Fall 2012 - Boyce Thompson Institute - Cornell University

INSIDE: Greetings from the President and CEO
BTI scientists play key role in ground-breaking tomato discoveries
BTI hosts three Human Frontier Science Program fellows
Education and Outreach update…And more
Summer / Fall 2012

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The Transcript is a bi-annual
newsletter for patrons and friends
of the Boyce Thompson Institute
for Plant Research. Articles
highlight BTI and other news from
our laboratories to bring you closer
to the important work happening
at 533 Tower Road,
Ithaca, New York.
Cover: Close-up of tomato.
Opposite page above: Cross
section of a tomato. Opposite page
below: Dr. James Giovannoni.
Photos: Sheryl Sinkow
From David Stern, CEO and President
Thank you for supporting the Boyce
Thompson Institute. We are
extremely fortunate to have
an interested and devoted group
of researchers, staff, alumni, board
members, donors and other friends
who are dedicated to our mission
of making important fundamental
discoveries in plant science. BTI’s
mission impinges on a number of
the pressing issues that are seen
and heard in the news every day:
threats to the food supply in the
face of chaotic weather, how to
best assure good health and
nutrition for our population and
what sources of alternative energy
can be developed for a more
sustainable future. Solutions to
these challenges are multifaceted,
but all require an understanding of
how plants function and interact with
the environment. Following
in the vision of BTI founder William
B. Thompson, BTI scientists are
helping to create solutions for
a better global future via
fundamental plant biology research.
In the course of carrying out our
research programs, BTI provides
stellar undergraduate, graduate and
postgraduate training to the next
generation of scientists and indeed,
encourages career and personal
growth for its entire staff. Through
a nationally recognized education
and outreach program directed
by Tiffany Fleming, BTI and its
partner institutions engage teachers
and high school students in innovative
citizen science plant research
projects (article on page six).
More than thirty students just
completed our summer internship
program, which not only provides
the opportunity to perform research
mentored by seasoned scientists,
but also includes lectures and other
activities to provide additional
context and experience. The BTI
internship experience can be
decisive in determining future
career direction, as it was for
Giulio Zampogna in Dr. Sorina
Popescu’s laboratory (article
on page eight).
BTI’s most visible research
achievement this year was
celebrated in June, when the
international Tomato Genome
Consortium culminated a decade
of work by decoding all 35,000
genes of the domesticated tomato.
A May cover article in the journal
Nature described the consortium’s
findings, and the implications not
just for tomato biology and
agriculture, but also for its many
continued on page 9

Homegrown Taste By
It has been a good summer for
consumers who love the taste of
homegrown tomatoes. BTI scientists
were involved in two collaborative
projects that led to major
discoveries about the taste and
nutrition of tomatoes. In May, the
international Tomato Genome
Consortium published their work
on the sequencing of the tomato
genome in the scientific journal
Nature. This work was the
culmination of years of work by
BTI scientists from the Giovannoni,
Mueller, Fei, Van Eck and
Martin laboratories. Secondly,
Cuong Nguyen from the
Giovannoni laboratory, in
collaboration with Anne Powell and
others at UC, Davis, published an
article in Science that highlights the
isolation and characterization of
a major gene involved in tomato
ripening.
On May 31 st the DNA sequence
of the tomato genome, Solanum
lycopersicum, was published in the
journal Nature, along with its wild
relative, Solanum pimpinellifolium.
This publication represents nearly a
decade of work by members of the
Tomato Genome Consortium, an
international collaboration between
Argentina, Belgium, China, France,
Germany, India, Israel, Italy,
Japan, the Netherlands, South
Korea, Spain, United Kingdom and
the United States. James
Giovannoni, a scientist at BTI and
the US Department of Agriculture,
ARS, led the US tomato
sequencing team, while the wild
tomato sequence was determined
at Cold Spring Harbor Laboratory.
Bioinformatic analysis of the
genome sequence, led by BTI
scientists Lukas Mueller and
Zhangjun Fei, indicates that
tomatoes possess 35,000 genes
arranged on 12 chromosomes,
more than the number
of genes
in humans. To
provide access
to the gene
sequences of the
tomato and related
species, Lukas
Mueller and his
team have
created the
interactive website,
solgenomics.net.
