2002 Annual Report - Donald Danforth Plant Science Center

Transcription

On November 1, the Danforth Center instituted
two awards to recognize individuals who have been
instrumental in the development of the St. Louis region
as a center for plant science and in the advancement
of plant science research. U.S. Senator for Missouri
Christopher S. "Kit" Bond and former President and
CEO of Monsanto Company Hendrik A. Verfaillie
received the Danforth Distinguished Service Award.
Dr. Mary-Dell Chilton, Principal Syngenta Fellow at
Syngenta Biotechnology, received the Danforth
Award for Plant Science.
The Danforth Distinguished Service Award recognizes
outstanding individuals or organizations that have
been important partners in the development of the
Donald Danforth Plant Science Center and/or in the
development of St. Louis as an international center
for plant science.
The Danforth Award for Plant Science recognizes
a prominent national or international leader for
outstanding achievement and service in the conduct
and/or advocacy of science for the benefit of
agriculture, food, nutrition, or human health.
The Honorable
Christopher S. "Kit" Bond
Mr. Hendrik A. Verfaillie
Dr. Mary-Dell Chilton
2 0 0 2 A n n u a l Re p o r t T he Power of Collaboration
The mission
of the Danforth Center is to
increase understanding of basic plant biology
apply new knowledge for the benefit of human nutrition
and health and improve the sustainability of agriculture worldwide
facilitate the rapid development and commercialization
of promising technologies and products
contribute to the education and training of graduate and
postdoctoral students, scientists, and technicians from around the world
Table of Contents
Chairman’s letter
Board of Trustees
President’s letter
Science Advisory Board
The Year in Review
Overview: Research at the Center
Donor Recognition
Friends Committee Members
Financial Report
2
2
3
3
4
7
11
15
16
Science Report
Roger Beachy
Claude Fauquet
Edgar Cahoon
Eliot Herman
Jan Jaworski
Joseph Jez
Erik Nielsen
Mark Running
Daniel Schachtman
Jeffrey Skolnick
Thomas Smith
Christopher Taylor
Yiji Xia
Liming Xiong
Oliver Yu
Brad Barbazuk
R. Howard Berg
Julia Gross
Nancy Mathis
18
20
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
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To Share the Excitement of Discover y
1
Donald Danforth Plant Science Center
Board of Trustees
William H. Danforth, M.D., Chairman
Chancellor Emeritus
Washington University
St. Louis, Missouri
Bruce Alberts, Ph.D.
President
National Academy of Sciences
Washington, D.C.
As I write this forward for the second annual report of the Donald Danforth
Plant Science Center, starvation threatens 38 million people in Africa. The
African food shortage has economic, political, and social roots; drought is also a
precipitating factor. But the need for locally grown nutritious food from plants
adapted to the local soil and other environmental conditions has never been
more evident.
Realizing the dreams of the Danforth Center—to use science for the benefit of
humankind, to help feed the hungry, and to protect the world’s environment for
our great-grandchildren; to provide discoveries that will help spark the next
generation of science-based industry; and to collaborate with partners to make
the Midwestern region a world center for plant science—seems to me to be
more important and more urgent than ever.
This report will document the progress made by our president, Roger Beachy,
and his colleagues in bringing together the scientists on whom all depends.
It will report on some specifics of the science and on steps toward assuring the
long-range financial sustainability of the Danforth Center.
I am personally very pleased with our progress and am grateful to the many
people who are making it possible. The morale within the Center is very high.
The strong commitment to our mission, that is to the realization of our dream,
is evident. I am thankful for the support shown by the St. Louis community
and especially for those who have joined our Friends group, so ably led by
Robert L. Virgil.
I am pleased also that the Center is serving as a catalyst for the development of
new commercial activities in the plant and life sciences. Our recently announced
partnership with The DESCO Group to build commercial wet laboratory space
on eight acres of the Danforth Center property will contribute to building our
local scientific community and to furthering regional goals for economic development.
The Donald Danforth Plant Science Center is still very young. While our major
contributions lie ahead, we are off to a wonderful start thanks to the scientists,
the staff, and the friends who are with us on this journey. It is an honor to work
with all of you.
Nancy Cantor, Ph.D.
Chancellor
University of Illinois at Urbana-Champaign
Champaign, Illinois
Martin C. Jischke, Ph.D.
President
Purdue University
West Lafayette, Indiana
David W. Kemper
Chairman, President,
Chief Executive Officer
Commerce Bancshares
St. Louis, Missouri
Alex F. McCalla, Ph.D.
Professor Emeritus
Department of Agricultural &
Resource Economics
University of California, Davis
Davis, California
John F. McDonnell
Retired Chairman of the Board
McDonnell Douglas Corporation
St. Louis, Missouri
Peter H. Raven, Ph.D.
Director
Missouri Botanical Garden
St. Louis, Missouri
Alfonso Romo Garza
Chairman/Chief Executive Officer
SAVIA, S.A. de C.V.
Garza García, N.L., Mexico
P. Roy Vagelos, M.D.
Retired Chairman/Chief Executive Officer
Merck & Co., Inc.
Bedminster, New Jersey
Hendrik A. Verfaillie
President/Chief Executive Officer
Monsanto Company
St. Louis, Missouri
Richard L. Wallace, Ph.D.
Chancellor
University of Missouri-Columbia
Columbia, Missouri
Mark S. Wrighton, Ph.D.
Chancellor
Washington University
St. Louis, Missouri
Usha Barwale Zehr, Ph.D.
Joint Director of Research
Maharashtra Hybrid Seeds
Jalna, India
William H. Danforth, M.D.
Chairman of the Board of Trustees
Ernest Jaworski, Ph.D.
Consultant
St. Louis, Missouri
Walter L. Metcalfe Jr., Counsel
Chairman
Bryan Cave LLP
St. Louis, Missouri
2
2002 Annual Report The Power of Collaboration
Science Advisory Board
Luis Herrera Estrella, Ph.D.
Director, Unidad de Biotecnologia
Irapuato, Mexico
John Johnson, Ph.D.
Professor, Department of Molecular Biology
The Scripps Research Institute
Norman G. Lewis, Ph.D.
Director, Institute of Biological Chemistry
Washington State University
Ronald Phillips, Ph.D.
Regents’ Professor
McKnight Presidential Chair in Genomics
Director, Center for Microbial and Plant Genomics
University of Minnesota
Natasha Raikhel, Ph.D.
Distinguished Professor of Plant Biology
Ernst and Helen Leibacher Chair
Director, Plant Cell Biology
University of California, Riverside
Clarence Ryan Jr., Ph.D.
Charlotte Y. Martin Professor of Biochemistry
Institute of Biological Chemistry
Washington State University
Marc C.E. Van Montagu, Ph.D.
Chairman, Institute for Plant Biotechnology for
Developing Countries
Professor Emeritus
University of Ghent, Belgium
The year 2002 marked the completion of the first year in our new facility.
The year was, by all measures, a great success.
One form of measurement is numerical. Throughout the year, the Center’s
principal investigators built their research groups, bringing highly qualified and
motivated people to their labs. All told, more than 120 scientists, post-doctoral
associates, students, interns, and technicians worked in 18 research groups during
2002. An additional 64 administrative and technical staff members supported
the Center’s research programs. These programs have been productive, and
research at the Center from 2000 to 2002 resulted in more than 80 scientific
publications and a number of technical discoveries. Our research has been
supported by grants and contracts from 16 different sources. The expansion
of each scientific team will continue through the next several years as additional
grants, contracts, and fellowships are awarded.
While such statistics are impressive, at the foundation of the Danforth Center’s
success lie the efforts of individuals working, not in isolation, but together.
Each Danforth Center employee is urged to expand her/his knowledge and
technical capabilities and to stretch the boundaries of science beyond the norm.
In addition, we understand that effective interactions among our employees
is essential to our success. Equally as important is the extent to which research
collaborations outside of the Danforth Center are established and fostered.
During 2002 our scientists developed many highly effective intra- and interinstitutional collaborations. Modern research in the biological sciences is vast
and broad in scope, and as we go forward our research collaborations will be vital
to achieving the mission of the Center.
Lastly, we have made great strides to develop a ‘culture’ at the Danforth Center
in which there is a friendly environment, a caring community of colleagues,
and, at the same time, a high level of professionalism. This culture adds value
to the spirit of collaboration and increases the personal satisfaction that results
from collaboration.
In this, the second annual report of the Donald Danforth Plant Science Center,
we highlight the opportunity for collaborations and note their importance for
both personal and professional growth. As you read you will learn more about
our science, our culture, and us.
Roger N. Beachy, Ph.D.
President
To Tackle Big ger Challenges
3
The Year in Review
2002
Staff News
Scientific Team Continues to Grow: The scientific staff at
the Danforth Center grew to more than 120 during 2002,
and the Center added four new principal investigators:
Dr. Eliot Herman and Dr. Edgar Cahoon, researchers with
the U.S. Department of Agriculture, Agricultural Research
Service; Dr. Liming Xiong, formerly of the University of
Arizona; and Dr. Joseph Jez, formerly at the Salk Institute
for Biological Studies. The team of principal investigators
now numbers fourteen.
Scientist Named to St. Louis Academy of Science:
Danforth Center principal investigator Dr. Claude Fauquet,
who directs the Center’s International Laboratory for
Tropical Agricultural Biotechnology (ILTAB), was elected
as a Fellow in the Academy of Science of St. Louis.
Dr. Fauquet is a leading expert on the biological diversity
and control of plant viruses. He heads the Center’s efforts
to develop improved varieties of cassava, a staple food crop
especially important in developing countries.
Dr. Claude Fauquet (third from left) talks in his laboratory
with colleagues (left to right) Dr. K.S. Ravi, Ben Fofana, and
Dr. Supriya Chakraborty.
Heather Ford, Research Associate in the Integrated
Microscopy Facility, with the confocal microscope.
Grant Highlights
Olin Foundation Supports Cassava Research: The Spencer
T. and Ann W. Olin Foundation granted $200,000 to the
Danforth Center to support ILTAB research for the
improvement of cassava. ILTAB is working to develop
cassava that resists attack by geminiviruses; virus infections
cause cassava yield losses of 35 to 50 million metric tons
per year in Africa.
National Science Foundation Funds Equipment: The NSF
awarded the Danforth Center $336,000 to acquire a
sophisticated confocal microscope for the Integrated
Microscopy Facility (IMF) directed by Dr. R. Howard Berg.
The IMF plays a critical role supporting research at the
Center to discover how cells function, and with the new
microscope the IMF has a full complement of equipment
that will enhance research at the Danforth Center.
4
The Year in Review
Center Wins $6 Million Maize Genomics Grant:
Funded by a $6 million NSF grant announced in
September, the Danforth Center was selected to lead a
multi-institution, multi-year effort to sequence the corn
(maize) genome. Coordinated by Dr. Karel Schubert,
Vice President for Technology Management and Science
Administration, this project establishes the Maize
Genomics Consortium (MGC) among four
organizations: the Danforth Center, Purdue University,
The Institute for Genomic Research, and Orion
Genomics (located in St. Louis). The MGC will evaluate
new methods for efficiently sequencing the complex set
of genes in corn; all data will be placed in publicly
accessible databases.
Science News
Hypoallergenic Soybeans Make National News:
Dr. Eliot Herman, USDA-ARS senior scientist and
Danforth Center principal investigator, received
national publicity in September for research that he
and collaborators conducted to produce hypoallergenic
soybeans, a breakthrough that could make a great
difference to those who suffer from food allergies.
Dr. Herman and his colleagues have found a way to
turn off the gene in soybeans that makes the primary
allergenic protein.
Dr. Eliot Herman (left), Gael Cockrell
(center), and Dr. Rick Helm (both with
the University of Arkansas) examine
the results of an allergy test on the
skin of a soybean-sensitive pig.
Center Joins Internet2 Consortium: The Danforth
Center joined Washington University and Saint Louis
University to form a consortium enabling access to
Internet2, a high-performance Internet system that
supports more sophisticated applications than the
commodity Internet. As the plant and life sciences
become increasingly dependent on information
technology, a strong infrastructure, such as I2 provides,
will be vital to the continuing leadership and success
of the Danforth Center.
Global Cassava Partnership Established: In October,
Danforth Center staff participated in a meeting in Italy
that resulted in the formation of the Global Partnership
for Cassava Genetic Improvement, a partnership to
promote and coordinate global investment in the genetic
improvement of cassava. The participating institutions,
which include the Danforth Center and some twenty
other institutions from Latin America, Europe, Africa,
and Asia, have agreed to work with growers to establish
goals, coordinate research, share findings, and build
scientific capacity in national institutions in
cassava-growing countries.
Annual Fall Symposium Held: Twelve speakers
from the member institutions of the Danforth Center
Alliance gathered to present their current research at the
Annual Fall Symposium on October 18-19. The event
has been held annually since 1999, serving to facilitate
interactions among regional scientists. This year’s topic
was “Altering Plant Metabolism to Improve Human
and Animal Nutrition.”
To Benefit from Wider Exper tise
5
The Year in Review
Other News
Distinguished Visitors
Rooftop Terrace Named for Dotty and Jeff Miller:
In September, the popular first-floor terrace at the
Danforth Center was dedicated to Dotty and Jeff Miller
in recognition of their generous support. The naming
was the first such dedication since the building opened
in October 2001 and is especially meaningful because it
acknowledges the continued involvement of members of
the Danforth family in ensuring the Center’s success.
Peace Prize Recipient Returns: Nobel Peace Prize
recipient Norman Borlaug visited the Danforth Center
in February, where he addressed a capacity crowd of 300
in the Southwestern Bell Auditorium. Dr. Borlaug, who
joined former President Jimmy Carter in St. Louis at an
event to launch the Center’s founding in 1998, spoke
about the challenges facing agriculture in the developing
world and outlined his ambitious scientific research
and development efforts, which, at the age of 88, he
continues to pursue.
(left to right) Abby Castle and Jeff Miller Jr.,
Dotty and Jeff Miller, Julie Miller Stewart, and
Jack Lampen at the dedication of the terrace.
Danforth Center Celebrates First Annual Awards
Dinner: The inaugural awardees (see inside front cover)
of the Danforth Distinguished Service Award and the
Danforth Award for Plant Science were honored at a
gala event entitled “An Evening of Exploration.” In
addition to attending the awards ceremony, about 250
people participated in hands-on activities that allowed
them to “be a scientist” for the evening, working with
some of the techniques and equipment used in research
at the Center.
