2014 IIGB - Institute for Integrative Genome Biology

Transcription

Institute for Integrative Genome Biology
FY 2013-14
ANNUAL REPORT
(Report must be typed or Word processed - handwritten forms will not be accepted. Four copies of this annual report should be routed to the Office of
Research.)
Institute Director: Natasha Raikhel
Title: Distinguished Professor, Plant Cell Biology; Ernst
and Helen Leibacher Endowed Chair
Department: Botany & Plant Sciences
College: College of Natural & Agricultural Sciences
Phone: (951) 827 - 6370
Email: nraikhel@ucr.edu
Period of Review: 2010-11
Name of Center:
____________________________________________
Director’s Signature
Date
____________________________________________
Department Chair’s Signature
Date
____________________________________________
Dean’s Signature
Date
************************************************
NOTICE OF ACTION
The Vice Chancellor for Research has reviewed the annual report and has scheduled a follow-up meeting with the
Center Director and Dean at _______________ on ________________ in _________________.
____________________________________________
Charles F. Louis
Vice Chancellor for Research
_____________________
Date
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Fiscal Year 2013-14
INSTRUCTIONS: Please submit four (4) copies of this review to the UCR Office of Research, University Office
Building Room 200 and (1) copy to the College Dean as appropriate. For information about the process for preparing
an annual report, please contact the Office of the Vice Chancellor for Research at 951.827.5535.
A1. GENERAL NARRATIVE: Please provide a short statement highlighting the main activities in which the center
has engaged during the review period and how they relate to the mission, goals and objectives of the research center and
to the challenges/issues/problems central to the work of the research center. How did the center contributed to UCR’s
graduate and undergraduate teaching programs? What activities did the center provide to UCR’s external communities?
MAIN ACTIVITIES RELATED TO MISSION, GOALS, AND OBJECTIVES:
Genomics Building PI Brainstorming Sessions:
It was decided at the IIGB Forum held June 14, 2013 that the IIGB PI luncheons initially started January 19. 2012 to
rejuvenate intellectual activities, learn about IIGB research projects, encourage problem-solving, and stimulate new
collaborations, would be on the second Thursday of each month in the Genomics Boardroom. Ted Karginov and Hailing
Jin agreed to coordinate the sessions. The format consisted of one PI presenting 15 minutes of his/her work involving a
research issue or problem, followed by input, advice and discussion.
The sessions allowed IIGB PIs to establish more helpful and productive relationships. More importantly, the sessions
created an active and stimulating intellectual atmosphere for producing imaginative science.
Speakers:
July 11: Anand Ray
August 8: Frances Sladek, “Role of circular RNA in human colon cancer”
September 12: Ted Karginov: presented work and ideas for future directions in studying mRNA co-regulation by
microRNAs and RNA-binding proteins
October 3: Sean Cutler, “Orthogonal Activation of ABA Signaling and Drought Stress Tolerance”
November 7: Timothy Close, “Opportunities to Engage in Cowpea Research at UCR”
December 5: Peter Atkinson, “Possible functional inferences from the unusual structure of an active eukaryotic hAT
transposase "
January 9: Morris Maduro, “Genome Editing Using CRISPR/Cas9 Technology”
February 6: Jiayu Liao, “Development of Quantitative FRET Technology for Basic and Translational Research in
SUMOylation and other Ubls”
March 6: Mike Allen, "Fungal-plant interactions of invasive plants in wildland ecosystems: partners and parasites"
April 3: Monica Carson "Identifying Links between Neurodevelopmental Disorders, TBI and Dementia using Gene
Expression Profiling” (CANCELLED Due to building emergency issues)
Expansion of Neil A. Campbell Science Learning Laboratory (November 1, 2013)
The opening of the second phase of the Neil A. Campbell Science Learning Laboratory was celebrated Friday,
November 1, 2013 with a reception attended by 50 people. Located in the University Laboratory Building, the Campbell
Learning Laboratory is named after a well-known biologist, author, and UC Riverside alumnus. The lab is home to “The
Dynamic Genome,” a laboratory-intensive learning program funded by a Howard Hughes Professor Grant to IIGB
distinguished professor Susan Wessler. In addition to offering unique research experiences to freshmen and other
undergraduate students, the Campbell Learning Lab provides outreach to local K-12 science teachers and students. The
second phase of the lab will allow the lab to reach out to more students
.
At the opening's reception, Chancellor Kim Wilcox, CNAS Dean Marylynn Yates and Distinguished Professor of
Genetics Susan Wessler delivered brief remarks to acknowledge donor Rochelle Campbell, who was also present at the
reception and whose generous contributions helped fund the laboratory as well as the recent expansion project. The
speakers highlighted the difference that the Learning Lab has already made to undergraduate students’ research
experience and the excellent fit that UCR has been for the lab.
Inside UCR: November 5, 2013: http://ucrtoday.ucr.edu/18918
CEPCEB 11th Annual Award Symposium (December 18, 2013) [Attachment B]
The eleventh annual CEPCEB awards symposium was a full-day event with 20 speakers selected from CEPCEB
postdocs, graduate students and professors, followed by award presentations to outstanding CEPCEB undergraduate and
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graduate students and postdocs and the 2013 Noel T. Keen Lecturer, Dr. Elliot Meyerowitz
(http://www.bbe.caltech.edu/content/elliot-meyerowitz). Dr. Meyerowitz is an HHMI-GBMF Investigator and the
George W. Beadle Professor of Biology at the California Institute of Technology. The event was organized by
CEPCEB members Julia Bailey-Serres, Venu Gonehal, Thomas Girke and Zhenbiao Yang, attended by 120
IIGB/CEPCEP researchers, and included lunch and an evening reception. Please see Attachment B for the program and
speakers.
2nd International Hemipteran-Plant Interactions Symposium (HPIS): June 22-25, 2014 [Attachment F]
In recognition of UCR's historic contributions to and current strengths in entomology, plant biology, and plant
pathology, IIGB organizers were selected to host the 2nd International Hemipteran-Plant Interactions Symposium
(HPIS). Hemipteran insects include many of the world’s most important economically damaging pests such as aphids,
whiteflies, psyllids, leafhoppers, and thrips, and their feeding directly damages plant cells, causing cell death.
Additionally, aphids, whiteflies, planthoppers, and thrips continue to devastate California’s agricultural and horticultural
crops. The three-day event was held on June 23-25, 2014 at HUB Rm 302 and connected 147 scientists, graduate
students and postdoctoral fellows from 18 states within the United States and 24 other countries and attendees
represented all continents of the world except Antarctica. The symposium featured 23 oral and 73 poster presentations
and included two satellite workshops: a pre-symposium Electrical Penetration Graph (EPG) Workshop (June 19-21,
2014) facilitated by Gregory Walker (UCR) and Freddy Tjallinji (Wageningen University, The Netherlands); and a
post-symposium workshop (June 26, 2014) discussing state of the art “big science” strategies and approaches to plantinsect interactions. In addition to IIGB, the symposium was sponsored by the Department of Botany and Plant Sciences,
the Department of Plant Pathology and Microbiology, the Department of Entomology; and the Department of
Nematology. Other sponsors are the US Department of Agriculture, the Citrus Research Board, Dupont and the U.S.Israel Binational Agricultural and Research Development Fund. IIGB organizers of the symposium included: Linda
Walling, Isgouhi Kaloshian Greg Walker and James Ng from UCR; Michelle Cilia from the Boyce Thompson Institute,
N.Y.; and Murad Ghanim from the ARO-Volcani Center, Israel. Please see Attachment F for the program and speakers.
CEPCEB Postdoc/Student Symposium: June 11, 2014 [Attachment C]
The1st Annual CEPCEB Post-doc (& Student) Symposium was held Wednesday, June 11, 2014 from 9am- 5pm in the
Genomics Auditorium. The intent of the symposium was to provide an opportunity for postdocs and advanced graduate
students to present their work to their peers, network with other researchers on campus, and obtain experience giving
oral presentations to a large audience. The event was attended by 83 researchers and included presentations by 12
postdocs/graduate students, three postdoc session chairs, one keynote speaker (Hailing Jin, Professor, Plant Pathology &
Microbiology), lunch and coffee breaks/refreshments. The organizing committee consisted of: Maureen Hummel
(Bailey-Serres lab), Jorge Lazano-Juste (Cutler lab), Laetitia Poidevin (Judelson lab), Brandon Le (Chen lab), Jeremie
Bazin (Bailey-Serres lab), Shengben Li (Chen lab), Ousmane Cisse (Stajich lab), Sofia Robb (Stajich lab), Pinky Kain
(Ray lab). Please see Attachment C for the program and speakers.
Creation of Consortium on Next-Generation Sequencing (NGS): March 26, 2014
Glenn Hicks, director of IIGB central facilities and an associate research plant cell biologist, is one of only 15
researchers along with UC Procurement leaders tasked with forming a consortium around next-generation DNA
sequencing (NGS), a powerful method that has helped scientists gain insight into many biological processes. Campus
Procurement and Contracts at UC San Francisco and the 15 researchers have secured funding of $17,000 from the UC
Office of the President to set up the two-day discussion and planning meeting.
Many UC campuses are experiencing high demand for NGS sequencing, with more projects and grants being funded to
use NGS for novel discovery and research. The goal of the consortium is to figure out how to collaboratively approach
the management of NGS equipment so that the UC system is better positioned to facilitate the needs of research at a
lower cost to scientists while stimulating innovation and collaboration.
The consortium meeting is expected to take place May 2015.
Inside UCR March 26, 2014: http://ucrtoday.ucr.edu/21293
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Academic Recruitments:
TWO FACULTY POSITIONS IN MAMMALIAN VIROLOGY/EPIGENETICS
In order to strengthen UCR’s expertise in state-of-the-art mammalian biology programs and be more competitive for
project grants and other funding opportunities sponsored by NIH and private foundations, two college searches were
conducted simultaneously in2013-14. The following individuals served on a college-search committee to recruit two
assistant professors in the area of mammalian virology/epigenetics.
Molecular and Cellular Biology Search Committee Members:
Xuemei Chen, Botany & Plant Sciences (Epigenetics Position Chair)
Natasha Raikhel, Botany & Plant Sciences
Yinsheng Wang, Chemistry
Ted Karginov, Cell Biology & Neuroscience
Iryna Ethell, Biomedical Sciences
Virology Search Committee Members:
Shou-Wei Ding, Plant Pathology & Microbiology (Virology Position Chair)
Ayala Rao, Plant Pathology & Microbiology
Anupama Dahanukar, Entomology
I-Chueh Huang, Cell Biology & Neuroscience
David Lo, Biomedical Sciences
An offer was made to Wenqian Hu from the Whitehead Institute for Biomedical Research for the molecular and
cellular biology assistant professor position, who turned it down. A subsequent offer was made to Katalin Toth from
Caltech – who also declined. This was a failed recruitment for FY14..
An offer was made to Ricardo Rajsbaum from the Icahn School of Medicine at Mount Sanai Hospital for the
Virology assistant professor position, who turned it down. An subsequent offer was made to James Brien from
Washington University School of Medicine in St. Louis, MO.– negotiations are pending.
TWO IIGB CENTER RECRUITMENTS:
CEPCEB Plant Cellular Biochemistry Search Committee Members:
Zhenbiao Yang, Botany & Plant Sciences (Biochemistry Position Chair)
Julia Bailey-Serres, Botany & Plant Sciences
Sean Cutler, Botany & Plant Sciences
Natasha Raikhel, Botany & Plant Sciences
Wenwan Zhong, Chemistry
An offer was made to Jaimie Van Norman from Duke University, who accepted the assistant professor position. And
additional offer was made using one of Natasha Raikhel’s future retention positions to Carolyn Rasmussen from the
University of Wyoming, who also accepted. Both will move into the Genomics Building: Jaimie Van Norman in
office/lab 4202B/4237 eff. 1/1/2015; and Carolyn Rasmussen in office/lab 3119B and 3126 eff. 7/15/14.
CDVR ARTHROPOD VECTOR HUMAN DISEASE
CDVR Arthropod Vector Human Disease Committee Members:
Alexander Raikhel (Department of Entomology) – chair
Karine Le Roch (Department of Cell Biology and Neuroscience) –affirmative action representative
Anand Ray (Department of Entomology)
Emma Wilson (Biomedical Sciences, School of Medicine)
I-Chueh Huang (Department of Cell Biology and Neuroscience)
The position was first offered to Zhiyong Xi, an Assistant Professor in the Department of Microbiology and Molecular
Genetics at Michigan State University. Dr. Xi rejected the offer. He became Associate professor during the search
process and did not want to come at an Assistant professor level. The position was then offered to Robin
Stevens, currently an assistant professor at the Department of Internal Medicine, University of Texas Medical Branch,
Galveston. After many meetings and conference calls, Dr. Steven’s rejected the offer.
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BIOINFORMATICS ACADEMIC COORDINATOR RECRUITMENT
As the current Director of Bioinformatics Facilities, Thomas Girke, became a full-time faculty appointment in the
Botany & Plant Sciences department effective July 1, 2012, a college-search recruitment was conducted for an
Academic Coordinator Level III to manage the IIGB/CEPCEB Bioinformatics Core Facility. Recruitments held in 2012
and 2013 were unsuccessful in securing an appropriately qualified candidate. The following members served on the
search committee in 2014:
Search Committee Members:
Thomas Girke, Botany & Plant Sciences (Chair)
Jason Stajich (Plant Pathology & Microbiology)
Julia Bailey-Serres (Botany & Plant Sciences)
Anandasankar Ray (Entomology)
Glenn Hicks (Botany & Plant Sciences)
Stefano Lonardi (Computer Sciences & Engineering) – Outside Member
On June 2, 2014, Rakesh Kaundal from Oklahoma State University accepted the position, beginning his role as
Bioinformatics Facility Director July 1, 2014.
Awards/Honors:
IIGB/CDVR Scientist Honored by City of Riverside (October 9, 2013)
IIGB/CDVR scientist Anandasankar Ray was recognized on October 8, 2013 as the Innovation Honoree of the Month
by the City of Riverside. Ray, an associate professor entomology, received the award from May Rusty Bailey.
In 2010, with help from UC Riverside’s Office of Technology Commercialization and the Innovation Economy
Corporation, Ray founded Olfactor Laboratories Inc. (OLI), in Riverside. The company is dedicated to insect research,
identifying the best odors for behavior control and designing products to protect people from mosquitoes.
Research performed initially in Ray’s laboratory — the identification of volatile odor molecules that can impair, if not
completely disrupt, mosquitoes’ carbon dioxide detection machinery — led to the research and development at OLI of
the Kite Mosquito Patch, the world’s first product that blocks mosquitoes’ ability to efficiently detect carbon dioxide,
their primary method of tracking human blood meals.
In the City Council Chambers, where Ray was honored, he said he was pleased to see research get translated into a
product that makes it to market.
UCR Today dated October 9, 2013: http://ucrtoday.ucr.edu/18318
Award for Exceptional Service to California Vegetable Industry (November 26, 2013)
IIGB distinguished professor John Trumble was named the recipient of the 2013 Oscar Lorenz Award, which
recognizes outstanding accomplishments in research and/or extension education benefiting the California vegetable
industry.
Trumble has provided exceptional service to the state’s vegetable industry for more than 30 years. He has been actively
developing integrated pest management (IPM) programs and conducting economic analyses of the cost benefits of IPM
versus chemical standard programs. A constant effort of his has been to reduce the use of the most toxic insecticides and
maximize the use of biocontrol and plant resistance strategies.
He is currently working on yet another new insect pest in California, the potato psyllid. This is a major pest throughout
the central United States, and has become a significant new problem for California on potatoes, tomatoes and peppers.
His research resulted in effective IPM protocols for this insect, including sampling strategies, pesticide use programs
designed to reduce pesticide resistance, enhanced biocontrol, and plant resistance approaches.He has also investigated
plant compensation for insect herbivory, evolutionary aspects of host plant selection by insect larvae, and the spatial
distribution of insects within plants and fields. All of these accomplishments have contributed to the success of
California’s vegetable industry.
UCR Today dated November 26, 2013: http://ucrtoday.ucr.edu/19354
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Initiatives/Motivational Events:
New Sound Enclosure for Genomics Auditorium Projector (May 2014)
Due to excessive noise produced by the integrated and powerful Panasonic Widescreen Projector with 1000 lumens,
numerous complaints were received by users of the Genomics Auditorium over the last few years regarding the
disruption to presentations and meetings. After researching several options including the purchase of a new projector
and consulting with Western AV (who designed and installed AV equipment in the building) and Media Resources on
campus, a Blizzard Stretch Hush 120V Projector Enclosure (custom-built) with internal fan from Tempest Lighting was
purchased and installed in May 2014 with funds generously provided by the Vice Chancellor for Research Michael
Pazzani.
New Security System in Genomics (April – October 2014)
Due to security breaches in a fourth floor lab in Genomics (4126) which created a sense of anxiety throughout the
building and disrupted research operations, the campus decided to hard-wire fob devices on all main lab doors in
Genomics. The process was initiated in April 2014 with the fourth floor and took six months to complete. This
initiative also required a major shared piece of equipment to be moved from a lab to an outside room (film developer
from Rm 4202A to 2221) and the purchase of three additional ice machines to minimize traffic between labs afterhours.
IIGB Forums (5/27/14) [Attachment A]:
An IIGB Forum was held during FY 2013-14 in an effort to encourage participation, stimulate ideas and input regarding
goals and objectives, increase morale, and inform faculty of important activities/announcements. The forum was held
Tuesday, May 27, 2014 to discuss ongoing IIGB recruitments and ideas regarding research focus areas for future
recruitment. Results of 2013-14 faculty recruitments were summarized by search committee chairs and the IIGB core
facility managers provided updates regarding new services and instrumentation. Ongoing and new initiatives were also
discussed and volunteers recruited. Please see Appendix A for detailed information.
RESEARCH SEMINAR ACTIVITIES [Attachment E]
Seminar Activities:
Previous and newly-appointed faculty and student seminar coordinators met at the beginning of the 13-14 fiscal year to
review IIGB/CEPCEB-related seminar goals and ways to improve their scope and education/research benefits. It was
determined that IIGB, CEPCEB and CDVR would once again coordinate seminars every two weeks so as not to
inundate IIGB researchers and promote maximal attendance. As in the previous year, $5K was allocated to IIGB,
CEPCEB and CDVR for their seminar series, and $3K was allocated to students to meet the stated goals for the IIGB
student series. All faculty and student coordinators met to review campus/IIGB seminar policies and emails were sent
to Institute and Center PIs soliciting speaker ideas.
All seminar activities are advertised on the UCR and IIGB homepage website (www.genomics.ucr.edu). The following
faculty members coordinated seminar activities within FY13:
IIGB Seminar Series [ATTACHMENT F]
IIGB seminars are devoted to systems biology and high-throughput genomics across all organisms. This seminar series
features prominent speakers in the field and is often announced, when appropriate, as an IIGB Distinguished Lecture.