BTI scientist Joyce
Van Eck provided important project
management for the consortium
and led outreach activities to ensure
that students and teachers were
Karen Kindle
exposed to this groundbreaking
research. In the 1990s, Greg Martin
worked with Cornell University
scientist Steve Tanksley to create
gene maps, which were the
foundation for the genomic work.
Interestingly, through this work,
scientists were able to determine
that the tomato genome underwent
a triplication event about 65
million years ago—around the
time of the mass extinction that
is thought to have wiped out the
dinosaurs. Although many of these
genes were lost over time, the
presence of the additional genes
probably provided
resilience during times
of extreme environmental
flux, an
important trait for
plants, which are
unable to move and
avoid life-threatening
changes.
BTI produced a video
about the tomato
genome paper, which
was played at a
reception honoring BTI scientists
involved in the project. The video
can be viewed by visiting BTI’s
website, bti.cornell.edu.
continued on page 11
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What’s Happening at BTI...
1 2 3
4 5 6 7
8 9 10
11 12 13
BTI President visits Washington, DC: 1) Nick Carpita (Purdue University), Sally MacKenzie (Nebraska), Julian Schroeder (University
of California, San Diego), Dick Sayre (Los Almos National Lab), Elizabeth Hood (Arkansas State), Pat Schnable (Iowa State) and
BTI’s President David Stern outside The White House in Washington, DC just after their Public Affairs Committee meeting for the
American Society of Plant Biologists. BTI Board May Board Dinner: 2) Greg Galvin, Sophia Darling, Patti FitzPatrick and Ezra Cornell
3) Jane Calder, Patti FitzPatrick and Johannes Mathieu 4) Kelli Monce, Lukas Mueller and Roy Park, Jr. 5) Paul Chomet and Edward Buckler
6) Laura Phillips and Alan Biloski, 7) Crispin Taylor. Summer 2012 Teachers, Interns and Staff: 8) Molly Shook, Elena Cravens and
Erin Matton 9) Dianiris Lucano and Sarah Hind 10) Kelsey Killoran, Amanda Gurung and Tiffany Fleming 11) Robert Langan, Samantha
Klasfeld, Paul Van Eck, Kristing Blacklock and Andrew Dunford 12 & 13) New York City teachers learning lab skills at BTI to take back to
their classrooms.

14 15 16 17
18 19 20
21 22 23
24 25 26 27
During Cornell University Frontiers in the Life Sciences Symposium: 14) Dr. Pamela Ronald (UC, Davis) talked to BTI and Cornell
University graduate students and postdoctoral associates about their careers. Tomato Genome Party: 15) James Giovannoni
16) Tomatoes and Champagne from the party. BTI Scientists at work: 17) Dr. Sorina Popescu with Giulio Zampogna 18) Greg Martin
19) Eric Richards 20) Maria Harrison 21) Dan Klessig 22) Joyce Van Eck BTI Annual Staff BBQ: 23) Fanhong Meng and In Sun Hwang
24) Sergey Ivanov, Dierdre Daniels and Kishor Bhattarai 25) Bushpa Bhattarai, Mamta Srivastava, Diva Shrivastava, Meeta Shrivastava,
Armando Bravo, Susana De la Torre and Kishor Bhattarai 26) Nick Reiter and Shalina LaBarr 27) Eloise Garzón and Hannah Yuzwa–the
future of BTI. Photos: Sheryl Sinkow, Rebecca Deveau and Betsy Ampofo.

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In the Hands of Students and Teachers
By Tiffany Fleming
Getting young students interested
and involved in plant science
research is a core goal of BTI’s
Education and Outreach
department. Since 2001, the Plant
Genome Research Program (PGRP)
has provided a very select group of
top undergraduate and high school
students with summer research
opportunities in BTI, Cornell and
USDA labs. Approximately 30
students annually receive this
intensive training and many of
those students then go on to
pursue advanced science degrees.
