- Author: Kathy Keatley Garvey
It did: their research revealed how TSWV (family Tospoviridae, order Bunyavirales) packages its RNA genome, a crucial step in virus infection.
Their newly published research, “The Genome of a Bunyavirus Cannot be Defined at the Level of the Viral Particle But Only at the Scale of the Viral Population,” appears in the current edition of the Proceedings of the National Academy of Sciences (PNAS).
The 18-member research team included scientists primarily from the French National Research Institute for Agriculture, Food and Environment (INRAE) at the Campus International de Baillarguet, Montpellier; Department of Entomology, University of Wisconsin; and the Department of Entomology and Nematology, University of California, Davis.
“Our work showed the genome of TSWV can only be defined at the population level, pointing at emerging properties when viral particles infect plants in groups,” said a key author Stéphane Blanc, research director of INRAE's Biology and Genetics of Plant-Pathogen Interactions. “As most virions contain an incomplete genome, TSWV is a multi-component viral system, where co-infection and complementation are key in the life cycle. These findings open a myriad of possibly distinct properties depending on the genetic composition of the group of virions co-infecting a cell.”
“The most challenging part of this work was to create a protocol reliably quantifying the two polarities of each segment,” said lead author Michel Yvon of INRAE. “The next important advance will be to demonstrate that co-infection of cells by a group of particles is key to the spread of infection.”
Ullman, an international authority on orthotospoviruses and one of the four main authors, took a sabbatical to work on the project. “My interest was in understanding how TSWV packaged its RNA genome,” she said. “While this sounds like a simple goal, it is quite complex because TSWV has negative sense and ambisense viral strands and many research tools common to studying other viruses, such as infectious clones were not available.”
“It was a delight to work with the fantastic team of scientists that Stéphane assembled, all very talented with skills in virology, cryoelectron microscopy and nanopore PCR,” Ullman commented. “I cannot imagine a more talented and diverse group of people to conduct this difficult work. I learned a great deal about virus purification from Michel Yvon, whose leadership, skills in virology, and patient teaching really moved our project forward."
German, professor emeritus and former chair of both the Departments of Plant Pathology and Entomology at the University of Wisconsin, died Aug. 27, 2023 at age 82.
“I am indebted to my husband, Jean-Marc Leininger who frequently drove me to the laboratory in Avignon where I was able to rear thousands of virus-infected plants and to store TSWV isolate,” Ullman added. “Jean-Marc not only transported me and my virus specimens, but also learned to mechanically inoculate plants and helped with every inoculation and virus harvest.”
UC Davis postdoctoral scholar Sulley Ben-Mahmoud of the Ullman lab was among the co-authors.
Funding was provided by grants from Montpellier University of Excellence (MUSE); Floriculture and Nursery Research Initiative, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS); and the Fulbright Scholar Program. The authors also acknowledged support from
- Santé des Plantes et Environnementor Plant Health and Environment (SPE)
- Centre National de la Recherche Scientifique (CNRS)
- Institute of Research for Development (IRD)
- Institut national de la santé et de la recherche médicale (INSERM)
- Centre for International Cooperation in Agronomic Research for Development (CIRAD)
- Plant Health Institute of Montpelier (PHIM)
Ullman noted the importance of the research in her Fulbright application: “Sustainable management of insect-transmitted pathogens is a key concern for food production in France and the United States. Both countries grow many of the same crops and growers face similar challenges from insect-transmitted plant viruses. Current management strategies rely heavily on pesticides that may cause significant health and environmental concerns, including damage to bees and other pollinators, as shown with neonicotinoid pesticides. Clearly, better knowledge about these insect-transmitted viral systems…has potential to reduce pesticide use by providing novel and innovative technologies to manage orthotospoviruses and thrips in France and the United States.”
Ullman, a former chair of the Department of Entomology and a former associate dean of the UC Davis College of Agricultural and Environmental Sciences, anticipates strong research relationships between UC Davis and Montpellier that will lead to grant applications for international research and scholarly exchange opportunities for scientists, students, and post-doctoral scholars.
