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The Onsa Network


RICHARD KLAUSNER. president of the National Cancer Institute. SAMBA, football and...genomics. ... mol culaire, cette institution qui g re le produit de l'imp t ... – PowerPoint PPT presentation

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Title: The Onsa Network

The Onsa Network
  • The São Paulo Virtual Genomics
  • Institute
  • These transparencies should be viewed as a
    complementary material to the paper ONSA, The
    São Paulo Virtual Genomics Institute Nature
    Biotechonology Vol.16, 795-796, 1998

Fapesps Genome from project to program - a
  • May 01.97 INITIAL IDEA
  • (A. Goffeau 06.13, S.Oliver)
  • 11.16.97 SELECTION OF LABS

ONSA The Original Architecture
  • Andrew Simpson (Ludwig ICR - SP)
  • USP (Reinach) - UNICAMP (Arruda)
  • UNICAMP (Setubal Meidanis)


  • Dec.97 COPERSUCAR and Sugarcane
  • Jan. 98 CGAP and the Cancer Project

  • Number of participating labs 21
  • NATURE VOL.406 JULY 13
  • Estimated genome size 2.1 Mb
  • Genome size revised 2.7 Mb

Sugarcane EST Project SUCEST
  • Goal sequence circa 50 000 genes of Sugarcane by
    April 2001
  • DNA coordinator Paulo Arruda (Unicamp)
  • Bioinformatics UNICAMP
  • 03.99 Call for application
  • 04.99 Choice of participant labs

  • Tumors Colon, Stomach, Head, Neck, Cervix
  • Call for applications April 99
  • Choice of labs June 99
  • Initial Goal 500.000 SEQUENCES - June 2001
  • Revised Goal 1.000.000 SEQUENCES - September

  • Xylella fastidiosa US 13 mi
  • Functional Genomics US 4 mi
  • CANCER US 10mi (1999) 10 mi (2000)
  • Xanthomonas axonopodis citri US 5 MILLION

The Enlarged ONSA
  • 65 labs through out the State of São Paulo
  • 300 researchers

  • Expected Conclusion December 2000


Brazilian scientists team up for cancer genome
Ricardo Bonalume Neto
  • (SÃO PAULO) Brazilian researchers have entered
    the competitive field of human genome sequencing
    with the signing of an agreement between the
    state funding agency of São Paulo (FAPESP) and
    US-based Ludwig Institute for Cancer Research.
  • Each will contribute US 5 million to two-year
    Human Cancer Genome Project. According to FAPESP,
    the programme is "aimed at providing sequences
    from genes expressed in tumours that are
    important within the context of public health in
    the state of São Paulo".
  • The project will sequence and analyse short DNA
    fragments created from the central coding
    portions of human genes. Although a US patent is
    being sought for the technique used to generate
    these expressed sequence tags (ESTs), the
    sequences will be freely available on the
    Internet. "No sequences will be patented. All the
    data will be promptly published", says Ed
    McDermott Jr., president of the Ludwig Institute,
    who visited Brazil to sign the agreement.
  • The programme follows on from the Organization
    for Nucleotide Sequencing and Analysis (ONSA), a
    network of 30 laboratories in the state of São
    Paulo now in the final steps of sequencing the
    complete genome of the plant pathogen Xylella
    fastidiosa. The groups will build upon their
    experience with this pathogen, which causes many
  • economically important plant diseases,
    notably citrus variegated chlorosis, which poses
    a major threat to São Paulo's orange farming (see
    Nature 389, 654 1997).
  • ONSA is a "virtual" institute that links the
    sequencing laboratories, keeping down costs and
    red tape. The acronym, which sounds like the word
    onça (jaguar) in Portuguese, mimics the Institute
    for Genomic Research (TIGR), according to José
    Fernando Perez, FAPESP's scientific director.
  • Five centres will carry out the sequencing, each
    helped by four other labs. The centres will be
    at the chemistry institute, the faculty of
    medicine at São Paulo, and the faculty of
    medicine at Ribeirão Preto, all from the
    University of São Paulo at the Paulista School
    of Medicine, São Paulo and at the Hemocentro of
    the University of Campinas. The programme aims to
    generate between 500,000 and 750,000 EST
    sequences, and about 200 million bases of human
    genome sequence.
  • The project will be monitored by a four-member
    committee, composed of Marcelo Bento
    Soares of the University of Iowa, John Sgouros of
    the Imperial Cancer Research Fund in Londo, and
    Webster Cavenee and Richard Kolodner of the
    Ludwig Institute in San Diego.