Iryna Ethell – Biomedical Sciences
Jason Stajich – Plant Pathology & Microbiology
CEPCEB Seminar Committee
Established in 2002, the CEPCEB seminar series (BPSC252: Special Topics in Botany) allows prominent speakers as
well as internal faculty and postdocs the opportunity to present and discuss noteworthy research discoveries in the fields
of plant cell and molecular biology and genomics.
Faculty Members:
Patricia Springer (Chair) –Botany & Plant Sciences
Thomas Girke – Botany & Plant Sciences
IIGB Student Seminar Series
The following three graduate students assumed responsibility for inviting three speakers for the 2013-14 academic year:
Lauren Dedow (Julia Bailey-Serres lab, Botany & Plant Sciences)
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CEPCEB Award Symposium
The 11th annual CEPCEB Symposium was held Wednesday, December 18, 2013. The following individuals assumed
roles in coordinating the event that included 20 postdoc, graduate student and faculty presenters and one invited
speaker.
Faculty Members:
Julia Bailey-Serres – Botany & Plant Sciences (chair)
Venu Gonehal – Botany & Plant Sciences
Zhenbiao Yang – Botany & Plant Sciences
CEPCEB REU Applicant Selection Committee
The following individuals reviewed the applications submitted for the NSF CEPCEB REU (Research Experience for
Undergraduates) program in plant and plant-pathogen cell biology (2010-15), which is geared towards providing
opportunities to students from two- and four-year colleges with limited research infrastructures who are interested in the
cellular and molecular biology of plants and their pathogens.
Howard Judelson – Plant Pathology & Microbiology (Project PI)
Patricia Springer – Botany & Plant Sciences
Thomas Eulgem – Botany & Plant Sciences
As the current CEPCEB REU grant will expire in one year, Thomas Eulgem is currently spearheading the effort to
submit a proposal for renewal for the period 2015 – 2020. Howard Judelson, currently PI on the existing grant, will
serve as co-PI on the renewal proposal.
CEPCEB Noel T. Keen Lecture and Award Committee
Established in 2002, the Center for Plant Cell Biology (CEPCEB) scholarship award fund sponsors an annual Special
Lecture and Awards Ceremony where an invited leading scientist presents his or her work and where postdocs, graduate
students and undergraduate students receive public recognition of their accomplishments. The Noel T. Keen Lecture has
become a top-notch lecture series. Previous lecturers have included: Fred Ausubel (Harvard), Jeffrey Dangl (University
of North Carolina at Chapel Hill), Chris Somerville (Stanford), Joanne Chory (Salk Institute), Bernhard Palsson
(University of California, San Diego) Gloria Coruzzi (New York University), Joseph Ecker (Salk Institute), Philip
Benfey (Duke University), Rob Martienssen (Cold Spring Harbor Laboratory), James Carrington (Donald Danforth
Plant Science Center) and Elliot Meyerowitz (CalTech).
CEPCEB Award Committee Members:
Faculty Members:
Venu Gonehal Reddy (Award Committee Chair) – Botany & Plant Sciences
Chia-en Chang – Chemistry
Stefano Lonardi – Computer Science & Engineering
Other Academics:
Glenn Hicks – IIGB Administrator, Genomics Core
Ruixi Li (postdoc) – Botany & Plant Sciences
Graduate Student:
Yuanyuan Zhao – Botany & Plant Sciences
CEPCEB Annual Award Symposium Organizers:
Faculty Members:
Julia Bailey Serres – Botany & Plant Sciences
Zhenbiao Yang – Botany & Plant Sciences
Venu Gonehal Reddy – Botany & Plant Sciences
CEPCEB Postdoc/Student Symposium Organizing Committee:
Maureen Hummel (Bailey-Serres lab)
Jorge Lazano-Juste (Cutler lab)
Laetitia Poidevin (Judelson lab)
Brandon Le (Chen lab)
Jeremie Bazin (Bailey-Serres lab)
Shengben Li (Chen lab)
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Ousmane Cisse (Stajich lab)
Sofia Robb (Stajich lab)
Pinky Kain (Ray lab)
CDVR Seminar Committee
Started in 2005, the Center for Disease Vector Research (CDVR) continues to bring leading as well as young
researchers together to discuss seminal discoveries related to molecular biology and the genomics of disease vectors.
Karine LeRoch – Cell Biology & Neuroscience
Anupama Dahanukar – Entomology
INSTITUTE’S CONTRIBUTIONS TO UCR’S GRADUATE AND UNDERGRADUATE TEACHING
PROGRAMS:
Contributions To Graduate Students
Annual CEPCEB Award Ceremony and Noel Keen Lecture (December 18, 2013):
Postdoctoral, graduate student, undergraduate student and high school students achieving research excellence in the
fields of plant cell biology, genomics, bioinformatics or engineering were recognized at the Eleventh Annual CEPCEB
Award Ceremony held on December 13, 2013 in the Genomics Auditorium. This year, the format of the symposium
was different in order to enable members and friends of CEPCEB to form new contacts and collaborations as well as
gain greater insight into the science performed in the Center.
Twenty graduate students, postdocs and faculty presented either research or “tech talks.” The innovative rapid-fire
"tech talks" and research presentations were part of this year's "Sensing" Symposium. The eight short "tech talks" were
five minutes in length, with time for only one or two questions. The purpose of these talks was to convey exciting
technology in the areas of genomics, proteomics, chemistry or biological modeling.
The purpose of the twelve (12) Research Talks that were 15 to 20 minutes in length was to inform and expose attending
biologists, engineers, computer scientists and chemists to exciting new project work.
Awardees:
The following outstanding CEPCEB researchers were selected by the CEPCEB award committee (Venu R. Gonehal,
Chia-en Chang, Stefano Lonardi, Glenn Hicks, Ruixi Li and Yuanyuan Zhao) and awarded $500 each:
•
•
•
•
Outstanding CEPCEB Postdoc(s): Joint award to Shengben Li from Xuemei Chen s lab
Outstanding CEPCEB Graduate Student: Ming Wang from Hailing Jin’s lab
Outstanding CEPCEB Neil Campbell Undergraduate Student: Grant Brady from Thomas Girke’s
lab.
Outstanding CEPCEB TechTalk Award: Anirban Chakraborty (graduate student) from Amit RoyChowdhury’s lab.
Graduate Student Mentoring:
USDA NIFA Fellowship: Tim Close’s student Mitchel Lucas, a PhD candidate in the Genetics, Genomics and
Bioinformatics Program was awarded a prestigious two-year (2013-15) United States Department of Agriculture,
Agriculture Food Research Initiative, National Institute of Food and Agriculture (USDA-AFRI-NIFA) predoctoral
fellowship for his project titled "Breeding Heat Tolerant Varieties of Cowpea by Exploiting Association Studies and
Legume Synteny."
His research project titled 'Breeding Heat Tolerant Varieties of Cowpea by Exploiting Association Studies and Legume
Synteny' addresses the AFRI Challenge Area 'Agricultural and Natural Resources Science for Climate Variability and
Change' and aims to contribute new knowledge concerning the inheritance, genetic control, and breeding of traits
important for agricultural production in the face of unpredictable climates.
Research will be guided by IIGB faculty members Dr. Timothy J. Close and Dr. Philip A. Roberts and will utilize
resources made available through UCR's Citrus Experiment Station.
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National Science Foundation’s Graduate Research Fellowship Program (GRFP) Awards: Three IIGB graduate
students were among 18 UCR recipients of NSF’s 2014 Graduate Research Fellowship Program (GRFP) awards. Oscar
Gonzalez (Neurosciences) from Maxim Bazhenov’s lab, Eric Robert Lucien Gordon (Entomology) and Jacklyn
Whitehead (Bioengineering) from Prue Talbot’s lab were among the awardees.
The NSF Graduate Research Fellowship Program provides three years of financial support within a five-year fellowship
period ($32,000 annual stipend and $12,000 cost-of-education allowance to the graduate institution) for graduate study
that is in a field within NSF’s mission and leads to a research-based master’s or doctoral degree.
Awards have historically been received by individuals who have become high-level achievers, contributors and leaders
in their fields. The program recognizes excellence and diversity among graduate students in the science and engineering
disciplines who are pursuing master’s and doctoral degrees at accredited US institutions. Underrepresented populations
are encouraged to apply and 13,000 applications were submitted this past year.
Research projects for IIGB’s GRFP winners are below:
Gonzales, a second-year student doing research with Maxim Bazhenov, a professor of cell biology and neuroscience, is
exploring how pathological synchronization arises in brain networks following traumatic brain injury. He has helped
develop a computer model to study which properties of the network lead to hyper-synchronization.
Gordon is in his second year of graduate studies. He works with Christiane Weirauch, an associate professor of
entomology, on exploring diversity and function of understudied bacterial symbionts of a group of true bugs including
plant bugs and lace bugs. The study will further our understanding of symbioses between insects and bacteria.
Whitehead is a first year bioengineering Ph.D. student working with Prue Talbot, a professor of cell biology. She is
working to develop a disease-in-a-dish model representative of brain development in utero by studying neural
differentiation of embryonic stem cells. This research is significant because it allows the modeling of in utero exposure
to various environmental chemicals in order to study their effects on prenatal development of the central nervous
system.
Contributions To Undergraduate Students
Tour of Genomics: Undergraduate Admissions Office (August 14, 2013)
On August 14, 2013, 38 career staff members from the Undergraduate Admissions Office were given a tour of a lab on
the first floor of Genomics as part of their training in recruiting undergraduate students for fall 2014. Wenbo Ma
presented interesting information about research being conducted in her lab and in the Genomics building, as well as
features of the shared Genomics building floorplan.
CEPCEB Research Experiences for Undergraduates (REU) Program (2010-15)
The NSF Research Experience for Undergraduates (REU) program was first awarded to CEPCEB researchers in 2002
for a period of three years, and renewed in 2005 for five years. In 2010, under PI Howard Judelson and co-PI Patricia
Springer, the REU Program was renewed for an additional five years. The 2010-2015 award titled “REU Site: Research
Experiences for Undergraduates in Plant and Plant-Pathogen Cell Biology” totaled $614,097.
As an NSF REU Site, CEPCEB brings research experiences to students of two- and four-year colleges who have limited
opportunity to learn about the excitement and career options that research in plant cell biology offers. Eight to twelve
students are accepted into the ten-week residential program. The program begins with a one-week workshop, in which
students are introduced to techniques and approaches used for analysis of plant and plant fungal pathogen cell function,
including basic molecular biology, genomic and bioinformatic analyses, and confocal microscopy methods used to
study live cells. Students then spend nine weeks working with a CEPCEB faculty mentor and a graduate or postgraduate
mentor on a research project of their choice. Students also participate in workshops to enhance learning skills and
professional development, and to discuss ethics in science. Thus far (incl. Summer 2013), 118 undergraduate students
have been trained in CEPCEB labs since the program’s inception, with 43 of them proceeding to graduate school. It is
estimated that approximately 40% have pursued studies related to plant biology.
Participating Faculty in the CEPCEB REU Program: http://cepceb.ucr.edu/reu/faculty.html.
The following 12 students participated in the 2012 REU Program in CEPCEB Labs and presented a poster session at the REU
Symposium on Friday, August 16, 2013.
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REU Student
College/University
CEPCEB Faculty
Jesus Banderas
Cuyamaca College, CA
Eulgem Lab
Quinton Brail
Cleveland State University, OH
Bailey-Serres Lab
Janel Case
Alan Hancock College, CA
Walling Lab
Sarah (Luna) Dietrich
Warren Wilson College, NC
Borkovich Lab
Seth Flanders
Whitworth University, WA
Roper Lab
Matthew Holmes
Haverford College, PA
Reddy Lab
Lauren Kivlen
Riverside Community College, CA
Nothnagel Lab
Mikayla Kravetz
Wells College, NY
Ma Lab
Andrea Krueger
University of Wisconsin-Stout, WI
Judelson Lab
Carolyn Meyers
Victor Valley Community College, CA
Chen Lab
Galen Rask
Swarthmore College, PA
Springer Lab
Alicia Vazquez
Cal State University, Channel Islands, CA
Larsen Lab
IIGB Faculty Contributions to Undergraduate Training:
Morris Maduro taught two MARCU-STAR trainees in the Bio 20 winter quarter class of 2014 (16 students total from
Honors program mostly). One undergraduate student completed her BSc and is starting as a graduate student at Yale
this fall.
IIGB Facilities Tours: [see below]
OUTREACH ACTIVITIES:
Twenty-one students from Riverside Community College participated in the Sequence to Success DNA Barcoding
Challenge, which involved analyzing fish samples and was coordinated by IIGB’s Alex Cortez, James Burnette III and
undergraduate researchers at the Neil A. Campbell Science Learning Laboratory.
These students visited campus as part of a three-week research experience program called the 2014 CNAS STEM
Community College Outreach Research Project. The program culminated in a poster session, which took place in the
Genomics Building on Saturday, March 22, 2014 and focused on research done by the these students and twenty-four
additional students also working on campus on a physics and astronomy project called the Experience Physics Pathway.
Both projects were sponsored by the Hispanic Serving Institution (HSI) STEM Pathway Project Grant, funded by the
U.S. Department of Education.
UCR Today March 27, 2014: http://ucrtoday.ucr.edu/21323
As part of UCR’s MARC U-STAR (Maximizing Access to Research Careers, Undergraduate Student Training in
Academic Research) Program: Ernest Martinez’s MARCU undergraduate students went to local high schools with
AVID programs to provide information about basic biomedical research at UCR and research careers.
Karine Le Roch presented a talk on malaria for the World Malaria Day (malaria, the facts, the history, the disease, the
treatments and the search for new antimalarial(s) to High Tech Middle School students in San Diego.
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Fiscal Year 2013-14
Isgouhi Kaloshiah’s graduate student, Dinusha Maheepala Mudalige, participated in 1) the Botany Program Plant
Discovery Day and 2) Served as a judge for the Science Fair of Alexandria Middle School in Riverside.
Norman Ellstand served as a participant on the Expert Panel Meeting – Gene Flow from CBSD Resistant Cassava to
Wild Relatives in Africa, VIRCA (Virus Resistant Cassava for Africa )/ Danforth Institute/Bill & Melinda Gates
Foundation, Mombasa, Kenya.
David Carter conducted a demonstration of the SEM (scanning electron microscope) at the 50th Anniversary
celebration of the UCR Botanical Gardens on Sunday, October 6, 2013. The event was open to the public and both
children and adults participated in the hands-on training.
Linda Walling presented the following talks, introducing a variety of public groups to her research:
May, 2014: Linda presented a talk on the dynamics of plant-insect interactions (30 min for elementary school students)
as part of Women in Match and Sciences Shadow Day.
October 1, 2013: As part of the Osher Life Society Lecture Series, Linda presented a 50-minute talk titled “Friends and
Enemies: Dynamic Interactions of Plants and Insects.”
Linda also tailored the talk above to Central Middle School students (Riverside, CA).
October 10, 2013: As part of the Long night of the Arts sponsored by the City of Riverside, Linda presented four
sessions of a 30-minute titled “Friends and Enemies: Dynamic Interactions of Plants and Insects.” Please see UCR
Today dated September 25, 2013: http://ucrtoday.ucr.edu/17814.
October 5, 2013: As an American Society of Plant Biologists (ASPB) invited speaker, Linda presented a short 15minute talk to the Society for Advancement of Chicanos and Native Americans in Sciences (SACNAS) titled
“Deceiving Your Host: Stealthy Feeding and Mixed Messages.”
Huiwang Ai’s lab collaborated with Riverside Unified School District and recruited a group of 4 high school students
for a short summer research program.
Stefano Lonardi presented talks to the Department of computer Science at the University of Verona, Italy, and the
Division of Biology and Biological Engineering at the California Institute of Technology in Pasadena, CA. He also
conducted a webinar organized by eXtension (http://www.extension.org/) for about 110 registered attendees titled
“Selective Sequencing Through Combinatorial Pooling” (http://www.extension.org/pages/67926).
Thomas Girke conducted a five-day next Generation Data analysis Workshop to researchers at UCR and also from
many countries December 12-16, 2013:
Next Generation Data Analysis Workshop (5 days, Dec 12-16, 2013)
1. Introduction to R
2. Programming in R
3. Visualizing and Clustering High-Throughput Data
4. Linux Part I: Linux Essentials
5. Linux Part II: Using IIGB's Linux Cluster
6. Basics on Analyzing NGS Data
7. Analysis of ChIP-Seq Data with R/Bioconductor
8. Analysis of SNP/Var-Seq Data with R/Bioconductor
9. Analysis of Small Molecules and HT Screens
10. Web-based Analysis of NGS Data
11. Analysis of RNA-Seq Data with R/Bioconductor
Jason Stajich conducted training workshops on the use of FungiDB (database resources for fungi that he developed)
tools at multiple international conferences.
High School Recipients of CEPCEB Plant Cell Biology Awards at Science Fairs (judged by CEPCEB faculty,
postdocs and students)
a. In 2002, CEPCEB initiated the CEPCEB Award Fund to recognize research excellence in plant cell
biology, genomics and bioinformatics by pre-college students, graduate students, and postdoctoral
researchers.
b. CEPCEB awarded Saumya R. Keremane of Martin Luther King High School the first place CEPCEB
Award of $500 at the RIMS Inland Science and Engineering Fair held on April 2, 2013 for her poster titled
“Gene Silencing in Bactericera Cockerelli, vector of Tomato Liberibacter.” CEPCEB also awarded a $100
honorable mention award to Sabrina Houston of Centennial High School from the Corona/Norco School
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Fiscal Year 2013-14
District for her poster titled “Solving Salt Stress: Chemical Genomics with Agricultural Implications.”
Images of both awardees were posted on the IIGB site at: http://genomics.ucr.edu/about/CEPCEB-awardfund.html .
a. David Carter, Venu Gonehal, Songqin Pan and Nolan Ung (Raikhel lab) represented CEPCEB as
judges at the event mentioned above.
c. The California State Science Fair was held on April 2, 2014.
a. David Carter and Shengben Li (Chen lab) served as judges for this event.
d. Songqin Pan served as a member of the Biochemistry Judging panel at the 2014 Intel International
Science and Engineering Fair held on May 12-13, 2014 in Los Angeles.
IIGB Facilities Tours: [see Attachment D]
In an effort to showcase Keen Hall’s advanced tools in bioinformatics, microscopy and imaging, proteomics and
genomics and assist in recruitment efforts of top-notch faculty and graduate students, IIGB’s academic staff regularly
participates in conducting tours to a wide range of groups. During fiscal year 2013-14, a total of 48 tours were
conducted throughout the cores. Many tours of Keen Hall were conducted as part of faculty recruitments (Mammalian
Virology/Molecular & Cellular Biology/BNPPS/Evolution & Development/Arthropod-Symbiont Interactions),
Biological Sciences Graduate Recruitment (CMDB, GGB, ENT, MIC, PB, Biomed, PPM), Research Experience for
Undergraduates (REU) programs, Visiting Professors, and other groups in an effort to assist in recruitments. These tours
have a real impact as guests are highly impressed by the quality of the facilities and personnel.
