Thomas Eulgem & Karine Le Roch collaborate on Arabidopsis thaliana PHD-finger protein EDM2: A prime example of across organisms and borderless scientific activities in IIGB

Thomas Eulgem
Karine Le Roch

A prime example of across organisms and borderless scientific activities in IIGB was achieved by Thomas Eulgem and Karine Le Roch, with a well-executed collaboration bringing together researchers working in very different areas of genome biology. The project was initiated in Thomas Eulgem’s lab as the PI on the critical roles of the chromatin-associated Arabidopsis thaliana protein EDM2 in coordinating plant immune responses. Karine Le Roch’s group contributed expertise and experience on epigenome profiling to the study.

The PLOS Genetics paper, “The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression”, can be viewed here.


Xuemei Chen, Robert Jinkerson, and Meng Chen received an NSF EAGER grant

Xuemei Chen, Robert Jinkerson, and Meng Chen received an NSF grant to establish a transformative RNA sequencing technology for studying plastids.

Plastids in plant cells (Image found here)

The plant cell stores its DNA in not only the nucleus but also the plant-specific organelles, the plastids. Plastid DNA can be transcriptionally programmed to instruct the differentiation of plastids into diverse types, such as the well-known photosynthetically active chloroplasts. In fact, plastids function far beyond photosynthesis in a variety of essential roles in development, metabolism, signaling, and immunity in plants. However, because each plant cell harbors tens to hundreds of plastids, current RNA sequencing approaches – even those using single cells – average plastid transcriptomic profiles, and thereby, potentially obscure biologically relevant transcriptomic variations that distinguish unique plastid types. As a result, our understanding of plastid types and their functions remains rudimentary.

A UCR team consisting of IIGB faculty Xuemei Chen, Robert Jinkerson, and Meng Chen have been awarded an NSF EAGER grant to tackle the long-standing problem in plant biology. The NSF EAGER (Early-concept Grants for Exploratory Research) mechanism supports radically different and potentially transformative research ideas or approaches. The two-year grant of $300,000, entitled “spRNA-seq: high-throughput transcriptome analysis of single plastids”, is aimed at establishing a cutting-edge technology to sequence RNA molecules from single plastids, namely single-plastid RNA sequencing (spRNA-seq). spRNA-seq allows the determination of molecular signatures of thousands of individual plastids in one experiment, making it possible to create a complete plastid-type atlas and elucidate their functions. This enabling technology is expected to revolutionize research on plastids and will generate novel insights into how plastids affect plant biology, ecology, and evolution.

Yanran Li receives NIH New Innovator Award

Yanran Li, an assistant professor of chemical and environmental engineering, has received a New Innovator Award from the National Institutes of Health’s High-Risk, High-Reward Research Program for a project to discover plant natural products of potential medicinal value and their biosynthesis through reprograming the plant innate immunity.

Li’s research seeks to engineer and redirect plant immune signaling to activate secondary metabolic pathways that are silent under normal conditions, in order to more efficiently discover novel plant natural products.

“I was first introduced to plant immune receptors during a lunch discussion with Wenbo Ma from plant pathology back in 2016 when I first joined UCR. We came up with the idea to reconstruct and engineer plant immune complexes in yeast,” Li said. “A generous collaborative seed grant from UCR’s Office of Research and Economic Development in 2018 helped me to extend the idea toward discovery of plant natural products in this successful proposal.”

Li’s project is one of the 50 High-Risk, High-Reward awards given by NIH in 2020 to exceptionally creative early career scientists proposing innovative, high-impact projects.

The research will be supported under NIH grant number DP2 AT011445-01. Read more about these awards and the recipients on the NIH website.

This UCR News article was written by Holly Ober and can be read in full here.