U.S. Senator for
Missouri Kit Bond (right)
participates in “An
Evening of Exploration.”
Helping Senator Bond
is Dr. Jitender Yadav of
the Danforth Center.
Center Featured in Prominent Publications: The
architecture of the Danforth Center was featured in an
extensive building study in the June 27, 2002 issue of
the Architects’ Journal. The article described the highly
technical and innovative yet functional and beautiful
facility. Chemical & Engineering News featured the
Danforth Center in its July 29, 2002 issue. The article
presented the Center’s mission, research initiatives, and
novel intellectual property policies.
6
USAID Administrator Takes Interest in Danforth
Center Programs: Andrew S. Natsios, Administrator of
the United States Agency for International Development
(USAID), visited the Danforth Center in November to
learn about the promise that agricultural biotechnology
research, training, and technology transfer hold for
improving agriculture, nutrition, and human health in
the developing world. During a series of briefings,
Administrator Natsios learned about the international
research, development, and training programs at the
Danforth Center.
Dr. Norman Borlaug
speaks at the
Danforth Center.
Dr. Egbichi Mbanaso (right)
talks with Andrew Natsios about
plant cell culture technology.
Afghanistan Minister Visits: In December, His Excellency
Sayed Hussain Anwari, the government of Afghanistan’s
Minister of Agriculture and Livestock, visited the
Danforth Center as part of a week-long study tour to
the United States. During his meeting with Danforth
Center president, Dr. Roger Beachy, Minister Anwari
discussed the many difficult challenges facing agricultural
production in his country. Dr. Beachy suggested ways
that partnerships for research, training, and development
with members of the Danforth Center Alliance might be
effectively used to address a number of these challenges
and advance crop science in Afghanistan.
Overview:
Research at the Center
Collaboration Is the New Standard
When you think of a scientist, you may conjure up an
image of a lone genius, a Galileo or a Newton, working
single-handedly to uncover the laws of nature. But in
modern-day research, to paraphrase an old saying, no
scientist is an island. The complexity of scientific
knowledge necessitates that scientists build collaborative
networks, sharing expertise to find answers to
research questions.
The Danforth Center was created with collaboration
in mind. The mission of the Center—to improve
agricultural crops to benefit human health and enhance
agricultural productivity—is by its nature an inclusive,
wide-ranging endeavor that thrives on a cooperative
attitude. The building, too, fosters collaboration through
its open spaces, its meeting rooms, and its system of
information-sharing technologies. To populate this grand
design, Center president, Roger Beachy has brought
together researchers who possess a complementary range
of technical skills and research experiences. A key
component of shared expertise at the Center is embodied
in the directors of the “core facilities”; these facilities
provide specialized equipment and knowledge needed for
the variety of research projects in progress.
Dr. Dilip Shah (right) with members of his laboratory,
Dr. Robert Spelbrink and Jennifer Hanks.
The Center also benefits from its alliance (termed the
Danforth Center Alliance) with major Midwestern
research institutions: the Missouri Botanical Garden,
Purdue University, the University of Illinois at UrbanaChampaign, the University of Missouri-Columbia, and
Washington University in St. Louis. This alliance offers
opportunities for Center scientists to expand their reach
into new areas and to extend their impact through
teaching. Our participation in the Internet2 consortium
provides high-speed, broad-band linkage to investigators
outside of the Danforth Center, enabling efficient and
dynamic sharing and analysis of data. Furthermore, the
Center enjoys the advantage of being an integral part
of the development of the plant and life sciences in the
St. Louis BioBelt.
Dr. Soojay Banerjee,
Research Scientist in
Dr. Thomas Smith’s
laboratory, places a
sample in the X-ray
detector used to
determine the
structure of proteins.
To Enhance Productivity
7
Dr. Terry Woodford-Thomas and a member of her laboratory,
Dr. Tomas Morovec, examine the leaf of a tobacco plant in
the Danforth Center’s greenhouse complex.
Dr. Edgar Cahoon, Dr. Thomas Smith,
and Dr. Oliver Yu discuss techniques for
characterizing proteins.
The Power of Collaboration
The Danforth Center is fortunate to have an
interdisciplinary group of scientists working together;
the unique training and experience of each scientist
adds to the strength of the Center as a whole.
Researchers with training in biochemistry benefit from
the knowledge of those specializing in cellular biology,
and vice versa. Scientists with expertise in soybean
biology compare notes with those working on maize or
other plants to uncover revealing differences or
similarities. Investigators with extensive knowledge of
root systems contribute unique insights to projects
that study plant growth and development.
A researcher’s training, then, is part of his or her
contribution to the collaborative endeavor. In addition,
the areas of research at the Center intersect to facilitate
collaboration. Consider research on how plants respond
to stress as an example: some projects at the Danforth
Center investigate the mechanisms used by plants to
adapt to environmental stress; others look at substances
within plants that confer defense against the stress caused
by pests and pathogens; and still other projects investigate
plant disease by studying how viruses infect, replicate,
and spread. The various ways of looking at stress
response will lead to more effective and timely ways to
minimize the effects of stress.
8
A collaboration to study nematode parasitism
demonstrates clearly how teamwork speeds scientific
research at the Danforth Center. Three groups of
Danforth Center researchers, each group capitalizing on
its particular expertise, are studying the process by which
nematodes feed on host plant roots. One group will
identify genes responsible for structures that transport
materials to the nematode, another group will investigate
the properties of the transport structures themselves, and
the third group will locate the structures in the root.
The separate groups, respectively, bring years of
experience to the table. Together the researchers will
obtain a more complete picture of the process than a
single group could achieve. The team will discover
methods for interfering with nematode feeding and help
to solve a major agricultural problem (infestation by
parasitic nematodes causes billions of dollars in crop
loss worldwide each year).
The atrium provides
the setting as
Dr. Karel Schubert (right)
consults with a member
of his laboratory,
Dr. Tahzeeba Hossain.
Another collaborative project studies the genes involved
in seed formation, taking advantage of the proficiencies
of each group in studying seed gene expression,
biochemical pathways, membrane biology, and transport
of materials in cells. The Center includes researchers
who are specialists in analyzing protein structures, and
many researchers collaborate with them to characterize
particular proteins.
Core facilities provide essential information and/or
technical skills for many of the collaborations. The
nematode project has benefited from working with the
Integrated Microscopy Facility. Similarly, the expertise
and equipment available in the Mass Spectrometry
Facility has enabled researchers to determine the
sequence and identity of the macromolecules of
interest to collaborating teams. The Plant Cell
Growth and Transformation Facility provides skills
needed to develop transgenic plants with specific
genetic characteristics.
The collaborative advantage extends outside the
Danforth Center. Center researchers have developed
projects with partners in the Danforth Center Alliance
and with researchers from a variety of U.S. and international institutions. Each partner adds depth and capacity
to each project. The Maize Genomics Consortium
(described in the “Year in Review” section) is an example
of interinstitutional collaboration that capitalizes on the
specific technical and intellectual resources of each
institution. The Center’s International Laboratory for
Tropical Agricultural Biotechnology (ILTAB) has
established global connections to collaborate with
researchers in the developing world to improve cassava.
In 2002, ILTAB also trained fifteen scientists from six
countries in Africa and Asia who will return to their own
countries with the skills to conduct research on crops
important to their homelands.
For more detailed information about ongoing research projects, refer to the
science report section of this book.
Chris Menne and Dr. Julia Gross confer in the Mass Spectrometry Facility.
In the background is some of the instrumentation available for
analyzing molecules.
To Increase Ef ficienc y
9
COLLABORATIVE PROGRAMS
Rhizosphere Research Community:
Led by Dr. Christopher Taylor, a group of scientists who
study the interaction of roots with the surrounding soil
environment has established the Rhizosphere Research
Community. The mission of this collaborative group is
to discover aspects of root biology important for plant
growth and crop productivity. They have combined the
efforts of people from several different fields of study
among institutions in the Danforth Center Alliance and
in the greater Midwest region. The communication
fostered by this research community will lead to new
research ideas. Participating researchers and students
will have access to training, to new techniques, and to
equipment that each participating institution brings
to the group.
Interns (left to right): Jim Collins, Rachel Maltman,
Julie Strandquist, Kerry Massman, Julie Plocher,
Devin Nichols, Laura Ernst, and Ben Millett.
Internship Program:
(left to right) James Kearns, Dr. Yiji Xia, and Lawrence Kent
discuss issues unique to research collaboration with
developing countries.
International Programs:
The Center is committed to using plant science to help
people in developing countries improve their lives.
Lawrence Kent, manager of International Programs, is
working to build partnerships with organizations in the
developing world to translate scientific discovery into
products that farmers or consumers can use to improve
their health, nutrition, and agricultural productivity.
Examples of such projects include enhancement of the
folate content of rice; development of cassava, sweet
potato, and rice that is resistant to virus diseases; and
plant-based immunotherapeutics.
10
Teaching is a vital collaborative activity, a way to share
knowledge and skills with the next generation of
scientists. Directed by Dr. Gwen Ericson, the Danforth
Center’s internship program brings undergraduates to
Center laboratories to gain practical research experience.
In the internship program, students are paired with
experienced mentors and spend ten weeks conducting a
research project. At the end of the training period, each
intern presents his or her research to an audience of
fellow scientists in the Southwestern Bell Auditorium.
In 2002, the third year of the program, the internship
program brought eight students from five regional
institutions to the Danforth Center.
Donor Recognition
2002
Honor Roll of Donors
Founding Donors
Friends Program Is Great Success: The Danforth Center
is grateful for the enthusiastic support of its donors
during the past year. As the honor roll of donors attests,
the Friends Committee, led by Dr. Robert L. Virgil,
attracted many community members and organizations to
the Friends Program during 2002 (the Friends Program
is a donor recognition society for those who provide
$1000 or more in annual support for the Center).
Annual gifts provided through the Friends Program are
essential to the success of the Danforth Center, because
they support the research in the Center’s laboratories.
All those who joined the Friends Program before June 30,
2002 were designated as charter members and are honored
on a permanent plaque in the lobby of the Danforth
Center. The charter member plaque was unveiled on
November 1, 2002 during the “Evening of Exploration”
(see page six).
The Danforth Foundation
Monsanto Company
The State of Missouri
Major Gift Donors
Spencer T. and Ann W. Olin Foundation *
SBC Foundation
Friends Program
Distinguished Research Sponsor $25,000 or more
Individual Gifts
Dr. and Mrs. William H. Danforth *
Mr. and Mrs. John F. McDonnell *
Organizational Gifts
Anonymous
William T. Kemper Foundation *
Spencer T. and Ann W. Olin Foundation *
Senior Research Sponsor $10,000 to $24,999
Individual Gifts
Mr. and Mrs. J. Hord Armstrong III *
Mr. Alvin Goldfarb *
Mr. † and Mrs. Charles Guggenheim *
Dr. and Mrs. P. Roy Vagelos *
Hendrik and Hilda Verfaillie *
Dr. and Mrs. Robert L. Virgil *
Interco Charitable Trust *
Fellows Research Sponsor $5,000 to $9,999
Individual Gifts
Anonymous
Dr. and Mrs. Roger N. Beachy *
Daniel A. Burkhardt and Connie Hager Silverstein *
Mr. and Mrs. John C. Danforth *
Mr. and Mrs. Norman L. Eaker *
Mr. and Mrs. John E. Klein *
Walter and Cynthia Metcalfe *
Mr. and Mrs. J. Patrick Mulcahy
Mr. and Mrs. Nicholas L. Reding *
Jim and Maebelle Reed *
Mr. and Mrs. John Sloop *
† Deceased
* Indicates Friends Program Charter Member
To Expand Knowledge and Lear ning
11
Dr. John H. Biggs, a
member of the Danforth
Foundation Board of
Trustees, examines
parasitic nematodes in
Dr. Christopher Taylor’s
laboratory during a visit
to the Danforth Center.
Honor Roll of Donors
Mr. and Mrs. Robert Tschudy *
Mary Ann and Michael Van Lokeren *
Dr. Virginia V. Weldon *
Scholar Research Sponsor $2,500 to $4,999
Individual Gifts
Ruth Palmer Blanke †
Dr. Robert J. and Kathryn W.
Calcaterra *
Mr. Rolf G. deLeuw
Arnold and Hazel Donald *
Mr. and Mrs. Donald F. Essen *
Mr. and Mrs. David C. Farrell *
Mr. Sam Fiorello and Dr. Rebecca
Messbarger *
Art and Jean Fitzgerald *
Dr. and Mrs. Robert T. Fraley *
Peter B. and Joanne S. Griffin *
Dr. and Mrs. Ernest G. Jaworski *
Mr. and Mrs. Kenneth Kranzberg *
Mr. and Mrs. Oliver M. Langenberg *
Ann and Lee Liberman *
Linda M. Martínez *
Dr. and Mrs. Philip Needleman
William and Anne Tao *
Mr. Richard P. Tolan, Ms. Tina M.
Hoechst, and Family *
Mr. and Mrs. James von der Heydt *
James and Stacey Weddle *
The Shepherd Foundation *
Wiethop Greenhouses Inc. *
Research Sponsor $1,000 to $2,499
Individual Gifts
Anonymous
Ann and Bruce Anderson *
Mr. and Mrs. Melvin C. Bahle *
Mr. and Mrs. Clarence C. Barksdale *
Mr. and Mrs. Charles L. Barnes *
Dr. Gerard F. Barry *
Mr. and Mrs. Jack Barsanti *
Mr. Brett Begemann *
Mr. and Mrs. Barry H. Beracha *
Mr. and Mrs. A. John Brauer III
James N. and Kathleen F. Brickey *
Ben and Janet Brink *
Mrs. Billie Broeker *
David L. and Kathleen A. Broughton *
Mr. and Mrs. Christopher W. Brown *
Mr. and Mrs. Spencer B. Burke *
Jane E. Burton *
Dr. Christopher I. Byrnes
Edgar and Rebecca Cahoon
Miss Carol B. Danforth *
Mr. Christopher B. Danforth *
Mr. and Mrs. David G. Danforth *
Mrs. Donald Danforth Jr. *
Mr. and Mrs. Donald Danforth III *
Mr. and Mrs. Harold W. Davies III *
Mr. and Mrs. Carl Deutsch *
Ed Doisy and Carla Qualy *
Mr. and Mrs. Patrick M. Donelan *
Sally and Derick Driemeyer *
Dr. William C. and Mrs. Glenda L.