When I began coordinating
education programs at BTI in 2008,
I approached the growth of our
programs largely from the
perspective of a classroom and
informal science educator. With an
understanding of the many needs
of science teachers and middle and
high school students, I set out to
develop Education and Outreach
programming at BTI to meet the
needs of these public groups and
our scientific staff. The department
has a goal to broaden the reach
and impact of BTI outreach activities
and to develop a national model for
authentic plant science education
in the classroom based on
collaboration among scientists,
teachers and students. We do this
through our Research Experiences
for Undergraduate programs, like
PGRP and Bioinformatics
internships, and also through
extensive teacher trainings and
research-based programs.
With support from the Northeast
SunGrant Initiative, the Helen
Graham Charitable Foundation,
NSF’s iPlant Collaborative and
USDA’s National Institute for Food
and Agriculture (NIFA) program,
plant biology research is now
being carried out in classrooms
across New York State. In addition
to providing under-resourced
schools with research materials,
Amanda Gurung, BTI’s Lab
Coordinator and Education
Specialist, regularly visits
classrooms, assisting and inspiring
students and teachers in authentic
research projects. Helping teachers
develop these research projects in
the classrooms is generating a lot
of excitement around plant science.
One teacher recently reported, “the
students are extremely engaged
throughout the activity with BTI
educators, and even make time
after school to continue their data
collection and experiments.”
Since January 2012, 58 teachers
have been conducting plant biology
research with their students through
a BTI teacher-training program.
This means that over 1,300 students
are currently performing plant
research as part of their

”the students are extremely engaged throughout the activity... and even
make time after school to continue their data collection and experiments.”
standard science curriculum.
Some of the research
questions include:
What varieties of switchgrass,
a potential bioenergy crop, germinate
best under stressful environmental
conditions?
How do cold treatments affect the
germination rates of different varieties
of switchgrass? Of Brachypodium,
a model grass species?
How do different switchgrass
pre-treatments affect enzyme efficiency
in converting cellulose to sugars?
In some classrooms, exposure to
plant science research has moved
beyond BTI programs and students
have generated their own
hypotheses. For example, students
in Ed Engelman’s Technology
Education class at Delaware-
Chenango-Madison-Otsego BOCES
in Sidney Center, New York asked,
“How can plants be used to create new
bioproducts to reduce consumer
dependency on plastics?”
They designed experiments using
plant starch polymers to create and
test auto crush zones and hoped
to compare their performance with
standard petroleum–based
materials. Their work inspired
teachers and students to go beyond
the education program and to start
asking—and researching—scientific
questions that relate to their
interests.
During the summer of 2012, BTI
hosted 31 teachers during a series
of teacher professional development
programs, where teachers learned
how to implement citizen science
lessons in their classrooms,
developed inquiry-based plant
science curricula and learned about
bioenergy and bioproducts research.
Additionally, we had an incredible
group of students participating in
our Research Experience for
Undergraduates program. We had
a total of 33 undergraduate and high
school students at BTI who gained
authentic research experience
working alongside BTI and Cornell
University scientists. These students
each presented their work at the
BTI Student Symposium in August.
Photo stream left to right: Mithzy Peña and
Amanda Gray; 2012 Plant Genomic Research
Program interns; David Thaler and Kevin
Hines; 2012 High School interns: Erin Matton,
Anna Knapp and Gabriella Gomez; Life
Science students performing research in the
classroom. Photos: Rebecca Deveau and
Amanda Gurung.
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Student turns research in Popescu Lab into Honors Thesis
by Bridget Rigas Garzón
In early 2010, Giulio Zampogna was
hired as a laboratory assistant in Dr.
Sorina Popescu’s laboratory. The
Los Angeles native was looking for
a way to gain lab experience while
completing his undergraduate
studies in plant science at Cornell
University. Through his passionate
drive and under Dr. Popescu’s
guidance, Giulio’s work at BTI
grew into his Cornell honors thesis.
In the beginning, Dr. Popescu
wanted Giulio to be trained in
molecular biology techniques,
so she paired him with scientists
to master basic lab skills. During
his first several months, Giulio
performed routine tests
and assisted postdoctoral scientists
and laboratory technicians. After
hours of dedication, he
mastered a number of
fundamental techniques and
created a protocol manual to help
him with his work.