Significance
In their significance statement, the authors wrote: “Bunyaviruses infect animals, plants, fungi, and protists. Despite their importance, fundamental aspects of their biology as basic as the definition of their genome remain elusive. The viral genome consists of several negative or ambisense RNA segments, and virions often miss segments and/or package complementary strands. We formally quantify this heterogeneity on the species Tomato spotted wilt orthotospovirus. Within individual virus particles, the number, the identity, and the polarity of the segments are widely variable. In contrast, we show that a stable genetic composition is an emerging property of the viral population, each of the RNA segments/polarities accumulating reproducibly at a specific frequency. This resembles the genome formula of multipartite viruses, suggesting that bunyaviruses may also function as multicomponent viral systems.”
Their abstract: “Bunyaviruses are enveloped negative or ambisense single-stranded RNA viruses with a genome divided into several segments. The canonical view depicts each viral particle packaging one copy of each genomic segment in one polarity named the viral strand. Several opposing observations revealed nonequal ratios of the segments, uneven number of segments per virion, and even packaging of viral complementary strands. Unfortunately, these observations result from studies often addressing other questions, on distinct viral species, and not using accurate quantitative methods. Hence, what RNA segments and strands are packaged as the genome of any bunyavirus remains largely ambiguous. We addressed this issue by first investigating the virion size distribution and RNA content in populations of the tomato spotted wilt virus (TSWV) using microscopy and tomography. These revealed heterogeneity in viral particle volume and amount of RNA content, with a surprising lack of correlation between the two. Then, the ratios of all genomic segments and strands were established using RNA sequencing and qRT-PCR. Within virions, both plus and minus strands (but no mRNA) are packaged for each of the three L, M, and S segments, in reproducible nonequimolar proportions determined by those in total cell extracts. These results show that virions differ in their genomic content but together build up a highly reproducible genetic composition of the viral population. This resembles the genome formula described for multipartite viruses, with which some species of the order Bunyavirales may share some aspects of the way of life, particularly emerging properties at a supravirion scale.”
- Author: Kathy Keatley Garvey
One UC Davis doctoral alumnus and 10 current or former members of the UC Davis Department of Entomology and Nematology are listed as among the world's top two percent of entomologists in a database announced by Stanford University with data from Elsevier's “science-wide author databases of standardized citation indicators.”
A separate list, gleaned from the main document, names the world's top entomologists, totaling 708. UC Davis alumnus Murray Isman, who received his doctorate in 1981 from UC Davis, studying entomology and toxicology, is ranked No. 2. He is the dean emeritus of the University of British Columbia's Faculty of Land and Food Systems and emeritus professor of entomology and toxicology at UBC.
The highest UC Davis entomologist/faculty member on that list is No. 22-ranked UC Davis distinguished professor Walter Leal of the Department of Molecular and Cellular Biology, former professor and chair of the Department of Entomology (now Department of Entomology and Nematology).
Other UC Davis entomologists on the list, in the order of ranking, are:
- Jay Rosenheim, No. 68
- Harry Kaya, 206
- Fumio Matsumura (1934-2012), 208
- James R. Carey, 232
- Robbin Thorp (1933-2019) 321
- Christian Nansen, 452
- Lester Ehler (1946-2016) 593
- Robert E. Page Jr., 548
- Frank Zalom, 557
Elsevier. Elsevier, a global information analytics company that helps institutions and professionals progress science, advance healthcare and improve performance, published its "science-wide author databases of standardized citation indicators" on Oct. 4, 2023. The ranking of scientists is at https://elsevier.digitalcommonsdata.com/datasets/btchxktzyw. It is a publicly available database "of top-cited scientists that provides standardized information on citations, h-index, co-authorship adjusted hm-index, citations to papers in different authorship positions and a composite indicator (c-score). Separate data are shown for career-long and, separately, for single recent year impact. Metrics with and without self-citations and ratio of citations to citing papers are given. Scientists are classified into 22 scientific fields and 174 sub-fields according to the standard Science-Metrix classification. Field- and subfield-specific percentiles are also provided for all scientists with at least 5 papers. Career-long data are updated to end-of-2022 and single recent year data pertain to citations received during calendar year 2022. The selection is based on the top 100,000 scientists by c-score (with and without self-citations) or a percentile rank of 2% or above in the sub-field. This version (6) is based on the October 1, 2023 snapshot from Scopus, updated to end of citation year 2022. This work uses Scopus data provided by Elsevier through ICSR Lab (https://www.elsevier.com/icsr/icsrlab). Calculations were performed using all Scopus author profiles as of October 1, 2023. If an author is not on the list it is simply because the composite indicator value was not high enough to appear on the list. It does not mean that the author does not do good work."