IIGB INSTRUMENTATION FACILITIES
The IIGB instrumentation facilities continued to meet the needs of campus researchers and stay abreast of scientific
trends, while vastly changing the nature of research being conducted at UCR. This has been accomplished through
upgrades, the acquisition of new technology, collaborations with a variety of researchers working on a broad range of
organisms, and regular training in the use of new instrumentation.
Bioinformatics Core
Expansions of Compute Infrastructure
In the past year, IIGB's computing infrastructure has continued to expand very rapidly to keep up with the rapidly
growing demands for CPU and storage resources within IIGB and our campus at large. The most relevant computational
resources offered by IIGB’s bioinformatics facility consist of two large Linux clusters with over 600 CPUs, seven highmemory servers, six web/database servers, over 250TB of fully backed-up disk storage space, over 500
bio/cheminformatic software tools, and many databases. This compute infrastructure is heavily used by over 150
researchers from 50 research groups in all life science, chemistry, engineering, computer sciences and statistics
departments at UCR. To sustain the rapidly growing demand for research computing resources at UCR, the Girke lab
(former director of facility) has been awarded two equipment grants from NSF and NIH in the total amount of almost
$1.5 million. In part, these funds will be used to purchase a new high-performance compute cluster specifically
designed for Big Data processing composed of over 3000 CPU cores, 512GB of RAM on each compute node and over
1.5PB of disk storage space. This new infrastructure will become available to the users of IIGB's bioinformatics facility
in early 2015. Moreover, the facility staff instructed in December 2013 another 5-day bioinformatics workshop on the
analysis of next generation sequencing data, microarrays, data visualization, programming, data mining and
cheminformatics. This event was attended by 75 researchers and students from UCR and many external universities in
the United States and Europe.
The extensive online material developed for these courses is currently accessed over 200,000 times per year by
researchers from many international locations. The facility staff has also been very active in supporting many data
analysis projects for IIGB research labs and writing the bioinformatic sections of publications and grant applications.
On average this involves over ten ongoing projects predominantly from various applications areas of next generation
sequencing (NGS) technologies, including small RNA profiling, RNA-Seq, ChiP-Seq, VAR-Seq, BS-Seq and de novo
assembly projects.
Microscopy Core
Nearly 200 users were trained on the new Leica SP5 confocal during FY2014, which now runs up to 14 hours of
bookings per day. Cross-training on the older systems has helped relieve pressure on the SP5, so everyone has access to
something for their data collection. However, there is clear demand for another instrument, especially with so many
new hires wanting extensive access to confocal imaging. There are now over 1700 microscopy users listed in the
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Fiscal Year 2013-14
booking system, from 15 departments in all three colleges. The Microscopy Core has been trying to negotiate with new
faculty hires regarding the use of some initial complement money for a joint purchase of a Leica SP8, rather than have
each new PI purchase lesser instruments for private use in his/her lab. But each PI has somewhat different imaging
needs. Much work has gone into designing a custom configuration which will do routine imaging and near Infra Red
spectroscopy, and can be based in the core facility (ongoing).
Instrumentation grants are more successful if they bring new technology to the requesting campus, rather than simply
more capacity, so we are evaluating super-resolution methodologies to see which might fit IIGB science. The Leica
SP8 confocal with (50nm) STED supre-resolution is the most promising since it works live with fluorescent proteins in
thick samples, but it is not compatible with chloroplasts. First attempts to use it on root tips did not damage the plant
with its very bright laser but didn't produce good images either. Nikon's (10nm) STORM system was here for a demo
in January, and was unable to provide any useful data to the labs trying it, due to very narrow sample and staining
constraints. Samples have to be fixed and bathed in a special buffer, and the dynamic range of signal needs to be quite
small or bright areas will not be seen. A more rugged and versatile microscopy technology is time gating, which is now
standard on Leica SP8 instruments, using their HyD detectors and pulsed white light or MP laser, but is not yet sold
with more economical single color lasers. Zeiss is releasing a new 880 scanner, which has a new Aryscan detector
which supposedly gives 100nm resolution but is not yet available for demo.
New technology added to the core this year includes a lens inverter, a mechanical cryostat, and a critical point dryer.
The inverter allows the direction of laser scanning to be flipped or rotated through two 90 degree angles. The more
sensitive SP5 can then be used as an upright microscope when needed; for example with the Reddy group for looking
down on Arabidopsis apical domes. And the Pathway HT can do top-down screens of samples, or even look sideways
to follow the sub-cellular gravitropic responses of roots.
The Microscopy Core added an EMS 850 critical point dryer to enable scanning electron microscopy of more delicate
vacuum-sensitive samples. The TM-1000 tabletop SEM does not need this to work, so most samples are still used fresh
or snap-frozen in isopentane, which allows the instrument to work at very high throughput. The critical point dryer in
CFAMM has been unreliable so the University needed an alternative. Having the core’s own system makes workflow
more friendly for biological samples. The Microscopy Academic Coordinator, David Carter, designed a 3D printed
cover-slip holder for use in the critical point dryer, but the type of plastic used in the Engineering printer was
incompatible with high pressure carbon dioxide, so a simple wire cage arrangement is being used instead. Hitachi just
launched a new TM-3030 which costs $73k and has low voltage for higher resolution imaging, and directional detection
for 3D modeling of imaged surfaces.
An epi-illumination white light cube was designed and built to allow observation of opaque materials on the SP5
confocal. This was in support of a bioengineering group working on texturing Titanium stent material, to make it more
friendly to cell colonization. We also had to figure out how to cut implanted stents in blood vessels, using cryostats and
new Tungsten Carbide blades.
Repairs were performed on almost all systems; the new SP5 needed a new 20x/0.75 objective lens due to chromatic
shift in Z. The Zeiss 510 needed a refurbish on its turret. The SP2 got a new fast Z stage for XZ imaging, and needed
renovation of its big UV laser, including a new UV deliver fiber. The Biomek FXp robot is always troublesome and
required work to its cytomat hotel and position sensor circuits. The luminescence dark box needed two re-works of its
LED focusing light shelf. The Pathway HT needed new lamps and light-guides, which had burned out. The TM-1000
SEM required a whole column rebuild and electronics diagnostic work to find a drift in focus. And the Arcturus laser
capture system frequently falls out of alignment. The cryostat had all its relays replaced, and an old Ames mechanical
cryostat donated by Greg Walker's lab was revived and actually cuts better 10 micron sections.
Software upgrades include the return of the MCID Elite system for quantitation of 2D images. There is a video
Informatics IGERT with Engineering which is now in its fourth year, and is struggling to maintain biologist
involvement. Bitplane has a sweet software developer program where they provide a whole extra copy of the $30k
Imaris 3D analysis suite for the engineers to do development work on, in exchange for development of at least one
software feature per year. Biologists get the very friendly user interface, and access to a large library of already written
modules; while engineers code in any one of many languages including C++ and Matlab. Upgrading to this full doublelicense costs $6000 and adds all modules of Imaris, including Filament Tracer ($8k value), which maps nodes and hairs
on neural trees or root systems. Unfortunately, the PI prefers to use only free software packages; and without
engineering buy-in there is little point of us doing it ourselves. If a small group with coding skills could be found, it is a
bargain and would be a huge help to software-hungry biologists.
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Fiscal Year 2013-14
Proteomics Core
An NIH grant awarded to proteomics core for LTQ-Orbitrap MS instrument
In early 2012, IIGB submitted a grant proposal to NIH Shared Instrumentation Program to request funds ($600,000) for
the purchase of an LTQ-Orbitrap Elite ETD LC/MS/MS system to upgrade our Proteomics core’s aging
instrumentation. Prof. Yinsheng Wang in Chemistry served as the proposal’s leading PI with Songqin Pan, Proteomics
Coordinator, as the co-PI. Ten other NIH-funded major users supported the proposal with their detailed project
descriptions. The proposal was well reviewed and funded, and we received the actual fund of $600,000 from NIH in
2013. After tireless negotiation, we were able to upgrade the proposed Elite system to the most up-to-date Orbitrap
Fusion system. Although the initial purchase agreement was for a second-hand demo machine, we eventually received a
brand-new Orbitrap Fusion instrument after our additional efforts. This is translated to a value of approximately
$100,000 we have saved.
Newly acquired capabilities due to Orbitrap upgrade
The newly-added Orbitrap Fusion MS system has been successfully coupled to 2-dimension nanoUPLC to perform
MudPIT experiments on daily basis although the two MS and LC systems are made by two different manufacturers.
Compared to the old Q-TOF system, the Orbitrap instrument shows 100x improvement in sensitivity with detection
limit as low as 0.1 femtomole, 40 times faster in scanning speed, and ultrahigh resolution up to 450,000. Compared to
Q-TOF being able to generate only CID spectrum, Orbitrap can generate three different types of spectra in parallel
including ETD, HCD, and CID. These different fragmentation technologies offer much more sequence information at
both peptide and protein level with improved confidence in identification and coverage of proteome. The ETD data
offers high degree of specificity in assignment of chemically modified amino acid residues and is particularly useful in
studies of protein post-translational medication (PTM) such as phosphorylation and glycosylation. With other
capabilities in top-down approach and SRM (selective reaction monitoring) targeted quantitative methods, the new
Orbitrap Fusion system has enabled our proteomics core to offer many more tools in proteomics research.
Ongoing proteomics projects:
Mike Adam: The Adam lab in Entomology is interested in characterization of venom peptides/proteins secreted during
stings by insect wasp. Wasp naturally attack/sting cockroach to affect the prey’s nerve system to change its behaviors
for wasp’s own benefit of reproduction. The venom peptides/proteins are thought to be the molecules that affect the
cockroach nerve system. Using MudPIT technology, Adam lab was able to discover many novel neuron peptides in
addition to the known ones in literature. They also profiled entire proteome of venom gland to determine the precursor
proteins/genes for these neuron peptides. Characterization of this system may help understand human neuron diseases
such as parkinson's disease. This study was well received at ASBMB annual meeting in 2014 and presented as the cover
story by ASBMBTODAY (April, 2014, Vol. 13, No. 4). A high-impact research manuscript is expected and now is in
preparation.
Wenbo Ma: Citrus stubborn disease (CSD) is a widespread bacterial disease found in most citrus-producing regions in
the United States. The disease is caused by Spiroplasma citri, an insect-transmitted and phloem-colonizing bacterium.
CSD causes significant tree damage resulting in loss of fruit production and quality. Detection of CSD is challenging
due to low and fluctuating titer and sporadic distribution of the pathogen in infected trees. Ma lab in the department of
plant pathology developed a novel diagnostic method using MudPIT proteomics. A pathogen-secreted protein,
CAK98563, was found abundant in CSD citrus trees with close correlation with the disease symptom. With CAK98563
protein as a disease marker, they developed an antibody against this protein and were able to detect the disease
development with high specificity. This new diagnostic tool may soon find its application in CSD control in citrus
industry. The study was published in Phytopathology in Feb 2014.
Natasha Raikhel: Raikhel lab in BPS has been working in the field of chemical genomics for many years. In their
large-scale screening of chemical libraries, they discovered many small molecules with abilities of perturbing cellular
endomembrane system in Arabidopsis seedlings. To determine the protein targets of these small molecules, Raikhel lab
employed the MudPIT proteomics approach to profile protein samples derived from affinity-based pull-down assays.
An exocytosis component protein, Exo70A1, was found by the proteomic method to specifically interact with small
molecule ES2. Further characterization of this ES2-Exo70A1 interaction has suggested that ES2 has a highly conserved
function in both plants and mammalian cells in cellular vesicle trafficking and exocytosis and that ES2 may have
pharmacological value in human diseases such as cancers and diabetes. A manuscript describing this study is in writing
for submission to Nature. A possible patent is under consideration.
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Fiscal Year 2013-14
Wenwan Zhong: Zhong lab in Chemistry has a focus on developing analytical tools to better assay interactions
between nanoparticles (NP) and cellular proteins in human. When nanoparticles enter a biological matrix such as human
blood, their molecules will be covered by cellular proteins to form a protein corona through NP-protein interactions
with subsequent effects on biological processes. The contents of protein corona are dependent on the dynamic nature of
cellular proteins and cellular environment and are interchangeable between different cellular proteins with fast binding
rates. To assay these protein coronas, Zhong lab has developed a method using flow filed-flow fraction (F4) combined
with MudPIT proteomics to distinguish fast binding proteins from slow binding. The research results were published in
Analytical Chemistry in Aug 2013.
Genomics Core
New Instrumentation and Sequencing
In this past year the Genomics Core has acquired an Illumina MiSeq next generation DNA sequencer. This was
provided via a HHMI equipment allocation to Prof Xuemei Chen. The MiSeq joins the HiSeq2500 within the IIGB
Genomics Core unit. This smaller and faster sequencer has specialized applications in understanding biodiversity both
within host organisms (for example human intestinal fauna) or in the environment which are rapidly growing areas of
biology and the biomedical sciences. It is also valuable for the rapid sequencing of small genomes and human exons
(gene coding regions). As within the HiSeq2500, this instrument system takes advantage of the high level of technical
expertise and infrastructure within the IIGB Genomics and Bioinformatics Cores. To introduce the MiSeq to the
campus, IIGB co-sponsored a day-long event which included seminar on the technology and its applications of interest
to UCR researchers. The event included raffles of prizes, including three MiSeq sequencing runs for which Dr. Hicks
negotiated free reagents from Illumina. This is an important way to promote use and provide faculty with opportunities
for new research on campus. In addition to this major addition, the Genomics Core also acquired a Blue Pippin device
which is a computer controlled device that is designed to isolate DNA fragments of precisely defined lengths. This is an
important for the preparation of samples for Illumina sequencing and further supports our major sequencing capabilities.
Dr. Brad White’s lab has been taking advantage of this capability of for the preparation of samples for a recent approach
known as RADSeq.
Other instruments acquired during the year included a new plate reader/luminometer. It is a device that was badly
needed since an older denoted device was retired several years earlier. With only a few such plate readers at UCR this
was a badly needed addition for general access across the biological sciences. This was funded by IIGB general funds.
Within the past year a Biorad gel doc device was acquired such that labs especially new labs with limited budgets would
have access. This and other items were negotiated from Biorad at low cost by the Director of Central Facilities, Glenn
Hicks. Very recently (August 2014) the core also acquired a fifth real time qPCR instrument (to examine gene
expression) to provide increased access for the many labs on campus that do not have such instruments. This parallels
the regular qPCR training workshops offered by the Genomics Core and the availability of supporting reagents at
significant discounts to UCR researchers. The Core has trained literally hundreds in qPCR, standardizing a higher level
of knowledge on campus.
Workshops and Training
Workshops are continuously offered to train campus researchers in the capabilities of relatively new and powerful
Illumina nextgen sequencing technology. The Illumina workshop introducing the MiSeq to campus had more than 100+
attendees. Earlier in the year, and following a successful two day laboratory workshop on small RNA sample
preparation (Completed Jan 20), the Genomics Core in partnership with New England Biolabs offered a two-day
seminar and lab training workshop in directional RNASeq. Instructors included IIGB staff and the product development
group that developed the NEB reagents. Reagents and sequencing reagents were provided by companies, Participants
providing their own RNA. Thus, in addition to training, this was a no cost way for investigators to also obtain
preliminary sequence data for new projects.
Hosted Events and Tours
Beyond events and training, the IIGB Genomics Core hosted a number of informational seminars in advanced
technologies to inform researchers of potentially useful approaches. This included seminars by Nanostring (higher
throughput markers), Fluidigm (single cell sequencing), and Bionano (genome mapping and assembly). To benefit UCR
researcher, the content of each seminar is overseen by Dr. Hicks to be sure that the content is research-based rather than
low content marketing of products. Dr. Hicks and the staff of the Genomics Core have conducted many tours including
virtually all biology-centered faculty recruitment candidates for CNAS and the SOM. From January through July 2014
alone there were 62 faculty recruitment tours. Additional tours included REU students, prospective graduate students,
UCR administrators, and external guests. This underscores the importance of IIGB facilities to UCR research and as an
important recruiting tool for faculty, staff and students, and as one public face for the university.
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Fiscal Year 2013-14
Outreach
The Genomics Core and Dr. Hicks has been very active in interacting and cooperating with other centers in SoCal
especially regional UC genome centers at UCI, UCSD and more recently UCLA as well as USC, Cedars Sinai, and
more recently Loma Linda University. More widely, centers at UCD, UCSF, and UCB are also active in
communications. The objective of this is to share information and resources. Dr. Hicks (and UCR Purchasing manager
David Gee) participated in a UCOP initiative to establish closer ties within the UC system in terms of nextgen
sequencing, including an actively used listserve which includes many UC campuses. Such unity will be an important
element of providing most competitive resources and expertise for UCR research. Outreach included judging in science
fairs at the K-12 levels in Riverside, the county and at the state level. IIGB and CEPCEB have wonderful facilities and
always elicit positive comments by virtually all visiting scientists and administrators for their permanent managers and
staff as well as the high centralized and efficient structure. As the campus grows in the next five years, strong support
and imaginative approaches will be required to remain at the cutting edge of relevant technology, equipment and as
important strong and relevant expertise.
.
The following additional research projects were collaborations among IIGB
researchers and/or facilitated by IIGB core facilities’ usage/technology.
IIGB Researcher Demonstrates How Aphids Self Sabotage (June 2, 2014)
A research team lead by IIGB member Isgouhi Kaloshian, a professor of nematology, showed how a bacterial protein in
aphid saliva triggers plant defense against aphids. Study results appeared online June 2, 2014 in the Proceedings of the
National Academy of Sciences.
By means of mass spectrometry, their work identified 105 proteins in the saliva of the potato aphid Macrosiphum
euphorbiae. Among these proteins were some originating from the proteobacterium Buchnera aphidicola, which lives
endosymbiotically within bacteriocytes in the hemocoel of the aphid. They demonstrated that one of these
endosymbiont-derived proteins, the chaperonin GroEL, is recognized by the plant immune surveillance system and
activates pattern-triggered immunity. Our findings for the first time demonstrates a direct role for insect symbionts in
their interactions with the plant host.
Kaloshian was joined in the research by Ritu Chaudhary (first author of the research paper) and Hagop S. Atamian at
UC Riverside; and Zhouxin Shen and Steven P. Briggs at UC San Diego. Shen and Briggs performed the mass
spectrometry. The researchers used the model plant Arabidopsis in their experiments with the aphids.
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UCR Today June 2, 2014: http://ucrtoday.ucr.edu/22930
PhysOrg News June 2, 2014: http://inlanddaily.com/tag/isgouhi-kaloshian/
Science Daily June 2, 2014: http://www.sciencedaily.com/releases/2014/06/140602162700.htm
Seed Quest June 2, 2014: http://www.seedquest.com/news.php?id_article=49416
BrightSurf.com June 3, 2014:
http://www.brightsurf.com/news/headlines/97225/The_betrayal_of_the_aphids.html
Ag Professional June 2, 2014: http://www.agprofessional.com/news/Aphid-saliva-triggers-plant-defense-tothe-aphids-261571671.html?llsms=863041&c=y
IIGB Associate Professor awarded $600,000 from NIH to Expand Data Storage Capacity on Campus (May 15,
2014)
The IIGB Bioinformatics Core has now received funding of $600,000 from the National Institutes of Health (NIH) to
support data-intensive research — also often called Big Data science. Specifically, the grant will make possible the
purchase of a complex instrument: a Big Data cluster with high-performance CPU resources and data storage space
equivalent to 5,000 modern laptops.