Finnie *
Mr. Edward V. Fischer Jr. *
Ms. Jane Goldberg *
Mr. and Mrs. Earle H. Harbison Jr. *
Harvey and Judy Harris
Mr. and Mrs. Whitney R. Harris *
Edward and Estelle Herman
Sally and Bruce Higginbotham *
Mr. and Mrs. David M. Hollo *
D. Michael Hollo Jr. *
Henry K. Hollo *
Laura H. Hollo *
Thompson D. Hollo *
Dr. and Mrs. Robert B. Horsch *
Mrs. Jane R. Huey *
Ms. Jeannette R. Huey *
Mrs. Jane Hunter
Eleanor and Allan Ivie *
Dr. Jan G. Jaworski *
Dr. Gregory R. and Mrs. Mary
Johnson *
Mr. David F. and Mrs. Lori W. Jones *
Lawrence Kent *
Drs. Ganesh and Nandini Kishore *
Luke Kissam and Kathryn Schanen
Kissam *
Janet M. and Newell S. Knight Jr. *
Robert H. Koff and Linda J. Riekes
Andrew and Diana Kohn
Chris and Sheree Lee *
Sally and Ned Lemkemeier *
Theresa E. Lynch *
Lisa J. and Mark A. Massa *
Paul and Midge McKee *
Mr. and Mrs. James McKelvey *
Mr. and Mrs. Thomas C. Melzer *
Mr. and Mrs. Jefferson L. Miller Jr.
Mr. and Mrs. I.E. Millstone *
Mr. Derek J. and Mrs. Jill M.
Montgomery *
Jane Nelson and Dale Isaak *
Mary Ann and Fred Noel *
Rick Oertli *
Mrs. William J. Oetting *
Dr. and Mrs. John C. O’Toole *
Gordon and Susan Philpott
Mr. and Mrs. Robert Wm. Prather IV *
Emily and Derek Rapp *
Mr. and Mrs. John R. Roberts *
Joseph and Lisa Roddy *
Karen Keeler Rogers *
Dr. and Mrs. Timothy Root *
Mr. and Mrs. Robert M. Sankey *
Samuel E. Schechter, M.D. *
James and Joan Schiele
Mrs. Donald O. Schnuck *
Warren and Jane Shapleigh
Dr. Raymond and Mrs. Alberta Slavin *
Frank and Teg Stokes *
Peggy Walter Symes
Mr. and Mrs. T.P.C. Taylor
Mrs. Diane M. Beers Thomas *
Mr. Lawrence E. Thomas *
Georgia and Bill † Van Cleve *
Mr. Christopher M. and Mrs. Elizabeth
A. Vancil *
Thomas J. Ward, D.D.S. *
Mark S. and Risa Zwerling Wrighton *
CASCO *
CPI Corp. *
Computer Sales International Inc. *
ESCO Technologies Inc. *
The Fox Family Foundation *
Knoll Inc. *
Osborn & Barr Communications *
St. Louis County Economic Council *
Stupp Bros. Bridge & Iron Co.
Foundation
Taylor Morgan Realty L.L.C. *
Additional Gifts - $1 to $999
Individual Gifts
Robert C. and Linda C. Ballard
Mr. and Mrs. Gene K. Beare
Dr. R. Howard Berg
Mr. and Mrs. George N. Bishop Jr.
Mr. William L. Bishop
Mr. and Mrs. William M. Graves III
† Deceased
12
Mr. Stephen L. Hampe
Mary and Jennifer McDonald
Mr. Dennis Plummer
Peter H. Raven
Jean and Jay Sosna
Mr. and Mrs. George H. Walker III
Mr. and Mrs. William E. Winter
Mrs. Jing Zhang
In honor of Senator Christopher Bond,
Mr. Hendrik Verfaillie, and
Dr. Mary-Dell Chilton
Mr. I.E. Millstone
Commercial Property Services Inc.
In honor of Dr. William H. Danforth
Mr. and Mrs. Gene K. Beare
Corporate Affiliates Program
In honor of Dr. and Mrs. William H. Danforth
Peter B. and Joanne S. Griffin
Ms. Jeannette R. Huey
Mimi and Jennifer McDonald
Mary Ann and Fred Noel
Director’s Circle $25,000 or more
Pioneer Hi-Bred International Inc. *
Builder’s Team Campaign
Corporate Donors
Lead Project Sponsor $50,000 or more
Hellmuth, Obata and Kassabaum
McCarthy Building Companies Inc.
Project Manager Sponsor $5,000 – $9,999
Vee-Jay Cement Contracting Co. Inc.
Project Coordinator Sponsor $2,500 - $4,999
C & R Mechanical Company
icon Mechanical
Internship Program Donors
Aon Risk Services
Applied Biosystems
Conviron
DuPont Protein Technologies
International
Dr. Gwen Ericson
Midwest BankCentre
Gifts-in-Kind
Dr. Tobias Baskin
Tribute and Memorial Gifts
In honor of Dr. Mary-Dell Chilton
Commercial Property Services Inc.
Tree in Entry Plaza given in honor of
Jan and Dale Fanter
Ms. Linda Fanter
In memory of Charles Guggenheim
Mel and Sue Bahle
Mrs. William Barnes III
Dr. and Mrs. John H. Biggs
Michael Brewer
Ann H. Brown
Ann S. Brown
Janet Brown
Charles and Bunny Burson
Dr. and Mrs. William H. Danforth
Kitty and John M. Drescher Jr.
Eleanor S. and Andrew J. Glass
Donald and Miriam Lay
Mr. and Mrs. Lee M. Liberman
Priscilla B. McDonnell
Cynthia and Walter Metcalfe
Susan D. and James J. Murphy
Mary Ann and Fred Noel
Elizabeth G. Perryman
Jane and Milton Rand
Mr. and Mrs. S. I. Rothschild Jr.
Harriot and Parker Smith
Mrs. Tom K. Smith Jr.
Helen B. and Donald H. Streett
J. K. Streett
Mr. and Mrs. Robert W. Streett
Jason Tartt
Mitchell Tartt
Nancy W. Tartt
Mr. and Mrs. Frank A. Thompson
Emily C. Volz
Carol B. Baker and Ross E. Wells
In loving memory of Joe Varner
Jane E. Burton
In honor of Dr. and Mrs. Robert L. Virgil
Ms. Jeannette R. Huey
In memory of James L. Wurm
Mr. and Mrs. David G. Danforth
Commercial Property Services Inc. – In honor of
Rafael Aguilar
Elliott Asbel
Ernesto S. Avino
Dave Barrow
Burton Belenke
Mr. and Mrs. Philip Benzil
Bette Baron and Lou Bernstein
Henry Blanton
Ron Branscombe
Keith Brock
Joan Chandler
Jack Chapin
Herbert Chestler
Ki H. Choi
Jennifer Chuck
Peter and Dianne Clancy
Judy Clark
James Clavijo
Debra Coburn
Richard Cohen
Bessie Connelly
David Dermer
Carlos Deupi
Fred Devitt
James Diefenbach
Joe Evich
Frank Fernandez
Paul Ferreigna
Margaret Ferreira
Matching Gift Companies
Altria Group Inc.
The Danforth Foundation
Monsanto Company
The Rockefeller Foundation
Phoebe and Spencer Burke
work with Danforth Center
Scientist Ray Collier in the mock
gene laboratory during the
“Evening of Exploration” event.
To Make More Rapid Prog ress
13
Howard and Caroline Fine
Eric Furman
Sarah and Gideon Gartner
Bob Gittlin
Bruce Gittlin
Allen Gordon
Terry Granot
Jeannette Greenberg
Howard and Lynn Halpern
Patricia Handler
Russell W. Heberling
Nancy and Coleman Hogan
Louis Izquierdo
Jeffrey Johnson
Alexander Jordi
Eugene Kaletsky
Robert Kaplan
Allan Kaulbach
Bob Keeley
Adolph Koeppel
Joel Koeppel
Anat Kremen
Jim Kurtzman
Jeffrey Lorenz
Maureen Luke
Debra Lundy
Michael Martone
Raymond Masucci
Albert Matsil
Phil McConaghey
Joan Carole Meyers
Maria Moré
Michele Moskowitz
Howard Orner
Denis Plante
Sheila Potsma
Sage Prigozen
Jim Riley
Valerie Robbin
J. R. Robinson
Elaine Roston
Joe Schlipman
Gary Severns
Robert M. Silva
Rand Skolnick
Georgean Smythe
Margaret Stenson
Neil Useden
Robert Vellone
Mark Verner
John and Suzanne Wagner
Timothy Wagner
Selwyn T. Werner Jr.
Regina West
Alice West-Price
Wesley White
Julie A. S. Williamson
Christopher Woodrum
Dr. William H. Danforth
thanks Nobel Peace Prize
Winner Dr. Norman E.
Borlaug for visiting the
Donald Danforth Plant
Science Center.
Bruce and Sally
Higginbotham
perfect their pipeting
skills at the “Evening
of Exploration” event.
Every attempt has been made to assure the accuracy of
this list. In case of error or omission, please contact the
development office at the Danforth Center.
14
Friends Committee Members
Robert L. Virgil, D.B.A.
Chair
Management Development Consultant
Edward Jones
Benjamin Brink
AP Materials
Spencer B. Burke
Director of Corporate Finance
A.G. Edwards and Sons Inc.
Daniel Burkhardt
Principal
Edward Jones
Arnold Donald
Chairman and Chief Executive Officer
Merisant Company
Hazel Donald
Community Volunteer
Patrick M. Donelan
Chairman
Allegiant Investment Counselors
Jane Goldberg
Community Volunteer
Joanne Sawhill Griffin
Corporate Vice President
Enterprise Rent-A-Car
Robert Horsch, Ph.D.
Vice President for Product
and Technology Cooperation
Monsanto Company
Ernest Jaworski, Ph.D.
Consultant
Donald Danforth Plant Science
Center
Gregory R. Johnson
Managing Director
Prolog Ventures LLC
John E. Klein
President and Chief Executive Officer
Bunge North America Inc.
Andy Kohn
President
Jerome Group
Derick Driemeyer
Retired
Linda Martínez
Partner
Bryan Cave LLP
William C. Finnie, Ph.D.
Managing Director
Grace Advisors Inc.
Jane Nelson
General Counsel/Secretary
CPI Corp.
Gregory Fox
Group President
Harbour Group Ltd.
Rick Oertli
Guarantee Electrical Company
Robert T. Fraley, Ph.D.
Executive Vice President and
Chief Technology Officer
Monsanto Company
Marie Oetting
Community Volunteer
Derek Rapp
Divergence Inc.
Nicholas L. Reding
Chairman
Nidus Center for Scientific Enterprise
Mark Schnuck
The DESCO Group
Charles M. M. Shepherd
Senior Partner
Shepherd, Taylor and Smallwood LLP
Attorneys at Law
Alberta C. Slavin
Community Volunteer
John Sloop
Partner
Edward Jones
Kenneth Steinback
Chairman and Chief Executive Officer
Computer Sales International Inc.
J.J. Stupp
Community Volunteer
Greg Sullivan
G. A. Sullivan
William K.Y. Tao, Sc.D.
President
Building Systems Consultant Inc.
William M. Van Cleve †
Senior Counsel
Bryan Cave LLP
Mary Ann Van Lokeren
Krey Distributing Company
† deceased
15
Selected Financial Data
Fiscal Year Ended December 31, 2002
Revenues and Expenditures (Dollars in Thousands)
REVENUES (CASH BASIS)
Corporate/Foundation Gifts
Individual Gifts
Grants and Contracts - Research
Grants - Capital Acquisition
Other Income
Revenue
$13,180
778
3,651
2,047
213
Source %
66.3%
3.9%
18.4%
10.3%
1.1%
Total
$19,869
100.0%
66.3%
18.4%
10.3%
3.9%
1.1%
Individual Gifts
Corporate/Foundation Gifts
Grants & Contracts - Research
Other Income
Grants -Capital Acquisition
OPERATING EXPENDITURES
Total Research/Science
Administration
Development and Public Relations
Total
Expenditures
$14,348
3,563
585
Expenditure %
77.6%
19.2%
3.2%
$18,496
100.0%
77.6%
3.2%
19.2%
Total Research/Science
Administration
Development and Public Relations
CAPITAL EXPENDITURES
Building Project Completion and
Startup Equipment Purchases
16
$4,630
Roger Beachy, Ph.D
Member and Principal Investigator
Research in the Beachy laboratory is directed to studies of virus infection
and development of strategies to control infection and disease.
Infection by tobamoviruses and strategies to control
infection and virus spread: The tobamoviruses tobacco
mosaic virus (TMV, hosts include tobacco and tomato)
and Cg (primary host, Arabidopsis) are useful models for
studies in molecular virology and pathogenesis. Our
research includes studies of the 30 kDa movement
proteins, coat proteins (CP), and CP-mediated resistance
(CP-MR), and characterization of host proteins that
influence resistance and susceptibility to tobamoviruses.
Coat protein mediated resistance: We developed transgenic
BY-2 cell lines with high levels of CP-MR to study cellular
and structural mechanisms of resistance. These studies
showed that certain mutants of CP can restrict infection
by restricting virus disassembly and by reducing the
production of movement protein. Details of these effects
are under study.
Transgenic plants in which the CP gene is controlled by
a chemical gene switch were recently developed for studies
to determine how the CP contributes to virus infection.
These studies will be complemented by genetic studies in
Arabidopsis to identify host genes that control CP-MR.
Colocalization of TATA Binding Protein (TBP) fused with CFP
and the transcription factor 2a (RF2a) fused with YFP from
rice using Fluorescence Resonance Energy Transfer (FRET).
Genes encoding the proteins were cointroduced to BY-2
protoplasts. a) Localization of CFP-TBP); b) Localization of
YFP-RF2a and c) colocalization of the two signals using
FRET. This study shows that TBP and RF2a are within 10 nm
each other in the nucleus.
Cell-cell spread of infection: Virus movement proteins (MP)
are essential for cell-cell and/or long-distance spread
of infection. The MP of tobamoviruses is required to
establish the cellular factories that
produce more virus particles. We are
combining genetics, cell biology, and
biochemistry to identify the cellular
and biochemical functions of the
protein. Using time-lapse fluorescence
microscopy, we follow the rate of
infection of TMV in lines of cells in
which cellular compartments can be
distinguished by fluorescent marker
proteins. This work will lead to
DsRed1-E5, a fluorescent protein,
identification of cellular components
in roots of transgenic Arabidopsis.
that are influenced by virus infection.
These studies are complemented with a genetic
approach to identify genes in Arabidopsis that are
essential for MP function.
