FAPESP

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• FAPESP

The State of São Paulo Research Foundation
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THE INSTITUTION

• States constitution 1 of its total tax
  revenue to FAPESP for the funding of scientific
  and technological research in all areas of
  knowledge.
• The creation of FAPESP in 1962, aimed at
  providing the State with an independent research
  support organization that should complement and
  articulate with the federal funding of research
  in the State. FAPESP is an autonomous body and
  works strictly on a peer review basis.
• Projected total investment to be made by FAPESP
  during the fiscal year 2004 is of approximately
  R 500 million. Traditionally 30 of FAPESPs
  investment is directed to fellowships and
  scholarships (graduate students and PosDocs)
• By law the administrative costs of FAPESP may not
  exceed 5 of its investment in research.

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MANAGEMENT

• FAPESPs Board of Trustees (CS) Each one of its
  twelve members has a six-year term of office. Six
  members are freely chosen by the States
  Governor. The other six are chosen by the
  Governor, each one from a list of three nominees
  chosen by the states research community.
• The Executive Board (CTA) consists of the
  President Director, the Scientific Director and
  the Administrative Director, each of them with a
  three-years term of office, chosen by the
  Governor, from a list of three nominees submitted
  by the Board of Trustees.

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The Onsa Network
Organization for Nucleotide Sequencing and
Analysis

• 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

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ASSUMPTIONS

• The strategic relevance of Biotech for a country
  like Brazil given its geo-economic features
  biodiversity, agriculture, cattlery, tropical
  diseases
• 2) Overall scientific competence, but slow
  development in Molecular Genetics
• 3) Insuficiency of traditional approaches to
  reach the goals with the needed speed

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GOALS

• Capacity building in genomics for both academic
  and applied research to help promoting the
  creation of a park of biotech companies in Brazil
• 2) Cutting edge science
• 3) Stimulate the scientific community to address
  problems of social and economic relevance

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Fapesps Genome from project to program - a
Chronology

• May 01.97 INITIAL IDEA
• MEETINGS WITH SCIENTISTS
• INTERNATIONAL CONSULTANTS
• (André Goffeau, Steve Oliver)
• INDUSTRIAL PARTNERS
• CHOICE OF ORGANISM
• 10.13.97 CALL FOR APPLICATIONS
• 11.15.97 DEADLINE FOR APPLICATIONS
• 11.16.97 SELECTION OF LABS

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Chronology (2)

• 05.01.98 SEQUENCING BEGINS
• 07.98 APPROVAL OF TH FUNCTIONAL GENOMICS PROGRAM
  UNDERSTANDING CVC FROM XfS GENOME CALL FOR
  PROPOSALS
• 01/99 FUNCTIONAL GENOMICS - 21 PROJECTS

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Chronology (3)

• 02.99 GENE PATENT SUBMISSION
• 03.99 BEGIN OF FUNCTIONAL GENOMICS
• Number of participating labs 21
• GENOME CONCLUSION
• INITIAL GOAL JUNE 2000
• ACTUAL CONCLUSION JANUARY 2000
• NATURE VOL.406 JULY 13
• Estimated genome size 2.1 Mb
• Genome size revised 2.7 Mb

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Chronology (4)

• 09/1999 Xanthomonas axonopodis citri
• 06/2001 Schistosoma mansoni

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Chronology (4)

• 08.2000 APPROVAL OF A NEW GENOME PROGRAM
• Agronomical and Environmental Genomes-AEG
• Number of participating labs 20
• . Genomes concluded
• - Leifsonia xyli (full genome)
• - Leptospira (full genome)
• - Pierces Disease - Xylella fastidiosa USDA
  (full genome)
• - Coffee (EST)
• - Eucalyptus (EST)
• . Genomes ongoing
• - Bovine (EST)

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Human Cancer Genome Project

• PARTNERSHIP LICR - FAPESP
• NOVEL METHODOLOGY
• ORESTES (OPEN READING FRAMES ESTs)
• DNA COORDINATOR - SIMPSON
• 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
  2000

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BUDGET

• Xylella fastidiosa US 13 mi
• Functional Genomics US 4 mi
• CANCER US 10mi (1999) US 10 mi (2000)
• LICR FAPESP
• SUGARCANE US 6 mi
• Xanthomonas axonopodis citri US 5 mi
• AEG - US 4 mi