Big Data has been identified as a contributor to the growth of the U.S. economy over the next few decades. The NIH
grant is expected to make UC Riverside more competitive in attracting new outstanding faculty and facilitating the
research of many existing programs. The grant is expected to benefit more than 160 scientists from more than 15
departments and several colleges at UCR.
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Fiscal Year 2013-14
UCR’s research compute infrastructure is provided by a central bioinformatics facility which is part of the Institute of
Integrative Genome Biology (IIGB). Thomas Girke, the grant’s principal investigator and a member of IIGB, is
currently the director of the bioinformatics facility. The new instrument will be housed in a brand-new server room of
the Genomics Building where many IIGB researchers work.
IIGB’s bioinformatics facility was formed in 2003. In 2008 it became the largest high-performance research compute
facility at UCR.
•
UCR Today May 15, 2014: http://ucrtoday.ucr.edu/22532
3D Model of the Malaria Parasite Genome (April 4, 2014)
A research team led by IIGB cell biologist Karine Le Roch generated a 3D model of the human malaria parasite
genome at three different stages in the parasite’s life cycle — the first time such 3D architecture was generated during
the progression of the life cycle of a parasite.
Le Roch's research team also found that those genes that need to be highly expressed in the malaria parasite — for
example, genes involved in translation — tend to cluster in the same area of the cell nucleus, while genes that need to be
tightly repressed — for example, genes involved in virulence — are found elsewhere in the 3D structure in a
“repression center.” The 3D structure for the malaria parasite genome revealed one major repression center.
Virulence genes in the malaria parasite are a large family of genes that are responsible for the parasite’s survival inside
humans. Le Roch’s team found that these genes, all organized into one repression center in a distinct area in the nucleus,
seem to drive the full genome organization of the parasite.
Study results appeared online last week in Genome Research; the research paper will appear in print in the June issue
of the journal.
To understand the biology of an organism or any cell type, scientists need to understand not only the information
encoded in the genome sequence but also how the sequence is compacted and physically organized in each cell/tissue,
and how changes in the 3D genome architecture can play a critical role in regulating gene expression, chromosome
morphogenesis and genome stability. In human cells, changes in chromosome organization and compaction can lead to
diseases such as cancer.
•
UCR Today April 4, 2014: http://ucrtoday.ucr.edu/21448
Understanding Plant Growth Development (March 13, 2014)
IIGB professor of cell biology Zhenbiao Yang led a research project that demonstrated the existence of an extracellular
auxin sensing system in plants and uncovered the decades-long mystery of how this system works to control plant
developmental processes. Study results appear in the Feb. 28, 2014 issue of Science.
Auxin is understood to be the most important and versatile plant hormone controlling nearly all aspects of plant growth
and development. But just how a small molecule like auxin could play such a pivotal role in plants baffled plant
biologists for decades. Now, IIGB plant cell biologists have discovered a new auxin sensing and signaling complex, one
that is localized on the cell surface rather than in the cell’s nucleus. The discovery provides new insights into the mode
of auxin action and uncovered how ABP1, an auxin-binding protein discovered more than 40 years ago, works. The
novel auxin sensing and signaling system makes possible the formation of the jigsaw shape of leaf epidermal cells and
many other auxin-mediated processes.
UCR Today dated March 13, 2014: http://ucrtoday.ucr.edu/21037
Local ABC new Interview on Crop Research Breakthrough (February 18, 2014)
ABC30 Action News Live (KFSN-TV Fresno) conducted an interview of IIGB Associate Plant Cell Biologist Sean
Cutler on February 18, 2014 and his major breakthrough related to the effects of quinabactin, a synthetic chemical that
triggers a molecular response protecting plants from drought.
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The online article and interview can be found at:
http://abclocal.go.com/kfsn/story?section=news/ag_watch&id=9436868.
Health Problems Caused by Third-hand Smoke (January 30, 2014)
IIGB cell biologist Manuela Martins-Green and colleagues conducted the first animal study of the effects of third-hand
smoke and proved that second-hand smoke and third-hand smoke are just as deadly as first-hand smoke. While firsthand smoke refers to the smoke inhaled by a smoker and second-hand smoke to the exhaled smoke and other substances
emanating from a burning cigarette that can get inhaled by others, third-hand smoke is the second-hand smoke that gets
left on the surfaces of objects, ages over time and becomes progressively more toxic. The results of the study provide a
basis for studies on the toxic effects of third-hand smoke in humans and serve to inform potential regulatory policies
aimed at preventing involuntary exposure to third-hand smoke. Martins-Green and colleagues studies the effects of
third-hand smoke on several organ systems of mice under conditions that simulated third-hand smoke exposure of
humans and found significant damage occurring in the liver and lungs. Wounds in these mice also took longer to heal
and these mice displayed hyperactivity.
Study results appear in PLOS ONE.
UCR Today dated January 30, 2014: http://ucrtoday.ucr.edu/20236
A Student’s Journey as a Scientist (January 28, 2014)
Irma Ortiz, whose parents immigrated to the US from Mexico, is the first in her family to graduate from college. Today,
Irma is a Ph.D. graduate student in IIGB geneticist Linda Walling’s lab, where she and her lab-mates identify and
deploy gene-based strategies for insect resistance in plants.
Ortiz’s honors include a National Science Foundation Graduate Research Fellowship “honorable mention,” accorded to
meritorious applicants. Because of a fellowship she received from the CAMP Bridge to the Doctorate program for her
first two years and a Ford Foundation Fellowship for the next three years, Ortiz can focus on her graduate work without
financial burden.
What drew Ortiz to agricultural research are the strategies scientists use to enhance plant success and plant resistance to
pests and pathogens. “I see the difficulties some Mexican families experience when they have a bad season,” she said.
“My grandparents worked on agriculture most of their lives. My parents depended heavily on that income. How then
could I not work in agriculture?”
Studying How Flies Detect Sweetness (January 13, 2014)
IIGB researchers led by assistant professor of entomology Anupama Dahanukar have performed a study that describes
just how the fly’s taste receptors detect sweet compounds, potentially offering tools to control insect feeding.
The study, which appears online this week in the Proceedings of the National Academy of Sciences, holds promise for
uncovering functions of taste receptors in insects that transmit diseases (for example, mosquitoes) or damage crops (for
example, beetles and weevils).
Although the researchers’ method is laborious, it is the only technique with which many different taste receptors have
been successfully expressed. It offers a platform to probe the specificity of individual taste receptors, potentially from a
variety of insects.
Island Tameness Supports Darwin’s Ideas (January 9, 2014)
IIGB biologist Theodore Garland, in collaboration with researchers from Indiana University-Purdue University Fort
Wayne and George Washington University published a study showing that island lizards are indeed “tame” as compared
with their mainland relatives. The study supported Charles Darwin's ideas about the importance of natural selection as a
mechanism by which populations of organisms would change — evolve genetically — across generations, eventually
becoming better and better suited to life in their current conditions. A corollary of Darwin’s revolutionary idea was that
organisms would also evolve to lose structures, functions, and behaviors they no longer needed when environmental
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circumstances changed. He noted that island animals often acted tame, and presumed that they had evolved to be so
after coming to inhabit islands that lacked most predators.
Study results appeared online in the Proceedings of the Royal Society B and will appear in the journal in print on Feb.
22.
Insights into the Origin of Flowers (December 19, 2013)
IIGB researchers are members of an international team — the Amborella Genome Sequencing Project — that has
sequenced the genome of the Amborella plant. The genome sequence sheds new light on the origin of flowering plants,
including all major food crop species. Susan Wessler, a distinguished professor of genetics, led the IIGB team of
members on the project. Study results appear in the 20 December 2013 issue of the journal Science. The research paper
includes a full description of the analyses performed by the project, as well as implications for flowering plant research.
Amborella (Amborella trichopoda) is unique as the sole survivor of an ancient evolutionary lineage that traces back to
the last common ancestor of all flowering plants. The plant is a small understory tree found only on the main island of
New Caledonia in the South Pacific. An effort to decipher the Amborella genome — led by scientists at Penn State
University, the University at Buffalo, the University of Florida, the University of Georgia, and UC Riverside — is
uncovering evidence for the evolutionary processes that paved the way for the amazing diversity of the more than
300,000 flowering plant species we enjoy today. Comparative analyses of the Amborella genome are already providing
scientists with a new perspective on the genetic origins of important traits in all flowering plants — including all major
food crop species.
UCR Today dated December 19, 2013: http://ucrtoday.ucr.edu/19652
$450K NIFA Grant to Improve Citrus Production and Health (November 20, 2013)
Two IIGB plant geneticists, Mikeal Roose and Timothy Close, received a $450,000 grant from the National Institute
of Food and Agriculture (NIFA) of the U.S. Department of Agriculture to develop a genetic tool that citrus breeders can
use to improve the efficiency with which citrus varieties are bred. To address exotic diseases, breeders need
sophisticated tools that rapidly characterize citrus varieties and hybrids and locate genes for disease resistance, fruit
quality, and other essential traits. Mikeal Roose and Timothy Close, the principal investigator and co-principal
investigator, respectively, of the two-year grant, will lead the project on developing a “high-density SNP genotyping
array” for citrus — an important tool that geneticists and molecular breeders use to do genetic analyses of animals and
plants.
UCR Today dated November 20, 2013: http://ucrtoday.ucr.edu/19253
Discovery of How Mosquitos are Drawn to Human Skin (December 5, 2013)
IIGB researchers headed by associate professor Anandasankar Ray reported on December 5, 2013 in the
journal Cell that the receptors in the mosquito’s maxillary palp that detect carbon dioxide also detect skin odors as well,
thus explaining why mosquitoes are attracted to skin odor even in the absence of CO2. The new finding — that the
CO2-sensitive olfactory neuron, designated cpA, is also a sensitive detector of human skin — is critical not only for
understanding the basis of the mosquito’s host attraction and host preference, but also because it identifies this dual
receptor of CO2 and skin-odorants as a key target that could be useful to disrupt host-seeking behavior and thus aid in
the control of disease transmission.
Currently, CO2 is the primary lure in mosquito traps. Generating CO2 requires burning fuel, evaporating dry ice,
releasing compressed gas or fermentation of sugar — all of which is expensive, cumbersome, and impractical for use in
developing countries. Compounds identified in this study, like cyclopentanone, offer a safe, affordable and convenient
alternative that can finally work with surveillance and control traps.
Ray was joined in the study by the three IIGB co-first authors Genevieve M. Tauxe, Dyan MacWilliam and Sean
Michael Boyle; and Tom Guda. Boyle is now a postdoctoral researcher at Stanford University.
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Learning about Malaria Parasites’ DNA (December 11, 2013)
Trying to understand the biology of the malaria parasite Pasmodium, IIGB researchers led by associate professor
Karine Le Roch discovered low levels of DNA methylation in Plasmodium’s genome that may be critical to the
survival of the parasite. A paper about the findings of Le Roch and her team, titled “Genome-wide Mapping of the DNA
Methylation in the Human Malaria Parasite,” appears in the December 2013 issue of the journal Cell Host & Microbe.
Plasmodium parasites sickened more than 200 million people globally in 2010 and killed about 660,000. The parasite is
now showing resistance to artemisinin, the most effective drug for treating infected people. DNA methylation is a
biochemical process involving the modification of DNA that plays an important role in development and disease. DNA
methylation is so essential for normal development that abnormal DNA methylation patterns have been linked with
many diseases, including cancers and neurological disorders, such as Alzheimer’s disease.
Mutations in the parasite have made it resistant to the most effective drugs on the market. “We need a new drug every
five years,” Le Roch said, “because the parasites always find a way to develop resistance against a drug.” Le Roch’s
ultimate goal is to map the regulatory networks controlling the entire life cycle of the Plasmodium parasite. She reasons
that researchers really need to understand the entire biology of the parasite and how it replicates.
Le Roch was joined in the study by IIGB's Nadia Ponts, Lijuan Fu, Elena Y. Harris, Jing Zhang, Duk-Won D. Chung,
Michael Cervantes, Jacques Prudhomme, Evelien M. Bunnik, Elisandra M. Rodrigues, Stefano Lonardi, Glenn R. Hicks
and Yinsheng Wang; and Vessela Atanasova-Penichon and Enric Zehraoui at the French National Institute for
Agricultural Research (INRA), France.
USAID Grants Develop Improved Cowpea Varieties (October 30, 2013)
In October 2013, IIGB researchers received substantial funding by way of two grants from the U.S. Agency for
International Development (USAID) to continue their work on developing better yielding varieties of cowpea through
new genomic resources and marker-assisted breeding — research by which UC Riverside directly impacts cowpea
production in several countries in Africa. Cowpea is a protein-rich legume crop that plays a key role in sustaining food
security for people and their livestock. Immensely important in many parts of the world, particularly drought-prone
regions, it plays a central role in the diet and economy of hundreds of millions of people in Africa and Asia.
The grants support USAID’s agricultural research and capacity building work under Feed the Future, the U.S.
Government’s global hunger and food security initiative. The two grants total nearly $7 million. The first, creating the
Feed the Future Innovation Lab for Climate-Resilient Cowpea, is a nearly $5 million grant that supports a new five-year
cowpea-breeding project with partners in four West African nations: Burkina Faso, Ghana, Nigeria and Senegal. The
second grant, titled “Genetic improvement of cowpea to overcome biotic stress and drought constraints,” extends a tenyear project and brings additional funding of about $2 million over four-and-a-half years to UCR through the Feed the
Future Innovation Lab for Collaborative Research on Grain Legumes as a sub-contract with Michigan State University,
East Lansing.
Timothy Close, a professor of genetics in the Department of Botany and Plant Sciences, is the principal investigator of
the $5 million grant and Philip Roberts, a professor of nematology, is the principal investigator on the $2 million
USAID grant. Close and Roberts will be joined in the analysis by Stefano Lonardi, a professor of computer science
and engineering and a co-principal investigator on the team, who will help process large amounts of data that the
research projects will generate. The research projects will support a number of IIGB graduate students, postdoctoral
researchers, support staff and visiting scientists in the labs of Close, Roberts and Lonardi.
UCR Today October 30, 2013: http://ucrtoday.ucr.edu/18766
Discovery of Virus-killing Power in Mammals (October 10, 2013:
Researchers led by IIGB microbiologist Shou-wei Ding discovered that, like plants and invertebrate animals, mammals
use the RNA interference (RNAi) process to destroy viruses within their own cells. Their findings were published in the
Oct. 11 2013 issue of the journal Science.
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Until then, scientists were unable to prove that mammals use RNAi for killing viruses, but ironically, it was Ding’s
earlier research into plants, nematodes and fruit flies that helped him find the key: viruses have been outwitting that
innate protection in our cells by using proteins to suppress our virus-killing mechanism. Remove the suppressor protein
from the virus, Ding’s research discovered, and the subject’s body will quickly eliminate the virus using the RNAi
process, which sends out small interfering RNAs (siRNAs) to kill the disease.
These findings have opened the door to new ways to combat dangerous human viruses.
How Fungal Pathogen Causes Mold in Fruits and Vegetables (October 3, 2013)
IIGB/CEPCEB molecular plant pathologist Hailing Jin and her team discovered the mechanism by which an aggressive
fungal pathogen infects almost all fruits and vegetables.
The team discovered a novel “virulence mechanism” — the mechanism by which infection takes place — of Botrytis
cinerea. This pathogen can infect more than 200 plant species, causing serious gray mold disease on almost all fruits
and vegetables that have been around, even at times in the refrigerator, for more than a week.
Study results appeared in the Oct. 4 2013 issue of the journal Science.
The new study represents the first example of a fungal pathogen delivering RNA effectors, specifically small RNA
effector molecules, into host cells to suppress host immunity and achieve infection of the host plant.
Small RNAs guide gene silencing in a wide range of eukaryotic organisms. In the case of Botrytis cinerea, small RNAs
silence the expression of host defense genes, resulting in the host plant cells being less able to resist the fungal attack.
The process is similar to how protein effectors weaken host immunity in the case of most pathogens.
Next, Jin and colleagues plan to continue investigating if the novel mechanism they discovered also exists in other
aggressive pathogens.
Discovery of Insect DEET Olfactory Receptors (October 2, 2013)
IIGB researchers led by Anandasankar Ray identified which olfactory receptors insects use to sense and be repelled by
N,N-diethyl-m-toluamide, also known as DEET. This was a major breakthrough in the field of olfaction.
Further, the team of researchers has identified three safe compounds that mimic DEET and could one day be used to
prevent the transmission of deadly vector-borne diseases such as malaria, dengue, West Nile virus, and yellow fever.
Study results appeared online Oct. 2, 2013 in Nature.
The method Ray’s team used to identify the receptors examined in an unbiased fashion all the sensory neurons in the
insect, which was the key to successfully finding them. In their experiments, the researchers used the genetic model
system Drosophila melanogaster (fruit fly) that was genetically engineered in such a way that neurons activated by
DEET glowed fluorescent green. The researchers thus found the receptors, called Ir40a receptors, lining the inside of a
poorly studied region of the antenna called the sacculus.
Using novel chemical informatics strategies, Ray’s lab screened half a million compounds against the DEET receptor to
identify substitutes. A computer algorithm the team developed identified which compounds are not only predicted to be
strong repellents but also found naturally in fruits, plants or animals. The algorithm predicted nearly 200 natural DEET
substitutes; of which the researchers tested ten compounds. Of these, eight were strong repellents on flies, of which four
were tested in Aedesmosquitoes and found to be strong repellents. Of the four compounds, three are already approved
by the Food and Drug Administration as food additives.
With the help of UC Riverside’s Office of Technology Commercialization (OTC), Ray is exploring options for
commercializing the technology. OTC has already filed two patents on the research. When commercialized, the findings
by Ray’s team could have wide applications.
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Discovery of Link between Intestinal Bacterial and White Blood Cell Cancer (July 15, 2013)
IIGB researcher and plant pathologist James Borneman was co-corresponding author on a paper in Cancer Research
showing that oral administration of a single type of bacteria lowered systemic genotoxicity, an intermediate marker of
many cancers. Along with researchers from UCLA's Jonsson Comprehensive Cancer Center, it was demonstrated that
specific types of bacteria that live in the gut are major contributors to lymphoma, a cancer of the white blood cells.
Up to 1,000 different species of bacteria (intestinal microbiota) live in the human gut. Intestinal microbiota number 100
trillion cells; over 90 percent of the cells in the body are bacteria. The composition of each person's microbiome — the
body's bacterial make-up — is very different, due to the types of bacteria people ingest early in their lives, as well as the
effects of diet and lifestyle.