Beginning in the summer of 2010,
Dr. Popescu gave Giulio the
opportunity to be directly involved
in a research project. He began
working closely with Dr. Magali
Moreau, a postdoctoral scientist
working on a collaborative project
at BTI between Dr. Popescu and
Dr. Daniel Klessig to identify and
characterize the cellular functions
of proteins that bind to the plant
hormone salicylic acid. Giulio’s work
with Dr. Moreau involved validating
putative salicylic acid-binding
proteins identified using Dr.
Popescu’s Arabidopsis thaliana
functional protein microarray.
At the end of the summer, Giulio
presented his work at the BTI
Student Symposium held every
August.
Dr. Popescu noted, “. . . it is really
important for students to go through
the discovery process—including the
disappointments and victories—to
come to their own conclusions.”
Giulio completed his honors thesis
and graduated from Cornell in May
2012, receiving a Bachelor of
Science degree holding the honors
of distinction in research and
summa cum laude. He attributes
much of his success to his work
with Dr. Popescu at BTI. This fall,
Giulio will begin his Ph.D. in
Immunology at the University
of Pennsylvania where he hopes
to research the evolution
of immunity.
“If Dr. Popescu hadn’t given me the
freedom to explore my own ideas,
I wouldn’t have moved the project
as far as I did. Dr. Popescu was
always encouraging me to take my
work further. It felt as though I was
given a primer to the Ph.D.
experience. BTI and Cornell helped
me realize my aspirations for a
career in research.”
Giulio Zampogna at the bench,
Summer 2012. Photo: Rebecca Deveau

From David Stern, CEO and President continued from page 2
close relatives in the Solanaceae
family such as potatoes, peppers
and eggplants.
The Giovannoni laboratory and
tomatoes were again in the news
shortly thereafter, when an article
in the journal Science described the
identification of a gene involved in
ripening and flavor (article on page
two).
The quality and innovation of BTI
research is well reflected in its
success in garnering external
support: our scientists receive
over $10M in annual funding from
the National Science Foundation,
National Institutes of Health, Gates
Foundation, Triad Foundation, the
US Departments of Energy and
Agriculture and other sources. The
BTI intellectual environment was
recently enriched by the arrival of
Dr. George Popescu from
Romania’s Institute for Laser,
Plasma and Radiation Physics.
Dr. Popescu brings expertise in the
analysis of large data sets, where
biological insights are revealed
through statistical analyses. In this
issue we profile several other
budding scientists at BTI,
including three postdoctoral
scientists who were awarded grants
from the Human Frontier Science
Program in a highly prestigious
international competition (article
on page ten).
BTI’s mission is grounded in the
conviction that fundamental
research will teach us how plants
function and respond to their
environment. The federal
government—in its role as a
facilitator of innovation—is the
primary supporter of this type of
research, which also contributes
to food and energy security.
As President and CEO, I have
been fortunate to participate in
a number of meetings where the
most promising and compelling
directions for plant research have
been discussed. One of these, the
Plant Science Research Summit,
brought together more than 140
national stakeholders at the
Howard Hughes Medical Institute
in September 2011. I am now
organizing a second phase of that
Summit, where we are creating
a community-wide 10-year
comprehensive strategy for
plant research.
In the face of our many societal
challenges, BTI will continue to
seize the opportunities offered by
plant research. Though the scale of
challenges is huge, the pace
of discovery continues to
accelerate. We cannot afford
to fail. As BTI scientist Dan Klessig
recently pointed out, “Plants can
survive without animals. The
reverse is not true.”
We hope that you, our BTI
supporters, enjoy this issue of
The Transcript. Please feel free
to contact our Director of
Development and External
Relations, Bridget Rigas Garzón,
(bmr6@cornell.edu, 607-254-2923)
if you have any questions or would
like a tour of BTI facilities.
David Stern
President and CEO
Photo above: plant protoplasts
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BTI Postdocs Earn Prestigious Awards
10
by Amara Pinnock
The Boyce Thompson Institute
currently hosts three Human Frontier
Science Program (HFSP) fellows:
Patrick Boyle and Johannes Mathieu
in Greg Martin’s laboratory and Silin
Zhong in James Giovannoni’s
laboratory.
