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July 4, 2000


Microarrays, testing, antibiotic markers, RAFI


AgBioView - http://www.agbioworld.org, http://agbioview.listbot.com

Date: Jul 05 2000 05:51:11 EDT
From: "prakash nijsure"
Subject: Dr Prakash Nijsure

Dear Prof Prakash

My name is Dr Prakash Nijsure. I am doing some research regarding
transformation of some legumes, and would like to use this fabulous
listserv/mailserv to present some questions about Microarrays to our vast
mailserv audience, as because I am seeking some answers from the experts,
industry representatives and so on.

My questions are What aremicroarrays? How they are useful in Biotech
world. Some references regarding microarrays. These are some of them. I
thank in advance for the help and guidance provided by the experts in
this area.

Yours sincerely

prakash nijsure

Date: Jul 05 2000 13:52:18 EDT
From: "Robert Vint"
Subject: Re: City panel fights 'Frankenfoods' : LETTERS TO THE EDITOR of
SanFrancisco Examiner

Dear Dr Prakash,

In your letter to the SF Examiner you say that biotech foods are fully
tested commodities yet you have also informed me that there really is no
independent published research. My understanding, having discussed the
situation with many consumers as well as regulatory bodies (in my capacity
as a representative of the UK food industry), is that the existing
unpublished corporately-sponsored research satisfies governments but that
it has no chance of satisfying consumers (not does is currently satisfy
the insurance industry).

Surely what is needed to resolve the crisis (and what should have been
launched when the issue hit the headlines over a year ago) is an
independent and open research program, designed in consultation with
non-governmental organisations that have wide public support, that will
lead to the publication and peer review of the results. The WHO, FAO, OECD
etc have not, to my knowledge, published any research results that provide
the kind of reassurance that is now clearly needed.

Should we not attempt to end the deadlock by trying to get the two sides
in this debate to agree on the kind of research that is needed to restore
public confidence?

Yours sincerely, Robert Vint.

Date: Jul 05 2000 14:31:34 EDT
From: david.nicholl@nabri.Novartis.com
Subject: (No Subject)

Dear Monalisa Ghose,

In addition to the selectable markers mentioned by Malcolm Livnigston
there has been development of positive selection markers. One example is
PMI (phosphomannose isomerase) which allows plant cells to break down
mannose into simple "sugars". Many plant species do not contain this gene
and therefore
starve to death on media in which mannose is the only carbohydrate source.
Transgenic cells with the PMI gene break down mannose into digestable
sugars while non-transformed cells die.

An informative article below summarizes this technology and was written by
AgBioView's own

C. S. Prakash
Center for Plant Biotechnology Research
Tuskegee University


Selectable marker genes are the sine qua non for the development of
genetically modified crops, and all such commercially released GM crops
have these marker genes. Marker genes render resistance in plant cells
against antibiotics or herbicides and thus enable scientists to
effortlessly select a rare transformed plant cell after co-introducing the
desired gene along with a marker. Antibiotic or herbicide added to the
plant culture media kills the normal plant cells while the few transformed
cells survive, grow, and develop into whole plants.

Beyond the laboratory, these markers have no role and thus their presence
in crops and food has provoked much public concern. The perceived risk of
marker genes to environmental safety and health has led scientists to
explore alternative systems such as the removal of marker genes using the
Cre-lox system or transposable elements, and the use of cytokinin
glucuronides with the GUS gene. A new selection strategy reported by
Danish scientists involves a novel selectable marker system using a gene
for an enzyme that
metabolizes mannose-6-phosphate, a plant growth-inhibiting phosphorylated
sugar, and thus the strategy may prove to be a better alternative to the
use of antibiotic marker genes (1).

The most widely used selectable marker is the nptII gene that codes for
neomycin phosphotransferase II, which confers resistance to antibiotic
kanamycin or geneticin. Considerable research on the nptII
has shown that it is safe for both the environment and the consumer (2).
However, such information is not available for other marker genes
including some herbicide resistance genes, which may carry a risk of
potential gene flow to weedy relatives. There are also some concerns that
antibiotic marker proteins could compromise the therapeutic efficiency of
orally administered antibiotic.

The new selectable system relies on the use of phospho- mannose isomerase
(PMI). PMI is fairly ubiquitous in nature; however, aside from leguminous
plants, it is not found in most plants, especially
cereals. Plant cells without this enzyme are unable to survive in a tissue
culture medium containing mannose-6-phosphate as a sole carbon source.
Incubation of plant cells in the presence of mannose-6-phosphate results
in phosphate and ATP starvation thus depleting energy from critical
functions such as cell division and elongation (3). The
mannose-6-phosphate toxicity in plant cells has also recently been shown
to cause apoptosis or programmed cell death through induction of an
endonuclease responsible for DNA
laddering (4).

The manA gene encoding PMI was cloned from E. coli by researchers at
Danisco Biotechnology. Plant cells transformed with this gene can convert
mannose-6-phosphate to fructose-6-phosphate, which is easily metabolized.
Morten Joersbo and colleagues (1) observed that use of mannose selection
in sugar beet resulted in a ten-fold increase in transformation frequency
when compared to traditional kanamycin selection. According to
researchers, such increased efficiency may occur because transformed cells
are actively encouraged to grow rather than just allowed to survive.