UCLA and UCR researchers wanted to determine whether differences in peoples' microbiomes affect their risk for
lymphoma, and whether changing the bacteria can reduce this risk. They studied mice with ataxia-telangiectasia (A-T),
a genetic disease that in humans and mice is associated with a high rate of B-cell lymphoma. They discovered that, of
mice with A-T, those with certain microbial species lived much longer than those with other bacteria before developing
lymphoma, and had less of the gene damage (genotoxicity) that causes lymphoma.
The scientists also were able to create a detailed catalog of bacteria types with promoting or protective effects on
genotoxicity and lymphoma, which could be used in the future to create combined therapies that kill the bacteria that
promote cancer (as antibiotics do) and increase the presence of the bacteria that protect from cancer (as probiotics do).
For additional information, please visit: UCLA Newsroom: http://newsroom.ucla.edu/portal/ucla/ucla-researchers-findlink-between-245945.aspx .
$2M Grant to Improve Undergraduate STEM Success (August 27, 2013)
IIGB/CEPCEB distinguished professor of genetics Susan Wessler is a co-principal investigator on a five-year grant of
$2 million from the National Science Foundation (NSF) to improve undergraduate success and retention in science,
technology, engineering and mathematics (STEM) majors, particularly for underrepresented students. Funding was
provided by the STEM Talent Expansion Program (STEP) of the NSF’s Division of Undergraduate Education. Only 10
large STEP grants were awarded nationwide by NSF during the current fiscal year funding cycle, out of 199 proposals
submitted.
The UC Riverside project, entitled “SL-CARE: Student Learning Communities and Research Engagement,” will focus
on dramatically expanding student participation in both first-year learning communities and early laboratory research
engagement courses in the College of Natural and Agricultural Sciences. Michael McKibben, the associate dean for
student academic affairs in CNAS, is the principal investigator of the grant.
The learning community cohorts are each comprised of 24 freshmen, offering participants an immediate peer group.
Members of each learning community take the same mathematics and science courses, and support one another. One of
the goals of SL-CARE is to break down any perceived barriers that entering freshmen may have, such as anxiety about
approaching faculty and the complexity of navigating university regulations and policies. The project also seeks to
expose students early to hands-on research, making their introductory science courses seem more meaningful and
relevant because they are participating directly in the process of scientific discovery.
For additional information, please visit: UCR Today August 27, 2013 (http://ucrtoday.ucr.edu/17216)
Gene Discovery Enhances Plant Immunity (August 14, 2013)
IIGB/CEPCEB geneticists Tokuji Tsuchiya and Thomas Eulgem reported in the Proceedings of the National
Academy of Sciences that they discovered a transposon that benefits its host organisms.
Working on the model plant Arabidopsis, Tsuchiya and Eulgem found that the COPIA-R7 transposon, which jumped
into the plant disease resistance gene RPP7, enhances the immunity of its host against a pathogenic microorganism that
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is representative of a large group of fungus-like parasites that cause various detrimental plant diseases.
The COPIA-R7 transposon affects RPP7 by interfering with the latter’s epigenetic code. In contrast to the well known
4-letter genetic DNA code, which provides instructions for the synthesis of proteins, the “epigenetic code” defines the
activity states of genes and determines to what extent their genetic information is utilized. Eulgem explained that the
transposition of transposons is typically inhibited by epigenetic silencing signals associated with their DNA. Such
epigenetic signals are like molecular “flags” or “tags” that are attached to special proteins, around which DNA is
wrapped.
A type of molecular flag, referred to as H3K9me2, prohibits transposons from being active and jumping in their host
genomes. Arabidopsis plants use H3K9me2-mediated messenger RNA processing to accurately set RPP7 activity to
precisely defined levels. In principle, scientists interested in crop improvement can now use the UCR discovery to
design new types of molecular switches based on H3K9me2-mediated messenger RNA processing. Using standard
molecular biological methods, transposon sequences that are naturally associated with this epigenetic signal can be
inserted into suitable genes and thereby alter the activity levels of these genes.
Next, Eulgem, an associate professor of plant cell biology and the senior author of the research paper, plans to expand
his lab’s research to how plants use the modulation of H3K9me2 levels at COPIA-R7 to dynamically adjust RPP7
activity when they are attacked by a pathogenic microorganism and to explore if this mechanism also applies to
additional genes.
For additional information, please visit:
• UCR Today August 14, 2013 (http://ucrtoday.ucr.edu/16990)
Patch Fights Mosquito-borne Diseases (July 26, 2013)
Initial research performed in the laboratory of IIGB/CDVR associate professor Anandasankar Ray and featured on the
cover of the journal Nature in 2011 led to the development of the world's first product that blocks mosquitoes' ability to
efficiently detect carbon dioxide, their primary method of tracking human blood meals. Ray’s lab identified volatile
odor molecules that can impair, if not completely disrupt, mosquitoes’ carbon dioxide detection machinery.
The intellectual property was licensed to Olfactor Laboratories Inc., a company that grew around the technology,
expanded the research, filed additional patents, and developed related technologies that led to the mosquito-warding
product
Called the Kite® Mosquito Patch, the product marks a significant advancement in the global fight against mosquitoborne diseases such as malaria, West Nile virus and dengue fever. The patch delivers mosquito-repelling compounds in
a simple, affordable and scalable sticker that can be used by individuals in regions impacted by malaria and other
mosquito-borne diseases. Simple and affordable, Kite is a colorful sticker, small enough to be worn virtually without
notice. It disburses the non-toxic compounds that provide individuals with up to 48 hours of protection from
mosquitoes. Estimated to cost a fraction of existing repellents, Kite is applied to clothing and can be used by people of
all ages, including infants and pregnant mothers. Kite’s technology is the culmination of years of development work on
a class of odor molecules, all of which are non-toxic compounds approved for human consumption by the U.S. Food
and Drug Administration.
UCR Today dated July 16, 2013: http://ucrtoday.ucr.edu/16352
Press Enterprise dated July 15, 2013: http://www.pe.com/local-news/riverside-county/riverside/riverside-headlinesindex/20130715-riverside-ucr-spawned-company-attacks-mosquitoes.ece
Chemical Discovery Improves Crop Yields (July 15, 2013)
A research team led by Sean Cutler, an IIGB/CEPCEB plant cell biologist, found a new drought-protecting chemical
that showed high potential for becoming a powerful tool for crop protection in the new world of extreme weather.
Named “quinabactin” by the researchers, the chemical mimics a naturally occurring stress hormone in plants that helps
the plants cope with drought conditions.
Working on Arabidopsis, a model plant used widely in plant biology labs, Cutler and his colleagues focused their efforts
on tinkering with one of the plant endogenous systems involved in drought responses. Plant leaves are lined with tiny
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pores, called stomata, which dynamically open and close to control the amount of water lost to the environment by
evaporation.
During drought the stomata close firmly to limit water loss. Behind the scenes, a small hormone called abscisic acid
(ABA) orchestrates the opening and closing of the pores. Since ABA itself is much too expensive for practical use in the
field by farmers, Cutler and his team searched through many thousands of molecules to identify inexpensive synthetic
chemicals that could activate the receptors by mimicking ABA. The team found and named quinabactin, a molecule
they show is almost indistinguishable from ABA in its effects, but much simpler chemically and therefore easier to
make than ABA. By studying how the new molecule activates the ABA receptors that are involved in drought tolerance,
the team also has learned more about the underlying control logic of the stress response system and provided new
information that can be used for others interested in developing similar molecules.
UCR Today dated July 15, 2013: http://ucrtoday.ucr.edu/16076
BBC News July 26, 2013: http://www.bbc.co.uk/news/science-environment-23253917
Other IIGB Research Projects:
Biofuel Production
Research in Eugene Nothnagel’s lab continues to focus on methylated sugars in plant cell wall polymers. They are
attempting to identify the methyltransferase that synthesizes 3-O-methyl-L-rhamnose in arabinogalactan proteins in the
moss Physcomitrella patens. During the period 7/1/13-6/30/14, we used recent updates of the Physcomitrella genome,
improved methods for conserved domain searches, and other new criteria to select five additional Physcomitrella genes
as new candidates to encode the target methyltransferase. Transgenic expression in tobacco was then selected as the
primary assay to test these five new candidate genes. Late in 7/1/13-6/30/14, each of the five new candidate genes from
Physcomitrella was transgenically expressed in tobacco. Evaluation of the transgenic tobacco plants is currently
underway. Engineering plants with higher or lower levels of polysaccharide O-methyltransferases could have
applications in biofuel production.
Plant Defense:
During this period, the Walling lab: (1) began a new project studying whitefly resistance in alfalfa using populations
selected for susceptibility and resistance. Using a genome-by-sequencing strategy, they mapped a major locus to
alfafla's chromosome 8. (2) demonstrated that tomato's wound-induced leucine aminopeptidase positively regulates
wound-induced genes but is a negative regulator of other stress response genes. These data indicate that LAP-A's role in
regulating nuclear gene expression is broader than initially recognized. Walling’s current NSF EAGER grant will
identify the nature of the LAP-A dependent chloroplast signal that controls nuclear gene expression. (3) In
collaboration with Li Fan's laboratory, the Walling lab determined the crystal structure of tomato's LAP-A. LAP-A is a
hexamer and unlike LAPs from other kingdoms, the tomato LAP-A binds two Mg 2+ ions in its reactive site and uses
sulfate as a co-factor. In conjunction with previous biochemical data, the crystal structure has allowed predictions of the
nature of LAP-A substrates. LAP-A is capable of hydrolyzing six heptamers at a time or five heptamers and one longer
polypeptide.
Virology:
Morris Maduro’s lab is completing a report on stochastic specification of endodermal ttisue in C. elegans for
publication later this year.
In collaboration with Dr. Jung at University of Southern California, I-Chueh Huang’s lab has identified that cholesterol
homeostasis is regulated by IFITM proteins. As cholesterol is an important component of cellular member, IFITMmediated accumulation of intracellular cholesterol resulted in viral entry block. In addition, they demonstrated that
IFITM proteins, especially IFITM1, blocks rift valley fever viruses but not papilloma viruses. During this period, they
also investigated the effect of an IFITM3 translational isoform, del21 IFITM3, encoded by rs12252-C on influenza A
virus infection. Different from previous studies, which concludes that del21 IFITM loses its ability to inhibit influenza
A virus replication and, therefore, rs12252-C is associated with poor clinical outcomes of influenza, their research
showed that del21 IFITM3 still strongly inhibits replication and entry of H1N1 influenza A viruses. These observations
suggested that factors other than viral entry restriction may contribute to the association between IFITM3
polymorphisms and the influenza prognosis.
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Sequencing of various citrus varieties in Mikeal Roose’s lab has improved scientists’ understanding of the origin of
important cultivar groups such as sweet oranges. UCR's contribution was one of the sequences analyzed, and additional
sequencing is in progress.
Computational Science/Bioinformatics:
Tao Jiang’s lab has developed new computational methods for (i) detecting differentially expressed genes by
combining RNA-Seq read counts with co-expression data, (ii) classifying microbial communities based on phylogenetic
information and (iii) assembling novel genomes with the help of closely related genome sequences. Their work on
isoform inference and differential expression was mentioned in Genetic Engineering & Biotechnology News
(http://www.genengnews.com/gen-articles/gene-expression-enters-transformative-times/5066/) .
Jason Stajich’s lab focused on genome sequencing recombinant inbred lines of rice and mapping transposable element
impact on phenotype and genome evolution. His lab developed a database of fungi resources – FungiDB http://fungidb.org and literature curation for Cryptococcus. They also established novel components in some fungal cell
walls and the resolution of a lineage of fungi in early branches of the fungal tree.
ORGANIZATIONAL AND MANAGEMENT STRUCTURE:
IIGB’s active membership is currently 93, from the following:
Depts (16):
Anthropology
Biochemistry
Bioengineering
Biology
Botany & Plant Sciences
Cell Biology & Neuroscience
Chemical & Environmental Engineering
Chemistry
Computer Science & Engineering
Electrical & Computer Engineering
Entomology
Mechanical Engineering
Nematology
Plant Pathology & Microbiology
Psychology
Statistics
Colleges/Schools (14):
Bourns College of Engineering (BCOE)
College of Agricultural & Natural Sciences (CNAS)
College of Humanities, Arts, and Social Sciences (CHASS)
School of Medicine (SOM)
Centers/Institutes (10):
Center for Conservation Biology (CCB)
Center for Disease Vector Research (CDVR)
Center for Glial-Neuronal Interactions (CGNI)
Center for Invasive Species Research (CISR)
Center for Nanoscale Science and Engineering (CNSE)
Center for Plant Cell Biology (CEPCEB)
Center for Research in Intelligent Systems (CRIS)
Institute for Research on World-Systems (IROWS)
Stem Cell Center
Water Science & Policy Center (WSPC)
During fiscal year 2013-14, the following faculty accepted an invitation to join the Institute for Integrative Genome
Biology.
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Weifeng Gu, Cell Biology & Neuroscience (eff. 1/1/14)
Naoki Yamanaka, Entomology (eff. 4/1/14)
The following faculty departed during fiscal year 2013-14:
Frank Sauer, Biochemistry (4/14)
There are currently 41 members in CEPCEB from 12 departments, and 22 members in CDVR from 6 departments.
Leadership:
The following assumed notable roles in FY 2013-14 within the IIGB Genomics Building:
Genomics Building Advisory Committee
Peter Atkinson, CNAS Divisional Dean
Natasha Raikhel, IIGB Director
Julia Bailey-Serres, CEPCEB Director (Alternate)
Anand Ray, CDVR Director
Sarjeet Gill, Professor, Cell Biology & Neuroscience
Stefano Lonardi, Professor, Computer Science & Engineering
Floor Contacts
Given the open design of the building, it is important that occupants of each floor have a primary contact for
inquiries, suggestions, and concerns. The following faculty have been designated with responsibility for
management of operations and space on their floor.
First Floor: Howard Judelson, Plant Pathology & Microbiology
Second Floor: Peter Atkinson, Entomology
Third Floor: Linda Walling, Botany & Plant Sciences
Fourth Floor: Natasha Raikhel/Julia Bailey-Serres, Botany & Plant Sciences
Emergency Contacts:
Building Supervisor for Emergency Conditions (BSEC):
Mien Van de Ven, SRA, Botany & Plant Sciences
Fran Holzer, SRA, Botany & Plant Sciences (Alternate)
Building Emergency Staff:
Blas, Michelle (Floor 1)
Ma, Kai-Wai (Floor 1)
Yamanaka, Naoki (Floor 2)
Chen, Yu-Chieh (Floor 2)
Mudal, Dinusha Maheepala (Floor 2)
Holzer, Frances (Floor 3)
Huan Wang (Floor 3)
Mandal, Jayati (Floor 3)
Li, Shengben (Floor 4)
Lavagi, Irene (Floor 4)
Sorenson, Reed (Floor 4)
26
FY 2013-14
OTHER ADMINISTRATIVE AND SUPPORT STAFF
For other administrative and support staff, please include Director along with other Center administrative support staff.
Source(s) of Funding
Name
Natasha Raikhel
Payroll Title
FTE
Director
Academic Administrator IV
0.00
1.00
Campus Allocation (Botany-100%)
Campus Allocation (60%); IIGB Genomics Sales &
Service Fund (40%)
Jocelyn Brimo
MSO II-Supervisor
1.00
Michelle Blas
Analyst II
1.00
Jennifer Douglas
Analyst I
1.00
CEPCEB Campus Allocation (96%); IIGB Genomics
Sales & Service Fund
IIGB Campus Allocation (46%); CEPCEB Campus
Allocation (34%); IIGB Genomics Sales & Service Fund
(20%)
Campus Allocation (100%)
Glenn Hicks
27
Fiscal Year 2013-14
ADVISORY COMMITTEE MEMBERS
For Advisory Committee members, please indicate name, title, and affiliation. Below the table, list dates of meetings held for the period under review and attach a
copy of the agenda for each meeting listed.
2013-14Genomics Building Advisory Committee
The Genomics Building Advisory Committee is authorized to assess space allocations (general purpose, conference/public,
research, bioinformatics training, and office/study) and make final decisions regarding unresolved procedural issues and concerns
affecting occupants on floors or throughout the Genomics Building. Committee membership includes the IIGB director, IIGB
center directors (Center for Plant Cell Biology (Alternate), Center for Disease Vector Research), two outside members (nonbuilding residents), and the divisional dean responsible for facilities and research as an ex officio member. Current members are
below.
Peter Atkinson, CNAS Divisional Dean, Life Sciences and Facilities
Natasha Raikhel, IIGB Director
Julia Bailey-Serres, CEPCEB Director
Anandasankar Ray, CDVR Director
Sarjeet Gill, Professor, Cell Biology & Neuroscience
Stefano Lonardi, Professor, Computer Science & Engineering
28
Fiscal Year 2013-14
IIGB PUBLICATIONS (Information dependent on PI response.)
CHEMICAL BIOLOGY
Z. Chen and H-w. Ai, “A Highly Responsive and Selective Fluorescent Probe to Image Physiological Hydrogen Sulfide”,
Biochemistry, 2014, DOI: 10.1021/bi500830d
Z. Chen, W. Ren, Q.E. Wright and H-w. Ai, “Genetically Encoded Fluorescent Probe for the Selective Detection of
Peroxynitrite”, J. Am. Chem. Soc., 2013, 135: 14940-14943.
CHROMATIN-MODIFYING COFACTORS AND GENE REGULATION
Zhang, N., Ichikawa, W., Faiola, F., Lo, S.-Y., Liu, X., and Martinez, E. (2014) MYC interacts with the human STAGA
coactivator complex via multivalent contacts with the GCN5 and TRRAP subunits. Biochim. Biophys. Acta (BBA)-Gene
Regulatory Mechanisms, 1839, 395-405.
COMPUTATIONAL BIOLOGY/BIOINFORMATICS
Yadav RK, Tavakkoli M, Xie M, Girke T, Reddy GV (2014) A high-resolution gene expression map of the Arabidopsis shoot
meristem stem cell niche. Development: 141, 2735–2744.
Worden N, Girke T, Drakakaki G (2014) Endomembrane dissection using chemically induced bioactive clusters. Methods Mol
Biol: 1056, 159-168.
Backman TW, Girke T (2014) Cheminformatic analysis of high-throughput compound screens. Methods Mol Biol: 1056, 145157.
Juntawonga P, Girke T, Bazina J, Bailey-Serres S (2014) Translational dynamics revealed by genome-wide profiling of ribosome
footprints in Arabidopsis. PNAS: 111, E203-212.
A. Polishko, E. Bunnik, K. Le Roch, S. Lonardi (2014) “PuFFIN: A Parameter-free Method toBuild Nucleosome Maps from
Paired-end Reads”, to appear in BMC Bioinformatics,.
H. Chen, S. Lonardi, J. Zheng (2014) “Deciphering Histone Code of Transcriptional Regulation in Malaria Parasites by Largescale Data Mining”, Computational Biology and Chemistry, vol. 50, pp. 3–10.