Scientists from China filtered the list to spotlight only entomologists. The list is at https://wxredian.com/art?id=9f6eea221698e282/.
- Author: Kathy Keatley Garvey
Danchin will speak on "Parasitic Success in the Absence of Sex: What Have We Learned from Nematode Genomes?" at 4:10 p.m., Monday, Nov. 20 in Room 122 of Briggs Hall. It also will be on Zoom. The Zoom link:
https://ucdavis.zoom.us/j/95882849672
Danchin, who specializes in genomics and adaptive molecular evolution, is with INRAE (French National Research Institute for Agriculture, Food and Environment) and is a senior scientist and scientific leader of the GAME team (Genomics and Adaptive Molecular Evolution) at ISA (Institut Sophia Agrobiotech), in Sophia-Antipolis, on the French Riviera.
"Root-knot nematodes are devastating plant parasites of worldwide importance. Interestingly, species that cause most damages reproduce entirely asexually," he writes in his abstract. "These nematodes are extremely polyphagous and have a wide geographic range. Theoretically, in the absence of sexual recombination animal species have lower adaptive potential and are predicted to undergo genome decay. To investigate how these species can be successful parasites on many hosts and in many places around the world, we have sequenced and analyzed their genomes. Out analysis confirmed these species are polyploid hybrids and the combination of several genotypes from different species might provide them with a general-purpose genotype. However, this does not explain how with a theoretically fixed genotype these species are able to overcome resistance genes or adapt to a new host. Therefore, we analyzed genomic variability across different populations and the possible mechanisms underlying genomic variations. In this presentation, I will provide an overview of our findings."
Etienne holds a doctorate in reproductive biology from the University of Paris (1980). He says on his website: "I am an evolutionary biologist working with genomes. I try to make biological sense of genomic singularities observed through comparative genomics. I have a special interest in plant parasites and I use bioinformatics as a tool to perform this research."
He lists his main research interests as:
- The impact of non tree-like evolution such as horizontal gene transfers and hybridization on species biology
- Evolution and adaptation of animals in the absence of sexual reproduction and the underlying mechanisms
- Genomic signatures of adaptation to a parasitic life-style
Seminar coordinator is Brian Johnson, associate professor, UC Davis Department of Entomology and Nematology. For Zoom technical issues, he may be reached at brnjohnson@ucdavis.edu. The list of seminars is posted here.
- Author: Kathy Keatley Garvey
Hammock, who holds a joint appointment with the Department of Entomology and Nematology and the UC Davis Comprehensive Cancer Center, was inducted along with 13 other Fellows on Nov. 14 during the annual Fellowship meeting. He joins the ranks of more than 500 Academy Fellows, a governing group of distinguished scientists and other leaders who have made notable contributions to scientific research, education, and communication.
“We're proud to announce 2023's distinguished pool of new Fellows—each of their contributions to science and society represent major advancements in their respective fields,” said Academy Dean of Science and Research Collections Shannon Bennett. “Our Fellows body is a group of future thinkers and innovators whose leadership inspires the next generation of scientists, science educators, story-tellers and change-makers. We look forward to forging a future with our new Fellows that advances the Academy's mission to regenerate the natural world through science, learning, and collaborative partnerships.”
