From your Director
Since the last Newsletter the Centre's DNA sequencing
facility has moved into a newly refurbished laboratory on the 8th
floor of the Microbiology Building. This has resulted in better
facilities and a more spacious environment and an overall improvement
of service to the members. The old Model 373 sequencer was recommissioned
for genotyping (Genescan). However there may not be enough usage
to justify the service contract on this instrument and plans are
afoot to convert the Model 373 sequencer to the BigDye chemistry
in order to take the sequencing overflow from the Model 377. This
will mean that the Genescan runs will be carried out on a prebooking
basis on the Model 377. The 7700 Taqman PCR machine is also housed
in the Centre's facilities and currently several groups are investigating
using SYBER Green for quantitative PCR (more about this elsewhere
in the Newsletter).
Another change was the launching of the new CGR
and the move to an on-line DNA submission system. The website has
been a pet project of mine, so you will have to bear with me if
I rabbit on about it. The use of the on-line DNA submission requests
has dramatically reduced the paper workload and the aggravation
level in keeping track of samples and the accounts.We used to expend
more time and energy in doing the paperwork than in carrying out
the actual DNA sequencing itself. You can image the cost effectiveness
of putting through a $6 DNA sequencing payment request through the
entire University accounting system. Some of the invisible benefits
have been the development of direct electronic invoicing to the
Registry Accounts by email. This not only cuts down the errors associate
with data entry but Tracee is now able to send to departmental account
managers a preview of the account charges prior to being sent to
Registry. This allows correction of account codes etc, before submission
for payment. In the past the University accounts system was used
to pick up the errors and there was the inevitable bouncing backwards
and forwards of account codes and a long paper trail . For instance
we would get a DNA sequencing request from some graduate student
(bless their little souls) who would scribble out some illegible,
non-existent and/or long-since-expired account code (in a desperate
bid to get some sequencing results). We would have carried out the
sequencing (in good faith) and then some weeks later had the time
to process the accounts by which time it would have bounced around
the system and finally been picked up by some irate departmental
The other feature of the website is that it provides
a 'virtual centre', a place where members can visit for news, for
announcements, for information, for looking up archival material
(such as this Newsletter) or searching for a profile on one of its
members. In some ways a Newsletter such as this is less vital for
keeping members informed as to the activities of the Centre. The
CGR membership policy is that you need to rejoin by filling in the
on-line membership form on the website. Your entry into the database
is 'updatable' by using the update form and you can use embedded
HTML codes to format your profile. You will need to remember your
username and password since only you have access to your data entry.
If you forget your password contact Tracee. A feature of a browser
like Netscape is that once you are logged in you remain logged in
until you "Quit" from Netscape &emdash; in other words the next
computer user could cause mischief to your profile. This also applies
to the DNA submission requests. Furthermore you may have to 'clear
the caches' around the network by 'reloading' before changes actually
appear on your computer screen.
There are plans to add other features to the website
such as a 'chat forum' and other 'searchable' features. I would
like you to feel that this is your website and that you can contribute
to it on any subject you like. As an example see the presentation
by Lynette and Claire: Marketing Yourself as a Successful Science
Graduate under the 'Activities' section.
The website gets a significant number of 'hits'
from overseas and I have to 'flick' people off who join from Japan,
Canada and the USA since they are not eligible for membership unless
they are associated with the University in some way.
As you are aware the Centre acts on behalf of the
Research Theme: Gene Structure and Function. This year the Research
Themes are being reviewed and will become part of the University
Audit. This review is something we have to take seriously since
funding priorities are established and based on these types of reviews.
For instance, the funding for the 'microarray genomic initiative'
(still to be announced!) is part of the University's strategic research
planning based on the perception of research excellence in this
area. Our review must be completed before August so as a PI you
can be expected to be asked for some statistical information on
papers published, postgraduate students, funding and other research
'outputs'. This will form part of the Theme's self-review which
will then be followed by an assessment by an external reviewer.
The Centre is involved in organising the Queenstown
Molecular Biology Meeting in August (see the website for details)
and in the International Science Festival being held in Dunedin
in June. The Science Festival theme is &emdash; The Global Village
&emdash; Join the Knowledge Revolution. So far our plans for the
Festival are to have a demonstration of how computers are used in
biomedical research and network communications. We hope to have
the use of 10 iMacs for the occasion with the venue being the Community
Centre (on Princes Street &emdash; around the corner from the Octagon).