E. M. Bunnik, A. Polishko, J. Prudhomme, N. Ponts, S. S. Gill, S. Lonardi, K. G. LeRoch (2014) “DNA-encoded nucleosome
occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum”, BMC Genomics,
vol. 15, no. 328.
M. Pottorff, P. A. Roberts, T. J Close, S. Lonardi, S. Wanamaker, J. D. Ehlers (2014) “Identification of candidate genes and
molecular markers for heat-induced brown discoloration of seed coats in cowpea [Vigna unguiculata (L.) Walp]”, BMC
Genomics, vol. 15 no. 328, 2014.
E. Bao, T. Jiang and T. Girke. (2014) AlignGraph: algorithm for secondary de novo genome assembly guided by closely related
references. Bioinformatics 30(12) pp. i319-i328, 2014; Also presented at the 22nd Annual International Conference on
Intelligent Systems for Molecular Biology (ISMB), July, 2014, Boston, MA.
O. Tanaseichuk, J. Borneman and T. Jiang (2014) Phylogeny-based classification of microbial communities. Bioinformatics
30(4):449-456.
E. Yang and T. Jiang (2014) GDNorm: An improved Poisson regression model for reducing biases in Hi-C data. To be
presented at the 14th Workshop on Algorithms in Bioinformatics (WABI), Wroclaw, Poland, Sept. 8-10, 2014.
N. Ponts, L. Fu, E. Y. Harris, J. Zhang, D.-W. D. Chung, E. Bunnik, M. C. Cervantes, J. Prudhomme, V. Atanasova-Penichon, E.
Zehraoui, E. M. Rodrigues, S. Lonardi, G. R. Hicks, Y. Wang, K. G. Le Roch (2013) “Genome-scale discovery of DNA
methylations in the human malaria parasite Plasmodium falciparum”, Cell Host & Microbe, vol.14, no.6, pp. 696–706.
E.W. Yang, T. Girke and T. Jiang (2013) Differential gene expression analysis using coexpression and RNA-Seq data.
Bioinformatics 29(17):2153-2161.
S. Roy, L. Poidevin, T. Jiang, and H.S. Judelson (2013) Novel core promoter elements in the oomycete pathogen Phytophthora
infestans and their influence on expression detected by genome-wide analysis. BMC Genomics 14:106.
Scranton MA, Fowler JH, Girke T, Walling LL (2013) Microarray Analysis of Tomato’s Early and Late Wound Response
Reveals New Regulatory Targets for Leucine Aminopeptidase A. PLoS ONE: 8, e77889.
Choy A, Severo MS, Sun R, Girke S, Gillespie JJ, Pedra J (2013) Decoding the Ubiquitin-Mediated Pathway of Arthropod
Disease Vectors. PLoS ONE: 8, e78077.
Wang Y, Backman T, Horan K, Girke T (2013) fmcsR: Mismatch Tolerant Maximum Common Substructure Searching in R.
Bioinformatics: 29, 2792-2794.
Zou Z, Saha TT, Roy S, Shin SW, Backman TW, Girke T, White KP, Raikhel AS (2013) Juvenile hormone and its receptor,
methoprene-tolerant, control the dynamics of mosquito gene expression. PNAS: 110: E2173-2181.
Yadav RK, Perales M, Gruel J, Ohno C, Heisler M, Girke T, Jönsson H, Reddy GV (2013) Plant stem cell maintenance involves
direct transcriptional repression of differentiation program. Mol Syst Biol: 9, 654ff.
29
Fiscal Year 2013-14
Luhua S, Hegie A, Suzuki N, Shulaev E, Luo X, Cenariu D, Ma V, Kao S, Lim J, Gunay MB, Oosumi T, Lee SC, Harper J,
Cushman J, Gollery M, Girke T, Bailey-Serres J, Stevenson RA, Zhu JK, Mittler R (2013) Linking genes of unknown
function with abiotic stress responses by high-throughput phenotype screening. Physiol Plant: 148, 322-33.
Bao E, Jiang T, Girke T (2013) BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences.
Bioinformatics: 29, 1250-1259.
Atamian HS, Chaudhary R, Cin VD, Bao E, Girke T, Kaloshian I (2013) In planta expression or delivery of potato aphid
Macrosiphum euphorbiae effectors Me10 and Me23 enhances aphid fecundity. Mol Plant Microbe Interact: 26, 67-74.
Yadav RK, Snipes S, Girke T, Reddy GV (2013) Gene expression analysis of shoot apical meristem cell types. Methods Mol
Biol: 959, 235-245.
Mustroph A, Zanetti ME, Girke T, Bailey-Serres J (2013) Isolation and Analysis of mRNAs from Specific Cell Types of Plants
by Ribosome Immunopurification. Methods Mol Biol: 959, 277-302.
Zhao H, Sun R, Albrecht U, Padmanabhan C, Wang A, Coffey MD, Girke T, Wang Z, Close TJ, Roose M, Yokomi RK,
Folimonova S, Vidalakis G, Rouse R, Bowman KD, Jin H (2013) Small RNA profiling reveals phosphorus deficiency as a
contributing factor in symptom expression for citrus Huanglongbing disease. Mol Plant: 6, 301-310.
DRUG DISCOVERY
Teasdale M., Prudhomme, J., Torres M., Braley M.; Cervantes S., Bhatia S., La Clair J., Le Roch K. †, and Kubanek J†.
Pharmacokinetics, metabolism, and in vivo efficacy of the antimalarial natural product bromophycolide A. ACS Medicinal
Chemistry Letters 2013. Oct 10;4(10):989-993. † Contributed equally to this work, Co-corresponding Authors.
Zafrir Ilan E, Torres MR., Prudhomme J., Le Roch K., Jensen PR., and Fenical W. Farnesides A and B, Sesquiterpenoid
Nucleoside Ethers from a Marine-Derived Streptomyces sp., strain CNT-372 from Fiji. J Nat Prod. 2013 Sep 27;76(9):18158. doi: 10.1021/np400351t. Epub 2013 Aug 29
ENTOMOLOGY, MICROBIOLOGY, IMMUNOLOGY
Hickman, A.B., Ewis, E.H., Li, X., Knapp, J.A., Laver, T., Doss, A.L., Tolun, G, Steven A.C., Grishaev, A., Bax, A., Atkinson,
P.W., Craig, N.L., Dyda, F. (2014) Structural Basis for Transposon End Recognition by Hermes, an Octameric hAT DNA
Transposase from Musca domestica. Cell, 158(2):353-367.
Wright, J. A., R. C. Smith, X. Li, N. L. Craig and P. W. Atkinson (2013). IPB7 transposase behavior in Drosophila melanogaster
and Aedes aegypti. Insect Biochem. Mol Biol. 43. 899-906.
GENOMICS/GENETICS
Polishko A., Bunnik EM., Le Roch K., Lonardi S. PuFFIN - A Parameter-free Method to Build Nucleosome Maps from Pairedend Reads BMC Bioinformatics, In press 2014.
Bunnik EM., Polishko A., Prudhomme J., Ponts N., Gill SS., Lonardi S. and Le Roch KG. DNA-encoded nucleosome
occupancy regulates transcriptional levels in the human malaria parasite Plasmodium falciparum. BMC Genomics. 2014 May
8;15:347. doi: 10.1186/1471-2164-15-347.
Ay F., Bunnik EM., Varoquaux N., Bol SM., Prudhomme J., Vert JP., Stafford Noble W., Le Roch KG. The three-dimensional
model of the P. falciparum genome reveals the role of genome architecture in regulating gene expression. Genome Res. 2014
Jun;24(6):974-88. doi: 10.1101/gr.169417.113. Epub 2014 Mar 26. Interviews and several media highlights around the
world.
Hamilton MJ., Lee M., and Le Roch KG. The ubiquitin system: an essential component to unlocking the secrets of malaria
parasite biology. Molecular BioSystems. 2014 Jan 30. [Epub ahead of print]
Bunnik EM., Chung DW, Hamilton M., Ponts N., Prudhomme J., and Le Roch KG. Polysome Profiling reveals Translational
Control of Gene Expression in the Human Malaria Parasite Plasmodium falciparum. Genome Biol. 2013 Nov
22;14(11):R128. [Epub ahead of print]
Ponts N., Fu L., Harris EY., Zhang J., Chung DW, Cervantes MC., Prudhomme J., Atanasova-Penichon V., Zehraoui E.,
Bunnik E., Rodrigues EM., Lonardi S, Hicks GR., Wang Y and Le Roch KG. Genome-scale discovery of DNA
methylations in the human malaria parasite. Cell Host & Microbe 2013 – Dec 11; 14 – 6(696-706)
Bunnik EM. and Le Roch KG. An introduction to functional genomics and systems biology. Advances in Wound Care. 2013
Nov;2(9):490-498.
Cervantes S., Bunnik EM., Saraf S., Conner CM., Escalante E., Sardiu ME, Ponts N., Prudhomme J., Florens L., and Le Roch
KG. The multifunctional autophagy pathway in the human malaria parasite, Plasmodium falciparum. Autophagy. 2013 Nov
11;10(1). [Epub ahead of print]
30
Fiscal Year 2013-14
GENOMICS
James, T.Y., Pelin, A., Bonen, L., Ahrendt, S., Sain, D., Corradi, N., Stajich, J.E (2013) Shared signatures of parasitism and
phylogenomics unite the Cryptomycota and Microsporidia. Current Biology. Vol. 23: 16 p.1548-1553. (Refereed, Electronic)
Website: http://dx.doi.org/10.1016/j.cub.2013.06.057.
Traeger, S., Altegoer, F., Freitag, M., Gabaldon, T., Kempken, F., Kumar, A., Marcet-Houben, M., Pöggeler, S., Stajich, J.E.,
Nowrousian, M (2013) The Genome and Development-Dependent Transcriptome of Pyronema confluens: a Window into
Fungal Evolution. PLoS Genetics. Vol. 9: 9 p.e1003820. (Refereed, Electronic)
Website: http://dx.doi.org/10.1371/journal.pgen.1003820.
Janbon, G., Ormerod, K.L., Paulet, D., Byrnes III, E.J., Chatterjee, G., Yadav, V., Hon, C., Billmyre, R.B., Brunel, F., Bahn, Y.,
Chen, W., Chen, Y., Chow, E.W., Coppée, J., Floyd-Averette, A., Gaillardin, C., Gerik, K.J., Goebels, C., Goldberg, J.,
Gonzalez-Hilarion, S., Gujja, S., Hamlin, J.L., Hsueh, Y., Ianiri, G., Jones, S., Kodira, C.D., Lam, W., Marra, M.A., Mesner,
L.D., Mieczkowski, P.A., Moyrand, F., Nielsen, K., Rossignol, T., Schein, J.E., Shun, S., Wood, I.A., Zeng, Q., Neuvéglise,
C., Newlon, C., Perfect, J.R., Lodge, J.K., Idnurm, A., Stajich, J.E., Kronstad, J.W., Sanyal, K., Heitman, J., Fraser, J.A.,
Cuomo, C.A., Dietrich, F.S (2014) The genome sequence of Cryptococcus neoformans var. grubii reveals complex
mechanisms of RNA expression and virulence plasticity. PLoS Genetics. Vol. 10: 4 p.e1004261. 26p. (Refereed, Electronic)
Website: http://dx.doi.org/10.1371/journal.pgen.1004261.
Inglis, D.O., Skrzypek, M.S., Liaw, E., Moktali, V., Sherlock, G., Stajich, J.E (2014) Literature-based gene curation and a
proposed genetic nomenclature for Cryptococcus. Eukaryotic Cell. Vol. 13: 7 p.878-883. (Refereed, Electronic)
Website: http://dx.doi.org/10.1128/EC.00083-14.
Treseder, K.K., Maltz, M.R., Hawkins, B.A., Fierer, N., Stajich, J.E., McGuire, K.L. (2014) Evolutionary histories of fungi are
reflected in their continental-scale biogeography. Ecology Letters. Vol. 17: 9 p.1086-93. (Refereed, Electronic)
Website: http://dx.doi.org/10.1111/ele.12311.
FUNCTIONAL GENOMICS
Haney, R., N. Ayoub, T. Clarke, C. Hayashi, and J. Garb. 2014. Dramatic expansion of the black widow toxin arsenal
uncovered by multi-tissue transcriptomics and venom proteomics. BMC Genomics 15:366.
Clarke, T., J. Garb, C. Hayashi, R. Haney, A. Lancaster, S. Corbett, and N. Ayoub. 2014. Multi-tissue transcriptomics of the
black widow spider reveals expansions, co-options, and functional processes of the silk gland gene toolkit. BMC Genomics
15:365.
Chaw, R., Y. Zhao, J. Wei, N. Ayoub, R. Allen, K. Atrushi, and C. Hayashi. 2014. Intragenic homogenization and multiple
copies of prey-wrapping silk genes in Argiope garden spiders. BMC Evolutionary Biology 14:31.
Lane, A., C. Hayashi, G. Whitworth, and N. Ayoub. 2013. Complex gene expression in the dragline silk producing glands of the
Western black widow (Latrodectus hesperus). BMC Genomics 14:846.
MICROBIAL ECOLOGY
Yamamoto ML, Maier I, Dang AT, Berry D, Liu J, Ruegger PM, Yang J, Soto PA, Presley LL, Reliene R, Westbrook AM, Wei
B, Loy A, Chang C, Braun J, Borneman J, Schiestl RH. 2013. Intestinal bacteria modify lymphoma incidence and latency by
affecting systemic inflammatory state, oxidative stress, and leucocyte genotoxicity. Cancer Research 73:4222-4232.
McHardy, Ian, Maryam Goudarzi, Maomeng Tong, Paul M Ruegger, Emma Schwager, John R
Weger, Thomas G Graeber,
Justin L Sonnenburg, Steve Horvath, Curtis Huttenhower, Dermot PB McGovern, Albert J Fornace, James Borneman,
Jonathan Braun. 2013. Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface
reveals exquisite inter-relationships. Microbiome 1:17.
McHardy Ian, Xiaoxiao Li, Maomeng Tong, Paul Ruegger, Jonathan Jacobs, James Borneman, Peter Anton, Jonathan Braun.
2013. HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota. Microbiome
1:26..
Tong M, McHardy I, Ruegger P, Goudarzi M, Kashyap PC, Haritunians T, Li X, Graeber TG, Schwager E, Huttenhower C,
Fornace AJ Jr, Sonnenburg JL, McGovern DP, Borneman J, Braun J. 2014. Reprograming of gut microbiome energy
metabolism by the FUT2 Crohn's disease risk polymorphism. ISME J. doi: 10.1038/ismej.2014.64.
Tong, Maomeng, Xiaoxiao Li, Laura Wegener Parfrey, Bennett Roth, Andrew Ippoliti, Bo Wei, James Borneman, Dermot
McGovern, Daniel N Frank, Ellen Li, Steve Horvath, Rob Knight, Jonathan Braun. 2014. A modular organization of the
human intestinal mucosal microbiota and its association with inflammatory bowel disease.
Ruegger PM, Clark RT, Weger JR, Braun J, Borneman J. 2014. Improved resolution of bacteria by high throughput sequence
analysis of the rRNA internal transcribed spacer. J Microbiol Methods. doi: 10.1016/j.mimet.2014.07.001.
PLANT DEVELOPMENT
Mittal, A., Balasubramanian, R., Cao, J., Singh, P., Subramanian, S., Hicks, G., Nothnagel, E.A., Abidi, N., Janda, J., Galbraith,
D.W., and Rock, C.D. (2014) TOPOISOMERASE 6B is Involved in Chromatin Remodeling Associated with Control of
31
Fiscal Year 2013-14
Carbon Partitioning into Secondary Metabolites and Cell Walls, and Epidermal Morphogenesis in Arabidopsis. Journal of
Experimental Botany, 65, 4217-4239.
PLANT GENOMICS
Wu, G. A., Prochnik, S., Jenkins, J. et al. (2014) Sequencing of diverse mandarin, pummelo and orange genomes reveals
complex history of admixture during citrus domestication. Nature Biotech doi:10.1038/nbt.2906.
PLANT DEFENSE
Scranton, M.A., Fowler, J.H., Girke, T., Walling, L.L. (2013) Microarray analysis of tomato's early and late wound response
reveals new regulatory targets for leucine aminopeptidase A. PLoS One, 8, e77889 19p
Duprez, K., Scranton, M.A., Walling, L.L. Fan, Li (2014) Crystal structure of the tomato wound-induced leucine aminopeptidase
sheds light on its substrate properties.Acta Crystallographica Section D, 70, 1649-1658.
PLANT IMMUNITY
Chaudhary, R., H. S. Atamian, Z. Shen, S. P. Briggs, and I. Kaloshian. 2014. GroEL from the endosymbiont Buchnera
aphidicola betrays the aphid by triggering plant defense. Proc. Natl. Acad. Sci. USA 111:8919-8924.
Peng, H.-C. and I. Kaloshian. 2014. The tomato leucine-rich repeat receptor-like kinases SlSERK3A and SlSERK3B have
overlapping functions in bacterial and nematode innate immunity. PLoS One DOI: 10. 1371/journal.pone.0093302
Weiberg, A., M. Wang, F.-M. Lin, H. Zhao, Z. Zhang, I. Kaloshian, H.-D. Huang, and H. Jin. 2013. Fungal small RNAs
suppress plant immunity by hijacking host RNA interference pathways. Science 342:118-123.
PLANT MOLECULAR BIOLOGY
Okamoto M, Peterson FC, Defries A, Park S-Y, Endo A, Nambara E, Volkman BF, Cutler SR (2013) Activation of dimeric
ABA receptors elicits guard cell closure, ABA-regulated gene expression, and drought tolerance. Proc Natl Acad Sci U S A
doi:10.1073/pnas.1305919110.
PLANT PATHOLOGY & MICROBIOLOGY
Xiang, Q. and Judelson, H.S. (2014) Myb transcription factors and light regulate sporulation in the oomycete Phytophthora
infestans. PloS One 9, e392086.
Gaulke C, Porter M, Han YH, Sankaran-Walters S, Grishina I, George M, Dang A, Ding SW, Jiang G, Korf I, Dandekar S (2014)
Intestinal epithelial barrier disruption through altered mucosal microRNA expression in human immunodeficiency virus and
simian immunodeficiency virus infections. J Virol 88:6268–6280
Jiang H, Lei R, Ding SW, Zhu S. (2014) Skewer: A fast and accurate adapter trimmer for Next-Generation Sequencing (NGS)
paired-end reads. BMC Bioinformatics 15:182. doi:10.1186/1471-2105-15-182.
Guo X, Zhang R, Wang J, Ding SW, Lu R. (2013) Homologous RIG-I-like helicase proteins direct RNAi-mediated antiviral
immunity in C. elegans by distinct mechanisms. Proc Natl Acad Sci USA 110:16085-90
Li Y, Lu JF, Han YH, Fan XX and Ding SW. (2013) RNA interference functions as an antiviral immunity mechanism in
mammals. Science 342:231-234 (featured in Science 342:207-208, Nat Struct Mol Biol 20:1239–41, Cell Host Microbe
4:374–378, Nat Rev Genetics doi:10.1038/nrg3616 and Nat Rev Microbiol 11:820)
Maillard PV, Ciaudo C, Marchais A, Li Y, Jay F, Ding SW, Voinnet O. (2013) Antiviral RNA interference in mammalian cells.
