Newsletter - December 2001
From Your Director
This newsletter has turned into something of annual report for the
year 2001 highlighting some of the events of the year and the outcomes
of the CGR Committee meetings. Getting a newsletter out seems to
have become a huge task -- one put aside pending other more urgent
matters. There is the question: Is a newsletter still necessary
or relevant given the website, email-lists and discussion groups???
The Centre for Gene Research is a grassroots organisation and like
any patch of grass it needs to be watered and fertilised and taken
care of otherwise it will become paved over with concrete slabs
of bureaucracy. I see this Newsletter as the equivalent of mowing
Early in 2001 we went around beating the bushes
for support for the replacement of the ABI 377 sequencer given that
the manufacture of this instrument had been discontinued and it
would be just a matter of time when it became obsolete. An appeal
went out to CGR members to support the purchase of an up-to-date
capillary sequencer. A total of 41 PIs responded with the
titles of their projects, the staff involved and the source of their
funding. This represented a total of 169 EFTs who were using
the DNA sequencing facility. The total membership of the CGR is
about 370, some of whom are postgraduate students and associated
members. A proposal was put together for the ABI 3100 capillary
sequencer and to make a long story short, the Equipment Committee
initially agreed in principle to the purchase of this piece of equipment.
But as time wore on we were asked to resubmit the request under
the CAWSEP -- the new capital works and significant equipment procedure
and then we put the request out for tendering. By the time the tendering
process was over there seemed to be less money available than originally
indicated and the Beckman CEQ2000XL came in at a significantly cheaper
price than the ABI 3100. Our arm was pretty much twisted by the
Equipment Committee to accept the CEQ2000XL offer or go back to
the end of the queue. After speaking to a couple of satisfied Australian
users of the CEQ2000XL we accepted the lesser option. One of the
fish hooks of accepting the grant for the new DNA sequencer was
that we were not to come back to the Equipment Committee again in
a few years time expecting another one. In other words we would
have to find money from elsewhere for the next sequencer upgrade.
At this stage we are NOT considering charging users depreciation
on the equipment -- this is definitely the least favoured and last
option. We are having on-going discussions with the Dean of the
School of Medical Sciences about possible alternate schemes.
Since early last year there have been increases
in the running costs of sequencing which the CGR has been absorbing.
For example, the cost of the ABI Big Dyes has increased from $12
per reaction to $17 or up by 40%. We can no longer afford to subsidize
these costs from our limited financial reserves and the cost will
go up. We have yet to evaluate the costs of running the CEQ2000XL
capillary sequencer but the initial indications are that they will
be very similar to the ABI costs.
The commissioning and the test runs of the CEQ2000XL
were something of a trial by fire since we we were hoping for a
transition period. However the ABI 377 broke down and we tried to
get as many sequences done before the Christmas break. The plan
is that we will run both the ABI 377 and the CEQ2000XL and offer
a choice to users with the understanding that the ABI 377 would
eventually be decommissioned. The initial runs from the CEQ2000XL
seem comparable to those from the ABI 377 -- certainly brilliant
for PCR products with some fine tuning required for sequencing from
plasmids. The main problem with plasmid DNA is that the capillaries
are very small and the viscosity of large pieces of DNA tends to
clog the capillaries. One of the many advantages of the CEQ2000XL
is that sample handling is very much easier and the background fluorescence
in the infra-red region is practically non-existent so that very
low concentrations of DNA can be accurately detected. Also since
each sample runs in its own capillary there is no bleeding
over from adjacent samples. A problem we still need to work
around is using ABI software to read the scf file format. While
the scf file format can be read by most third party software packages
like DNAStar, Sequencher and GCG, it can not be read by the ABI
software. We will soon have conversion software (a la Peter Stockwell)
that will convert scf files to the ABI file format and allow you
to continue using the free ABI software.
One of the main uses of the CEQ2000XL at other
centres is fragment analysis and the detection of alleles, etc.
This is something we will be exploring further and will hold a workshop
on this topic.
Some of the other activities in 2001 was the launching
of the new CGR website with its own URL (cgr.otago.ac.nz). Websites
are quite hungry for content and we are always looking for fresh
content on a regular basis. We get a good rating by the GOOGLE search
engine and consistently get into the top 10 for gene research
from 1.3 million websites!! This is mainly to due (to the good design!)
to the content which comes from the HTML versions of the PCR PowerPoint
presentations and other resource materials on this website. Content
On August 28th we held a combined Annual CGR Poster
Night with the Research Themes: (i) Functional Genomics, Gene Expression
and Proteomics; (ii) Oral Microbiology and Dental Health;(iii) Virology.