Hammock, a member of the UC Davis faculty since 1980, was nominated by colleagues James R. Carey, UC Davis distinguished professor, and Robert E. Page Jr., UC Davis distinguished emeritus professor and emeritus provost of Arizona State University. The CAS Board of Trustees selects the Fellows.
Hammock discovered that regulating degradation of insect hormone mediators is as important as biosynthesis in development. He applied this toward the development of green chemical and the first recombinant viral pesticide. He asked if the same systems of metabolism of chemical mediators could be important in other species, notably man, resulting in the discovery of a new group of human chemical mediators. By inhibiting a key enzyme in this pathway, beneficial natural mediators increased there by showing benefit in treating multiple diseases including arthritis, cancer, Alzheimer's with the resulting drug candidates currently in human trials to treat pain.
Hammock co-discovered a human enzyme termed Soluble Epoxide Hydrolase (sEH), a key regulatory enzyme involved in the metabolism of fatty acids. It regulates a new class of natural chemical mediators, which in turn regulates inflammation, blood pressure and pain. Hammock and his lab have been involved in enzyme research for more than 50 years.
Hammock founded the Davis-based pharmaceutical company, EicOsis LLC, formed in 2011 to develop an orally active non-addictive drug for inflammatory and neuropathic pain. The former chief executive officer, he now serves on the board of directors.
He is a fellow of the National Academy of Inventors and the National Academy of Sciences., and the Entomological Society of America. He is the recipient of scores of awards, including the first McGiff Memorial Awardee in Lipid Biochemistry; and the Bernard B. Brodie Award in Drug Metabolism, sponsored by the America Society for Pharmacology and Experimental Therapeutics. At UC Davis he received the Distinguished Teaching Award and the Faculty Research Lectureship. In 2020, he received a Lifetime Achievement Award from UC Davis Chancellor Gary May.
Hammock has authored or co-authored more than 1,400 peer-reviewed publications and holds more than 95 patents in agriculture, environmental science and medicinal chemistry.
Hammock is known for his expertise in chemistry, toxicology, biochemistry and entomology. Early in his career, he founded the field of environmental immunoassay, using antibodies and biosensors to monitor food and environmental safety, and human exposure to pesticides. His groundbreaking research in insect physiology, toxicology led to his development of the first recombinant virus for insect control.
A native of Little Rock, Ark., Hammock received his bachelor's degree in entomology (with minors in zoology and chemistry) magna cum laude from Louisiana State University, Baton Rouge, in 1969. He received his doctorate in entomology-toxicology from UC Berkeley in 1973. Hammock served as a public health medical officer with the U.S. Army Academy of Health Science, San Antonio, and as a postdoctoral fellow at the Rockefeller Foundation, Department of Biology, Northwestern University, Evanston, Ill.
In the Army, he served as a medical officer at Fort Sam, Houston, and what he saw--severely burned people in terrible pain--made a lasting impression on him and steered him toward helping humankind.
2023 Fellows. Among the new CAS Fellows is Beth Rose Middleton Manning, professor of Native American Studies and designated emphasis chair at UC Davis who also was supported by the NIEHS Superfund Program. She focuses on environmental policy, cultural site protection, and climate adaptation with Native nations and communities.