Science 342:235-238 (Li Y is a postdoc in my lab).
PROTEOMICS
Shi J, Pagliaccia D, Morgan R, Qiao Y, Pan S, Vidalakis G, Ma W (2014) Novel diagnosis for citrus stubborn disease by
detection of a spiroplasma citri-secreted protein. Phytopathology. 104(2): 188-95.
Ashby J, Schachermeyer S, Pan S, Zhong W (2013) Dissociation-based screening of nanoparticle-protein interaction via flow
field-flow fractionation. Anal Chem 85(15): 7494-501.
VIROLOGY
Amini-Bavil-Olyaee S, Choi YJ, Lee JH, Shi M, Huang IC, Farzan M, Jung JU. 2013. The antiviral effector IFITM3 disrupts
intracellular cholesterol homeostasis to block viral entry. Cell Host Microbe.; 13(4):452-64.
Mudhasani R, Tran JP, Retterer C, Radoshitzky SR, Kota K, Altamura LA, Smith JM, Packard BZ, Kuhn JH, Costantino J,
Garrison AR, Schmaljohn CS, Huang IC, Farzan M, Bavari S. 2013. IFITM-2 and IFITM-3 but not IFITM-1 restrict rift
valley fever virus. J Virol.; 7(15):8451-64.
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Fiscal Year 2013-14
Bailey CC, Kondur HR, Huang IC, Farzan M. 2013. Interferon-induced transmembrane protein 3 is a type II transmembrane
protein. J Biol Chem.; 288(45):32184-93.
Warren CJ, Griffin LM, Little AS, Huang IC, Farzan M, Pyeon D. 2014. The antiviral restriction factors ifitm1, 2 and 3 do not
inhibit infection of human papillomavirus, cytomegalovirus and adenovirus. PLoS One; 14;9(5):e96579. PMCID:
PMC4020762
Williams DEJ, Wu WL, Grotefend CR, Nguyen NT, Chung C, Chung YH, Farzan M, Huang IC. 2014. IFITM3 polymorphism
33
Fiscal Year 2013-14
DISTINGUISHED AWARDS RECEIVED OR HELD BY INSTITUTE PARTICIPANTS
Please list prestigious awards received or held by Center participants from professional organizations, industry, etc.
Recipient Name
AI, HUANG, Cell Biology &
Neuroscience
AI, HUANG, Cell Biology &
Neuroscience
MORIKIS, DIMITRIOS,
Bioengineering
LUCAS, MITCHEL
Genetics, Genomics and
Bioinformatics Graduate
Program (T. Close Lab)
RAY, ANANDASANKAR
Entomology
RAIKHEL, ALEXANDER
Entomology
BAILEY-SERRES, JULIA
Botany & Plant Sciences
MARTINEZ, ERNEST
BIOCHEMISTRY
Name of Award
Year Award
Received
Hellman Fellow (UCR)
2013
NSF CAREER Award
2014
Carolyn K. McGillvray Memorial Award for Macuolar Degeneration Research, BrightFocus
Foundation
Food and Agricultural Sciences National Needs Graduate and Postgraduate Fellowship (NNF),
awarded by the USDA National Institute of Food and Agriculture
2013
City of Riverside Mayor's Innovation Honoree of the Month Award
2013
UCR Faculty Research Lecturer for 2013
2013
Thomson Reuters Highly Cited Researcher
2014
Director, MARC U-STAR Undergraduate Research Training Program funded by NIH -General
Medical Sciences
2013
34
2013
FY 2013-14
EVENTS SPONSORED BY CENTER
Title of Event
IIGB/CEPCEB/CDVR/GGB
/ IGERT Seminars
IIGB Tours
CEPCEB REU Poster
Symposium
CEPCEB 11th Award
Symposium
Southern California
Instrumentation Facility
Consortium
Type of Event
Date of Event
Number of
Attendees
Names of
Featured Speakers
Title and Affiliation of
Featured Speakers
Seminar Series
See Attachment E
~25
See Attachment E
Tours of
Instrumentation
Facilities (microscopy,
bioinformatics,
proteomics,
genomics)
Poster Symposium
See Attachment D
See
Attachment D
Microscopy: David Carter
Bioinformatics: Thomas Girke
Proteomics: Songqin Pan
Genomics: Glenn Hicks
August 16, 2013
~50
REU Students
Lecture/Award
Ceremony
December 18, 2013
~90
George W. Beadle Professor of
Biology/HHMI-GBMF Investigator, California
Institute of Technology
Workshop/Meeting
May 16-17, 2013
12
Noel T. Keen Special Lecturer:
Elliot Meyerowitz;
Internal Speakers: see
Attachment B
Charles Nicolet, Ph.D.
Vincent Funari,, Ph.D.
Technical Director, Genomics Core
Cedars-Sinai Medical Center
Melanie L. Oakes, PhD
Genomics High-Throughput Facility Manager
University of California, Irvine
Academic Coordinator, Imaging/Microscopy
Asst. Professor/Dir. of Bioinf Facilities
Academic Coordinator, Proteomics
IIGB Academic Administrator
Director of Sequencing Technology,
University of Southern California
Suzanne Sandmeyer
IIGB Forum
Forum
May 27, 2014
1st Annual CEPCEB
Postdoc Symposium
Symposium
June 11, 2014
2nd International
Hemipteran Plant
Interactions Symposium
Symposium
June 22-26, 2014
~50
147
Natasha Raikhel
Julia Bailey-Serres
Anandasankar Ray
Xuemei Chen
Shou-wei Ding
Thomas Girke
Glenn Hicks
Songqin Pan
Keynote Speaker: Hailing Jin;
Internal Speakers: See
Attachment C
UCR Organizers:
Linda Walling, James Ng,
Gregory Walker, Isgouhi
Kaloshian
Other Invited Speakers: See
Attachment F
35
Professor/Director of Genomics Highthroughput Facility
University of California, Irvine
IIGB Director
CEPCEB Director
CDVR Director
Professor, Botany & Plant Sciences
Professor, Plant Pathology & Microbiology
Assoc. Professor, Botany & Plant Sciences
Academic Administrator, Institute for
Integrative Genome Biology
Academic Coordinator, Proteomics
FY 2013-14
SPACE UTILIZED BY CENTER
Fiscal Year Period:
Center Name:
Please provide explanations or descriptions as required. Changes to number of square feet, space configuration, or space use
should be described.
Space Description
Square Feet
Office Support
2316 (2018 Keen Hall; 1102/1102A
Genomics)
1646*
Research
6905**
Meeting Space
Special Use
Miscellaneous
273 (misc. storage, incl. AV
equipment)
Total Assigned Space
11.140
* Space related to offices, office equipment, and support services at Keen Hall and Genomics building
** Research and support space at Keen Hall and Genomics Building.
36
Fiscal Year 2013-14
SPONSORED FUNDING PROPOSALS AND AWARDS
Current Awards: IIGB
Proposal Title
Exploration, Conservation
& Development of Marine
Biodiversity in Fiji
Understanding the Role of
Nucleosome Turnover in the
Malaria Parasite Infectious
Cycle
The Spatial Organization of
the Plasmodium Genome
Throughout its Infectious
Cycle
Gene silencing as an
antiviral defense in animal
cells
Genetic dissection of the
RNAi-mediated antiviral
immunity in C. elegans
Understanding the global
virus distribution in tomato
and development of
translation genomic tools to
accelerate tomato breeding
for virus resistance
CPGS: Genome-wide
impact of mPing
transposition on rice
phenotypic diversity.
New Active Transposons
for Mosquito Genomics
Functional Characterization
of the Long Non-Coding
RNA Scirocco in
Development and Cancer
Functional Definition of
MYC Acetylation (F31)
Core promoter-selective
transcription by RNA
polymerase II
Collaborative Research:
Functional Genomics of
Spider Silk Synthesis and
Fiber Performance within
the Western Black Widow
and among Cob-Web
Weaving Spiders
High-throughput synthetic
biology for natural products
discovery
EAGER: Leucine
Aminopeptidase - Regulator
of the Stress-Induced
Co-PIs
Funding
Agency
Period of Funding
Le Roch
NIH
5/2009 – 4/2014
$110,000
Lonardi
NIH
9/2010 – 8/2015
$1,600,000
Le Roch
and Noble
NIH
7/2013 – 6/2017
$1,000,000
Ding
NIH
5/2012 – 4/2017
$2,495,946
NIH
5/2010 – 4/2014
$1,150,600
NIFA, USDA
10/2012 – 9/2016
NSF
William M.
Keck
Foundation
3/2011 – 2/2015
NIH
3/2014 – 8/2017
$913,360
NIH
9/2011 – 8/2016
$172,765
Martinez
NSF
9/2010 – 8/2015
$659,669
Hayashi
NSF
6/2010 – 6/2015
$200,713
9/2013 – 8/2014
$65,000
8/2014 – 7/2015
$126,142
PI
Total Award
Hay
Le Roch
Ding
Maduro
Ding
Wessler
Stajich
Wessler
Atkinson,
Stajich
Martinez
Hurd
Martinez
Borkovich
Stajich,
Larive
UCR
Chancellor
Walling
Pan
NSF
37
1/1/2011 –
12/31/2013
$498,655
$4,798,864
$1,000,000
Fiscal Year 2013-14
Stromal Proteome
Hemipteran-Plant
Interactions Symposium
RDR1 regulation and
function in plant virus
defense
The role of RNA-dependent
RNA polymerase 1 in plant
virus defense
Algorithms and Software
Tools for Epigenetics
Research
WaterSENSE
Developmental Buffering in
a Gene Regulatory Network
Development And
Application Of A HighDensity SNP Genotyping
Array For Citrus
MRI: Acquisition of a Big
Data Compute Cluster for
Interdisciplinary Research
Reducing losses to potato
and tomato late blight by
monitoring pathogen
populations, improved
resistant plants, education,
and extension
Feed the Future Innovation
Lab: Advanced Tools for
Breeding ClimateResilient Cowpeas
Acquisition of a Scalable
Storage Cluster for Data
Intensive NIH Research
CC*IIE Networking
Infrastructure: UCR's
Science DMZ
Impact of maternal obesity
during pregnancy on the
development of the fetal
immune system
Collaborative Research:
ABI Innovation: GenomeWide Inference of mRNA
Isoforms and Abundance
Estimation from Biased
RNA-Seq Reads
Novel Bacteria Affect DNA
Damage in Mice
The mechanisms of IFITM-
Walker
Walling,
Kaloshian,
Ng
USDA
1/2014 – 9/2014
$35,510
Ding
US Israel BNSF
11/2012 –
10/2016
$80,000
Ding
BARD (USIsrael)
8/2012 – 7/2015
$162,000
NSF
7/2013 – 6/2016
$1,000,000
NSF-IGERT
2012-2017
$3,000,000
NSF
2013-2015
$550,000
USDA-NIFA
9/1/2013 –
8/31/2015
$450,000
Girke
Close
Allen,
Stajich,
BaileySerres,
Lonardi
NSF
8/2014 – 5/2015
$548,476
Judelson
Girke
USDA-NIFA
3/2011 – 2/2016
$9,100,000
US-AID
9/2013 – 8/2018
$4,972,542
NIH
5/2014 – 4/2015
$592,816
Girke
NSF
12/1/2014 –
11/30/2015
$499,893
Girke
UCR Seed
Grant
7/1/2014 –
6/30/2015
$62,500
NSF DBI
UCR Seed
Grant
NIH/NISID
9/1/2013 –
8/31/2016
7/1/2014 –
6/30/2015
7/1/2013 –
Lonardi
Atkinson
Le Roch
Yates,
Gauvain,
Deolalikar,
Walker
Maduro
Roose
Close
Girke
Jiang
Bornemann
Huang (I-
Roberts,
Lonardi
Lonardi
(Senior
Personnel)
Xinshu,
Xiao
(UCLA)
Jiang,
McCole
38
$771,000
($570,000 to
UCR)
$73,000
$245,000
Fiscal Year 2013-14
mediated restriction
C)
microRNAs and their
targets critical for shifting
the balance of T cellmediated immunity
Karginov
Sun, Z.
CNBS/CUBRI
3/14/14 – 3/14/15
$100,000
The functions of IFITM
proteins in control of
influenza A virus infection
NIH/NIAID
7/1/2013 –
6/30/2014
$380,000
UCR Seed
Grant
7/1/2014 –
6/30/2015
$70,000
Dietary Effects on the GutBrain Axis
Huang (IC)
Sladek
Bornemann,
CurrasCollazo,
Jiang, Lytle
6/30/2014
39
Fiscal Year 2013-14
On the second table below, please list all pending and planned proposals in fiscal year under review and indicate the total
amount of the request.
NON-SPONSORED RESOURCES
Sources of Funding(IIGB)
Funding Provided by UCR Institutional Sources
Amount
CNAS Staff
funding
CNAS
Operating
Budget
$321,256
$78,651(including CWF & GEL)
Funding Provided by UC System Sources
Funding from Endowments or Gifts
Funding from Other Sources (Please List)
Noel Keen
Memorial
Endowment
Fund 47675
Genomics
Bldg.
Foundation
Vrs. Dnrs.
Sources of Funding(CEPCEB)
Funding Provided by UCR Institutional Sources
$1,576.22
$3,874.73
$405,358 Total
Amount
CNAS
Staff
funding
CNAS
Operating
Budget
$285,234
$8,488(including CWF & GEL)
Funding Provided by UC System Sources
Funding from Endowments or Gifts
CEPCEB
Award
Fund
43890
40
$4,750
$298,472 Total
Fiscal Year 2013-14
Attachment B
IIGB FACULTY FORUM
Tuesday, May 27, 2014: 12:00pm
Genomics Auditorium, Rm 1102
–AGENDA–
I.
Announcements (N. Raikhel, S.W. Ding, X. Chen, Z. Yang, A. Ray, T. Girke)
A. New Members (Natasha Raikhel)
i. New Members – Introduction
1. Naoki Yamanaka (Entomology, CDVR replacement for Joao Pedra)
ii. New Staff
1. Jennifer Douglas, IIGB Analyst I (replacing Guille Vallejo)
B. New Center Directors (Natasha Raikhel)
i. CDVR: Anand Ray (eff. 7/1/14); Currently Peter Atkinson
ii. CEPCEB: Julia Bailey Serres (eff. 7/1/13)
C. Recruitments
i. Status of IIGB-related Faculty Recruitments:
1. Virology (Shou-wei Ding)
a. Search Committee: Shou-wei Ding (Chair), Ayala Rao, Anupama
Dahanukar, I-Chueh Huang, David Lo
b. Offer: initially to Ricardo Rajsbaum from Icahn School of
Medicine in Mount Sanai Hospital (rejected); currently to James
Brien from Washing Univ. School of Medicine in St. Louis, who
has requested position for wife, Dr. Pinto. (pending)
2. Molecular and Cellular Biology (Xuemei Chen)
a. Search Committee: Xuemei Chen (Chair), Natasha Raikhel,
Yinsheng Wang, Ted Karginov, Iryna Ethell)
b. Offer: initially to Wenqian Hu, Whitehead Inst. for Biomedical
Research (rejected); then to Katalin Toth, Caltech (also
unsuccessful).
3. CEPCEB Plant Cellular Biochemistry (Zhenbiao Yang)
a. Search Committee: Zhenbiao Yang (Chair), Natasha Raikhel,
Sean Cutler, Wenwan Zhong, Julia Bailey-Serres
b. Offers Accepted: Jaimie Van Norman, Duke University; Carolyn
Rasmussen, University of Wyoming (NR’s retention position)
4. CDVR Arthropod-Vector Human Disease (Anand Ray)
a. Search Committee: Alex Raikhel (Chair), Karine LeRoch, Anand
Ray, I-Chueh Huang, Emma Wilson
b. Offer: initially to Zhiyong Xi at Michigan State University
(rejected); then to Robin Stevens from the University of Texas
Medical Branch, Galveston (also rejected).
ii. Bioinformatics Academic Coordinator (Thomas Girke)
a. Search Committee Members: Thomas Girke (chair), Julia BaileySerres, Glenn Hicks, Stefano Lonardi, Anand Ray, Jason Stajich
b. Offer: Rakesh Kaundal, Oklahoma State University. Accepted
and Started 7/1/14.
II.
Faculty Recruitment 2015 (2): (N. Raikhel)
• Two Asst. Professors: Natasha Raikhel and Shou-wei Ding retentions
• Areas of Focus (solicitation – send to N. Raikhel/S.W. Ding)
III.
IIGB Instrumentation Core Update
i. New Equipment
1. NSF MRI: Acquisition of a Big Data Compute Cluster for Interdisciplinary
Research ($880 award)
2. Bioinformatics: S10 Award for Big Data Storage Cluster (Thomas Girke)
Thomas stated that $660,000 was obtained from NIH (S10) for one year
41
Fiscal Year 2013-14
Attachment B
of funding and $880,000 was obtained from NSF. David Lo mentioned
that a systemwide clinical genomics center is being created and he and
Thomas Girke are representatives from UCR.
3. Genomics: MiSeq (acquired through X. Chen’s HHMI Appt; an Illumina
benchtop sequencer); Qubit nucleic acid/protein quantification; library
preps and pooling (Glenn Hicks)
4. Proteomics: LTQ Orbitrap Fusion Mass Spectrometer: $715K (Songqin
Pan). Songqin reported that the new Mass Spectrometer is 50-100x
more sensitive than the existing QTOF.
5. Microscopy: Objective Inverter Optical Adapter for Leica SP5; Critical
Point Dryer; Z-Stages and Lenses for Leica SP2 (David Carter) David
reported that the Leica SP5 is almost used to saturation and he is trying
to add capability to existing confocals in the core. Zhenbiao suggested
wubmitting a NIH High-end instrumentation proposal.
ii. Instrumentation Facility Consortiums/Meetings Update (Glenn Hicks)
Glenn will host the next systemwide meeting to discuss a leasing program for
state-of-the-art instrumentation since the UC campuses are obligated to stay at
the front of technology to remain competitive.
iii. New High-End Instrumentation Proposals in FY15 (Glenn Hicks)
Glenn reported that a proposal was submitted for an Illumina next-generation
sequencer.
IV.
New/Ongoing IIGB Initiatives (N. Raikhel)
A. Sound Enclosure for Projector in Genomics Auditorium (installed May 23, 2014)
B. Fob Security Expansion in Genomics Building
i. All labs will be fob accessible and documented (third and fourth floor devices
installed)
C. IIGB PI Luncheon Brainstorming Sessions (N. Raikhel)
i. Current Coordinators: Hailing Jin/Ted Karginov)
ii. Goal: Problem-solving, Collaborations, Open to all IIGB PIs; held on monthly
basis
iii. Interest level – dismal; eliminate sessions?
IIGB PIs decided to continue this program another year with the same
coordinators but perhaps at another time (early a.m. or late p.m.) since the noon
hour is not convenient.