The venue was the upstairs. "Scholar's Bar", Staff Club
and about 80 people attended. There were four student poster prizes
of $150 each, sponsored by CGR and the research themes. The prizes
were presented by Martin Kennedy, the visiting Poster Night guest
The Centre for Gene Research Poster Prize was awarded
to Elizabeth Duncan for the poster entitled: A cDNA MICROARRAY APPROACH
TO CANDIDATE GENE DISCOVERY IN FACIAL ECZEMA RESEARCH. E. J. Duncan,
D. Hyndman, T. Wilson and S. H. Phua AgResearch Molecular Biology
Unit, Department of Biochemistry
The Functional Genomics, Gene Expression, and Proteomics
Research Theme Poster Prize was awarded to Marjan Askarian-Amiri
for the poster entitled: IDENTIFICATION OF SITES OF INTERACTION
OF THE TRANSLATIONAL RELEASE FACTOR WITH RIBOSOMAL. Marjan Askarin-Amiri,
Debbie-J Scarlett and Warren P. Tate.
The Oral Microbiology and Dental Health Research
Theme Poster Prize was awarded to Mehdi Rahimi for the poster appropriately
entitled: FORENSIC PCR ANALYSIS OF BACTERIA RECOVERED FROM BITE
MARKS. M. Rahimi, N.C.K. Heng, J.A. Kieser and G.R. Tompkins
The Virology Research Theme Poster Prize was awarded
to Dongho Kim for the poster entitled: NUTRIENT REGULATION OF UCP2
& UCP3 EXPRESSION IN C2C12 CELL LINE. Dongho Kim and Mary P.
In October we held a users workshop on sequencing
and Real-Time PCR based around the ABI equipment where we went over
some of the DNA sequencing problems and the latest information on
the 7700 PCR protocols.
The ABI 7700 PCR equipment is heavily used and
fully booked and in some ways has become the victim of its own success.
In a six month period we clocked up 300 runs which means that the
equipment is running at full capacity for most of the time.
In October we had a fascinating seminar on the
protein chip technology, the Ciphergen Proteinchip and finally ended
the year (December 7th) with the Microarray Forum organised by Kyoko
Koishi and Jo Stanton.
In 2002 I began the third year of my second term
as Director of the CGR and there are times when I have worried about
where the CGR sits among the themes and schemes scenario. The challenge
is to find an administrative home because when things go wrong we
are really in a free-fall situation -- an orphan without a home.
We can continue to be a grassroots organisation as long as we can
remain financially viable and therein lies the challenge for the
Ever wanted to get a handle of this bioinformatics stuff or thrash
out some ideas of your own?
Amonida Zadissa, a Bioinformatics Ph.D. with AgResearch,
and Grant Jacobs, formerly a Research Fellow at Biochemistry now
operating as BioinfoTools, held the first meeting on Tuesday 12th
February at 4.00pm. The venue was the Reading Room on second floor
at the Biochemistry Department. The details of remaining meetings
will be finalised at this first meeting. Meetings will likely be
held every two weeks. You will be informed by email when upcoming
meetings are, who is speaking and their chosen topic.
People form any university department, local commercial
venture, institution, or whatever are welcome. Students are strongly
encouraged to join. If you are interested in joining, send an email
to firstname.lastname@example.org. Emails sent t this account will
be forwarded to both organisers automatically.
Let anyone else you feel may be interested know.
Below are some brief thoughts about the BC. The overall aim should
be to share and learn approaches to bioinformatics problems. Presentations
should encourage discussion and be aimed at a fairly general level.
People can always ask for more detail if they want it.
Topics don't have to be picked from a recent paper:
use this as an opportunity to read up a topic your have been meaning
to dig into because it interests you. Pretty much anything will
go for topics, but we discourage blow-by-blow accounts of using
some "pretty user-interface" unless it genuinely offers
something new. More interesting would be discussion of the concepts
behind bioinformatics methods, datasets that pose interesting bioinformatics
problems and the issues involved in analysing them, etc., than exactly
how to run some specific software or web site.
Chris Brown (Biochemistry Department) has suggested
that each speaker introduces their won work briefly before giving
their presentation, which we think is an excellent idea. The main
talk can be your own work it you feel so inclined. Talks shouldn't
be allowed for discussion with a maximum of an hour for the whole
meeting. If anyone has further suggestions/ideas, we're happy to
hear them, just send us an email.
Hope to see your there!
Amonida & Grant
Real Time PCR News
This year has seen a large increase in the number of users, which
is great to see. There has however been a down side in that at times
it has been operating 24 hours a day and your have had to book a
week or two in advance to get on.
Towards the end of the year we had the first ever
Users Workshop. We had two "experts" from Applied Biosystems
Australia here. They gave a general seminar on real time PCR (Taqman)
technology and the latest developments form their company. this
was an open lecture. After the tea break there was an opportunity
for the users to hear about more practical matters and discuss their
own problems/experiences. Over the next day there was also the chance
to have a one on one session which many people took advantage of.
As I only use it periodically I found it an excellent refresher
course and introduction into the SYBR green analysis. From the feed
back I had everybody found it a worthwhile exercise. Perhaps we
can make this an annual event. I have continued to pass on all information
sent by Applied Biosystems, sorry to those who receive it directly.
A hard copy is placed in a folder under the ABI 7700 o the 8th floor
of Micro. This year Richard, fro Applied Biosystems, has written
a Compendium for users. It includes troubleshooting, tips and frequently
asked questions. Copies of the latest version are on the CGR/PCR
server. Things have run smoothly over the year with only the odd
problem. Hopefully 2002 we run smoothly.