Regulation of gene expression of Rice tungro
bacilliform badnavirus (RTBV): This virus is
responsible for a severe disease of rice in Asia.
Previous work showed that transcription factors RF2a
and RF2b control virus gene expression. Our current
work involves characterizing the role(s) of specific
domains of these factors in regulating gene expression
using in vivo and in vitro studies. In recent studies we
used chemically regulated gene expression and synthetic
zinc finger proteins to test the function of synthetic
and native proteins in controlling expression of the
RTBV promoter. A goal of this work is to identify
proteins that can reduce RTBV replication and disease
in rice plants.
Recent Publications
18
Bendahmane M, Szecsi J, Chen I, Berg RH, Beachy RN. 2002.
Characterization of mutant tobacco mosaic virus coat protein that interferes
with virus cell-to-cell movement. P Natl Acad Sci USA 99:3645-3650.
Ordiz MI, Barbas III CF, Beachy RN. 2002. Regulation of transgene
expression in plants with polydactyl zinc finger transcription factors.
P Natl Acad Sci USA 99:13290-13295.
Zhu Q , Ordiz M, Dabi T, Beachy RN, Lamb C. 2002. Rice TATA binding
protein interacts functionally with transcription factor IIB and the RF2a
bZIP transcriptional activator in an enhanced plant in vitro transcription
system. Plant Cell 14:795-803.
Stege JT, Guan X, Ho T, Beachy RN, Barbas III CF. 2002. Controlling
gene expression in plants using synthetic zinc finger transcription factors.
Plant J 32:1077-1086.
Lab Members:
Sebastian Asurmendi, Ph.D., Post Doctoral Associate
Jennifer Bick, Lab Assistant
Yangjian Chen, Student
Shunhong Dai, Ph.D., Post Doctoral Researcher
Masaaki Fujiki, Ph.D., Research Scientist
Shigeki Kawakami, Ph.D., Research Scientist
Moses Koo, Ph.D., Research Scientist
Yi Liu, Ph.D., Post Doctoral Scientist
Isabel Ordiz, Ph.D., Post Doctoral Fellow
D.V.R. Reddy, Ph.D., Visiting Scientist
Cecilia Rovere, Ph.D., Visiting Scientist
Carolina Serrano, Graduate Student
Maria Soto-Aguilar, Ph.D., Post Doctoral Associate
Zhihong Zhang, Ph.D., Post Doctoral Associate
Karel Schubert, Ph.D., Domain Member
Yajuan Cao, Ph.D., Post Doctoral Associate
Tahzeeba Hossain, Ph.D., Research Scientist
Dilip Shah, Ph.D., Domain Associate Member
Jennifer Hanks, Research Assistant
Robert Spelbrink, Ph.D., Post Doctoral Associate
Terry Woodford-Thomas, Ph.D., Domain Associate Member
Tomas Moravec, Ph.D., Post Doctoral Associate
Kerry Massman, Summer Intern
Executive Assistant: Bernadette Kurtz
Administrative Assistant: Kathleen Mackey
Karel Schubert, Ph.D., Domain Member
Research in the Schubert group has focused on
the interactions between plants and symbiotic and
pathogenic microorganisms, insects, and parasitic
nematodes; carbon and nitrogen assimilation in plants;
plant energetics; bioprospecting and discovery of
naturally occurring bioactive metabolites, proteins and
genes; and the engineering of metabolic pathways.
Our experimental approaches include biochemistry,
structural biology, molecular and cellular biology, and the
application of modern genomics, proteomics, and
metabolomics tools. Current research has focused on the
biofortification of folates in foods. Folate deficiency is
the most common nutrient deficiency in the world
leading to increased incidence of birth defects, cancer,
cardiovascular disease, and reduced cognitive development.
Dr. Tahzeeba Hossain and Dr. Schubert are engineering
pathways of de novo folate biosynthesis to enhance the levels
and bioavailability of folates in cereals. Other research
includes investigations by Dr. Schubert and Dr. Yajuan
Cao on the cellular, molecular, and biochemical
mechanisms of regulation of key enzymes of nitrogen
assimilation in soybean and a collaboration with The
Institute for Genomic Research, Purdue University, and
Orion Genomics to compare different strategies to
sequence the maize genome.
Dilip M. Shah, Ph.D., Domain Associate Member
Plant diseases caused by fungal pathogens are responsible
for substantial losses of crop yields worldwide. Effective
and sustainable control of fungal pathogens remains one
of the most important challenges of modern agriculture.
My lab is investigating the potential of small antifungal
defensin peptides to confer disease resistance in crops.
Recent Publications: Schubert
Salles II, Blount JW , Dixon RA, Schubert KR. 2002. Phytoalexin induction
and ß-1.3-glucanase activities in Colletotrichum trifolii infected leaves of alfalfa
(Medicago sativa L.). Physiological Molecular Plant Pathology 61:89-101.
Cao Y, Schubert KR. 2001. Molecular cloning and characterization of a
cDNA encoding soybean nodule IMP dehydrogenase. Biochim Biophys Acta
1520:242-246.
Recent Publications: Shah
Gao A-G, Hakimi S, Mittanck C, Wu Y, Stark D, Shah DM, Liang J,
Rommens C. 2000. Fungal pathogen protection in potato by expression of
a plant defensin peptide. Nature Biotechnol 18:1307-1310.
Defensins are small cysteine-rich antifungal peptides
expressed constitutively in specific tissues of plants and
in response to pathogen infection. A defensin peptide
isolated from the seed of alfalfa has been previously
shown to confer resistance to a fungal disease in a
transgenic crop. We have recently cloned genes encoding
two highly diverged antifungal defensins from a model
legume Medicago truncatula. We are performing a
structure-function analysis of these peptides and
investigating the expression of these genes during
development and in response to biotic and abiotic
stresses. Research in the future will focus on revealing
the precise roles of these peptides in plant defense.
Ultimately, this research will lead to novel strategies for
disease control in transgenic crops.
Terry Woodford-Thomas, Ph.D.,
Domain Associate Member
Design, production and analysis of plant-based vaccines:
The technology is being developed to use agricultural
plants for the production and delivery of oral vaccines
designed to induce protective immunity against infectious
disease pathogens of humans and animals. One aspect
of the work is aimed at refining our knowledge of how
modified, chimeric plant viruses, such as TMV, can be
used as vaccine vectors and efficient platforms for the
display of immunodominant disease epitopes. Based on
structural and functional analyses, peptide sequences
encompassing epitopes known to trigger disease immunity
are being incorporated into distinct regions of the viral
coat protein for surface display. Strategies are being
examined which could potentially allow for the elicitation
of both B and T cell responses in order to generate
multivalent and combination vaccines, as well as to target
vaccines to the mucosal immune system for improved
vaccine delivery. Studies on vaccine potency, efficacy,
safety, as well as potential allergenicity and oral tolerance
effects are also being conducted. A second aspect of the
research focuses on the production of subunit vaccines
and therapeutic antibodies in genetically enhanced plants
including tobacco, maize, and soybean. The current
prototype diseases for studies on plant virus-based gene
expression and vaccine production in plants include
HIV/AIDS and rabies.
19
Claude Fauquet, Ph.D
In 2002, we established international collaborations to improve cassava
and build research capacity in developing countries as well as continuing
our research on the biology of geminiviruses and virus resistance.
The International Laboratory for Tropical Agricultural
Biotechnology (ILTAB) is a research and training
organization at the Danforth Center dedicated to tropical
agriculture. Its mission is threefold: to advance the
application of molecular biology and biotechnology
for tropical crop improvement, to promote building of
research capacity in developing countries, and to help
coordinate global biotechnology research on tropical crops.
Two scientists from Africa,
who are part of our
capacity-building program,
observe transgenic cassava
plants for virus resistance
evaluation: Kwando Ayeh
from BINARI, Ghana (left)
and Dr. Ada Mbanaso
from NRTCRI, Nigeria
(right).
Geminivirus resistance in cassava: ILTAB continues its
research on the biology of geminiviruses and resistance
mechanisms in crop plants. Employing the replicase
strategy, we have produced transgenic cassava plants
showing high resistance or immunity to a variety of
geminivirus species infecting cassava in the tropics. The
genetically modified plants have been fully characterized
and challenged with the pathogens under controlled
greenhouse conditions. At this time, we are working to
obtain the documentation required to carry out field
trials of the most promising plant lines in Africa. With
a target date for beginning these field trials of 2004, this
will be the first trial of transgenic cassava in the tropics.
We have also been developing a novel strategy for
blocking replication of geminiviruses in plant cells.
In collaboration with a commercial company in India,
we have demonstrated that transgenic expression of a
single-stranded DNA-binding protein (called g5) imparts
resistance to a range of genetically unrelated geminivirus
species in both tomato and tobacco. We believe that this
technology has the potential to impart resistance to all
geminiviruses in any crop species and help address the
billions of dollars lost to these pathogens each year.
Research at ILTAB is continuing to develop this exciting
technology and to transfer the g5 gene to cassava.
Biology of geminiviruses: In developing countries,
geminiviruses are responsible for the emergence of new,
potentially destructive crop diseases. ILTAB is studying
a collection of geminiviruses from Africa and Asia to
better understand geminivirus biology, synergistic
interactions, and evolutionary mechanisms. This research
is essential for the development of resistance strategies
robust enough to perform in farmers’ fields in the tropics.
We are in the process of identifying ORFs of
geminiviruses that play complementary roles in synergism
and silencing and co-suppression of their host. We have
also made some progress on understanding the
specificity of DNA replication of geminiviruses, and
we will expand this study to newly discovered geminivirus
satellites known as Beta molecules.
Pseudo-recombinant viruses
between two Indian geminiviruses
are more virulent. From left to
right; wild type TOLCGV-Var,
pseudo-recombinant between
ToLCNdV-Svr DNA-A and
ToLCGV-Var DNA B, wild type
ToLCNdV-Svr, and healthy
Nicotiana benthamiana.
Recent Publications
Brugidou C, Opalka N, Yeager M, Beachy RN, Fauquet CM. 2002. Stability
of Rice yellow mottle virus (RYMV) and cellular compartmentalization
during the infection process in Oryza sativa (L). Virology 297:98-108.
Fargette D, Pinel A, Halimi H, Brugidou C, Fauquet CM, van Regenmortel
MHV. 2002. Comparison of molecular and immunological typing of isolates
of Rice yellow mottle virus. Arch Virol 147:583-596.
20
Taylor NJ, Fauquet CM. 2002. Microparticle bombardment as a tool in plant
science and agricultural biotechnology. DNA Cell Biology 21:963-977.
Zhou X, Xie Y, Tao X, Zhang Z, Li Z, Fauquet C. 2002. Characterization of
DNA-beta associated with begomoviruses in China and evidence for co-evolution
with their cognate viral DNA-A. J Gen Virol 84:237-247.
Chatterji A, Beachy R, Fauquet CM. 2001. Expression of the oligomerization
domain of the replication-associated protein (Rep) of Tomato leaf curl New Delhi
virus interferes with DNA accumulation of heterologous geminiviruses. J Biol
Chem 276:25631-25638.
Lab Members:
Kwadwo Ayeh, Research Associate
Supriya Chakraborty, Ph.D., Visiting Scientist
Brotati Chattopadhyay, Ph.D., Lab Technician
Ben Fofana, Graduate Student
Nicole Kokora, Graduate Student
Rachel Maltman, Summer Intern
Ali Mkezo Mashata, Ph.D., Visiting Scientist
Egbichi Mbanaso, Ph.D., Visiting Scientist
Francis Ogbe, Ph.D., Research Scholar
Chellappan Padmanabhan, Ph.D., Post Doctoral Associate
Denise Peterson, Lab Technician
Justin Pita, Graduate Student
Vanitarani Ramachandran, Ph.D., Research Associate
K.S. Ravi, Ph.D., Visiting Scientist
Byongchul Shin, Ph.D., Post Doctoral Associate
Nigel Taylor, Ph.D., Assistant Domain Member
Jitender Yadav, Ph.D., Post Doctoral Fellow
Xueping Zhou, Ph.D., Research Associate
Administrative Assistant:
Pat Cosgrove
Participation in capacity-building for developing countries:
With support from the U.S. Agency for International
Development and Monsanto Company, ILTAB has
continued to train African researchers in cassava
biotechnology and molecular virology. This program
builds research capacity in these countries and contributes
to our efforts to deliver improved planting materials to
farmers in developing countries. Fifteen scientists from
six countries in Africa and the Indian subcontinent
worked at ILTAB during 2002. One such scientist is
Dr. Francis Ogbe who has now returned to the National
Root and Tuber Crop Research Institute in Nigeria; we
will collaborate with Dr. Ogbe to establish the first field
trials of transgenic cassava in that country.
Global cassava improvement plan: An important
outcome of the Fifth International Meeting of the
Cassava Biotechnology Network (CBN-V), hosted by the
Danforth Center in November 2001, was a commitment
to establish a global, coordinated plan for the agronomic
improvement of cassava. In 2002, working with the
Rockefeller Foundation, we organized a meeting of
cassava researchers that resulted in establishment of the
Global Partnership for Cassava-Genetic Improvement.
An integrated plan, GPC-GI links efforts in biodiversity,
biotechnology, and breeding with the needs of farmers
and cassava consumers. ILTAB and the Danforth Center
have obtained both endorsement and logistical support
for the plan from the United Nations Food and
Agricultural Organization (FAO).
Dr. Nigel Taylor, Assistant
Domain Member in ILTAB.
21
Edgar Cahoon, Ph.D.
U.S. Department of Agriculture, Agricultural Research Service
Associate Member and Principal Investigator
My research is aimed at increasing the value of soybeans
by enhancing the storage components of the seed.
Soybean is the second most widely grown crop in the
United States and the number one cash crop in Missouri.
The annual production of soybeans in the United States
has increased by over one million bushels during the past
twenty-five years, but the bushel price received by farmers
has changed little in this time period. My research is
aimed at increasing the value of soybeans by genetically
enhancing the storage components of the seed. A
particular focus of my research is the modification
of the fatty acid composition of soybean seed oil to
make it better suited for nutritional, animal feed, and
industrial uses.