Hailing Jin is awarded a $1.89M NIH grant and $900k NSF/USDA grant

Hailing Jin

Hailing Jin received a prestigious 5-year Maximizing Investigators Research Award (MIRA R35) from the NIH on “Cross-kingdom RNA communications between plant and fungal pathogens”, for a total of $1.89M. MIRA is designed to increase the efficiency of NIH funding by providing investigators with greater stability and flexibility, thereby enhancing scientific productivity and the chances for important breakthroughs. The program will also help distribute funding more widely among the nation’s highly talented and promising investigators. MIRA grants are generally for 5 years and are for both established investigators and early stage investigators. Jin’s grant is for established investigators.

Jin also received a $900k grant from the NSF/USDA titled “Development of innovative RNA-based anti-fungals to control plant fungal disease.”

Plant pathologists Caroline Roper and Shou-Wei Ding honored by international society

Caroline Roper
Shou-Wei Ding

Caroline Roper, an associate professor of plant pathology; and Shou-Wei Ding, a professor of plant pathology; are among the 2020 award winners from an international professional organization of plant pathologists.

The American Phytopathological Society, or APS, regularly honors individuals who have made significant contributions to the science of plant pathology. Roper and Ding were presented with their awards at the APS annual meeting held online Aug. 4, 2020.

Roper received the Lee M. Hutchins Award due to her series of seven papers published in APS journals in the last 10 years, including Molecular Plant-Microbe Interactions and Phytobiomes. The award is presented to authors of published research on basic or applied aspects of diseases of perennial fruit plants.

Ding received the Noel T. Keen Award for his research on the molecular basis of plant antiviral defense and virus counterdefense. The award recognizes research excellence in molecular plant pathology.

This Inside UCR article was written by Steven Valenzuela and can be read in full here.


Chemistry professor Yinsheng Wang receives $7 million NIH grant

Yinsheng Wang

Yinsheng Wang, a UC Riverside distinguished professor of chemistry, has won a highly competitive research grant from the National Institute of Environmental Health Sciences, or NIEHS.

Wang was one of five scientists nationally to receive the Revolutionizing Innovative, Visionary Environmental Health Research, or RIVER, award which provides grant funding to mid-career and established researchers and supports groundbreaking projects in environmental health sciences. The institute, which announced the grants July 7, provided another six awards in a separate category for early career researchers.

Wang will study how alkylated DNA lesions affect genomic stability and can lead to diseases. His project was among those chosen to provide a greater understanding how specific genetic mechanisms can worsen diseases as part of environmental exposure.

The RIVER grant provides $7 million in funding for eight years to support research projects in the Wang laboratory.

“The RIVER award seeks scientists that have demonstrated the potential for continued innovative research and supports the majority of their established independent research program,” said Jennifer Collins, RIVER coordinator for NIEHS.

This Inside UCR article was written by Imran Ghori and can be viewed here.

Study provides insights into how Zika virus suppresses the host immune system

Jikui Song (left) and Rong Hai

A research team led by Jikui Song and Rong Hai at the University of California, Riverside, has outlined how the Zika virus, which constituted an epidemic threat in 2016, suppresses the immune system of its host.

The study appears in Nature Structural & Molecular Biology.

The research involved first solving the crystal structure of a complex between a large fragment of ZIKV NS5 and STAT2. This crystal structure guided the researchers in solving the cryo-EM structure of ZIKV NS5 and STAT2, which then led them to come up with a model for how ZIKV NS5 suppresses human STAT2.

Next, the researchers will work on the structure and function of SARS-CoV-2 proteins to identify new targets against COVID-19.

Song and Hai were joined in the study by Z. Hong Zhou at UCLA, also a senior author of the research paper. Other coauthors include UCR’s Boxiao Wang and Stephanie Thurmond. Kang Zhou at UCLA and Maria T. Sánchez-Aparicio at the Icahn School of Medicine at Mount Sinai share co-first authorship with Wang and Thurmond.

Song was supported by a grant from the National Institutes of Health, or NIH, and a University of California Cancer Research Coordinating Committee Faculty Seed Grant. A second NIH grant funded both Song and Hai.

The research paper is titled “Structural basis for STAT2 suppression by flavivirus NS5.”

This UCR News article was written by Iqbal Pittalwala and can be read in full here.