Other new Academy Fellows:
Peter Alagona, PhD
Professor, Environmental Studies
University of California, Santa Barbara
Nicole Ardoin, PhD
Associate Professor, Social Sciences and Emmett Family Faculty Scholar
Stanford University
Junko Habu, PhD
Professor of Anthropology
University of California, Berkeley
Vanessa Handley, PhD
Director of Conservation Science and Global Conservation Consortium for Cycads Chair
University of California, Berkeley
Terry Jones, PhD
Professor of Anthropology
California Polytechnic State University
Marjorie Matocq, PhD
Foundation Professor, Department of Natural Resources and Environmental Science
University of Nevada, Reno
Derrick Rossi, PhD
CEO, Convelo Therapeutic
CEO, New York Stem Cell Foundation
Partner, Castle Rock Entertainment
Harvard University
Robert Bullard, PhD
Distinguished Professor of Urban Planning and Environmental Policy and Director of the
Bullard Center for Climate and Environmental Justice
Texas Southern University
Franck Marchis, PhD
Senior Planetary Astronomer
SETI Institute
Melissa Nelson, PhD
Professor of American Indian Studies
Arizona State University
Daniel Pauly, PhD
Professor of Fisheries
University of British Columbia
Aomawa Shields, PhD
Clare Boothe Luce Associate Professor of Physics and Astronomy
University of California, Irvine
The list of UC Davis Department of Entomology and Nematology faculty or former faculty who are Fellows:
UC Davis distinguished professors James R. Carey, Walter Leal (now with College of Biological Sciences) and Frank Zalom; distinguished professor emeritus Robert E Page Jr. (chair emeritus of the Department of Entomology and provost emeritus of Arizona State University; Professors Phil Ward and Neal Williams; and department affiliate Catherine Tauber (formerly of Cornell)
The late Robbin Thorp (1933-2019), UC Davis distinguished emeritus professor, and Maurice Tauber (1931-2014, a UC Davis visiting professor/scientist and formerly of Cornell) also were CAS Fellows.
See more information about the CAS Fellows here.
- Author: Kathy Keatley Garvey
When the UC Davis College of Agricultural and Environmental Sciences (CA&ES) honored UC Davis distinguished professor Lynn Kimsey, director of the Bohart Museum of Entomology, as the recipient of its 2023 Exceptional Faculty Award, she was asked to trace her interest in insects and to recall some of her fondest UC Davis memories.
One of the funniest memories, Kimsey related, occurred at Briggs Hall in 1986 when noted UC Davis entomology professor Richard "Doc" Bohart (1913-2007) received a 21-Insect Net Salute at the campuswide dedication of the museum in his honor. Entomology faculty and students lined up with their insect nets, forming an archway as Doc Bohart sauntered through. UC Davis Chancellor James Meyer (1922-2002) conducted the dedication. At the time, Kimsey was a postdoctoral scholar in the Doc Bohart lab. He had earlier served as her major professor.
The CA&ES awards dinner, held Nov. 2 in the Athletic Recreation Center (ARC) Ballroom, celebrated five award recipients. In addition to Kimsey, spotlighted were: Alumnus of the Year, James Finch, 1989; Early Career Alumnus, Jeffrey Sparks 2014; Distinguished Friend of the College, Tony Turkovich; and Exceptional Staff Award, Lisa Nash Holmes.
CA&ES Dean Helene Dillard praised the recipients for serving "their communities and the university in a way that exemplifies the spirit of our college and the campus." Prior to the award presentations, the crowd watched a video of each recipient.
Why did she choose to study at UC Davis? "It was one place in the state that had an entomology program," said Kimsey, who holds two entomology degrees from UC Davis: a bachelor's degree (1976) and a doctorate (1979). "I got to pursue my bug interests. I know it was kind of weird, but even as a little kid it was fun." A portrait of her at age 5, holding an insect net, graces the Bohart Museum.
"Uc Davis," Kimsey added, "has been my home for decades."
Kimsey, a recognized authority on insect biodiversity, systematics and biogeography of parasitic wasps, urban entomology, civil forensic entomology, and arthropod-related industrial hygiene, is a 34-year member of the UC Davis entomology faculty. She has directed the Bohart Museum since 1990.
When "Doc" Bohart founded the museum in 1946, it included only 400 insect specimens at its Briggs Hall location. Under Kimsey's tenure, it has grown to a global collection of eight million insect specimens in Room 1124 of the Academic Surge Building, 455 Crocker Lane, and is the seventh largest insect collection in North America.