Brazil to sequence first plant pathogen
Ricardo Bonalume Neto
  • São Paulo. The creation of a network of
    laboratories in São Paulo state, Brazil, to
    sequence the complete genome of a microorganism
    was announced last week by the Foundation for the
    Support of Research of the State of São Paulo
  • The Organisation for Nucleotide Sequencing and
    Analysis will first tackle the bacterium Xylella
    fastidiosa, the causal agent of many economically
    important plant diseases, particularly citrus
    variegated chlorosis, which poses a major threat
    to São Paulo's orange cultivation. This is
    thought to be the first plant pathogen genome to
    have been sequenced.
  • Citrus variegated chlorosis, first reported in
    1987, has been found only in Brazil and
    Argentina. São Paulo and Florida are the two most
    important citrus-growing areas in the world, São
    Paulo producing 87 per cent of Brazil's -- and 30
    per cent of the world's -- citrus crop. According
    to FAPESP, the total cost of the project is
    US11.6 million, to be spent over two years.
    Sequencing completion is predicted by 2000.
  • Xylella fastidiosa was chosen because sequencing
    might help in the control of the pest, with
    obvious gains to the state's economy. It will
    also help to forge links between research centres
    and the private sector, which is contributing to
    the cost of the project.
  • The state says that it is keen to create a
    network of laboratories that will "significantly
    increase the number of laboratories in the state
    capable of using modern molecular biology
  • The project will be overseen by a five-member
    steering committee onsisting of three
    international experts in genome sequencing and
    two researchers from São Paulo state. Two of the
    experts, André Goffeau of the University of
    Louvain in Belgium and Steve Oliver of the
    University of Manchester Institute of Science and
    Technology, helped to set up the project, and
    were also involved in the sequencing of the
    Saccharomyces cerevisiae genome.
  • The committee will select one laboratory to house
    a bioinformatics centre. Two large central
    sequencing laboratories will be chosen to
    generate a large part of the sequence data. These
    laboratories will also act as training and
    support centres for other members of the network.

  • GENOMES 2000
  • Intimate Portraits of Bacterial Nemeses

Michael Hagmann
  • A Genome Cinderella Story
  • In 1987 orange growers in the Brazilian state of
    São Paulo first noticed the telltale signs of a
    new disease conspicuous yellow patches on
    individual leaves. The fruits on these spotted
    trees turned out to be small, hard, and gave
    little juice, rendering them commercially
    useless. Today, citrus variegated chlorosis
    (CVC)--as the disease is known--threatens the
    entire citrus industry in São Paulo state, the
    world's largest exporter of concentrated orange
    juice. The disease affects more than 30 of all
    trees and causes losses estimated at 100 million
    each year.
  • Now scientists have a new tool to attack this
    devastating microbe. On 12 April a team reported
    at the meeting that they had deciphered the
    2.7-million-base-pair genome of Xylella
    fastidiosa, the causative agent. X. fastidiosa is
    the first bacterial plant pathogen ever to be
    fully sequenced. What's more, the feat was pulled
    off not by one of the sequencing superstars in
    the United States or Europe but by a consortium
    of some 30 labs in São Paulo state--groups with
    little or no previous genomic expertise.
  • This coup earned the Brazilian scientists ample
    praise from their international peers. Raves
    biochemist André Goffeau of the École Normale
    Superieure in Paris "The quality of the
    sequence is superb. It's incredible how fast
    they've done it, given that 2 years ago they
    didn't even have the sequencing machines." The
    X. fastidiosa genome "is quite a big deal," says
    Edwin Civerolo, a plant pathologist with the U.S.
    Department of Agriculture (USDA) who works at the
    University of California, Davis. Indeed, the work
    is so impressive that the USDA and the state of
    California have just enlisted--to the tune of
    250,000--the Brazilian team to sequence a
    related strain of X. fastidiosa that causes
    Pierce's disease and is threatening vineyards
    across California.
  • The X. fastidiosa genome project was conceived in
    1997 when Fernando Perez, scientific director of
    the State of São Paulo Research Foundation
    (FAPESP), a state-run public funding agency,
    became concerned about the lack of genomics
    research in Brazil. After consulting some of
    Brazil's top life scientists, Perez and his
    scientific advisers decided that Brazil should
    embark on its own genome project. But what to