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BUDGET

• Onsa Network total budget (from 1997 to 2003)
• US 39 million
• of total budget of FAPESP 2,4 average over
  the period

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The Enlarged ONSA

• 65 labs through out the State of São Paulo
• 300 researchers
• 10 Bioinformatic Centers

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PARTNERS
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MEDIA VISIBILITY

• NATURE
• SCIENCE
• New York Times, Washington Post, Le Figaro,
• La Nación, The Economist
• NEWSPAPERS
• MAGAZINES
• RADIO
• TV SERIES - 5 PROGRAMS

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GOALS x RESULTS

• 1) Improvement of produced science
• 2) Qualification of human resources
• 3) Social-economic importance of performed
  research
• 4) Development of Biotecnology in Brazil

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COLLATERAL BENEFITS

• Domestic and Internacional Visibility (USDA,
  Inst. Ludwig)
• 2) Relationship between research system and media
• 3) Recognizement by Public Authorities, Private
  Sector and Society at large of the competence of
  Brazils research system
• 4) International leadership in Bioinformatics

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MEDIA VISIBILITY

• NATURE
• SCIENCE
• NEWSPAPERS
• New York Times, Washingon Post, Le Figaro, La
  Nación, The Economist, etc.
• MAGAZINES
• TV SERIES
• State of S.Paulo Govt. - Award MÉRITO
  CIENTÍFICO

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Samba, Football and Genomics The Economist
(July/2000).

• Xylella fastidiosa
• Sugarcane
• Human Câncer
• Clinical Genome
• Xanthomonas
• Schistosoma

• AEG
• Eucalyptus
• Leifsonia
• Leptospira
• Grapevyne Xylella
• Bovine
• Coffee

• Principal Publications
• Xylella fastidiosa, Nature (13/jul/00)
• Xanthomonas campestris, Nature , 23 de maio de
  2002 Onsa, the São Paulo Virtual
• Genomics Institute, Nature Biotechnology ,
  setembro de 1998
• Genoma do Câncer - tecnologia ORESTES, PNAS,
  Proceeding of The National Academy of Sciences of
  The United States of America , março de 2000
• Cromossomo 22, PNAS, novembro de 2000
• Genoma do Câncer, PNAS, outubro de 2001.
• Xylella da Uva, Journal of Bacteriology ,
  fevereiro de 2003.
• Nature Genetics - Schistosoma mansoni , vol. 35,
  no. 2, October 2003.
• The generation and utilization of a
  cancer-oriented representation of the human
  transcriptome by using expressed sequence tags,
  PNAS, Proceeding of The National Academy of
  Sciences of The United States of America ,
  October 2003.

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SUBPRODUCTS

• BIOINFORMATICS
• PATENTS Genes and Metodology
• CLINICAL RESEARCH

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MAIN PUBLICATIONS

• Xylella fastidiosa, Nature (july 13,2000)
• Xanthomonas campestris, Nature , May 23, 2002
  Onsa, the São Paulo Virtual
• Genomics Institute, Nature Biotechnology ,
  September 1998
• Genoma do Câncer - tecnologia ORESTES, PNAS,
  Proceeding of The National Academy of Sciences
  of The United States of America , March 2000
• Cromossomo 22, PNAS, November 2000
• Genoma do Câncer, PNAS, October 2001.
• Xylella da Uva, Journal of Bacteriology ,
  February 2003.
• Nature Genetics - Schistosoma mansoni , vol. 35,
  no. 2, October 2003.
• The generation and utilization of a
  cancer-oriented representation of the human
  transcriptome by using expressed sequence tags,
  PNAS, Proceeding of The National Academy of
  Sciences of The United States of America ,
  October 2003

