
on" work. The results are reproducible & the amount of
starting material calculated for you, what could be easier. The
biggest delay has been waiting for probes to arrive. The probe design
programme is user friendly & to date has created probes that
work well. I have not worked out my current costs but the convenience
of no down-stream manipulations makes it well worth it.
The greatest interest in the ABI PCR machine at present seems to
be its use for quantitative PCR. Its other main use is for allelic
discrimination. My work using this machine has been looking at two
single nucleotide polymorphisms in sheep situated 8bp apart. By
using probes specific for each allele (labeled with different fluorescent
reporter dyes) in the PCR assay it is possible to determine whether
an animal is homozygous (and if so for allele 1 or for allele 2)
or heterozygous. This process is efficient and allows high throughput.
As no post PCR analysis (gel running etc.) other than ~15min of
computer is required, time involved is minimal. I find it takes
me about 25 minutes to set up the PCR for 96 animals, 2 hours to
run the PCR and about 15 minutes to analyze my results to completion.
I have found the machine to be user friendly and results so far
have been excellent (reproducible, consistent and clear). If you're
wondering about the cost, my PCR assay costs about $2 per sample.
I will keep you up to date with developments. If you have any questions
please contact me.
||The following members of the CGR were
successful in the latest round of Marsden Fund grants:
David J Galloway, Biochemistry Department; Principal Investigator
Do New Zealand's native grasslands and forests like lichens?
The project will use large, fast-growing lichens in the genus Pseudocyphellaria,
from tussock grassland and rainforest biomes in New Zealand, to
find out how these unique symbiotic systems can exploit both low-light
and high-light levels for photosynthesis and nitrogen-fixation in
biomes that are naturally nitrogen-limited. The investigators' skills
in lichen systematics, nitrogen fixation and in cyanobacterial photosynthesis,
will be strongly linked in this novel interdisciplinary study which
will attempt to explain, in biochemical terms, the contributions
that diazotrophic lichens make as "biological fertilisers"
to the maintenance of biodiversity in our grasslands and forests.
Parry Guilford, Biochemistry Department; Principal Investigator.
E-cadherin: An evolutionary link between bacterial immunity
and cancer susceptibility.
We have recently shown that mutation of the E-cadherin gene is responsible
for inherited predisposition to stomach cancer in several extended
Maori families. It is likely that mutations in this gene are common
in the Maori population and may have provided a survival advantage
which outweighs the increased risk of cancer. We are going to test
the hypothesis that variation in this gene leads to resistance to
the bacteria which cause Listeria. This knowledge will lead to a
better understanding of the causes of cancer and may provide innovative
strategies for treating bacterial infections.
Sally P A McCormick, Biochemistry Department; Principal Investigator.
Designer peptides to inhibit atherosclerosis
Heart disease is a leading cause of early death in Westernised countries
including New Zealand where it claims over 6500 lives per year.
A major risk factor for developing heart disease is high blood levels
of lipoprotein(a), a cholesterol-rich lipoprotein formed in the
blood by the binding of a low density lipoprotein to the apo(a)
protein. There is currently no drug available to lower lipoprotein(a)
levels. This research aims to develop a new strategy to prevent
lipoprotein(a) formation and has the potential to provide an effective
new therapy for people with high plasma lipoprotein(a) levels who
are at high risk of developing heart disease.
Michael P Murphy, Biochemistry Department; Principal Investigator.
Modification of mitochondrial function within living cells.
We have developed a targeting system that uses the mitochondrial
membrane potential to deliver novel, bioactive compounds to the
mitochondrial compartment of animal cells. These compounds will
be used to measure and modify crucial aspects of mitochondrial function
within intact cells. This will lead to new insights into the role
of mitochondria in the production of reactive oxygen species and
programmed cell death. This work will also lead to new methods to
modify the expression and replication of mitochondrial DNA.
Russell T M Poulter and John F Cutfield, Biochemistry Department;
The origin of vertebrate retroviruses: Horizontal transmission
Research by Russell T M Poulter at Otago has resulted in the discovery
of the first vertebrate retrotransposon (termed sushi). This mobile
genetic element was found in the genetic material of the fugu fish.
This is a finding of major significance in the understanding of
retroelements, the class of genetic elements that includes the vertebrate
retroviruses such as HIV (the causative virus of AIDS). It is proposed
to investigate two phylogenetic questions: (1) Are the vertebrate
retroviruses derived from this newly described class of vertebrate
retrotransposon? (2) Can the origin of these vertebrate retrotransposons
be traced to the horizontal transfer of a 'jumping-gene' from a
fungus to an ancient vertebrate?
John Sullivan, Microbiology Department; Principal Investigator.
Decoding the symbiotic island of Mesorhizobium loti
The aim of this proposal is to define the genes contained on the
500 kb symbiosis island of Mesorhizobium loti by nucleotide sequence
analysis. The symbiosis island is a large genetic element located
on the chromosome that converts nonsymbiotic rhizobia to strains
able to fix nitrogen with a legume host. It belongs to the same
group of genetic elements as pathogenicity islands that confer virulence
on otherwise benign bacteria. Sequencing will reveal the bacterial
genes required for the Rhizobium-legume symbiosis, and will provide
insight into the evolution and acquisition of these genetic elements
that allow bacteria to interact with plants or animals.