(No Transcript)
Brazil, a new Mecca for genomics?
  • The agency settled on Xylella fastidiosa, a
    bacterium that infects orange trees, a major
    source of income in São Paulo, and causes Citrus
    Variegated Chlorosis. This choice also brought in
    additional funding from the citrus growers'
    association (Fundecitrus).
  • ONSA
  • A major goal of this first genome project was to
    bring sequencing technology to as many
    laboratories as possible, thus propelling them
    into the genome age. Therefore, the concept of
    setting up a single sequencing centre was
    rejected from the start. Instead, bids were put
    up for laboratories interested in participating
    in the project, and those that were selected
    received equipment (ABI370 sequencers), reagents,
    and ample technical advice. In total, 30 labs
    were selected for the Xylella project, dispersed
    geographically throughout the state of São Paulo.
    In addition to the sequencing labs, the project
    steering committee designated a DNA co-ordinator
    (for the handling and distribution of clones)
    and a bioinformatics centre. The bioinformatics
    group, located at the University of Campinas
    (about 80 km from São Paulo), was made
    responsible for all of the data handling, from
    base calling to final assembly verification. The
    sequencing labs submitted trace files only, and
    were paid on the basis of the amount of
    non-vector, high-quality sequences (based on
    phred scores) that could be extracted from their
    data. The entire process was automated using Web
    pages, and enabled the bioinformatics group to
    keep very close tabs on the daily progress of the
    project as a whole.
  • Historical perspective
  • High-throughput sequencing is a highly
    specialised trade, practised in a very limited
    number of laboratories in the developed world. It
    can be estimated that a dozen labs are
    contributing over half the total sequence data
    currently being deposited in the public
    databases, with another 50 or so accounting for
    the bulk of the rest. All of these labs are
    located in North America, the larger European
    countries, Australia and Japan. It may thus come
    as a surprise that the latest entrant in this
    select club hails from Brazil, and more
    specifically the state of São Paulo.
  • São Paulo has a law stating that 1 of the tax
    revenue collected by the state has to be given to
    an independent agency that supports scientific
    research, known as FAPESP (Fundação de Amparo à
    Pesquisa do Estado de São Paulo). As São Paulo is
    the richest state in Brazil, this amounts to a
    considerable amount of money (USD 250 Mio in
    1998). By law, FAPESP is also forbidden to spend
    more than 5 of its money on administrative
    costs. The combination of ample funding and
    political independence gives the Foundation a lot
    of freedom to develop innovative scientific
  • In 1997, FAPESP decided that Brazil should not
    miss out on the scientific and economic
    opportunities that can be derived from genome
    sequencing, and should be able to produce its
    own data, analyse them, and use the results for
    local scientific projects. To start off, it was
    decided that a good target rganism should be
    bacterial, and of interest to the local economy.