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companies

• http//www.alellyx.com.br

Alellyx is a biotechnology company focused on
applied genomics for agriculture. Alellyx was
created in March 2002, by five Molecular
Biologists and Computer Scientists. The founders
of Alellyx were pioneers in academic genome
projects in Brazil. These projects resulted in
the whole genome sequences of several bacteria
that cause plant diseases, such as Xylella
fastidiosa and Xanthomonas axonopodis pv. citri,
both citrus pathogens, Xylella fastidiosa that
causes Pierce's Disease in grapes, and
Agrobacterium tumefaciens, a well-known tool in
the biotechnology industry. The founders have
also participated in the genome sequencing (EST)
projects of economically important crops such as
sugar cane and eucalyptus. Genome sequencing is
just the first step in modern biotechnology
development. Alellyx will push forward this
development, creating and using a large applied
genomics platform to increase the productivity,
competitiveness, and quality of commercially
important crops. The initial focus will be on
soybean, orange, grape, eucalyptus, and sugar
cane. Alellyx has its own research laboratories
and a still-expanding team of about 20
scientists. It uses information available from
public databases, but it also generates
information in-house. Alellyx maintains close
ties with Universities and Research Centers and
it will pursue partnerships with national and
international agroindustrial companies. The
company is funded by Votorantim Ventures and by
contracts with selected companies.
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companies

• http//www.scylla.com.br

Scylla Bioinformatics started in May 2002,
through the initiative of five bioinformaticians
originated from the group that created the
innovative solutions that contributed to the
reverberating success of the first Brazilian
genome projects, including the complete genomes
of bacterial species Xylella fastidiosa and
Xanthomonas citri, and sugarcane EST, allowing
Brazil to occupy a prominent position in the
global genomic research arena. Our team is
composed by people holding PhD degrees, with a
solid theoretical background and large experience
in developing solutions for genomic and
post-genomic investigations. Scylla's team also
includes young, highly qualified developers with
solid academic background and impressive skill.
The union between experience and youth creates
the perfect environment for research and
development of solutions that combine quality,
efficiency, and innovation.
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companies
A CanaVialis tem como objetivo desenvolver novas
variedades e garantir a utilização ótima das
variedades de cana-de-açúcar nos canaviais. Para
isso a empresa atuará juntamente com seus
clientes em todas as etapas do processo
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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.
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LE FIGARO
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.
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Los Angeles TimesBy Melinda FulmerApril, 15,
2000
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Calif. Vintners Put Hopes in Brazil's Labs
Work on Decoding a Devastating Microbe Reflects
New Rules of Global Science

• By Abigail Trafford
• Washington Post Staff Writer
• Saturday, December 29, 2001 Page A01
• SAO PAULO, Brazil -- The Botany Department at the
  University of Sao Paulo is a spare, gray
  two-story building surrounded by uneven grass.
  The lights are turned off in the hallways to save
  electricity. Power outages have been a problem.
• But inside its walls lies perhaps the best hope
  to protect California's 2.7 billion wine
  industry from a devastating predator. A team of
  Brazilian scientists has cracked the genetic code
  of the bacterium Xylella fastidiosa, which has
  decimated vineyards in Southern California and is
  rapidly heading north.
• Under a unique combined project, the U.S.
  Department of Agriculture, the California
  Department of Food and Agriculture and the
  American Vineyard Foundation are funding the
  work. The U.S. government turned to Brazil for
  help because "Brazil is now the leader in this
  area of agriculture," said Edwin L. Civerolo of
  the USDA's Agricultural Research Service. "We did
  not have the experience or infrastructure to do
  the work."
• Brazil's accomplishment illustrates the new rules
  of science in the global economy. Researchers
  anywhere in the world who do quality research and
  master the Internet can leapfrog national borders
  and challenge the traditional citadels of science
  in the United States and Europe. Brazil's
  achievement took money, focus and the right
  microbe.
• The work on the genome is complete, according to
  results reported this month at a San Diego
  research symposium on Pierce's disease -- the
  name for the ailment caused byXylella fastidiosa.
  It is the first step toward designing targeted
  strategies to block the disease in the grapevines
  at the cellular level.

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Brazil experts help California battle wine
plague28 Feb 2003 1300

• By Todd Benson
• SAO PAULO, Brazil, Feb 28 (Reuters) - California
  wine growers are a step closer to tackling a
  deadly pest that is ravaging the state's
  vineyards, and they have Brazilian scientists to
  thank for it.
• At the request of the U.S. Department of
  Agriculture, a team of 30-odd researchers here
  has mapped the DNA code of Xylella fastidiosa,
  the bacteria that causes Pierce's disease and is
  threatening the livelihood of California's 2.7
  billion wine and grape industry.
• While the discovery isn't enough in itself to
  save Chardonnay lovers from the threat of
  Pierce's disease just yet, it offers a complete
  blueprint of the bacteria's genetic make-up. That
  could provide new clues on how to stop its spread
  and, ultimately, find a cure.
• "This study is a huge step in the right
  direction," said Patrick Gleeson, executive
  director of the American Vineyard Foundation, a
  Napa Valley-based research group that donated
  75,000 to the Brazilian study.
• Pierce's disease has long been a nagging problem
  for California wine growers, decimating vineyards
  in the Los Angeles basin as far back as the
  1880s. Spread by sap-feeding insects known as
  sharpshooters, the disease blocks the flow of
  nutrients and kills vines within two years of
  infection.
• For nearly a century, growers managed to limit
  the damage caused by the disease -- which gets
  its name from the American scientist who first
  identified it, Newton B. Pierce -- by using
  insecticides and lopping off infected shoots
  before it spread through the whole plant.