Goodbye to Mark Dalphin
||The rumours are true. Mark Dalphin
is leaving the University of Otago and the Centre for Gene Research
for a job with the drug company, Amgen, in California. While he vigourously
denies the rumoured "six-figured" salary that is promised
to "Bioinformatics Professionals", he isn't unhappy with
what he has been offered.
Fortune Magazine in picking their "100 Best Companies to work
for in America" (Jan 12, 1998) picked Amgen as number 74, saying:
Leader of biotech industry nearly quintupled work force this
decade. Employees showered with benefits: stock options, subsidized
on-site child-care center, free beer busts every Friday night, free
refreshments, quarterly parties, on-site gym, 15 days' vacation
in first year, host of on-site conveniences (film processing, flower
At least he won't miss the Biochemistry Department's Happy Hour,
though it will be hard to replace the Emerson's Weis Beir.
Amgen is located in Thousand Oaks, about 1 hour's drive West-Northwest
from Los Angeles (airport) on the US101 freeway. A further 45 minutes
driving would bring one to Santa Barbara. A 30 minute drive South
on twisty roads thru the Santa Monica Mountains brings you to the
Pacific Ocean, and to the North is Los Padres National Forest. The
two neighboring towns, Simi Valley and Moorpark, along with Thousand
Oaks, are consistently the "safest cities" (placed one,
two and three on the list) in the USA. These are towns of about
100,000 people each: boring, middle-class suburban towns with large
tracts of big family homes, mostly built from 1970 onwards. Median
household income is about US$60,000 per year.
The climate looks nice, though a bit on the hot side: January average
lows of 5C and average highs of 15 with a mean of 10C.
July lows of 15, highs of 30 and mean of 20C. And then there
is the rain. Or rather, lack of rain: about 10 inches per year of
which 7.5 inches fall in January. Gentle winds too with an average
relative humidity of 50%. The place is dry!
The downside to all this is the high cost of living in the area.
Two bedroom apartments cost between US$700 - US$1200 per month.
The median cost of a three bedroom family home with two car garage,
large section, etc is US$280,000! Food costs about the same as here;
cars of similar vintage to cars here, cost about the same, but everyone
drives newer cars. And then there is insurance! How about US$2,000
per year per car? And vehicle registration is 2% of the vehicle's
sales price. At least the petrol costs about 1/2 what it does here.
Mark will be working in the new Genomics Group at Amgen, attempting
to locate protein coding sequences in genomic DNA sequence prepared
from some in house sequencing projects. He will be part of a team
of 10 other scientists working on the same or similar projects.
Novel coding sequences will be examined for potential as thereputic
agents and promising candidates will be turned over to Molecular
Biologists for cloning and creation of transgenic animals for testing
the effect. Bad guesses are frowned upon.
Assuming the American Embassy provides the required visas in time,
Mark will be leaving with his wife, Ruth, at the end of November.
GCG Course Will Not Be Held This Year
||With Mark leaving Dunedin, the GCG
Course will not be held this year. In addition, there is a strong
possibility that our current GCG package will be upgraded to something
newer, which would require a re-write of the GCG Course material.
The Centre for Gene Research expects to have a new, updated Sequence
Analysis Course operating next year.
A Glimmering In the Far Distance
||Amidst the doom and gloom that surrounds
science in New Zealand just at present with scenarios of few scientific
jobs for New Zealand and a general economic depression I was delighted
to find something positive. Well, sort of delighted. The glimmering
was to be found at the recent Protein Society meeting in San Diego.
The nature of this meeting has changed markedly over the last 10 years.
Early in the decade, those attending were almost all from academic
institutions, but now the majority of attendees were from industry,
primarily from the biotechnology industry.
I suppose this reflects the adoption by industry of protein engineering
as a way of producing new products and making money. Perhaps what
is surprising is the range of companies that have adopted this approach.
The biggest companies and the small biotechnology startup companies
were all represented at the conference.
From New Zealand it is hard to judge the significance of this development.
However, consider that about a third of the newly rich in the USA
acquired their wealth from biotechnology, mostly by creating a startup
company and selling it when the product proved successful. Furthermore
consider that there are more biotechnology laboratories and companies
on one road in San Diego than there are in the whole of New Zealand.
Biotechnology is alive and well in the USA and making a great deal
of money. Accordingly these companies are hiring talented people
as fast as they can. On senior academic at the Protein Society commented
that it was getting increasingly difficult to hire really good people
because they were all going to much better paying jobs in industry.
I found this a startling comment because for a number of years the
post-doctoral job market has very much been slanted in favour of
the hirer. Things, it seems, are changing.
So what was the glimmering in the distance? Post-doctoral positions
in industry in the United States, particularly in California and
around Boston are abundant. Companies are hiring people with experience
in "proteomics" and structural biology by the handful.
Sadly, these jobs are in the United States and it seems likely that
unless science (and biotechnology) is much better funded in New
Zealand, those that leave New Zealand are even less likely to return.
Much could be said of the folly of allowing talented people to
disappear like this. It seems blindingly obvious that this is not
in the best interests of New Zealand. It is equally blindingly obvious
that the best advice that can be given to a young scientist looking
for a career past their PhD is to look to the far North East. Eldorado
it might not be, but it is certainly better than scratching around
looking for non-existent positions in an over-competitive environment
in New Zealand.