The HFSP is a prestigious
program for funding research in the
life sciences. Implemented by the
International Human Frontier
Science Program organization based
in Strasbourg, France, the awards
support innovative and interdisciplinary
basic research on complex
mechanisms of living organisms.
Supported projects can range from
molecular and cellular approaches
to biological systems to cognitive
neuroscience. HFSP emphasizes
on original, international collaborations
between scientists from
different fields and countries such
as physics, mathematics, chemistry,
computer science and engineering.
To be chosen as a HFSP fellow is a
high honor and requires substantial
contributions to the science
community in order to be
considered. BTI is honored to be
hosting three fellows in two of our
laboratories performing tomato
research. We introduce you to the
researchers and their current
projects.
Patrick Boyle Martin Laboratory
Originally from Canada, Patrick
Boyle is a postdoctoral scientist
working with Dr. Greg Martin.
His research focuses on
understanding how bacteria cause
disease in tomatoes, specifically
exploring tomatoes’ natural defense
mechanisms. By studying what
the pathogens target within the plant,
Patrick believes he can
understand the critical components
of disease resistance. He hopes that
his research can be used towards
the development of environmentally
friendly disease resistance methods
in crops. Similarly, he believes the
technology he is developing can
potentially be applied to further
understand how pathogens cause
disease in other host systems,
including humans.
Patrick appreciated the honor
of becoming a HFSP fellow
because the program typically
funds “avant-garde” research and
gives him the opportunity to take
risks. Ultimately, he hopes to
enhance our understanding of the
battle that exists between pathogens
and their hosts and to develop
technology that can be applied to
other pathogen-host interactions.
Johannes Matthieu Martin Laboratory
From Germany, Johannes
originally worked in developmental
plant biology and classical genetics,
and eventually decided to study
biochemistry. He met Dr. Greg
Martin when he attended, Dr.
Martin’s lecture on effectors in his
home country. Now working at BTI
with Dr. Martin, Johannes’ research
focuses on bacterial effectors—
pathogen proteins that are injected
into host plant cells to overcome
plant resistance mechanisms. He
hopes to be able to visualize the
transfer of these effectors into the
plant cells, in vivo, to witness the
actual process. This feat has never
been accomplished in plant
research. It is hoped that by
understanding how this process
occurs in real time, scientists will be
able to develop novel strategies to
limit bacterial infection in plants and
other organisms.
Johannes was pleased to become
a HFSP fellow because he felt that
the program takes scientists out of
their comfort zones and exposes
them to new environments, often
working in different cultures and
studying new organisms. In
Johannes’ words, he “likes to push

Prestigious Awards continued from previous page
boundaries and explore projects that
are not always possible with
traditional research.” Like a
precocious child, his curiosity is
never satisfied. He loves figuring
out how things work and ultimately
hopes that his work leads to
discoveries that have a useful
outcome in plant health.
Silin Zhong Giovannoni Laboratory
Silin Zhong would say that his
research is driven by curiosity rather
than pursuing a fixed target. From
China, Silin initially studied
biochemistry, but became interested
in genetics after reading the story
about cloning Dolly the sheep.
His first research project was in
plant genetics and he soon learned
that he preferred plant genetics
to animal genetics.
Working in Dr. James Giovannoni’s
laboratory, Silin’s HFSP project is
Homegrown Tomatoes continued from page 3
But knowing the sequence of a
gene does not necessarily mean
that you know what each gene
does. That’s why the publication
on uniform ripening in tomatoes
in the June 29 th issue of Science
is so important. Naturally, tomatoes
ripen unevenly, with lighter and
deeper coloring found on the same
fruit. In the late 1920s, commercial
breeders stumbled across a natural
mutation that caused tomatoes to
ripen uniformly. This “uniform
ripening” mutation is nearly
ubiquitous in the $2 billion a year
US commercial tomato market,
where customers expect perfectly
colored, red fruit. Interestingly, BTI
and UC, Davis researchers
discovered that this same mutation
also accounts for reduced sugars
and nutrients, which may affect fruit
flavor. “This is an unintended
consequence,” says Giovannoni,
explaining why commercial growers
continue to select for the trait.