This is a call for volunteers and ideas to 'raise the awareness
of science to the public' and to promote the Centre.
Finally a closing reminder: if you want to continue
to be a member of the Centre for Gene Research, please fill out
the on-line membership form (http://microbiology.otago.ac.nz/cgr)
in the "Join" section.
GMOs, Killer Tomatoes and Utopian
The last few weeks have seen a flurry of news media
interest in genetically-modified organisms. Much of the comment
has been along the lines of "Frankenstein Food May be Bad for Ozone
Layer" and the tone has been generally against the idea of genetic
manipulation of food. Indeed, the most vocal of these critics have
concerns about the whole idea of genetic manipulation on any grounds.
Those scientists that have spoken out have been forced into a defensive
position and have been criticized for being apologists for such
companies as Monsanto. One thing is clear; there has been little
informed debate about the issue, but instead, the airing of many
But why has there been such an interest in genetically
modified organisms? Part of the answer is probably related to the
appearance of ERMA as a regulatory body. ERMA has made available
a great deal of information about genetic modification in New Zealand.
Opponents of such manipulation are able to find out what is happening
in this area much more easily than they could in the past and they
are appalled by what they have found.
Does this mean ERMA is a bad thing? I would say,
on balance, that it is not. Although many researchers have been
caught as minnows in a net set for much bigger fish, there can be
little doubt that the release of genetically modified organisms
to the environment is something not to be done lightly. It is less
clear that the cloning of a favouritegene into E. coli is something
that should be supervised so closely. Certainly there is little
evidence for any danger associated with the routine cloning of most
genes. Exposing large number of people to novel organisms, in theory
at least, is potentially a much more serious issue.
It is here that the serious problem crops up. The
distinction between the potential and actual risks is all the difference
in the world. It is easy to imagine apocalyptic visions of mutant
killer tomatoes. It is much harder to decide if the vision is plausible.
To do so requires considerable knowledge of both theoretical and
practical molecular biology. Too often we are left with spectacle
of the technically-informed defending genetic manipulation against
those whose concerns are of principle. Each side might be speaking
a different language.
Perhaps what we are seeing is process by which
Society forms an ethical view. Genetically modified food has been
only a theoretical possibility until recently, but now we have to
make a decision. Is such genetically modified food a good or a bad
thing? We are not in a position to put off making a decision; if
we do nothing, the food will appear, but do we have good grounds
for saying no? The difficulty with such decision making is that
in principle each opinion is as good as another. To my mind however,
informed and uninformed opinions are not of equal weight.
Much of the debate in the news media at present
pits those who are opposed to genetic manipulation on principle
against those who argue for it on practical grounds. Of course I
don't mean to say that all opponents of genetically modified food
know little of molecular biology, nor that all molecular biologists
are in favour of it, but there is a tendency for both these things
to be true.
What can be done to make sure that the debate is
informed? Decisions will be made and, in the end, we will be faced
with regulations or legislation designed to deal with the issue
of genetically modified food. Sitting back and doing nothing in
the hope that the problem will go away won't work. Actively supporting
genetic manipulation is not to every molecular biologist's taste.
Perhaps the most useful and important thing we can do is to try
and keep the debate informed. We should offer information about
molecular biology for those who are interested (perhaps through
the CGR Web site). We should be prepared to counter those who claim
ridiculous things. Genetically modified glucose in Easter Eggs is
just plain silly.
Genetic manipulation offers neither utopia nor
dystopia. The world will not be made an immeasurably better place
where noone is hungry by the introduction of genetically modified
food, but neither will civilization's end be hastened by eating
transgenic plants and animals.
One thing has come out of the debate that seems,
to me at least, incontrovertible. Genetically modified food, like
all food, should be labelled for what it is for we should have the
right to choose or avoid something for whatever reasons seem appropriate
News from the IBSC
As you are no doubt all aware, the HSNO legislation
requires that the development or importation of a genetically-modified
organisms receives prior approval from ERMA (or for "Low-Risk" development,
the UOO Institutional BiologicalSafety Committee acting under delegated
authority from ERMA). Those of you with ACNGT approvals carried
over to HSNO through publication in the NZ Gazette will no doubt
have enjoyed your two seconds of fame as your name scrolled across
the screen on "Holmes" a couple of weeks ago! There is no doubt
that the use of recombinant DNA technology will continue to attract
public scrutiny, which emphasises the importance of ensuring that
your work is fully covered.