Los Angeles Times By Melinda FulmerApril, 15,
Cinderella Genes Brazil was the poor sister of
genome research, until its scientists pulled of
two world-class coups By Mac Margolis

August 6 - Brazilian biochemist Sandro de Souza,
32, ha landed a dream job at Harvard University.
His boss was physicist and Nobel
laureate Walter Gilbert, practically a deity in
the world of DNA sequencing. Then the
phone rang. A friend asked Souza to join a new
genome research project - in Brazil,
of all places. To his surprise, Souza took a deep
breath and accepted. "I wondered what
would become of me," he recalls.
THAT WAS TWO whole years ago, before Brazil, a
backwater of genetic research, metamorphosed into
an international powerhouse. Last month
researchers at Sao Paulo's fapesp research
institute announced that they had cracked the DNA
code of Xylella fastidiosa, a bacterial pest that
destroys a third of Brazil's orange crop each
year. It is the first time scientists had ever
mapped the structure of the genome of a plant
pathogen - a "landmark achievement," as the
British journal Nature put it. As if that
weren't enough, a week later Souza's own group
announced that it had successfully mapped the
structure of some 500,000 human
expressed-sequence tags (EST) in malignant
tumors. ESTs are tiny bits of DNA that scientists
use to piece together the far longer sequence of
base pairs that make up a gene. The more ESTs you
know for a particular tumor, the better your
chance of being able
to decode the entire structure of its genome and
eventually to find a cure. Only the United States
and Britain have identified more human ESTS. Ali
of a sudden, Souza and his fellow Brazilians are
sitting pretty at the top of an important field
of research. "This is the leading edge," said
Richard Klausner, president of the National
Cancer Institute, who works closely with the
Brazilians. "TheBrazilian team has shown that
emerging nations can participate as equals in
cutting-edge research. How did Brazil pull off
such a feat? Slowly at first, then all at once.
The slow part was Fapesp's rise to the research
big leagues. Fapesp takes a 1 percent share of
Sao Paulo's state tax revenues, which has allowed
the 50-year-old institute to nourish a fat
endowment and fund quality research into
everything from airplane dynamics to weather
"The Brazilian team has shown
that engineering nations can
particpate as equals in cutting- edge
research." RICHARD KLAUSNER president of the
National Cancer Institute
The Economist
July 22nd-29th, 2000 - Ed. no. 8180
Brazilian science Fruits of co-operation
Peter Collins S A O P A U L O
SAMBA, football and...genomics. The list of
things for which Brazil is renowned has suddenly
got longer. Only a few days after publishing, on
July 13th, the first-ever sequence of the genome
of a plant pathogen, scientists at Sao Paulos
state research agency, Fapesp, were due to
announce, on July 21st, another successthe
composition of 279,000 human expressed-sequence
tags, small pieces of DNA that allow genes to be
located along chromosomes. Only in America and
Britain have more than that number of human ESTs
been identified. Though they are of global
significance, both of these advances are also of
particular interest to Brazilians. A number of
the ESTs in question are derived from genes
linked to cancer of the head and neck, which for
some reason is unusually common in Brazil. And
the plant pathogen sequenced, Xylella fastidiosa,
is an insect-borne bacterium that has been
ravaging Brazils orange groves, causing their
trees to produce shrivelled fruit and costing
growers an estimated 100m a year. As if
sequencing X. fastidiosa were not enough of an
achievement in itself, the project was finished
two months ahead of schedule and 2m under its
original 15m budget, even though it involved
co-ordinating a "virtual institute" made up of 35
laboratories scattered across the state. The man
who did that co-ordinating, Andrew Simpson, says
there were two reasons for arranging things this
way. The alternative, building a giant,
bricks-and-mortar institute would have been
costly and time-consuming. And dividing the work
between many laboratories maximised the sharing
of know-how among Sao Paulos scientists.
The Economist
July 22nd-29th, 2000 - Ed. no. 8180
This sudden leap in scientific expertise has had
a long run-up. Ever since the 1960s, Fapesp has
been guaranteed, by law, a fixed share of all
the tax collected in Sao Paulo (first 0.5, later
1) and independence from the political meddling
that is endemic in Brazilian public institutions.
And whereas other states research agencies have