New tools in the fight against lethal citrus disease

​​ Simplified metabolic model and its striking similarity to a road map. (Metallo&Vander Heiden)

Scientists are closer to gaining the upper hand on a disease that has wiped out citrus orchards across the globe. New models of the bacterium linked to the disease reveal control methods that were previously unavailable.

In this case, researchers created the first models of the bacterium associated with Huanglongbing or HLB, also known as citrus greening disease. The team’s work is described in a new paper published in Nature’s npj Systems Biology and Applications.

This research project involved a collaboration between UC Riverside, UC San Diego, Texas A&M University, and the U.S. Department of Agriculture. In addition to James Borneman, members of the modeling team included UCR plant pathologist Georgios Vidalakis and UCSD systems biologist Karsten Zengler.

The research team made models for six different strains of the bacterium known as CLas and doing so enabled them to identify as many as 94 enzymes essential for the bacterium’s survival. These enzymes can now be considered targets for the creation of new antibacterial treatments.

In addition, the team identified metabolites required for the bacteria to grow.

Knowing the metabolites needed for CLas’ growth could enable scientists to cultivate it in a laboratory setting. It is not currently possible to grow CLas on its own, hindering scientists’ ability to study it and ultimately to manage it.

This UCR News article was written by Jules Bernstein and can be read in full here.

IIGB Director Katie Dehesh to serve as ASPB President

IIGB is extremely proud to announce that Katie Dehesh has been elected to serve as ASPB President in 2021, with her President-Elect duties starting October 2020.

Katie Dehesh, IIGB Director

Katie first joined the American Society of Plant Biologists in 1998 and is currently serving on the Hoagland Award Committee. From 2013 to 2019, she also served on the ASPB Publications Committee. As president, she will strive to provide more opportunities for students, postdoctoral fellows, and early career colleagues through increased social engagement and awareness in various public sectors, private sectors, and to the plant biology community.

With Katie’s leadership and vision, ASPB will thrive as a platform to allow for collaboration and understanding between educators, governmental granting agencies, politicians, businessmen, and farmers. Together, their voices will be amplified and will empower young plant scientists to advance their research and education, which is a core value of ASPB’s mission.

As Katie would say, be powerful!

Adler Dillman Awarded $1.8M NIH Outstanding Investigator Award

It’s likely that billions of people are unaware they have been infected with parasitic worms. A UC Riverside scientist has won $1.8 million to try and understand why.

Pictured above: Dr. Adler Dillman

The National Institutes of Health granted an Outstanding Investigator Award to Adler Dillman, an assistant professor of parasitology, so he can shed light on the mystery of worm infections that escape detection by human immune systems.

Unlike other grants, the Outstanding Investigator Award funds a research program rather than a specific project. This increases the flexibility for scientists to follow new research directions as opportunities arise instead of adhering to objectives proposed in advance of the studies. Spread out over five years, these funds will enable Dillman to hire a postdoctoral researcher, support graduate researchers, and purchase biochemistry equipment.

Recently, Dillman was also the recipient of a UCR Office of Research and Economic Development grant. For that project, Dillman is working toward a pesticide based on nematode venom, and on modifying crops to secrete a version of the toxin in the venom, which would give them natural resistance to insect attacks.

“Nematodes are devastating parasites of humans, capable of modulating our biology in numerous ways, including suppressing our immune systems,” Dillman said. “The goal of my lab is to understand this modulation and to characterize the chemical pathways that allow it to happen.”

Dillman said one of the things that most interests his students is the idea that parasites aren’t necessarily always bad. The hygiene hypothesis proposes that in places with highly developed sanitation systems, human immune systems don’t develop properly because they are not challenged by infection.

“There’s compelling data that parasites could even be used to treat autoimmune disorders such as Crohn’s or inflammatory bowel disease,” he said. “Parasitic worms are just the coolest things you could study because there are so many strange interactions, both positive and negative, that occur between the worms and their hosts.”

The complete news article can be read in full at UCR News.

Author: Jules Bernstein