“Producers currently don’t get
researching the molecular and
genetic basis of fruit development.
He would like to understand exactly
what controls the growth of tomato
fruit. He hopes the knowledge he
gains from this research will be
readily applied to other fruits and
vegetables that are nutritionally
important and a vital part of the
human diet.
Silin believes that the HFSP award
has been important to his career,
as he now feels a higher
responsibility towards his research
direction. Instead of carrying out
research assigned to him by a
project advisor, he thinks of the
projects more broadly to include
possible key collaborations and
further experiments. He has warmly
welcomed this increase in
accountability and credits Dr.
Giovannoni’s support and
encouragement to his success.
a penny more for [flavor] quality.”
Cuong Nguyen, with colleagues at
BTI, conducted genetic analysis to
determine that the uniform
ripening gene was located at a
specific location on chromosome
10. Using genome sequence
information from solgenomics.net,
the team identified the gene that
controls ripening and the genetic
lesion that causes the mutation.
The gene encodes a transcription
factor, which regulates genes that
control photosynthesis in the
tomato fruit, ultimately affecting
the accumulation of sugars, carbohydrates
and carotenoids (color and
nutrition). Ann Powell, a research
biochemist who led the UC, Davis
team on the research, says that the
study “is a rare chance to translate
scientific findings to the real world…
it provides a strategy to re-capture
quality characteristics that had
been unknowingly bred out of
modern cultivated tomatoes.”
Photo: Tomatoes from Dr. James Giovannoni’s research greenhouses. Photo: Sheryl Sinkow
11

Mark Your Calendars:
September 10 -
December 17
February 7
Board of Directors
Barbara A. Baird, Ph.D. †
Andrew Bass, Ph.D. †
Alan J. Biloski, Ph.D.
Kathryn Boor, Ph.D. †
Peter Bruns, Ph. D.
Thomas Burr, Ph.D. †
Paul Chomet, Ph.D.
Mary E. Clutter, Ph.D.
Ezra Cornell
William E. Fry, Ph.D. †
Gregory Galvin, Ph.D.
Gregory J. Hartz
Roy H. Park, Jr.
Laura A. Philips, Ph.D, MBA
Kira S. Sheinerman, Ph.D.
Crispin Taylor, Ph. D.
† Cornell University appointed
Setaria viridis Photo: Sheryl Sinkow
Graphic Design Camilo Rosero
Editor Bridget Rigas Garzón
Coordinator Amara Pinnock
For more Information on BTI contact:
Bridget Rigas Garzón
bmr6@cornell.edu
(607) 254-2923
9:00 a.m.
Monday Morning Seminars
BTI Auditorium
6:00 p.m.
President’s Winter Gathering
BTI Atrium
Research Oversight Committee
Peter Bruns. Ph.D., Chair
Barbara Baird, Ph.D.
Edward S. Buckler, Ph.D.
Thomas Burr, Ph.D.
Paul Chomet, Ph.D.
Mary E. Clutter, Ph.D.
Michael Scanlon, Ph.D.
Crispin Taylor, Ph.D.
President & CEO
David B. Stern, Ph.D.
Vice President for Research
Eric Richards, Ph.D
BTI lead scientists receive $10M
a year in research support from
government and other sources.
Here is a selection of recent
grant awards:
$934,659 for the Harrison Laboratory
National Science Foundation
Beneficial symbioses of bacteria and fungi
$614,439 for the Richards Laboratory
National Science Foundation
Genetic instability in Arabidopsis
$356,068 for the Mueller Laboratory
Advanced Technologies (Cambridge) Limited
Postdoctoral scientists research support
$265,533 for the Van Eck Laboratory
National Science Foundation
Development and function of C4 photosynthesis
$205,386 for the Jander Laboratory
National Science Foundation
Plant defenses by an insect-vector virus
$200,000 for the Mueller Laboratory
Nestlé Research Center
Bioinformatics for coffee and cocao
Follow us on:
Boyce Thompson Institute for Plant Research
533 Tower Road
Ithaca, New York 14853-1801
bti.cornell.edu