such guarantees routinely ignored, Fapesps
growing prestige over the years has made it
increasingly hard for local politicians to
interfere or pinch its money. By late 1997 it was
possible for the agency to decide that, although
there had until then been only some limited
sequencing of individual genes, the states
laboratories were ready to jump into a huge
project and sequence a complete organism. The
success of the X. fastidiosa project seems to be
breeding more successand more money. The
Brazilian citrus growers association, which
helped to finance the project, is now offering to
pay to decode the bug that causes another
serious disease, citrus canker. The Ludwig
Institute, in Switzerland, is contributing half
of the 10m cost of the teams human-cancer
project. Brazilian sugar growers are helping to
finance another new project, to sequence the
genome of sugarcane. And the American Department
of Agriculture is to pay for a team to sequence a
strain of X. fastidiosa that causes Pierces
disease in grapevines, which is currently
afflicting Californias vineyards. The lesson
of all this is that there is no reason why
countries such as Brazil cannot compete in
leading-edge science if they put their minds to
it. Brazils share of the scientific papers
published in international journals has risen
from 0.4 to 1.2 over the past 15 years. With
its largest state having now demonstrated the
benefits of co-operation and a secure source of
financing, and with more than 200 young
geneticists trained as a result of the X.
fastidiosa project alone, that share may well
go on rising.
July 18, 2000 Agriculture Takes Its Turn in the
Genome Spotlight By CAROL KAESUK YOON
In a scientific first, and a coup for science in
Brazil, a team of more than 200 researchers there
has for the first time deciphered the complete
DNA sequence of an organism that causes a plant
disease. Though other genome sequencing efforts
-- for example, in humans or the laboratory
staple fruit fly -- have attracted more
attention, the Brazilian target, an odd little
bacterium known as Xylella fastidiosa,
distinguishes itself as the first to be decoded
of the countless nasty species that together cost
farmers and foresters many billions of dollars
each year. This particular organism can cause
diseases in oranges, grapes, almonds, plums,
peaches, alfalfa, oaks, elms and other plants.
Xylella fastidiosa Genome Project
electron micrograph of the
Xylella fastidiosa.
"Everyone is quite thrilled," said Dr. Andrew
Simpson, a molecular biologist at the Ludwig
Institute for Cancer Research in São Paulo,
Brazil, and one of the team leaders. "It's
probably the biggest ever scientific project in
Brazil." The team has been feted by the
president of Brazil and serenaded by orchestras,
and a new scientific prize was invented just to
be given to the team. It was an achievement for
developing nations' science as well, Dr. Simpson
said, as this was the first complete sequence to
come from outside the United States, the United
Kingdom or Japan.
Jeudi 13 Juillet, 2000
GÉNÉTIQUE Décryptage du génome dune bactérie
ravageant les agrumes brésiliens Les mécanismes
de la virulence dévoilés
L'annonce du décryptag complet du génome de la
bactérie Xylella fastidiosa constitue un double
événement. Non seuloment, c'est la première fois
qu'un micro-organisme pathogène pour les végétaux
est sequencé, mais, surtout, ce travail
remarquable, publié aujourd'hui dans la revue
Nature, est 1'ceuvre d'un consortium de
laboratoires brésiliens. Le fait que ce pays
émergent dans le domaine de la bio1ogie se soit
impliqué dans ce projet, avec le soutien de
I'Institut national de la recherche agronomique,
ne doit rien au hasardla bactérie séquencée est
un redoutable ravageur des agrumes et le Brésil,
qui produit le tiers des oranges vendues dans le
monde, compte bien utiliser ces connaissances
pour maîtriser ce fléau.
Jeudi 13 Juillet, 2000
Le Brésil parmi les grands En parvenant à
séquencer le génome de la bactérie Xylella
fastidiosa, le Brésil se hisse au niveau des
puissances ltlt biologiquesgtgt de la planète
Etats-Unis, Grande-Bretagne, France, Japon,
Allemagne. L'nitiative est venue, il y a trois
ans, de la Fondation pour le soutien de la
recherche scientifique et technique de I'Etat de
San Paolo (FAPESP). Soucieuse de développer la
biologie moléculaire, cette institution qui
gère le produit de l'impôt destiné à la
recherche, lançait par ce biais une sorte de plan
keynesien de relance appliqué à la seience. La
FAPESP a fourni à chacun des trente laboratoires
qui ont répondu à son appe1 d'offres un