To increase the value of soybean oil, we have undertaken
to identify genes for novel fatty acid modifying enzymes
from non-agronomic plant species. These genes can then
be transgenically expressed in soybean seeds to produce
oils with enhanced properties, particularly for industrial
applications. We have identified a number of "new"
enzymes. These include enzymes that are referred to as
"fatty acid conjugases," which generate conjugated double
bonds in fatty acid substrates. Fatty acid conjugase genes
that we have isolated from plants such as Momordica charantia
and Calendula officinalis have been expressed in soybean
seeds to produce oils with improved properties as drying
agents in paints, inks, and varnishes. More recently, we
have identified a divergent cytochrome P450 from
Euphorbia lagascae that introduces epoxy groups in fatty
acids. Expression of this enzyme in soybean seeds
resulted in the production of epoxidized oils that
potentially can be used in plasticizers, adhesives,
and paints.
Oil comprises nearly
20 percent of the
weight of soybean
seeds. The fatty acid
composition of the oil
can be genetically
modified to enhance
the nutritional,
animal feed, and
industrial uses of
the seed.
Current research is directed towards identifying
biochemical factors that limit the accumulation and
proper metabolism of novel fatty acids in transgenic
soybeans to engineer high levels of novel fatty acids in
soybean seed oils. We are also exploring approaches for
improved identity preservation of transgenic soybeans,
particularly those with improved industrial properties.
With the development of these transgenic soybeans there
will be an increased need to segregate seeds for food use
from those destined for non-food use. Research has been
initiated to alter the seed coat color of soybeans as a
means of readily distinguishing seeds engineered with
non-food traits.
Recent Publications
22
Cahoon EB, Ripp KG, Hall SE, McGonigle B. 2002. Transgenic production
of epoxy fatty acids by expression of a cytochrome P450 enzyme from
Euphorbia lagascae seed. Plant Physiol 128:615-624.
Cahoon EB, Shanklin J. 2000. Substrate-dependent mutant complementation
to select fatty acid desaturase variants for metabolic engineering of plant seed oils.
Cahoon EB, Ripp KG, Hall SE, Kinney AJ. 2001. Formation of conjugated
∆8, ∆10 double bonds by ∆12-oleic acid desaturase related enzymes:
biosynthetic origin of calendic acid. J Biol Chem 276:2637-2643.
Cahoon EB, Marrillia EF, Stecca KL, Hall SE, Taylor DC, Kinney AJ. 2000.
Production of fatty acid components of meadowfoam oil in somatic soybean
embryos. Plant Physiol 124:243-251.
Cahoon EB, Carlson TJ, Ripp KG, Schweiger BJ, Cook GA, Hall SE, Kinney AJ.
1999. Biosynthetic origin of conjugated double bonds: production of fatty acid
components of high-value drying oils in transgenic soybean embryos. P Natl Acad
Sci USA 96:12935-12940.
Eliot Herman, Ph.D.
U.S. Department of Agriculture, Agricultural Research Service
My research program focuses primarily on modifying soybean proteins to improve
composition, produce novel products, and reduce allergenicity.
The primary focus of my research program is producing
modifications of soybean proteins to improve composition,
produce novel products, and reduce allergenicity. This will
increase soybean utilization as both food and feed. Parallel
objectives are to investigate the control and regulation of
protein expression and accumulation, including collateral gene
expression as the consequence of genetic modification. My
laboratory has additional secondary projects that include two
broad investigations with multi-institutional interactions.
These projects include one focusing on the gene expression
and cell biology of plants exposed to subfreezing
temperatures and another on dinoflagellate genomics.
A
B
Immunogold assay of P34 cross-reactive
proteins in a suppressed and nonsuppressed
line. Figure A: abundant P34 label in a late
maturation cell of a control soybean. Figure B: a
transgenic cell in which P34 accumulation was
suppressed. The morphology of the protein
storage compartment, which contains P34, is
identical in both types of cells, indicating that P34
suppression does not alter the formation or
structure of the seed protein storage compartment.
The immunodominant human allergen of soybean seeds is
a cysteine protease family member called P34 or Gly m Bd
30K. P34 is accumulated at high levels in maturing seeds and
in small quantities in vegetative tissues, where it may have a
pathogen-resistance role. Among cysteine proteases, P34 is
unique in possessing a glycine substitution for an otherwise
invariant cysteine in the active site. Among soybean sensitive
people, P34 accounts for a large majority of IgE crossreactivity. Soybean sensitivity is also widespread among
farmed animals ranging from pigs to salmon. Human IgE
binding epitopes have been mapped, and the allergenic
epitopes consist of fourteen distinct sites.
A seed-specific silencing of P34 has been achieved, and
homozygous lines completely lacking P34 are now growing in
field tests. P34-silenced soybean seeds have identical protein
composition and protein/oil ratios compared to the wild
type. The P34-silenced lines grow normally and are
apparently identical to the wild type in the development of
the plant and in the formation of the seed. The protein
storage vacuoles that would sequester the P34 protein are not
altered in the silenced line. Proteomic analysis of the P34silenced line in comparison with the wild type demonstrates
there are no other collateral changes in protein composition in
response to P34 suppression. These results show that it is
feasible to use biotechnology to suppress a major human
allergen in crops, implying that widespread use of this
approach can improve the safety of food for sensitive people.
Lab Member:
Kelsi Scott, Lab Manager
Recent Publications
Hinz G, Herman EM. Sorting of storage proteins in the plant golgi apparatus.
In: Robinson D, editor. Plant golgi apparatus. Sheffield, England: Sheffield
Academic Press (in press).
Kinney AJ, Jung R, Herman EM. 2001. Cosuppression of the subunits of
∝-conglycinin in transgenic soybean seeds induces the formation of endoplasmic
reticulum-derived protein bodies. Plant Cell 13:1165-1178.
Okinaka Y, Yang CH, Herman EM, Kinney A, Keen T. The P34 syringolide
elicitor receptor interacts with a soybean photorespiration enzyme NADH
dependent hydroxypyruvate reductase. Plant Mol Microbe Interact (in press).
Chrispeels MJ, Herman EM. 2000. UPDATE-ER-derived compartments function
in storage and as mediators of vacuolar remodeling via a new type of organelle,
precursor protease vesicles (PPV). Plant Physiol 123:1227-1233.
Nielsen N, Herman EM. The future prospects for broadening soybean
utilization by altering glycinin. In: Renard D, Valle GD, Popineau Y, editors.
Plant biopolymer science. Cambridge, UK: Royal Society of Chemistry;
2002. p 13-23.
23
Jan Jaworski, Ph.D.
We investigate the biosynthetic pathways involved with seed oil biosynthesis
with an eye toward oils with useful applications.
Fatty acid elongation: The purpose of this research area
Plants accumulate oil in their seeds to provide both the
is to conduct a structure-function analysis of condensing
energy and carbon necessary for a germinating seed to
enzymes involved in fatty acid elongation to better
grow into a plant. Seeds from crops are a rich source of
understand their catalysis and substrate specificity. This
edible vegetable oils. However, nature has provided the
class of enzymes, also referred to as 3-ketoacyl-CoA
plant kingdom with a broad assortment of oil
synthases (KCS), initiates the series
compositions, and some unusual oils
of reactions that lead to the twomay have useful industrial
carbon extension of fatty acids. We
applications. A major challenge
have engineered the membraneis to identify the genes responsible
bound KCS with an N-terminal Hisfor producing unusual oils that can
Tag and developed a yeast expression
be used to produce a transgenic crop
system that generates a fully active
capable of synthesizing large
KCS. Using this easily purified
quantities of the oil. The Jaworski
enzyme for mechanistic and substrate
lab focuses on research that will
specificity studies, we have concluded
lead to a better understanding of
that the membrane-bound KCS
pathways involved with oil
appears to be most closely related
biosynthesis as well as of some
to
the soluble condensing enzyme
of the enzymes used.
Fatty acid and oil biosynthesis in seeds is a
chalcone synthase. Using a similar
complex process taking place in several parts
Modification of seed oil
of the cell.
approach, we are analyzing the
composition: This research is part
substrate specificity and catalytic
of an ambitious project, funded by The Dow Chemical
capacity of several KCS homologs.
Company, with participation by its affiliate Dow Agro
Sciences LLC, designed to solve the basic challenges of
modifying oilseeds. A key aspect of this research
Lab Members:
initiative is to obtain genes that will allow the production
Lin Chen, Ph.D., Post Doctoral Associate
of unusual fatty acids in common crops such as soybean.
Fan Deng, Ph.D., Post Doctoral Fellow
We have also extended our capabilities to analyze
Jixiang Han, Ph.D., Post Doctoral Associate
intermediates of fatty acid metabolism using highJia Li, Lab Technician
performance liquid chromatography coupled with
Shirley Ng, Research Associate
fluorescence and mass spectrometric detectors.
Janet Oriatti
Recent Publications
Blacklock BJ, Jaworski JG. 2002. Studies into factors contributing to
substrate specificity of membrane-bound 3-ketoacyl-CoA synthases.
Eur J Biochem 269:4789-4798.
Ghanevati M, Jaworski JG. 2001. Active-site residues of a plant
membrane-bound fatty acid elongase ß-ketoacyl-CoA synthase, FAE1 KCS.
Biochim Biophys Acta 1530:77-85.
Ghanevati M, Jaworski JG. 2002. Engineering and mechanistic studies of
Arabidopsis FAE1 ß-ketoacyl-CoA synthase, FAE1 KCS. Eur J Biochem
Dehesh K, Tai H, Edwards P, Jaworski JG. 2000. Overexpression of
3-ketoacyl-acyl carrier protein synthase IIIs (KAS III) reduces the rate of
lipid synthesis. Plant Physiol 125:ll03-1114.
269:3531-3539.
24
Todd J, Post-Beittenmiller D, Jaworski JG. 1999. KCS1 encodes a fatty acid
elongase 3-ketoacyl-CoA synthase affecting wax biosynthesis in Arabidopsis
thaliana. Plant J 17:119-130.
Joseph Jez, Ph.D.
Assistant Member and Principal Investigator
The goal of my research is the investigation of the molecular basis of
natural product biosynthesis and plant hormone signaling.
The goal of my research is the integration of biochemistry,
protein engineering, and X-ray crystallography to investigate
the molecular basis of biological processes in plants with
emphasis on natural product biosynthesis and plant
hormone signaling.
Molecular basis of natural product biosynthesis: Plants
are amazing chemists capable of generating an arsenal of
secondary metabolites with a wide range of biological
activities. Understanding the biosynthesis of these
compounds at a structural and mechanistic level forms the
basis for manipulating their assembly. Currently, we are
focusing on phytochelatins and flavonoids.
Phytochelatins are glutathione-derived peptides essential
for heavy-metal tolerance in plants. As the enzyme that
generates these protective compounds, phytochelatin synthase
is an attractive target for crystallographic and protein
engineering studies aimed at elucidating the molecular basis
for generation of phytochelatins and manipulating their
production. The ability to create improved or novel
phytochelatins may lead to a system for plant-based
heavy-metal detoxification of soils.
Structural biology of plant hormone responses: The plant
hormone auxin controls a variety of growth and developmental
processes. The current model for the auxin-response is that
Aux/IAA proteins repress the auxin-response pathway by
negatively regulating auxin-response factors (ARFs),
transcription factors that bind to auxin-response elements
(AREs). Auxin promotes the ubiquitination of Aux/IAA
proteins by targeting them to the SCFTIR1 ubiquitin-ligase.
Subsequent degradation of Aux/IAA proteins results in
activation of ARFs and de-repression of genes involved in
auxin-mediated growth and development. The overall aim of
this project is to develop a structural perspective of how the
auxin response is regulated, investigating the nature of the
Aux/IAA protein–ARF interaction that represses expression
of auxin-response genes, characterizing specific interactions
between Aux/IAA proteins, ARFs, and/or both types of
protein, and studying the recognition of AREs by ARFs.
Plant and bacterial
polyketide synthases
generate diverse natural
products by modulating
the size of the active site
cavities of these enzymes
to generate compounds
like chalcones (top), used
as precursors for floral
pigments, and methylpyrones (bottom), which
form the backbone of
anti-pathogen glucosides.
Plants use flavonoids as floral pigments, inducers of Rhizobium
nodulation genes, and anti-microbial phytoalexins. Chalcone
synthase (CHS) and chalcone reductase (CHR) represent a
branch point in flavonoid biosynthesis. Despite extensive
structural and biochemical studies, the interplay between
CHS and CHR remains poorly understood. By isolating and
characterizing the acyl-enzyme and CoA intermediates of
CHS by quench-flow methods, mass spectroscopy, and X-ray
crystallography, we will develop a detailed understanding of
the individual steps in the reaction pathway.
Recent Publications
Jez JM, Bowman ME, Noel JP. 2002. Expanding the biosynthetic repertoire
of type III polyketide synthases by altering starter molecule specificity.
Jez JM, Bowman ME, Noel JP. 2001. Structure-guided programming of
polyketide chain-length determination in chalcone synthase. Biochemistry
49:14829-14838.
Jez JM, Bowman ME, Dixon RA, Noel JP. 2000. Structure and mechanism of
the evolutionarily unique plant enzyme chalcone isomerase. Nature Struct Biol
7:786-791.
Ferrer J-L, Jez JM, Bowman ME, Dixon RA, Noel JP. 1999. Structure of
chalcone synthase and the molecular basis of plant polyketide biosynthesis.
Nature Struct Biol 6:775-784.
Jez JM, Austin MB, Ferrer J-L, Bowman ME, Schröder J, Noel JP. 2000.
Structural control of polyketide formation in plant-specific polyketide
synthases. Chem Biol 7:919-930.
25
Erik Nielsen, Ph.D.
My laboratory focuses on the analysis of regulatory molecules involved in
deposition of cell walls in plants.
The long-term goal of this research project is to study
how membrane trafficking events are involved in proper
deposition of plant cell wall components at the molecular
level. Plant cell walls are comprised of a complex mixture
of polysaccharides, lignin, suberin, waxes, and proteins.
The cell wall provides mechanical support for the plant
and serves as the interface to neighboring cells and the
environment. Because the majority of a plant’s biomass is
accumulated in cell walls, understanding how carbohydrates
are incorporated into this structure has important
ramifications for the use of plants as a source of biofuels
and in food-based applications. Despite this importance,
there is still little understanding of the nature and
organization of the membrane trafficking pathways
in plants responsible for sorting and delivery of cell
wall components from Golgi complexes to the
plasma membrane.
A
B
C
D
To begin studies of the post-Golgi membrane trafficking
pathways involved in secretion of cell wall components
in plants, we focused on the potential roles of Rab
GTPases, a class of regulatory molecules that control
membrane trafficking events in eukaryotic cells.