"The importance of what Dr. Kimsey does and the importance of insect specimens in museums cannot be overstated," wrote nematologist Steve Nadler, professor and then chair of the Department of Entomology and Nematology, in his letter of nomination. "They are a valuable resource for the agricultural community, public health, forensic entomology, medicine and criminology, environmental biology, and the pest control industry, as well as the public."
Nadler described Kimsey as a visionary with a “let's-do-this” viewpoint that defines her. "Her work is nothing short of exemplary; she has made the museum the place to be—not only for scientific collaborators but for the public."
The Bohart draws an average of 15,000 visitors a year, adds an average of 30,000 new specimens annually, and loans an average 7000 specimens yearly to scientists worldwide. It supports campus classes with specimens, live insects and exhibits in keeping with its mission: “Understanding, documenting and communicating terrestrial arthropod diversity.”
It is also the home of an insect-themed gift shop (proceeds benefit the Bohart's educational activities) and a live “petting zoo” that includes Madagascar hissing cockroaches, stick insects and tarantulas.
The nomination packet included letters of support from numerous colleagues and friends. They included longtime colleague Arnold Menke of Bisbee, Ariz., whose major professor, like Kimsey, was Doc Bohart; professor Jason Bond, the Schlinger Endowed Chair, UC Davis Department of Entomology and Nematology, and CA&ES associate dean; Frank Zalom, UC Davis distinguished professor emeritus; James Carpenter, American Museum of Natural History curator; and Fran Keller, who was Kimsey's doctoral student.
Wrote Bond: "Professor Kimsey is an internationally recognized expert in insect systematics and taxonomy who specializes in the evolution and taxonomy of two wasp families. She has made an incredible number of contributions to the field of insect systematics that includes > 120 peer reviewed papers, along with a number of book chapters, books, and monographs...Her publications are found in among the top journals appropriate for her field."
"Lynn is an outstanding taxonomist with many publications on various wasp groups, and other insects," wrote Menke. "She has international recognition for her taxonomic work. Included in her bibliography are several books including the world revision of the wasp family Chrysididae with R. M. Bohart in 1990 which is a landmark publication."
Menke praised Kimsey for developing "an outstanding public relations situation," adding that "She has fostered in children (and adults) an appreciation of insects and their world. Lynn has all sorts of living creatures for them to touch and experience first hand. Because of this Lynn has caused many students to take entomology as a career. I know of no other entomological institution that has done what Kimsey has in the Bohart Museum. High school students are interns in the museum, as are undergraduates. Lynn also guides the study of her graduate students at the museum. In addition, she publishes a newsletter in full color (Bohart Museum Society Newsletter) in which she covers stories about insects that are very informative. For example, one of the last issues has an article on fleas which is comprehensive, and doubtless of great interest to people who have encountered these noxious creatures."
The nominating team also described Kimsey as a favorite among the news media, with her ability to translate complex subjects into lay language, and her love of people. Over her 34 years at UC Davis, she has granted thousands of interviews to news outlets, including British Broadcasting System, New York Times, National Geographic, Associated Press, and Los Angeles Times.
Kimsey served as president of the International Society of Hymenopterists from 2002-2004, and as a member of the board of directors of the Natural Science Collections Alliance in 2000 and 2001. The Pacific Branch, Entomological Society of Ameica (PBESA) singled her out for its highest honor, the C. W. Woodworth Award, in 2020. She received the PBESA Systematics, Evolution, and Biodiversity Award in 2014 and was a member of 'The Bee Team' that won the PBESA Outstanding Team Award in 2013. The UC Davis Academic Senate honored her with its Distinguished Scholarly Public Service Award in 2016 in recognition of her outstanding work.
Kimsey served as the vice chair of the UC Davis Department of Entomology in 2005-2006 and again in 2009-2010 and chaired the department in 2008-2009. She plans to retire in 2024 but will continue her research and public service at the Bohart Museum.
Related Story:
Amazing Story About What Entomologist Lynn Kimsey Recorded in San Francisco Bay 50 Years Ago--Bug Squad blog, Aug. 23, 2021