The IBSC has just completed its assessment of the
first round of applications (about 30) to develop genetically-modified
organisms in containment under HSNO. The round was a learning experience
for both applicants and the IBSC. Basically when assessing applications,
the IBSC is acting under delegated authority from ERMA and the decisions
have the same legal status (essentially district court level) asdecisions
made by ERMA. Hence the IBSC must give the application the same
level of scrutiny as ERMA would. This means that all questions in
the application form must be addressed and full information provided,
including the glossary, and copies of all literature cited must
be attached. Once the IBSC has made its decision, a copy of the
decision form and the application are provided to ERMA. These are
public documents and ERMA will provide a copy to anyone requesting
one. (There is provision in the application form for confidential
information to be so designated and kept confidential). This is
one reason why the University of Otago has set the policy that all
applications are in the name of the Institution and one reason why
the location of the laboratory conducting the work is not listed.
In fact, the actual laboratory is also not really relevant from
ERMA's point of view - permission is given to develop a particular
organism under a specified set of containment conditions. The location
of the laboratory is relevant to the IBSC as one of the terms of
reference of the IBSC is to ensure that the University is complying
with containment controls - hence the IBSC requests that information
on the cover sheet that is required with all applications.
Applications received in the first round varied
considerably in the care that had been taken in their preparation
and in the level of information provided, and hence in the number
of times they were returned to applicants and in the amount of time
the IBSC had to expend on them. Several people had put a lot of
care and effort into their applications and this was much appreciated;
others..... INDEED THE IBSC IS OF THE OPINION THAT THE LEVEL OF
CARE REQUIRED IS SIMILAR TO THAT YOU WOULD TAKE WITH A GRANT APPLICATION.
We will within the next couple of weeks place a "model" application
on the network to provide guidance on the type and quantity of information
required. This will be placed in the "Biological Safety" Folder
on the shared disk "CGR Results", the same disk that Tracee places
the sequencing results on. The Folder also contains application
forms and two files that provide further information on the process
to be followed: "IBSC pres. Feb 99 HO", and "GMO Information and
As far as proposed new ERMA charges are concerned,
ERMA have dropped their proposal to charge all applications $800
to cover the cost of public notification. To quote, "I would advise
that on the basis of a review of the legal situation IBSC decisions
are no longer notified and thus the notification fee does not apply".
One small piece of good news! Hence there are no direct charges
for "low-risk" development applications. I have not heard any further
word on the proposal to charge an initial instalment fee of $5000
for importation applications. The IBSC sent in a strongly-worded
submission on this as did other universities but I would not hold
my breath, as ERMA are required by the Government to be self-funding
by 2001. In an attempt to minimise the effect on U. Otago, the IBSC
has submitted five importation applications to ERMA on behalf of
University researchers, while the old fee of $750 plus GST still
applies. If these are approved by ERMA, they will cover a broad
range of transgenic E. coli, transgenic S. cerevisiae, transgenic
gene knock-out mice, transgenic "over-expressing" mice, and transgenic
murine cell-lines. Thanks to Iain Lamont and Chris Brown (Dept.
Biochemistry) and Mat Walton (Malaghan Institute) for their efforts
in preparing these applications. We will keep you informed of progress.
Approval of a GMO under HSNO makes it a restricted
organism under the Biosecurity Act. This means the organism must
be handled in a MAF-approved Containment Facility. The University
is in the process of registering (hopefully) all labs involved in
GMO work in Dunedin as part of a single Containment and Transitional
Facility. The Facility comprises eleven sectors with Sector Managers
as follows: AgResearch Molecular Biology Unit, Department of Biochemistry
(Dr Allan Crawford); Department of Anatomy and Structural Biology
(Associate Professor Ian Mclennan); Department of Biochemistry (Dr
Russell Poulter); Department of Botany (Dr Paul Guy); Department
of Laboratory Animal Sciences (Dr John Schofield); Department of
Microbiology (Dr Glenn Buchan); Department of Oral Sciences and
Orthodontics (Dr Geoffrey Tompkins); Department of Pathology (Professor
Antony Braithwaite); Department of Physiology (Mr Nairn Smith);
Department of Zoology (Mrs Carleen Mitchell); Wellcome Research
Building (Dr Paul Hessian). The Containment and Quarantine Manual
has been approved by MAF, and the Facility has just been inspected
by the MAF Supervisor. We expect approval next week. The MAF Supervisor
was mainly concerned about security and access - labs need to be
locked when there is nobody in them and freezers in public areas
must be kept locked. In addition signs stating "Restricted Area
- No Unauthorised Access" must be posted on lab doors. Microbiology
also posts "BioHazard" signs. These precautions make sense to me
and I think in the current environment we need to be very security-conscious.