D. NSF-CEPCEB REU Program in Plant and Plant-Pathogen Cell Biology (H. Judelson)
i. Update: Howard noted that Thomas Eulgem will write a renewal proposal since
this grant ends in FY15.
E. IIGB/CEPCEB/CDVR Seminars (N. Raikhel)
i. Every two weeks, not weekly
ii. PI Involvement in encouraging attendance
iii. Seminar Coordinators (same for 2014-15):
1. CEPCEB Seminars
a. 2013-14 Coordinators:
Parry Springer/Thomas Girke
2. IIGB Seminars
a. 2013-14 Faculty Coordinators:
Iryna Ethell/Jason Stajich
3. CDVR Seminars
a. 2013-14 Faculty Coordinators:
Karine Le Roch/Anupama Dahanukar
4. Student Seminars
a. 2013-14 Student Coordinator:
This has been changed to a postdoc symposium in 2014-15 and
is headed by Laetitia Poidevin
F. CEPCEB Symposium and Award Ceremony (Julia Bailey-Serres)
i. Date: December 12, 2014
ii. 2014 Noel T. Keen Lecturer: Eva Benkova, Institute of Science and Technology
Austria (IST Austria)
42
Attachment B
Fiscal Year 2013-14
iii. Symposium similar to last year: need organizers (last year was Venu Reddy and
Thomas Girke)
iv. 2013-14 Award Committee Members: Venu Reddy Gonehal (chair), Chia-en
Chang, Stefano Lonardi, Glenn Hicks, Ruixi Li (Raikhel lab), Yuanyuan Zhao
(Chen Lab)
v. 2014-15 award committee membership: need new chair; new members?
Isgouhi Kaloshian volunteered to chair this committee.
vi. Pre-college Awards
1. State Science Fair held on April 29, 2014
a. Awardees:
i. First Place: : SAUMYA R. KEREMANE (Martin Luther
King High School, Riverside); Poster Title: “An Ecofriendly RNA Interference-based Insect Control for
Management of Citrus Greening Disease Using a Model
System”
ii. Second Place: EMILY S. WANG; Poster Title:
“Illumination Disease Pathways :Developing Bright
Fluorescent Proteins to Improve FRET Biosensing”
b. Judges: David Carter, Shengben Li (Chen lab)
2. RIMS Inland Science and Engineering Fair held on April 2, 2014
a. Awardees:
i. First Place: SAUMYA R. KEREMANE (Martin Luther
King High School, Riverside); Poster Title: "Gene
Silencing in Bactericera Cockerelli, vector of Tomato
Liberibacter"
ii. Honorable Mention: SABRINA HOUSTON (Centennial
High Schools, Corona/Norco); Poster Title: "Solving Salt
Stress: Chemical Genomics with Agricultural
Implications"
b. Judges: David Carter, Venu Gonehal, Songqin Pan, Nolan Ung
(Raikhel lab)
3. Intel International Science and Engineering Fair held on May 12-13,
2014 in Los Angeles
a. Judge: Songqin Pan
G. CEPCEB Postdoc/Student Symposium (Julia Bailey-Serres)
1. Date: June 11, 2014
2. Full-day Symposium
3. Organizing Committee: Maureen Hummel (Bailey-Serres lab), Jorge
Lazano-Juste (Cutler lab), Laetitia Poidevin (Judelson lab), Brandon Le
(Chen lab), Jeremie Bazin (Bailey-Serres lab), Shengben Li (Chen lab),
Ousmane Cisse (Stajich lab), Sofia Robb (Stajich lab), Pinky Kain (Ray
lab)
H. Career Day 2014 (Anand Ray)
i. Coordinator: Anand Ray
ii. Open to IIGB postdocs and students
iii. Date: Friday, October 3, 2014
iv. Faculty Committee Volunteers?
Bradley White and Xinping Cui volunteered to be on this committee.
I. 2nd International Hemipteran-Plant Interactions Symposium (HPIS) (Linda Walling)
(Isgouhi Kaloshian)
i. Committee Members: Linda Walling, Isgouhi Kaloshian, Gregory Walker, James
Ng
ii. Date: June 22-25, 2014
iii. Expected attendance: 120
V. Questions/Comments?
Karine Le Roch mentioned that a California Pathogen Symposium will be held in October. This is
the fourth time this symposium has been organized; Anand Ray is assisting.
43
Fiscal Year 2013-14
Attachment B
44
Fiscal Year 2013-14
Attachment C
45
Fiscal Year 2011-12
Attachment D
2013-14 IIGB INSTRUMENTATION FACILITY TOURS
FY13/14
Total
Number
of
Attendees
Title
Genomics
Proteomics
Microscopy
Bioinformatics
Biomedical Sciences Dept
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
12
5
12
5
12
Evolution & Development
Faculty Recruitment,
Mammalian Virology Faculty
Recruitment, ArthropodSymbiont Interactions Faculty
Recruitment, Graduate
Student Recruitment Day
89
88
89
88
89
Prospective Etox PhD
students
6
6
6
6
6
1
1
1
1
1
1
1
1
1
1
3
3
3
3
3
17
Vector-Pathogen Interactions
Entomology/CDVR positions Susanta Behura
Prospective Etox Grad
students
Entomology/CDVR positions Yuemei Dong
1
1
1
1
1
19
Corona High School AP visit
65
65
65
July
August
14
19
21
26
29
September
3
5
9
11
11
October
November
December
January
1/10, 1/14,
1/16, 1/17,
1/22, 1/24,
1/28, 1/29,
1/31
February
2/4, 2/7,
2/7, 2/10,
2/11, 2/13,
2/18, 2/20,
2/25, 2/28
BNPPS Faculty Recruitment,
Evolution & Development
Faculty Recruitment,
Epigenetics Faculty,
Mammalian Virology Faculty
Recruitment
March
11
14
14
14
46
Fiscal Year 2011-12
21
24
Candidate Student
April
2
2
18
21
23
Entomology/CDVR positions Rubing Chen
Dept of Nematology
Candidates
CDVR -final interview
candidate Dr. Robin Stephens
Dept of Nematology
Candidates
Attachment D
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
May
16
1
20
Dept of Nematology
Candidates
Dept of Nematology
Candidates
Dept of Nematology
Candidates
1
1
1
1
1
1
1
June
17
19
School of Medicine
1
1
1
1
1
School of Medicine
1
1
1
1
23
School of Medicine
1
1
1
1
1
199
125
134
191
Subtotal
47
200
ATTACHMENT E
CEPCEB/IIGB/CDVR (FY 2013-2014 Seminar Schedule)
Location: Genomics Auditorium
Time: 12:10 pm Fridays
SERIES
SPEAKER
TITLE
HOST
August ‘13
CEPCEB
9
Ulla Bonas
Institute for Biology and
Genetics
Martin Luther University,
German
TAL and other bacterial pathogen
effectors and their host targets
Hailing Jin
September ‘13
CEPCEB
27
Hong Ma,
Fudan Univ
Control of anther cell division and
differentiation by cell-cell signaling and
transcriptional networks
Michelle Digman,
UC-Irvine
Philip Felgner,
UC-Irvine
Advanced Methods in Imaging
Microscopy to Study Protein Dynamics
Exploring the antibody universe with
high density proteome microarrays
Natasha Raikhel
October ‘13
IIGB Student
Seminar
CVDR
4
18
Lauren Dedow
Karine Le Roch
November ‘13
CVDR
CEPCEB
1
15
Craig Montell,
UCSB
Christoph Benning
Michigan State University
Unraveling the molecular and cellular
basis of behavior and decision making
in Drosophila
Lipid remodeling in response to abiotic
stress
Anupama
Dahanukar
Thomas Girke
December ‘13
CVDR
CEPCEB
6
18
George Dimopoulos,
Johns Hopkins
Elliott Meyerowitz
CalTech, Pasadena
Can we target the beast in the belly with
the mosquito immune system and
microbiome?
Tissue mechanics and tissue shape
control cell-cell signaling and
morphogenesis in a plant stem cell
niche
Karine Le Roch
Julia Bailey-Serres
January ‘14
CEPCEB
10
IIGB
17
IIGB
31
Masaru Ohme-Takagi;
National Institute of Advanced
Industrial Science and
Technology
Carlos Bustamante
Stanford
Yue Feng
Emory University
Functional analysis of plant transcription
factors using chimeric repressors: a
novel gene silencing technology
Population genetics in the personal
genome era
Regulation of BDNF-TrkB function by
neuronal activity and FMRP
Thomas Eulgem
Jason Stajich
Iryna Ethell
February ‘14
IIGB Student
Seminar
14
Sarah Hake
UC- Berkeley
A new angle on patterning the maize
leaf
Lauren Dedow
March ‘14
CEPCEB
CVDR
7
14
Keiko Torii
University of Washington
(Seattle)
Elissa Hallem
UCLA
Patty or Natasha
Anupama
Dahanukar
48
ATTACHMENT E
April ‘14
IIGB
CDVR
4
18
Yi Xing
UCLA
Global analysis of pre-mRNA alternative
splicing
Elizabeth Winzeler
TBA
Jason Stajich
Karine Le Roch
May ‘14
IIGB
2
Xiaolan Zhao
IIGB Student
Seminar
16
Doug Muench
University of Calgary
CEPCEB
30
Rob Last
11
Postdoc/Student Symposium
Day
A SUMO Atlas shoulders the DNA damage
response
Xuemei Chen
TBA
Lauren Dedow
Metabolites, enzymes and evolution:
glandular trichomes of domesticated and
wild tomato
Thomas Girke
June ‘14
CEPCEB
TBA
49
Julia Bailey-Serres
ATTACHMENT F
PROGRAM
HPIS 2014: June 22-25
2nd International Hemipteran-Plant Interactions Symposium
SUNDAY, JUNE 22, 2014
18:00
Registration/
Opening Reception
Botanic Gardens
MONDAY, JUNE 23, 2014
8:00
Registration/Coffee
HUB 302
8:30
Opening Remarks
GREG WALKER
Department of Entomology, UC Riverside
Welcome Address
KIM WILCOX
UC Riverside Chancellor
Phloem and Xylem Physiology and Vascular Sap-Feeding Hemipterans I
Session Chair: GREG WALKER
8:50
Plenary Address
FREDDY TJALLINGII
Plant Penetration and Feeding by Aphids
9:25
Submitted Presentation
BEATA GABRYS
Evolutionary Stability of Aphid Probing Behaviour:
Constants and Variables
9:45
MANOHARIE SANDANAYAKA
Does Candidatus Liberibacter solanacearum Modify
the Feeding Behaviour of its Vector Tomato Potato
Psyllid?
10:05
Coffee/Tea/Snack
HUB 302 (Poster Area)
Phloem and Xylem Physiology and Vascular Sap-Feeding Hemipterans II
10:30
Plenary Address
AART VAN BEL
Sieve-Element Calcium as One of the Middlemen in
Aphid-Plant Interactions
11:05
KARLA MEDINA-ORTEGA
Phloem Occlusion Inhibits Sap Ingestion by Green
Peach Aphid on Faba Bean
11:25
NABIL KILLINY
Asian Citrus Psyllid-Host Interactions: Comparisons
Between Phloem Sap and Honeydew Chemical
Composition
11:45
NATHALIE BOISSOT
Insights into the Genetic Control of Resistance to Aphis
gossypii in Melon: What We Learned from the Diversity of
Aphids
50
ATTACHMENT F
12:05
VICKI TOLMAY
Russian Wheat Aphid Resistance in the Cultivar
TugelaDn: An Overview
12:25
Lunch
HUB Eateries (First Floor)
Interactions Between Plants and Non-Vascular-Feeding Hemipterans
14:00
Plenary Address
MARGARET ALLEN
Genes, RNA, and Extraoral Digestion
Molecular Biology of Hemipteran-Plant Interactions I
Session Chair: LINDA WALLING
14:35
Plenary Address
MARK MESCHER
Virus Effects on Chemically Mediated Interactions
among Host Plants, Aphid Vectors, and Other Insects
15:10
CLARE CASTEEL
The Role of Ethylene in Vector-Virus Interactions with
Host Plants
15:30
Coffee/Tea/Snack
Molecular Biology of Hemipteran-Plant Interactions II
Session Chair: LINDA WALLING
16:00
Plenary Address
GEORG JANDER
A Genetic and Biochemical Basis for Natural Variation in
Maize Aphid Resistance
16:35
JOE LOUIS
Mir1 Mediated Maize Defense Against Aphids
16:55
Interactions
GARY THOMPSON
Toward Building miRNA Regulatory Networks for PlantAphid Interactions
17:15
Announcements
HUB 302
17:25
Discussion
Moderator: GARY THOMPSON
18:00
Poster Session
Even Number Posters, HUB 302 (Poster Area)
TUESDAY, JUNE 24, 2014
Molecular Biology of Hemipteran-Plant Interactions III
Session Chair: ISGOUHI KALOSHIAN
9:00
Plenary Address
JYOTI SHAH
Plant Defense Against the Polyphagous Green Peach
Aphid
9:35
IWONA MORKUNAS
The Interrelationship Between the Sequence of
Enhanced Generation of Signal Molecules and Defence
Responses of Pisum sativum to Pea Aphid Infestation
51
ATTACHMENT F
9:55
XIANGFENG JING
How Insects Exploit Sugar-Rich Phloem Sap: A
Molecular Perspective
10:15
Coffee/Tea/Snack
Molecular Biology of Hemipteran-Plant Interactions IV
Session Chair: ISGOUHI KALOSHIAN
10:35
Plenary Address
SASKIA HOGENHOUT
Plant-Insect Interaction: An Intricate Balance of Plant
Defense Induction and Suppression
11:10
TETSUYA KOBAYASHI
Genetic Mapping of the Rice-Resistance-Breaking Gene
of the Brown Planthopper Nilaparvata lugens
11:30
AKIKO SUGIO
What Are the Molecular Mechanisms of Plant
Specialization in the Pea Aphid Complex?
Interactions Among Hemipterans, Their Symbionts and Host Plants I
Session Chair: MURAD GHANIM
11:50
Plenary Address
NANCY MORAN
Genomic Insights into the Roles of Symbionts in SapFeeding Insects
12:25
Lunch
Interactions Among Hemipterans, Their Symbionts and Host Plants II
14:00
Plenary Address
MARTHA HUNTER
Exploring the Mechanism of Fitness Benefits of a
Facultative Symbiont of Whiteflies
14:35
ADI KLIOT
Tritrophic Interactions Between Insect-Virus-Bacteria:
the Whitefly Bemisia tabaci, the Endosymbiont
Rickettsia and Tomato Yellow Leaf Curl Virus
14:55
ALLISON HANSEN
Widespread Expression of Ancient Symbiont Small
RNAs in Aphids
15:15
Coffee/Tea/ Snack
Interactions Among Hemipterans, Their Symbionts and Host Plants III
15:45
Plenary Address
16:20
Announcements
16:30
Discussion
Moderator: ANGELA DOUGLAS
17:00
Poster Session
Odd Number Poster (HUB 302 (Poster Area)
ANGELA DOUGLAS
Bacterial Symbionts as Enablers of Phloem Sap
Utilization
52
ATTACHMENT F
WEDNESDAY, JUNE 25, 2014
Transmission of Plant Pathogens by Hemipteran Vectors I
Session Chair: JAMES NG
8:30
Plenary Address
STÉPHANE BLANC
Canonical Circulative Non-Propagative Transmission
May Not Apply to the Transmission of Nanoviruses by
Aphid Vectors
9:05
JESUS NAVAS CASTILLO
The Minor Capsid Protein of the Crinivirus Tomato
Chlorosis Virus Interacts with Two Bemisia tabaci
Proteins in the Yeast Two-Hybrid System
9:25
ANGEL CHEN
Recombinant Lettuce Infectious Yellow Virus Minor
Coat Protein-Mediated Inhibition of Virion Retention in
Bemisia tabaci Disrupts Virus Transmission
9:45
Plenary Address
STEWART GRAY
Circulative, Nonpropagative Transmission: A Carefully
Tuned Orchestra of Virus, Vector and Host Proteins
10:25
Coffee/Tea/Snack
Transmission of Plant Pathogens by Hemipteran Vectors II
Session Chair: JAMES NG
10:45
Plenary Address
11:20
11:40
JING WEI
Specific Cells in Whitefly Salivary Glands Control
Retention and Transmission of Begomoviruses
12:00
MARÍA SÁNCHEZ GUZMÁN
Manipulation of Hormone Homeostasis on the Tripartite
Interaction Among Tomato Yellow Leaf Curl Virus,
Bemisia tabaci and Tomato
12:20
Lunch
HENRYK CZOSNEK
Interfering with Begomovirus Transmission to Plants by
Silencing Genes of their Whitefly Vector
AYAN DAS
Binding of Allium sativum Leaf Agglutinin (ASAL) with
GroEL Related Receptor Interferes with Insect
Mediated Plant Virus Transmission Machinery
Transmission of Plant Pathogens by Hemipteran Vectors III
Session Chair: MICHELLE CILIA
14:00
MARTIN DRUCKER
Activation of Viral Transmission Induced by Vector
Action on a Host: A General Phenomenon?
14:20
ELAINE BACKUS
Glassy-Winged Sharpshooter Can Use a Mechanical
Mechanism to Inoculate Xylella fastidiosa Into
Grapevines
53
ATTACHMENT F
14:40
JEANNETTE RAPICAVOLI
Implication of Lipopolysaccharide in the Vector-Microbe
and Plant-Microbe Interactions of the Bacterial
Phytopathogen, Xylella fastidiosa
15:00
PIOTR TREBICKI
Elevated CO2 and its Effects on Wheat, Barley Yellow
Dwarf Virus and its Aphid Vector: Results from the Field
(FACE) and Growth Chamber Experiments
15:20
Coffee/Tea/Snack
Transmission of Plant Pathogens by Hemipteran Vectors IV
15:40
Plenary Address
BRYCE FALK
RNA Interference (RNAi) Strategies for Targeting
Vascular Feeding Hemipteran Vectors of Plant
Pathogens
16:15
Discussion
Moderator: BRYCE FALK
16:45:
Closing Remarks
19:30
Closing Banquet
Arroyo Vista Café, UCR alumni & Visitors Center
OMICs WORKSHOP —
THURSDAY, JUNE 26, 2014
9:00
Welcome
Genomics Building Auditorium, Rm 1102A
Opening Remarks
MURAD GHANIM
Agricultural Research Organization, Volcani Center,
Israel
OMICs
9:15
Plenary Speaker
ZHANGJUN FEI
Deep Sequencing of Small RNAs for Plant Virus
Identification
9:50
Plenary Speaker
CECILIA TAMBORINDEGUY
Psyllid Vitellogenesis
10:25
Coffee
Genomics Lobby
10:45
Plenary Speaker
JIM BRUCE
Protein Interactions in Cells: Finding Connections
11:20
Plenary Speaker
CAROLYN SLUPSKY
Effect of Insects and Pathogens on Citrus Metabolism
11:55
Discussion
54

2014 IIGB - Institute for Integrative Genome Biology

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