Specifically, we have begun characterization of the
intracellular distribution of an Arabidopsis thaliana
Rab GTPase, AtRabA4b. AtRabA4b shares significant
similarity to Rab GTPases that control post-Golgi
trafficking pathways in both yeast and mammals and to
plant Rab GTPases that are up-regulated in rapidly
expanding plant tissues. Using fluorescence microscopy
techniques we have determined that this plant Rab
GTPase accumulates to a high degree at the tip of
growing root hair cells, an area to which expansion and
hence secretion of cell wall components is restricted.
Based on this data, our current working hypothesis is that
AtRabA4b labels a membrane compartment involved in
delivery of cell wall components to the plasma membrane
in root hair cells. The aims of this project are (i) to
further characterize the role of the AtRabA4b-labeled
compartment in tip-based growth in the root hair cell
and cell expansion in other cell types in plants and (ii) to
identify other plant proteins that either interact directly
with AtRabA4b, or indirectly by way of trafficking
through the AtRabA4b compartment.
Lab Members:
Root hair cells of A. thaliana seedlings expressing
EYFP-AtRabA4b (A, C), or EYFP-AtRabF2a (B, D) were
imaged either with transmitted light (A, B) or with
epi-fluorescence illumination (C, D). EYFP-AtRabA4b
localized to the tips of root hair cells (A, C; arrows).
In contrast, EYFP-AtRabF2a distributed randomly in
these cells (D, arrows).
Adita Akbani, Ph.D., Research Assistant
Mario Izaguire, Graduate Student
Mary Preuss, Ph.D., Post Doctoral Associate
Aaron Schmitz, Lab Technician
Jannie Serna, Lab Technician
Julie Strandquist, Summer Intern
Hankuil Yi, Graduate Student
Recent Publications
Vernoud V, Horton AC, Yang Z, Nielsen E. 2002. Analysis of the small
GTPase gene family of Arabidopsis thaliana. Plant Physiol (in press).
Nielsen E, Severin F, Hyman AA, Zerial M. In vitro reconstitution of
endosome motility on microtubules. In: Vernos I, editor. Methods in
molecular biology. Totowa, NJ: Humana Press, Inc; 2001. p 135-146.
Nielsen E, Christoforidis S, Uttenweiler-Joseph S, Miaczynska M, Dewitte F,
Wilm M, Hoflack B, Zerial M. 2000. Rabenosyn-5, a novel Rab5 effector,
is complexed with hVPS45, and is recruited to endosomes through a
FYVE-finger domain. J Cell Biol 151:601-612.
Sönnichsen B, De Renzis S, Nielsen E, Rietdorf J, Zerial M. 2000. Distinct
membrane domains in the endosomal recycling pathway visualized by
multi-color imaging of Rab4, 5, and 11. J Cell Biol 149:901-913.
Nielsen E, Severin F, Backer JM, Hyman AA, Zerial M. 1999. Rab5 regulates
motility of early endosomes on microtubules. Nature Cell Biol 1:376-382.
26
Mark Running, Ph.D.
Meristems are the undifferentiated tissues that allow plants to adapt their forms to the
environment; our lab investigates the signaling processes responsible for meristem function.
Plants of the same species can vary markedly in their
appearance depending on the environment in which they
are grown: the numbers and positions of branches, leaves,
and flowers, the length and thickness of the stem, and the
depth and complexity of the root system are all signs of
the plant adapting its form to its environment. This reflects
a developmental flexibility not seen in animals such as
mammals, where the basic body plan is laid down early in
embryogenesis. What allows for this flexibility is the presence
of meristems, the study of which is the focus of the research
in my lab.
One mutant of particular interest, pluripetala (plp), showed
more meristem activity in leaves. These plants also showed
signs of altered native meristem function, such as shorter
stems, misplaced stems, extra flowers, and extra flower parts.
The PLP gene encodes a key protein involved in protein
prenylation, a post-translational lipid modification that aids
in membrane localization, particularly of signal transduction
proteins. Our efforts now are in identifying the signaling
pathways in which the PLP gene acts and in determining the
relationship of these pathways with other genes regulating
meristem function.
Meristems are simple in structure, typically composed of
small, undifferentiated cells with a uniform appearance. Each
meristem must integrate a wide variety of environmental and
genetic cues to initiate organs and stems in specific patterns,
while relying on internal signals to stably maintain a constant
number of cells for future growth. The goal of the research
in my laboratory is to understand the signaling processes
responsible for meristem function.
We designed a genetic screen to rapidly identify novel
mutants in genes that are critical for meristem activity in
the model plant Arabidopsis thaliana. We first induced
the formation of meristems in leaves, and then looked
for mutants that affect the function of these meristems.
We have found many mutants that showed either increased
or decreased meristem activity in the leaves and are
characterizing the role of the corresponding genes
in meristem function.
The pluripetala gene acts together with other genes to
limit meristem cell division. Instead of a normal stem,
shown at left, the pluripetala clavata3 double mutant
plant produces a huge mass of bunched flowers from its
overactive meristem.
Lab Members:
Kevin Lehnbeuter, Lab Technician
Qin Zeng, Post Doctoral Associate
Julie Plocher, Summer Intern
Recent Publications
Running MP. 2001. Nuclear staining for confocal microscopy. In: Weigel
D, Glazebrook J, editors. Arabidopsis: a laboratory manual. Cold Spring
Harbor: Cold Spring Laboratory Press. p 100-103.
Fletcher JC, Brand U, Running MP, Simon R, Meyerowitz EM. 1999. CLAVATA3 communicates cell fate decisions in the Arabidopsis shoot meristem.
Science 283:1911-1914.
Running MP, Hake S. 2001. The role of floral meristems in patterning.
Curr Op Plant Biol 4:69-74.
Jacobsen SE, Running MP, Meyerowitz EM. 1999. Disruption of an RNA
Helicase/RNAse III homologue in Arabidopsis causes unregulated cell division in
floral meristems. Development 126:5231-5243.
Running MP, Scanlon M, Sinha N. 2000. Maize genetics 2000 – and
beyond. Plant Cell 12:829-835.
27
Daniel Schachtman, Ph.D.
The overall focus of the Schachtman laboratory is to understand the mechanisms that roots
use to regulate mineral uptake from soils and to sense changes in soil conditions.
To understand mineral acquisition in plant roots, we have
been studying the physiological function and structural
biology of membrane transport proteins in plant cell
membranes. At present, we are focusing on a family of
potassium transporters (KUP/KT/HAK) and on a
family of zinc transporters (ZIP). Our work on the
KUP transporters is aimed at understanding the function
of each member of the family. Future work on zinc
transporters will be aimed at understanding how protein
structure determines functional characteristics such as
zinc and cadmium selectivity.
Roots not only take up minerals from soil, they also
are very sensitive monitors of soil conditions. When
nutrients are deficient in the soil, roots must employ
various strategies to ensure that plants obtain sufficient
amounts of minerals for growth. To understand signal
transduction pathways and the regulation of gene
expression under nutrient deficiency, we have initiated
microarray analysis, which we hope will provide an
entry point for understanding how roots sense
potassium deficiency.
Under conditions of water deficit, roots transmit
signals to leaves, which in turn reduce water usage. To
understand more about the identity and transport of
the long distance signals that plant roots transmit to
shoots, we have embarked on a collaborative genomics
project with groups at the University of Illinois at
Urbana-Champaign and the University of MissouriColumbia. We will profile a range of metabolites and
the proteins in xylem sap in search of novel signals; we
will also study gene expression profiles in the roots
that are sending the signals.
Lab Members:
Sung-ju Ahn, Ph.D., Post Doctoral Associate
Laura Ernst, Summer Intern
Ellen Marsh, Research Associate
Carolyn Neal, Lab Technician II
Ryoung Shin, Ph.D., Post Doctoral Associate
Cathy Kromer
"Root System of Prairie Plants" by Heidi Natura.
© 1995 Conservation Research Institute.
Recent Publications
Ramesh S, Eide DJ, Schachtman DP. 2003. Differential metal selectivity
and gene expression of two zinc transporters from rice (submitted).
Storey R, Schachtman DP, Thomas MR. 2003. Root structure and
cellular chloride, sodium and potassium distribution in salinized grapevines.
Plant Cell Environ (in press).
Amtmann A, Fischer M, Marsh EL, Stefanovic A, Sanders D, Schachtman
DP. 2001. The wheat cDNA LCT1 generates hypersensitivity to sodium
in a salt-sensitive yeast strain. Plant Physiol 126:1061-1071.
Liu W , Fairbairn DJ, Reid RJ, Schachtman DP. 2001. Characterization
of two HKT1 homologues from Eucalyptus camaldulensis that display intrinsic
osmosensing capability. Plant Physiol 127:283-294.
Schachtman DP. 2000. Molecular insights into the structure and function
of plant K+ transport mechanisms. BBA-Biomembranes 1465:127-139.
28
Jeffrey Skolnick, Ph.D.
In the Laboratory of Computational Genomics, we develop computational
tools for predicting protein function from sequence.
The Laboratory of Computational Genomics develops
computational tools used for comparing and interpreting the
sequence information generated by genome sequencing
projects. The tools we create are algorithms for predicting
protein function from sequence, including both ab initio
folding and threading methods. Our ab initio folding
approaches are capable of predicting low resolution structures
for a substantial fraction of small, single domain proteins,
and our threading algorithms can assign structures to at least
half of the sequences in an average genome. We can use
these predicted structures to assign biochemical function,
to dock ligands to identify the binding site, to predict
protein-protein interactions, and to assign the proteins to
known pathways.
A unified approach to protein structure prediction:
Our group has developed a unified methodology, TOUCHSTONE, to predict protein structure from sequences. The
methodology uses a newly developed, iterative threading
algorithm called PROSPECTOR. If there is no significant
match to a template structure, the predicted consensus
contacts and secondary structure extracted from the top
twenty scoring structures are used as restraints in ab initio
folding. On average, about one-third of the contacts are
correctly predicted and seventy-five percent are correctly
predicted within two residues. Application to a representative
test set of sixty-five proteins gives the native state in one of
the well-defined clusters in fifty-one cases. We have also
predicted the tertiary structure of all the small proteins in
the M. genitalium genome.
Conversely, if a global template is identified by PROSPECTOR,
then a generalized comparative modeling approach called
GeneComp uses the template alignment and predicted contacts
and secondary structure (not necessarily from the template
structure) as restraints in the ab initio folding algorithm.
We have also extended PROSPECTOR to predict multimeric
interactions, and the resulting method seems to be quite robust,
predicting over 2,100 dimeric complexes in the yeast genome,
500 of which have been experimentally observed. We have also
developed a methodology to assign proteins to known pathways.
Lab Members:
Adrian Arakaki, Ph.D., Research Fellow
Marcos Betancourt, Ph.D., Assistant Domain Member
Eckart Bindewald, Ph.D., Post Doctoral Associate
Michal Boniecki, Graduate Student
Dominik Gront, Graduate Student
Daisuke Kihara, Ph.D., Senior Post Doctoral Associate
Michal Kolinski, Web Master
Andrzej Kolinski, Ph.D., Domain Member
Wei Li, Ph.D., Post Doctoral Associate
Hui Lu, Ph.D., Post Doctoral Associate
Long Lu, Graduate Student
Piotr Pokarowski, Ph.D., Post Doctoral Assistant
Andras Szilagyi, Ph.D., Post Doctoral Associate
Weidong Tian, Graduate Student
Jorge Vinals, Ph.D., Visiting Scientist
Prince Xavier, Ph.D., Research Associate
Xiequn Xu, Ph.D., Post Doctoral Associate
Yang Zhang, Ph.D., Post Doctoral Associate
Julie Heger
In September 2002, Dr. Skolnick accepted a position as director
of the Center for Excellence in Bioinformatics at the University of
Buffalo, a campus of the State University of New York.
Recent Publications
Vinals J, Kolinski A, Skolnick J. 2002. Numerical study of the entropy
loss of dimerization and the folding thermodynamics of the GCN4
leucine zipper. Biophys J 83(5):2801-2811.
Lu L, Lu H, Skolnick J. 2002. MULTIPROSPECTOR: An algorithm
for the prediction of protein-protein interactions by multimeric
threading. Proteins 49(3):350-364.
Skolnick J, Kolinski A. 2002. A unified approach to the prediction of protein
structure and function. Adv Chem Phys 120:192-201.
Zhang Y, Kihara D, Skolnick J. 2002. Local energy landscape flattening:
Parallel hyperbolic Monte Carlo sampling of protein folding. Proteins
48(2):192-201
Sikorski A, Kolinski A, Skolnick J. 2002. Computer simulations of
protein folding with a small number of distance restraints. Acta Biochim
Pol 49(3):683-692.
29
Thomas Smith, Ph.D.
My laboratory is interested in a number of different projects
using crystallography to elucidate the biological functions of proteins.
The Smith laboratory is currently involved with several
projects that combine crystallography with biochemistry
and other biophysical techniques to investigate the
biological functions of proteins.
alterations, to perform complex regulatory functions in
higher-order organisms. Further evolutionary analyses
will help us understand the metabolic role of GDH in
the various kingdoms.
Human rhinovirus: To understand the mechanism of
antibody-mediated neutralization of viruses, we have
determined the structures of several neutralizing
antibodies and antibody/virus complexes and have used
mass spectroscopy to monitor the dynamic processes
involved in the release of the viral genome into the target
cell. These studies have the potential of facilitating the
development of synthetic vaccines as well as changing the
way we view the early steps in the viral infection process.
Fungal toxins: We have been examining the structure and
mechanism of action of several fungal toxins. In the case
of the toxin KP4, we have shown that cAMP abrogates
KP4 effects, suggesting that KP4 affects calcium gradient
dependent signal transduction pathways. Such studies
may allow for development of products that protect
against fungal infections. It may be possible to reduce
the contamination of grains by fungi that produce
cancer-causing anaphlatoxins.
Glutamate dehydrogenase (GDH): Found in all
organisms, GDH catalyzes the reversible oxidative
deamination of L-glutamate to 2-oxoglutarate. We have
continued to use crystallography to identify the location
of the allosteric regulators and better understand the
structural mechanism of their control. From structural
and genomic information, we have found that this
ancient enzyme evolved, through relatively small
Insect transmission of plant viruses: Cucumber mosaic
virus (CMV) is transmitted by aphids in a “nonpersistent”
manner—it does not circulate or replicate in the aphid.
We have determined the structure of this virus and of
the virus complexed with antibodies raised against the
transmission loop. Better understanding of the structural
mechanism of insect transmission of viruses will lead to
better protection of plants against viral infection.