In operational terms,there is a need to maintain a paper trail such
that uncleared biologicals can be tracked from import through to
final disposal, and also a register of microorganisms (either imported
or GMOs). Of course, people working in the MAF-approved facility
will be expected to have read and to comply with the Containment/Quarantine
Manual. Further information will be forthcoming from your Sector
Manager in the next couple of weeks, who will also have a copy of
the Manual. for those working with organisms other than microbes,
transgenic mice need to be held in a Containment Facility for Vertebrate
Laboratory Animals. We are in the process of registering the DLAS,
with John Schofield as Manager. MAF have yet to release the Containment
Standard for Plant, but when they do....
Finally, there is a need for a rapid avenue for
information dissemination. The IBSC is distributing information
via the CGR email list-server but it is apparent this has been missing
a lot of relevant people. If you are not registered, you will miss
out. Joining the CGR does not automatically subscribe you to the
list - you need to register separately. Tell your friends!
Real-time PCR News
The ABI 7700 has now been in operation for almost 1 year. To date
all the users are pleased with the results. It is good to see another
group using the technology. The SYBR green dye profile has been
installed so there is no longer the need to buy probes. Whlie this
technology has not yet been used on the machine two groups are about
to give it ago. The Primer Express software has been used by many
people and is available to anyone to design primers (& probes).
After discussions with Applied Biosystems and based
on nearly 12 months usage they have offered a discount of 5% on
consumables required to run the machine, including the 40nM & 0.2uM
scale fluorogenic probes. If we increase our purchases/usage then
the discount will be greater, likewise if if drops we loose the
discount. There is still the offer of a special discount (approx.
20%) for new users which can be arranged through the NZ rep Stacey
Nelson. The CGR has purchased tubes/caps/retainers for selling to
users. This allows the purchase of small numbers, 100-200 tubes
rather than 20000. This service is merely to help people initially
start & if you plan long term usage then buy your own tubes. They
will NOT operate as a store and if abused the service will be with
Please contact me for details on the discount or
any other matters on use of the ABI 7700. Look forward to hearing
from you & seeing greater usage of the technology.
Vascular Biology - Looking
for a Research Portfolio
The Department of Surgery invites all interested parties to asymposium
on vascular biology in the Sayers Common Room on the 29 April 1999
from 10am to 4pm. The aim of this symposium is to identify and explore
avenues for collaborative research in vascular biology and examine
the possibilities and initiate research portfolio(s) in the area
of vascular biology and disease.
The keynote speaker and facilitator is the William
Evans Fellow, Professor M David Tilson, of the Columbia UniversityDepartment
of Surgery. He is well known for his wide-ranging research on the
etiology of abdominal aortic aneurysms (AAA), and was one of the
first researchers to draw attention to the strong genetic component
Previously, Professor Tilson has done research
on the types and expression of elastases and proteases involved
in the formation of abdominal aortic aneurysms. More recently, his
work has focused on relationships between the immune system and
AAA. IgG from the abdominal aortas of AAA patients undergoing elective
repair was used to identify an 80 kd protein in the vascular wall
found in the majority of AAA patients. The autoantigen is a microfibril-associated
glycoprotein with homologies to the tenascin superfamily. An expression
library was made with mRNA from the adventitia of an AAA patient
and several clones immunoreactive with IgG from AAA patients have
been partially characterized. These clones share motifs with vitronectin,
fibrinogen and IgK. In collaboration with the Vascular Biology Group
at Otago one was mapped by FISH to chromosome 2 near the Ig kappa
Professor Tilson using serology and Cornelia Weyand
of the Mayo Clinic using molecular methods have found an association
between HLA-DRB1 alleles and AAA. To test this association in our
AAA patients the Vascular Biology Group is using a molecular method
to type our large database of AAA patient samples for HLA-DRB1 to
a resolution equivalent to that obtained by serology.