In the traditional selection system using antibiotics or herbicides, the
transgenic cells convert the selective agent to a detoxified compound that
may still exert a negative influence on the plant cells. Further, the
release of toxic metabolites by dying adjacent cells may also inhibit the
growth of transformed cells. In contrast, mannose selection essentially
provides a metabolic advantage to the transformed cells while the
untransformed cells are starved and progressively lose their viability,
according to Joersbo et al.

Novartis Agribusiness Biotechnology Research, Inc., which has licensed the
PMI gene selection system, has found this marker to be very effective in
the selection of wheat and maize transgenics with an
astoundingly high frequency of transformation of 25% and 50%,
respectively. Novartis scientists have found that PMI protein is very safe
as is evident from many studies including mouse toxicity assays
(3). The protein was readily digested in simulated mammalian gastric and
intestinal fluids indicating a low allergenic potential. Sugar beet and
maize plants containing the manA gene had identical biochemical profiles,
yield, and nutritional composition when compared to control plants. The
gene encoding this activity has been cloned from several bacteria and
yeast species and also from humans. PMI has also been purified and studied
from yeast, bacteria, pigs, and humans.

The PMI-mannose appears to be an ideal selectable system for plant
transformation as it obviates the need for antibiotic or herbicide markers
and also provides improved recovery of transformed plants. Researchers
interested in obtaining the manA gene and more information about this
system may contact Dr. Andy Beadle at andrew.beadle@seeds.novartis.com.

1. Joersbo M, et al. 1998. Analysis of mannose selection used for
transformation of sugar beet. Molecular Breeding 4:111-117.

2. Fuchs R, et al. 1993. Safety assessment of the neomycin
phosphotransferase II (NPTII) protein. Bio/Technology 11:1543-1547.

3. Privalle LS, Meghji M, and Powell L. 1999. Safety assessment of a novel
plant selectable marker: Phosphomannose isomerase. Abstract No. 395.
Annual Meeting of the American Society of Plant
Physiologists (July, 1999; Baltimore, MD).

4. Stein JC and Hansen G. 1999. Mannose induces an endonuclease
responsible for DNA laddering in plant cells. Plant Physiology 121:1-9.

I hope this information helps.

David Nicholl

Subj: RAFI, property rights, Divine and Sacred
DateWed, 5 Jul 2000 9:43:58 AM Eastern Daylight Time
From: Hope Shand
Subject: RAFI, property rights, Divine and Sacred

This message is in response to Andrew Apel's diatribe against RAFI -- the
Rural Advancement Foundation International, a Canadian-based civil society

Mr. Appel is entitled to his views, but I hope that other members of this
listserve will form their own pinions about RAFI without relying on Mr.
Appels' poorly-informed, misinterpretation of RAFI's work and activities.
See for yourself, by visiting: http://www.rafi.org

Mr. Appel believes that RAFI has a lot of credibility with the
"eco-reactionary" community. I would also point out that RAFI has worked
with a number of international organizations, either through contracts,
joint publications, or consultancies. These include, for example, the U.N.
Development Programme, the U.N. Food and Agriculture Organization, the
International Development Research Centre of Canada, and the Dag
Hammarskjold Foundation of Sweden. Our credibility, I believe, expands
far beyond
the "eco-reactionary community."

Mr. Appel incorrectly states that RAFI is in favor of intellectual
property for the developing
world. I can't imagine how Mr. Appel came to that conclusion, but he is
confused. RAFI was perhaps the first civil society organization to
campaign against plant intellectual property laws (PVPA or plant breeders'
rights) beginning in the late 1970s. We oppose the patenting of life
forms, in general -- and we don't make a distinction between intellectual
property for the South and the North. RAFI has vocally opposed TO/TRIPs
provisions which obligate developing countries to adopt plant intellectual
property laws.

RAFI coined the term "biopiracy" back in 1992 and we are pleased that the
issue is a subject of debate and controversy -- it should be. We think
it's wrong that intellectual property is being used to claim exclusive
monopoly control over the innovation and knowledge of rural and indigenous
peoples. Biopiracy isn't necessarily illegal -- but it is immoral and
unacceptable, in RAFI's view. Biopiracy is the inevitable consequence of
international agreements such as the Biodiversity Convention that have no
real capacity to regulate bioprospecting or to ensure benefit-sharing.

Mr. Appel is also confused about RAFI's position on Terminator technology.
RAFI has spearheaded an international campaign against Terminator
technology because we oppose technologies and laws that attempt to
eliminate or restrict the right of farmers to save and exchange seed, and
to breed their own crops. The act of seed saving is fundamental to
agriculture, to global food security, to survival on this planet. We
believe that genetic seed sterilization endangers farmers, biodiversity
and global food security. If commercialized, the impact of Terminator
seeds would be far greater in the South because over 1.4 billion
people depend on farm-saved seeds as their primary seed source. But RAFI
also believes that Terminator is dangerous for farmers and food security
in the North - and we've always said so.

All of RAFI's publications, including annual reports, are posted on our
web site. Anyone who would like to receive news and analysis from RAFI
can join our listserve.


Hope Shand
Research Director

Please note new address, phone and fax:

Hope Shand, Research Director
118 E. Main St., Rm. 211
Carrboro, NC 27510

tel: 919 960-5223
fax: 919 960-5224
email: hope@rafi.org