Shown here is an cryo-electron
microscopy image reconstruction of
cucumber mosaic virus (CMV) bound
with antibodies to the aphid transmission site. The background is a portion
of the raw data used for the
reconstruction. The reconstruction is
shown in the middle where the virus is
colored gray and the antibody is
green. The image on the lower right
is a representation of a portion of the
virus with the antibody contact area
highlighted in white.
Lab Members:
Aron Allen, Lab Technician
Soojay Banerjee, Ph.D., Research Scientist
Umesh Katpally, Graduate Student
Ming Li, Ph.D., Research Associate
Steven Sarfaty, Lab Technician
Baoxian Wei, Ph.D., Research Associate
Joni Patton
Recent Publications
Bowman VD, Chase ES, Franz AWE, Chipman PR, Zhang X, Perry KL,
Baker TS, Smith TJ. 2002. An antibody to the putative aphid recognition
site on cucumber mosaic virus recognizes pentons but not hexons. J Virol
Smith TJ, Schmidt T, Fang J, Wu J, Siuzdak G, Stanley C. 2002. The structure
of apo human glutamate dehydrogenase details subunit communication and
allostery. J Mol Biol 318:765-777.
76:12250-12258.
Smith TJ, Chase E, Schmidt T, Perry K. 2000. The structure of cucumber
mosaic virus and comparison to cowpea chlorotic mottle virus. J Virol 74:
7578-7586.
Gage MJ, Rane SG, Hockerman GH, Smith TJ. 2002. The virally encoded
fungal toxin KP4 specifically blocks L-type voltage-gated calcium channels.
Mol Pharmacol 61:936-944.
30
Smith TJ, Chase ES, Schmidt TJ, Olson NH, Baker TS. 1996. Neutralizing
antibody to human rhinovirus penetrates the receptor-binding canyon. Nature
(London) 383:350-354.
Christopher Taylor, Ph.D.
Data obtained from our work will lead to a better understanding
of how nematodes feed and new methods for nematode control.
Plant parasitic nematodes are among the most destructive
plant pathogens, causing losses exceeding $77 billion annually
to twenty-one agronomic crops worldwide. Of these plant
parasitic nematodes, root-knot nematodes (Meloidogyne spp.) are
capable of reproducing on over 2,000 species of plants and
are responsible for approximately fifty percent of the overall
nematode damage. Symptoms of plant infestation by
root-knot nematodes may include knot- or gall-like
formations on the roots. These knots, or galls, inhibit the
ability of the root to uptake nutrients and water.
Microscopic analysis of root-knot nematode feeding sites:
To determine if Arabidopsis is a good model for examining
giant cells and the role of transport proteins in nematode
feeding and nutrition, we determined whether Arabidopsis
giant cells contain all of the hallmarks of giant cells found
in previously studied crop plants. Giant cells were examined
using both light and transmission electron microscopy. The
isolated Arabidopsis giant cells showed all the classic hallmarks
of nematode-induced giant cells. Giant cells were large
(Figure 1.A), had thickened and highly invaginated cell wall
labyrinths (Figure 1.B), were multinucleated (Figure 1.D), and
were filled with dense cytoplasm. Additionally, several feeding tube structures (Figure 1.C) were found.
Molecular analysis of root-knot nematode feeding sites:
Analysis of gene expression during root-knot nematode
infestation was initiated using microarrays. RNA was
isolated from one-, two-, and four-week-infested Arabidopsis
roots and used as a probe on the 24,000-gene chip produced
by Affymetrix. Analysis of the expression data showed that
genes associated with cell cycle, cell wall generation, hormone
production and sensing, amino acid and protein biosynthesis,
transcription, signal transduction, and transport of small
molecules were up-regulated.
B
C
A
D
Root-knot nematode
in Arabidopsis root
prepared by high
pressure freezing and
freeze substitution.
Figure A: thick plastic
section of nematode
feeding site. Giant cells
(GC) and nematode (N)
are shown. TEM
pictures: Figure B:
transfer cell wall
labyrinth (CW) of giant
cell (marked by arrow);
Figure C: transverse
section of feeding tube
(FT); Figure D: numerous
nuclei (N) of a giant cell.
Using a variety of techniques (including gene knockouts,
RNA interference, and application of specific inhibitors) we
will investigate the role of those genes associated with the
biosynthesis and transport of small molecules. Data
obtained from these experiments will lead to a better
understanding of how nematodes feed and new methods
for nematode control.
Lab Members:
Byron Bertagnolli, Lab Assistant
Beth Burgwyn, Ph.D., Post Doctoral Associate
Ray Collier, Research Technician II
James Collins, Summer Intern
Lily Gavilano, Ph.D., Visiting Scientist
Ulrich Hammes, Ph.D., Post Doctoral Associate
Kevin Lutke, Lab Technician
Nathalie Walter, Lab Assistant
Recent Publications
Opperman CH, Acedo GN, Skantar AM, Saravitz DM, Song W , Taylor CG,
Conkling MA. 1994. Bioengineering resistance to sedentary endoparasitic
nematodes. In: Bird DM, DiGiorgio C, Lamberti F, editors. Advances in
molecular plant nematology. New York: Plenum. p 221-230.
Yamamoto YT, Taylor CG, Acedo GN, Cheng CL, Conkling MA. 1991.
Characterization of cis-acting sequences regulating root-specific gene expression
in tobacco. Plant Cell 3:371-382.
Opperman CH, Taylor CG, Conkling MA. 1994. Root-knot nematodedirected expression of a plant root-specific gene. Science 263:221-223.
31
Yiji Xia, Ph.D.
Our study of aspartic proteases will provide novel insights into molecular
mechanisms underlying many important biological processes in plants.
Aspartic protease is one of five classes of endopeptidases
and has been implicated in regulating a wide range of
biological pathways, including processing of peptide
prohormones, receptors, and other regulatory proteins.
In yeast and animals, aspartic proteases usually comprise
a small gene family of eight to fourteen members.
In contrast, we have identified sixty-six putative aspartic
protease genes through analysis of Arabidopsis genome
sequences. The disproportional expansion of this family
in plants suggests that aspartic proteases might play
important roles in a wide variety of developmental and
physiological processes unique to plants. This notion has
been supported by the identification of the CDR1 and
CDS1 genes and our preliminary phenotype characterization of T-DNA insertion mutants of over thirty aspartic
protease genes in Arabidopsis (atasp).
CDR1 encodes an apoplastic aspartic protease. CDR1
was identified through analysis of a gain-of-function
mutant (cdr1-D) which was originally isolated through
a genetic screen of activation-tagged Arabidopsis lines
by its enhanced resistance to infection by a virulent
Pseudomonas syringae strain. The mutant phenotype is
caused by hyper-activation of the CDR1 gene by the
35S enhancer. Suppression of CDR1 using antisense
technology resulted in reduced resistance to infection by
P. syringae strains. Preliminary molecular characterization
suggests that CDR1 generates an endogenous peptide
signal that mediates local and systemic disease
resistance pathways.
cds1-D is another gain-of-function mutant isolated
from the same screen in which cdr1-D was identified.
In contrast to cdr1-D, cds1-D exhibited enhanced
susceptibility to infection by the virulent P. syringae
strains. The cloned CDS1 gene encodes another putative
aspartic protease. We have used GeneChip technology to
elucidate the gene networks regulated by CDR1/CDS1
and identified some candidate genes acting downstream of
the CDR1/CDS1-mediated defense response.
We have been taking a multidisciplinary approach to
determine the biological function of the other aspartic
protease genes in Arabidopsis. We have obtained T-DNA
insertion lines for over thirty AtASPs and have assigned
several AtASPs to different biological pathways. Our
long-term goal is to elucidate in detail the cellular and
physiological roles of the individual AtASPs. The study
will provide novel insights into molecular mechanisms
underlying many important biological processes in plants.
On left: Mutation in AtASP38
causes abortion of male gametophytes (the pollen grains that
stained gray). On right: Analysis
of the promoter activity of
AtASP38::GUS transgenic
Arabidopsis plants reveals that
AtASP38 expression is gametophyte specific. Shown is an
inflorescence from a transgenic
plant stained for the GUS activity.
Lab Members:
Charles Dietrich, Ph.D., Post Doctoral Associate
Michiyo Matsuno, Ph.D., Post Doctoral Associate
Ben Millett, Summer Intern
Jing Zhang, Research Associate
Recent Publications
Xia Y, Borevitz J, Blount J, Dixon R, Lamb C. 2002. Biopanning by
activation tagging. Recent Adv Phytochem 36 (in press).
Delledonne* M, Xia* Y, Dixon R, Lamb C. 1998. Nitric oxide functions as
a signal in plant disease resistance. Nature 394:585-588. *Joint first authors.
Borevitz* J, Xia* Y, Blount J, Dixon R, Lamb C. 2000. Activation tagging
identifies a conserved MYB regulator of phenylpropanoid biosynthesis.
Plant Cell 12:2383-2394. *Joint first authors.
Xia Y, Nikolau BJ, Schnable PS. 1997. Developmental and hormonal regulation
of the Arabidopsis CER2 gene which codes for a nuclear localized protein required
for the normal accumulation of cuticular waxes. Plant Physiol 115:925-937.
Xia Y, Nikolau BJ, Schnable PS. 1996. Cloning and characterization of CER2, an
Arabidopsis gene that affects cuticular wax accumulation. Plant Cell 8:1291-1304.
32
Liming Xiong, Ph.D.
Our laboratory is studying the mechanisms for stress signal transduction
in the model plant Arabidopsis.
Adverse environmental conditions such as drought and
extreme temperatures greatly impair crop productivity.
These environmental conditions are likely sensed by
specific receptors and are transmitted to cellular machinery
to activate adaptive responses. Our laboratory is interested in
understanding the mechanisms for stress signal transduction
in the model plant Arabidopsis. Knowledge gained in the study
may help us to devise better strategies for breeding crop
plants with increased tolerance to stress.
Drought tolerance: Drought occurs in virtually every
agriculture area. Yet, very little is known about how plants
deal with drought stress: genetic analysis of plant drought
stress responses is impeded by difficulties in manipulating
drought in a quantitative way and our limited awareness of
plant phenotypes specifically conferred by drought stress.
Recently we obtained Arabidopsis mutants that show altered
drought resistance and that will serve as useful tools for
further studying plant drought stress signal transduction
and drought tolerance.
Stress hormone-biosynthesis and signaling: The plant
hormone abscisic acid (ABA) regulates a wide range of
cellular processes including responses to environmental
stresses. ABA levels in plant cells remain low under nonstressful conditions but can increase dramatically during
seed maturation and in response to stresses, suggesting that
ABA biosynthesis is highly regulated. Nonetheless, very
little is known about the mechanism of this regulation.
The recent identification of genes that encode for ABA
biosynthesis enzymes offers an opportunity to understand
how ABA biosynthesis is modulated. Our study attempts
to reveal stress-signaling pathways that culminate in de novo
ABA biosynthesis.
Light the path for stress signals: To facilitate the
study of stress signal transduction, the mustard plant
Arabidopsis was engineered to express a stressinducible luminescence. These plants appear normal
but glow when stressed. The false color image in the
background shows cold-induced luminescence in a
population that contains both wild type (less bright
ones) and a mutant strain (brighter ones). The mutant
plants are defective in a gene that attenuates stress
signaling. These mutant seedlings also glow more
strongly when treated with the plant hormone abscisic
acid. The wild type (on the left) and mutant (on the
right) seedlings and the structure of abscisic acid are
superimposed on the image background.
Plant nutrient efficiency and tolerance to soil acidity: Low
soil fertility is a major constraint for crop production in
many developing countries. One of the major nutrients,
phosphorus, is of particularly low availability as a result of
high fixation in tropical and subtropical acidic soils.
Our laboratory uses a genetic approach to uncover processes
in roots that control phosphorus efficiency. Since
phosphorus efficiency and tolerance to high acidity are
closely linked traits, the study will shed light on mechanisms
of plant tolerance to soil acidity as well.
Recent Publications
Xiong LM, Shumaker KS, Zhu JK. 2002. Cell signaling during cold,
drought and salt stress. Plant Cell 14:S165-S183.
Xiong LM, Lee H, Ishitani M, Tanaka Y, Stevenson B, Koiwa H, Bressan
RA, Hasegawa PM, Zhu JK. 2002. Repression of stress-responsive genes
by FIERY2, a novel transcriptional regulator in Arabidopsis. P Natl Acad Sci
USA 99:10899-10904.
Xiong LM, Gong ZZ, Rock CD, Subramanian S, Guo Y, Xu WY, Galbraith
D, Zhu JK. 2001. Modulation of abscisic acid signal transduction and
biosynthesis by an Sm-like protein in Arabidopsis. Dev Cell 1:771-781.
Xiong LM, Ishitani M, Lee H, Zhu JK. 2001. The Arabidopsis LOS5/ABA3
locus encodes a molybdenum cofactor sulfurase and modulates cold and
osmotic stress-responsive gene expression. Plant Cell 13:2063-2083.
Xiong LM, Lee BH, Ishitani M, Lee H, Zhang CQ , Zhu JK. 2001. FIERY1
encoding an inositol polyphosphate 1-phosphatase is a negative regulator of
abscisic acid and stress signaling in Arabidopsis. Gene Dev 15:1971-1984.
33
Oliver Yu, Ph.D.
Our investigation of isoflavonoid biosynthesis will reveal mechanisms
of plant-microbe interactions at different levels.
Isoflavonoids play key roles in many plant-microbe
interactions. They are the major phytoalexins of
legumes that inhibit the growth of invading pathogens.
Isoflavones, together with other flavonoid compounds,
also serve as signal molecules and chemo-attractants for
symbiotic rhizobia. The isoflavonoids are synthesized
from a branch of the general phenylpropanoid pathway
that exists in all higher plants. In legumes, a cytochrome
P450 enzyme, isoflavone synthase (IFS), commits
flavonoid substrates to isoflavones. These isoflavones are
further metabolized to pterocarpans and other phytoalexins.
The transcriptional regulation and coordinate
expression of the isoflavonoid biosynthesis pathway is
under investigation. The promoter region of the IFS
gene from soybean was isolated, ligated to a reporter
gene, and transformed into soybean and Arabidopsis.
Observation of the transgenic plants demonstrated that
the IFS promoter had root-specific and defense-inducible
expression patterns. A putative DNA-binding protein
specific to a cis-element of the promoter has recently
been identified.