Dr Greg Jones from the Department of Physiology,
University of Melbourne will be speaking on his work using a rat
model of vascular fragility. Other topics of discussion include
vascular compliance, the clotting system, endothelial cell signaling,
Apo-Lipoproteins, the genetics of vascular disease and the extracellular
The program will also focus on interactive sessions
to explore possible portfolio development and giving impetus to
For further details on the symposium, please contact
Dr. Jeremy Rossaak at firstname.lastname@example.org.
Anyone interested in contacting Professor Tilson whilst he is here,
please contact the department secretary, Dawn Howe-Dennison at (33)8835
With the increasing focus on gene products and a consequent upswing
in use of the Protein Microchemistry Facility it is timely to briefly
review the services available in 1999.
For those of you new to the protein game and perhaps
wanting to check out a recombinant protein or just quantify it we
endeavour to offer a simple 'one stop shop' where you can get the
appropriate analyses done and (if you feel so inclined) learn something
about the procedures involved. Recombinant protein expression offers
several traps for the unlucky and the unaware (eg incorrect signal
removal through to inadvertant expression of the wrong protein),
most of which can be rapidly exposed by sequence or mass analysis.
Amino acid composition analysis remains the best
way to quantify your protein, subject to it being reasonably pure.
This is often the best starting point since accurate quantification
can benefit the following more detailed (and expensive) analyses.
For example, instead of trying to guess if there is enough protein
on your blot for sequencing do a composition analysis and find out
for sure. If no sequence is forthcoming then this also provides
firm evidence that the terminus is blocked, as is common for natural
Mass spectrometry can substantially extend what
you learn from SDS-PAGE. With over 100-fold greater mass accuracy
than gels it is usually a simple job to establish whether your (whole)
protein is of the expected size. Supplement this with peptide mass
fingerprint analysis (eg compare actual with theoretical tryptic
peptide masses computed from the cDNA sequence) or amino acid composition
analysis and you will likely have solid evidence that you have what
Sequence analysis remains the most definitive way
to confirm protein identity. On the down side it only tells you
about the bits that you actually sequence (surprise surprise) so
significant errors or modifications might go unnoticed. A complete
sequence analysis can be an expensive and time consuming proposition
but many shortcuts can be made using peptide mass fingerprint analysis,
if the desired sequence is known.
To broaden our service repertoire we have established
links with other groups in New Zealand and Australia who have instrument
capabilities that complement or extend our own. Our access to automated
C-terminal microsequencing is of particular relevance to those of
you wanting to check out 'the far side' of your recombinant proteins
definitively. We also have available a variety of supplies for small
time users (eg sequence grade enzymes, sequencer-friendly PVDF membranes)
The Otago University Bionode is now available (http://angis.otago.ac.nz).
The system is provided by Encompass Bioinformatics.
Encompass grew out of the Australian National Genomic Information
Service (ANGIS) which provides bioinformatics support for most of
the Universities and Research institutes in Australia. This linkage
has not previously been available outside Australia.
The service provides a range of bioinformatics
tools via several interfaces running on the Sun Ultra computer 'angis'.
Easy access is available though the web interface,
using Netscape v3.1 or higher. This interface allows you to:
- Manage files remotely with file manager - WebFM;
- Use the GCG package through a simplified Web
interface - WAG. We recommend you try this. Most of the EGCG programs
have also been installed in WAG. These include Phylip programs
for phylogenetic analysis;
- Search databases (including GenBank, EMBL,
SwissProt) through SeqSearch - BLAST and FastA database sequence
matching QueryDB - smooth database text searching These databases
will be updated weekly;
- Browse Code - the quick way to obtain an entry
if you know its database code or accession number;
- Undertake Linkage analysis - WebLCP;
- Convert sequence files from one format to another
- ReadSeq. And undertake other useful data management tasks.
Most tasks will be able to be done via WebANGIS
but for more specialised tasks A TelNet and XANGIS interface is
available. Examples of these uses would be Sequence assembly using
the Staden package, or ACEDB databases. An introductory booklet
that focusses on the WebANGIS interface is available for download
or can be purchased for a nominal amount from the CGR.
A more complete set of four books 'The ANGIS Bioinformatics
Handbook' (angis.otago.ac.nz/Education/Materials/book.html) is available
in the Science Library. This will be revised in June, and may then
be freely downloadable so don't rush out to buy it ($100 AUS).
More information on getting access OU Bionode is
available here: http://biochem.otago.ac.nz:800/chrisb/bionode.html
Thanks to the School of Medical Sciences, CGR,
and members of the Biochemistry Department for implementing it.