séquenceur dont le prix unitaire avoisine les 700
000 francs. Ces efforts ont payé. Mieux, les
Etats-Unis viennent de commander aux
Brésiliens le séquençage d'une souche de
X.fastidiosia qui s'attaque à leurs vignobles. Et
qui pourrait bien un jour menacer l'Europe et la
France. Pas étonnant que ce grand pays ait été
invité aux côtés de la Chine, de l'Inde et du
Mexique à participer, fin juin, à Bordeaux, à la
réunion des ministres de la Recherche du G8.
Wednesday, 12 July, 2000, 1801 GMT 1901 UK
Brazil hails scientific first
Xylella fastidiosa was first identified in 1987
By BBC News Online's Jonathan Amos South
American researchers have decoded the first
genome for a bacterium that causes disease in
plants. Xylella fastidiosa infects citrus crops
and has been known to devastate plantations in
Brazil where one third of the world'soranges are
now produced.
Wednesday, 12 July, 2000, 1801 GMT 1901 UK
"The bacteria thrive in the xylem, which are like
the veins of the plant transmitting the sap from
the roots to the leaves," Dr Simpson said.
"Basically, they clog up these tubes so that the
extremities and leaves of the plant get
undernourished and don't get enough water. "The
fruits become very small and hard, and have no
juice in them."
This disease results in smaller, less juice fruit.
This disease is known as citrus variegated
chlorosis (CVC). It was first identified in
Brazil in 1987 but it was another six years
before X. fastidiosa was shown to be the cause.
Farmers are keen for scientists to develop new
ways of combating the disease. In the Sao Paulo
region alone, 400,000 people are involved in the
citrus business, exporting orange concentrate
valued at over 1.5bn a year.
Wednesday, July 12, 2000
Genes of Plant Disease Mapped" By JEFF BARNARD,
Associated Press Writer
For the first time, scientists have reported
mapping the genes of a plant disease, an advance
that could lead to new approaches to fighting a
bacterial scourge that ravages orange groves and
other crops. The work also sheds light on the
way bacteria infect both humans and plants and
thwart their defenses. This sort of
information is going to open up crop protection
strategies the way genome sequencing is opening
up new pharmaceutical strategies to control
infectious diseases" in people, said Charles J.
Arntzen, president of the Boyce Thompson
Institute at Cornell University.
New York Times - July 12, 2000
Genes of Plant Disease Mapped By The Associated
For the first time, scientists have reported
mapping the genes of a plant disease, an advance
that could lead to new approaches to fighting a
bacterial scourge that ravages orange groves and
other crops. The work also sheds light on the
way bacteria infect both humans and plants and
thwart their defenses. This sort of
information is going to open up crop protection
strategies the way genome sequencing is opening
up new pharmaceutical strategies to control
infectious diseases'' in people, said Charles J.
Arntzen, president of the Boyce Thompson
Institute at Cornell University. Sponsored by
the State of Sao Paolo Research Foundation in
Brazil, 200 scientists in 34 molecular biology
labs worked for two years to sequence the genome
of the bacteria Xylella fastidiosa.
There is a common misconception that only
advanced industrialized nations have the
wherewithal and skilled human resources needed to
achieve cutting-edge science. This misconception
is fanned by the number of researchers from
developing countries who find it necessary to
obtain their research training abroad - and
frequently decide not to return, citing a lack of
scientific opportunity. But it is given the lie
by a paper published in this issue which
describes the result of a project carried out by
a consortium of research centres in the state of
São Paolo in Brazil to sequence the bacterium
Xylella fastidiosa. This bacterium causes a
disease that affects citrus fruit and other
important crops, resulting in many millions of
dollars of damage each year. As the first public
sequence of a free-living plant pathogen, the
paper represents a significant scientific
milestone. But it also sends a clear political
signal, namely both the desire and ability of
countries such as Brazil to play in the big
league. The sequencing project was deliberately
chosen by the project's main funding agency,
FAPESP, to play a catalytic role in helping
research teams equip themselves for the challenge
of the post-genome era. It was also intended to
send a signal to Brazils young scientists that
they do not need to leave the country to engage
in world-class science. In both respects, it
appears to have succeeded.