The structural enzymes in multi-step metabolic pathways
form large enzyme complexes called “metabolons.” These
metabolons promote the physical association of enzymes
and the direct exchange of substrates and products
between enzymes catalyzing sequential steps of a
metabolic pathway. The regulation of isoflavonoid
biosynthesis is governed by specific and controlled
interaction of the key enzymes. When a maize transcription
factor that specifically activates the transcription of the
maize phenylpropanoid pathway was ectopically expressed
in soybean seed, the isoflavonoid profiles of the transgenic
beans were altered significantly. One component of the
isoflavones, daidzein, was drastically increased while the
other component, genistein, was reduced to an
undetectable level. Current research is focusing on
how the maize transcription factor affects specific
associations between key pathway genes and leads to
altered isoflavone profiles.
The investigation of isoflavonoid biosynthesis will reveal
mechanisms of plant-microbe interactions at different
levels. This information will facilitate the metabolic
engineering of this important pathway in both soybean
and non-legume crops.
Lab Members:
Maria Gonzalez, Student
Zhenhua Guo, Ph.D., Post Doctoral Associate
Chris Menne, Research Assistant
Devin Nichols, Summer Intern
Lyle Ralston, Ph.D., Post Doctoral Associate
Senthil Subramanian, Ph.D., Post Doctoral Associate
Subcellular localization of IFS1::EYFP under control of the
CaMV 35S promoter, transiently expressed in tobacco epidermal cells. The IFS1::EYFP fusion is targeted to the cortical ER.
Recent Publications
34
Yu O, Shi J, Hession AO, Ellis S, Moghaddam M, Odell JT. 2002.
Maize C1 and R transcription factors alter the composition of seed
isoflavones in transgenic soybean. Nature Biotech (submitted).
Jung W , Yu O, Lau SMC, O’Keefe DP, Odell J, Fader G, McGonigle B. 2000.
Identification and expression of isoflavone synthase, the key enzyme for
biosynthesis of isoflavones in legumes. Nature Biotech 18:208-212.
Yu O, Jung WS, Shi J, Crose RA, Fader GM, McGonigle B, Odell JT.
2000. Production of the isoflavones genistein and daidzein in
non-legume dicot and monocot tissues. Plant Physiol 124:781-793.
Jung W , Yu O, Fader G, Odell J, McGonigle B. 1999. Nucleic acid fragments
encoding isoflavone synthase. WO 00/44909, US Patent 60/117769,
60/144783, 60/156094.
Brad Barbazuk, Ph.D.
Assistant Domain Member and Senior Bioinformatics Specialist
Our work
investigation
biosynthesis
will reveal
Our
aims ofto isoflavonoid
develop improved
strategies
for mechanisms
isolating of plant-microbe
interactions
at different
levels.of maize.
and
sequencing
the genes
Maize is both a classical genetic model for plant research
and an economically important crop. Sequencing the
maize genome will greatly influence our understanding of
the molecular basis of important agronomic traits, gene
regulation, genome evolution, plant development, and
biology. A consortium consisting of the Donald
Danforth Plant Science Center, The Institute for
Genomics Research (TIGR), Purdue University, and
Orion Ge-nomics has been awarded a National Science
Foundation (NSF) plant genome grant to develop and
evaluate high-throughput and robust strategies to isolate
and sequence maize genes.
Because the maize genome is exceptionally large and
nearly eighty percent consists of repetitive elements, the
consortium has proposed two strategies for targeting
gene-rich regions: methyl-filtration and high-Cot
selection. Methyl-filtration, a technique developed
at Cold Spring Harbor
Laboratory and licensed
to Orion Genomics,
exploits the finding that
the majority of
retrotransposon and
repetitive sequences
in maize are
methylated.
Propagating maize genomic clones in methyl-restrictive
hosts results in a library enriched for non-repetitive gene
sequences. High-Cot libraries produced by Professor
Jeff Bennetzen at Purdue University exploit the different
rates of re-annealing observed for maize genome sequences
originating from the abundant repetitive fraction versus
those representing the gene-rich regions. The High-cot
libraries specifically select the low abundance, gene-rich
regions. Clone sequencing, quality control, and sequence
processing is being performed by TIGR.
We are characterizing the collection of sequences
obtained by both methods for gene en-richment, gene
coverage, and biases. These methods may provide a costeffective alter-native to maize whole genome sequencing,
and we anticipate that this analysis will iden-tify the best
strategy for delivering a comprehensive genome resource
to the scientific community.
In traditional large-insert clone map based sequencing methods, the target
genome is cloned into large insert vectors (BACs, PACs) (A), which are
assembled into a fingerprint map. A minimally redundant set of clones is
selected and sequenced to completion. For maize, up to eighty percent
of the resultant sequence will be composed of retrotrans-posons and repetitive
DNA, and these sequences tend to be methylated. Reduced representation
methods, such as methyl-filtration (B), target gene-rich regions
Recent Publications
Chen M, et al. 2002. An integrated physical and genetic map of the
rice genome. Plant Cell 14:537-545.
The Genome International Sequencing Consortium. 2001. Initial
sequencing and analysis of the human genome. Nature 409:860-921
Hukriede N, et al. 2001. The LN54 radiation hybrid map of zebrafish
expressed sequences. Genome Res 11(12):2127-32.
Barbazuk WB, Korf I, Kadavi K, Heyen J, Tate S, Wun E, Bedell JA,
McPherson JD, Johnson SL. 2000. The syntenic relationship of the
zebrafish and human genomes. Genome Research 10:1351-1358.
The Genome International Sequencing Consortium. 2001. A physical
map of the human genome. Nature 409:934-41.
35
R. Howard Berg, Ph.D.
Director, Integrated Microscopy Facility
The Major Research Instrumentation program (MRI) of
the National Science Foundation funded a grant to the
Danforth Center to purchase an optical sectioning
microscope for live cell imaging. This instrument, a Zeiss
LSM 510 Meta NLO imaging workstation, can produce
3-D images of living cells by using either confocal or
multiphoton optical sectioning. The instrument has
argon, green HeNe, and red HeNe lasers for confocal
microscopy and a Coherent Mira 900F titanium-sapphire
laser for multiphoton excitation. The advantages of
multiphoton excitation include deeper imaging capability,
excitation using IR radiation, which is less harmful to
living tissue, and reduced phototoxicity.
TEM image of a Golgi stack
in high pressure-frozen/thin
sectioned material.
3-D reconstruction, from confocal
optical sections, of a tobacco BY-2
protoplast showing colocalization of
TMV viral proteins (green=Movement
Protein, blue=Coat Protein) and plant
ER (DsRed retained in the ER lumen) (in
collaboration with Sebastian Asurmendi
and Roger Beachy). To see this in a
rotating animation, go to www.danforthcenter.org/imf
The ability to excite many different fluorescent dyes
with a single multiphoton laser line is well matched with
the Zeiss system’s spectral imaging “Meta” detector.
This innovative detector uses a diffraction grating,
coupled with an array of thirty-two photomultiplier
tubes, to sort the emitted light according to wavelength
and produce an image whose individual pixels contain
spectral information. Computer algorithms extract the
location of each type of fluorescent molecule in the
sample by reference to the IR reference spectra. This
important advance opens the possibility of simultaneously
imaging up to eight different fluorescent proteins in one
living cell.
36
TEM image of nematode cytoplasm
in high pressure-frozen sample
from plant roots infected with the
nematode (in collaboration with
Chris Taylor).
To ease the work load on the multifunctional Zeiss
system, we have acquired a second confocal microscope.
The modestly priced Nikon C1 confocal system is
designed for routine confocal optical sectioning. It has
an argon and two HeNe lasers and z-axis control.
The electron microscope equipment funded by our first
MRI award has been installed, including a Balzers High
Pressure Freezer and a LEO 912 AB energy filter
transmission electron microscope (TEM). The high
pressure freezer is used to physically fix plant tissues by
ultrarapid freezing, giving the best possible preservation
of cells for electron microscopy. The energy filter of
the TEM adds a great deal of flexibility in optimizing
specimen contrast. The filter’s ability to reduce chromatic
aberration enhances the imaging of thick sections (up to
~ 1µm). Coupled with the tilting stage goniometer, this
allows electron tomography study of cellular components.
With the energy filter, Electron Energy Loss
Spectroscopy can be used to analyze elemental or mass
distribution in cells.
We are involved in collaboration in research grants at the
Danforth Center, Washington University, and University
of Missouri-Columbia. The facility director spoke on
three-dimensional imaging of virus protein distribution in
plant cells at the annual meeting of the Microscopy
Society of America.
Lab Member:
Heather Ford, Research Associate
Recent Publication
Bendahmane M, Szecsi J, Chen I, Berg RH, Beachy RN. 2002.
Characterization of mutant tobacco mosaic virus coat protein that
interferes with virus cell-to-cell movement. Proc Natl Acad Sci USA
99:3645-3650.
Julia Gross, Ph.D.
Co -Manager, Mass Spectrometry and Bioseparations Facility
Current instrumentation:
The Mass Spectrometry and Bioseparations Facility
(MSB) provides services to the scientists of the Donald
Danforth Plant Science Center and the scientific
community at large. The analytical capabilities of the
MSB increased this year with the acquisition of a QTOF
mass spectrometer (QSTAR Pulsar XL, Applied
Biosystems) and an LC Packings nano-bore liquid
chromatography interface.
The MSB Facility makes an effort to learn about the
client’s research, as well as to offer general
analytical support and advice. Seminars are given on a
regular basis to educate scientists about the usage and
advantages of mass spectrometry. The MSB Facility
and the Mass Spectrometry Resource of Washington
University in St. Louis organized a two-day symposium
at the Donald Danforth Plant Science Center
(November 11-12, 2002), which was attended
by more than 150 people.
• MALDI-TOF with SymBiot PS1 system (Voyager-DE
STR, Applied Biosystems).
• QSTAR PULSAR XL (Applied Biosystems) with
Electrospray, Nanospray, MALDI source
• LC Packings nano-bore liquid chromatography unit
for QSTAR
• GC-MS (GC-Q Polaris, ThermoFinnigan)
• BioCad 700E with fraction collector (Applied Biosystems)
• Biacore 2000 (Biacore Inc.)
• System Gold HPLC (Beckman Coulter) with diode array
and fluorescence detectors
• Cary Eclipse Fluorometer (Varian)
Information about instrumentation, setup of the facility,
and service sample submission can be found on the Internet:
www.danforthcenter.org/msb
Lab Member:
Charles Gloeckner, Research Associate III
Nancy Mathis, Manager,
Plant Cell Culture and Transformation Facility
The purpose of the Plant Cell Culture and
Transformation Facility is to provide a common facility
where a wide range of plant transformation and culture
systems can be done efficiently.
The facility consists of the transformation room, media
prep area, and kitchen. The main transformation room
contains eight tissue culture hoods, including necessary
equipment such as centrifuges, microscopes, incubators,
shakers, plus electroporators and biolistics guns for gene
delivery. Three large walk-in tissue culture rooms within
the lab add several hundred square feet of growing area
and include both platform shakers and shelf space,
making it convenient to access plant cultures. Special
care has been put into providing the equipment needed
and as many supplies as possible so as to optimize the
facility for researchers wishing to do their own tissue
culture work. An internal website has been developed for
ease of requesting transformations and information about
tissue culture methods, recipes, and fee schedules.
Plant species cultivated in the past year included
Arabidopsis, cassava, rice, tobacco, lettuce, Medicago,
soybean, and canola.
Plant transformation and maintenance services
provided by the facility have produced over 2000 plant
and calli lines at this time, with numbers expected to
increase dramatically over the next year. Facility services
can also provide outside scientists with plant production
or training; the first visiting scientists, from Romania,
were trained early this year.
37
S EMINAR S PEAKERS I N 2002:
Dr. Mavis Agbandje-McKenna
University of Florida
Dr. Jonathan Arias
University of Maryland
Dr. Adi Avni
Tel Aviv University
Tel Aviv, Israel
Dr. Tim Baker
Purdue University
Dr. David Bird
North Carolina State University
Dr. Wesley Bruce
Pioneer Hi-Bred International
Dr. Daniel R. Bush
University of Illinois
at Urbana-Champaign
Dr. Joel I. Cohen
International Service for
National Agricultural Research
The Hague, The Netherlands
Dr. Laszlo N. Csonka
Purdue University
Dr. Dean Dellapenna
Michigan State University
Dr. Vibha Dhawan
The Energy and Resources Institute
New Delhi, India
Dr. David Ehrhardt
Carnegie Institution of Washington
Stanford, CA
Dr. Bernard Epel
Tel Aviv University
Tel Aviv, Israel
Dr. Gad Galili
The Weizmann Institute of Science
Rehovot, Israel
Leonard Gianessi
National Center for
Food and Agricultural Policy
Washington, D.C.
Dr. Warren Gish
Washington University in St. Louis
Dr. Bob Goldberg
University of California, Los Angeles
Dr. Andrew Hanson
University of Florida
Dr. Jeffrey Harper
The Scripps Research Institute
Dr. Greg Hockerman
Purdue University
Dr. Leroy Hood
Institute for Systems Biology
Seattle, Washington
Dr. Leon Kochian
Cornell University
Dr. Hilary Koprowski
Thomas Jefferson University
Dr. David Lightfoot
Southern Illinois
University-Carbondale
Dr. Rob Martienssen
Cold Spring Harbor Laboratory
Dr. N. Appaji Rao
Indian Institute of Science
Bangalore, India
Dr. Ilya Raskin
Rutgers University
Glen Rogan
Monsanto Company
Dr. Julian Schroeder
University of California, San Diego
Dr. Peter Singer
University of Toronto
Dr. Anthony Sinskey
Massachusetts Institute of Technology
Dr. Chris Somerville
Carnegie Institution of Washington
Stanford, CA
Dr. Phil Stahl
Dr. Jeffrey M. Staub
Monsanto Company
Dr. Dan Szymanski
Purdue University
Dr. John C. Walker
University of Missouri-Columbia
Dr. Amy McGough
Purdue University
Dr. Florence Wambugu
A Harvest Biotech
Foundation International
Nairobi, Kenya
Dr. Elizabeth D. Owens
Monsanto Company
Dr. Brenda S.J. Winkel
Virginia Tech
Dr. Himadri Pakrasi
Dr. Mark Young
Montana State
Dr. Craig S. Pikaard
Dr. Hector Quemada
Western Michigan University

2002 Annual Report - Donald Danforth Plant Science Center

Transcription

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