• MORE AGGRESSIVE PEST
• But in the early 1990s, a new, more aggressive
  pest called the glassy-winged sharpshooter made
  its way to California from the southern United
  States, probably in a nursery shipment, and
  started to spread the disease with astonishing
  speed.
• Since the arrival of the glassy-winged
  sharpshooter, which is strong enough to feed on
  tougher stems that cannot be cut off without
  killing the vine, close to 6,000 acres (2,400
  hectares) of wine grape vineyards in California
  have been damaged by Pierce's disease, costing
  growers millions of dollars in lost revenue.
• The bug, which feeds and breeds on more than 130
  plants, is also putting other key California
  crops at risk, including almonds, citrus, stone
  fruits and oleander. The threat is so big that
  federal, state and local governments have spent
  more than 65 million dollars since 1998 to fight
  the sharpshooter.
• "If you ask people in the wine industry here what
  their priorities are, Pierce's disease and the
  glassy-winged sharpshooter are at the top of the
  list," said Jay Van Rein of the California
  Department of Food and Agriculture, which has a
  20 million annual budget to fund research and
  other projects aimed at controlling the disease.
• Desperate for a cure, the California wine
  industry and the USDA sought help in Brazil, a
  farming powerhouse that has made significant
  strides battling a similar disease that attacks
  citrus groves.
• Two years ago, a group of researchers in Sao
  Paulo state put Brazil on the scientific map by
  becoming the first anywhere to decipher the
  genome of a plant pathogen. After years of
  grueling laboratory work, they cracked the DNA of
  the strain of Xylella fastidiosa that causes a
  lethal disease in orange trees called Citrus
  Variegated Chlorosis, or CVC.

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Good Job Crianças da Califórnia escrevem cartas
para cientistas brasileiros Revista Pesquisa
Fapesp, Edição 74, 04/02

• Lori Connelly é professora de uma turma de alunos
  da terceira série de uma escola de San Luis
  Obispo, cidade do interior da Califórnia, Estados
  Unidos. Cercada de vinícolas, a região é uma
  grande produtora de vinhos nobres e vive sob o
  pânico de ser atingida pela doença de Pierce,
  praga que ataca as videiras, causada por uma
  variedade da bactéria Xylella fastidiosa , que
  tanto estrago provoca nos laranjais. Em agosto de
  2000, o Departamento de Agricultura dos Estados
  Unidos propôs à FAPESP uma parceria para
  seqüenciar a Xylella da videira, aproveitando a
  experiência brasileira na área.
• Tendo à frente as pesquisadoras Marie-Anne Van
  Sluys e Mariana Cabral de Oliveira, ambas da
  Universidade de São Paulo, e João Paulo Kitajima,
  da Universidade Estadual de Campinas, os
  brasileiros se uniram aos norte-americanos e
  realizaram o trabalho. A professora Lori, a
  partir de uma reportagem do New York Times ,
  mostrou aos alunos, todos entre 8 e 9 anos, como
  é possível trabalhar em cooperação com pessoas de
  qualquer lugar do mundo, com sucesso. Vinte e
  nove estudantes escreveram, então, cartas de
  agradecimento aos cientistas brasileiros.
• "Lori ensinou às crianças que os pesquisadores de
  todo o mundo são iguais e foi além das diferenças
  entre países pobres e ricos", diz Andrew Simpson,
  do Instituto Ludwig de Pesquisa contra o Câncer,
  coordenador do primeiro projeto genoma da FAPESP,
  o da Xylella . Todas as cartas têm o mesmo tom da
  escrita por Warren Stevens Crendall "Obrigado
  pelo trabalho duro que vocês fizeram".

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