Murphy, a fourth-year UC Davis student majoring in neurobiology, physiology, and behavior, received $1563 to study “Codon Optimization: Cracking the Genetic Code.” A codon is a unit of three nucleotides that together codes for an amino acid, the building block of proteins in all organisms. Using the fly, Drosophila melanogaster, as a model system, Murphy is exploring the functional significance of codon bias, a phenomenon in which certain codons are favored over others even though they may code for the same amino acid.
Murphy has worked in the Chiu lab since 2011. “Katie is one of the most talented and hardworking student I have ever encountered,” Chiu said. “I can't think of anyone else who is more deserving of this award.”
Murphy is one of a select group of students in the Research Scholars Program in Insect Biology, organized and directed by professor Jay Rosenheim and assistant professors Louie Yang and Joanna Chiu. The program aims to provide undergraduates with a closely mentored research experience in biology.
The Provost's Undergraduate Fellowship supports undergraduate students doing research or creative projects under the guidance of UC Davis faculty members. Students from all discipline areas are eligible to apply
As a Provost fellow, Murphy will present her work at the annual UC Davis Undergraduate Research Conference, which takes place April 25–26 in Freeborn Hall.
In 2012, Murphy received a UC President's Undergraduate Research Fellowship for her research on "Transgenic Yeast as an Organic Pesticide," exploring the use of RNAi technology in combating the invasive pest, the spotted-wing Drosophila suzukii. She also received a 2013 McBeth Memorial Scholarship and a 2010 Voorhies Memorial Scholarship.
Murphy is a 2010 graduate of Kelseyville High School (Lake County) and valedictorian of her class.
“My favorite subject in high school was biology,” she recalled. “My favorite project was when we dissected a cat in anatomy. In college, I lucked into a lab job where my boss and co-workers were willing to teach me and allowed me the freedom to take on my own projects, an opportunity that few undergrads get.”
Following graduation, she plans to travel and continue her current research projects.
The work is expected to accelerate basic and applied research, leading to better monitoring and control strategies for the pest.
Officially published Dec. 1 in the journal G3 (Genes Genomics and Genetics), the open-access research has been available online for several weeks and drawing global attention.
“To enable basic and applied research of this important pest, Drosophila suzukii, we sequenced the genome to obtain a high-quality reference sequence,” said molecular geneticist Joanna Chiu of the UC Davis Department of Entomology and Nematology. Chiu and Professor David Begun of the UC Davis Department of Evolution and Ecology led the genomics team of collaborative researchers from four institutions.
The posting of the genome and comparative sequence analysis on the publicly accessible SpottedWingFlyBase web portal could lead to more species-specific weapons to combat the destructive pest, Chiu said. Scientists are looking at its biology, behavior, food and odor preferences, and pesticide resistance.
“Many researchers are working hard to study the biology of this insect through basic and applied projects, and we hope our efforts in presenting our genomic data in a user-friendly web portal will democratize the sequence data and help facilitate everyone’s research, especially those who do not have expertise in genome and sequence analysis,” she said.
The spotted wing drosophila, a native of Asia that was first detected in the United States in 2008, is wreaking economic havoc on crops such as blueberries, cherries, blackberries and raspberries. This fly lays its eggs inside the ripe or ripening fruit, and the developing larvae feed on the soft fruit, crippling crop yields.
Chiu teamed with scientists at UC Davis, Oregon State University (OSU), the China National Gene Bank and the American Museum of Natural History as part of a $5.8 million project on the biology and management of spotted wing drosophila, funded by a U.S. Department of Agriculture Specialty Crops Research Initiative grant to OSU entomologist Vaughn Walton and a team of investigators including Professor Frank Zalom of the UC Davis Department of Entomology and Nematology, who is the lead UC Davis investigator.
Zalom, recently inducted as president of the nearly 7000-member Entomological Society of America, said that the G3 article “presents a high quality reference sequence of Drosophila suzukii, examination of the basic properties of its genome and transcriptome, and description of patterns of genome evolution in relation to its close relatives.”
As of Nov. 27, SpottedWingFlyBase has drawn more than 3000 page views from 20 countries, including the U.S., France, Italy, Belgium, China, Spain, Japan, Germany, and Great Britain, Zalom said. “Given this impressive response and the worldwide importance of Drosophila suzukii, I expect that the G3 article will become very highly cited and cast Dr. Chiu as a central figure in future Drosophila suzukii genomic studies related to topics such as insecticide detoxification, odorant reception and regulatory entomology.”
OSU entomologist Vaughn Walton, lead investigator of the USDA grant, said: “Scientists from all over the world are interested in knowledge locked inside the fly’s genetic material.” He also pointed out that the genome work may relieve the fears of countries wishing to export American fruit, but not the pest. By finding the fly’s unique genetic signature, scientists hope that DNA testing will quickly determine if ready-to-be-shipped fruit contains spotted wing drosophila larvae.
The UC Davis team included the Joanna Chiu lab and the Frank Zalom lab, both in Department of Entomology and Nematology, and David Begun’s Drosophila evolutionary genetics lab in the Department of Evolution and Ecology. They collaborated with Walton and spotted wing drosophila project leader Linda Brewer of OSU; Ernest Lee from the American Museum of Natural History, and Xuanting Jiang and Guojie Zhang of the China National Genebank, BGI-Shenzhen.
Other UC Davis scientists involved in the research included doctoral candidates Kelly Hamby of the Zalom lab, Rosanna Kwok of the Chiu lab, as well as postdoctoral researchers Li Zhao, Christopher Hamm, Julie M. Cridland and research technician Perot Saelao of the Begun lab.
The SpottedWingFlyBase is a dedicated online resource for Drosophila suzukii genomics but also includes comparative genomic analysis of Drosophila suzukii with other closely related Drosophila species.
The article is available at the G3 website at: http://www.g3journal.org/content/early/2013/10/14/g3.113.008185.abstract.
More information is provided by Oregon State University at the SpottedWingFlyBase portal at http://spottedwingflybase.oregonstate.edu/ or the Spotted Wing Drosophila website at http://spottedwing.org/
-- Joanna Chiu, UC Davis Department of Entomology and Nematology, (530) 752-1839
-- Frank Zalom, UC Davis Department of Entomology and Nematology, (530) 752-3687, firstname.lastname@example.org
Using state-of-the-art genome sequencing and bioinformatics, the researchers resolved a long-standing, unanswered evolutionary question. Scientists previously thought that ants and bees were more distantly related, with ants being closer to certain parasitoid wasps.
Ants, bees and stinging wasps all belong to the aculeate (stinging) Hymenoptera clade -- the group in which social behavior is most extensively developed, said senior author and ant specialist Phil Ward, professor of entomology at UC Davis.
"Despite great interest in the ecology and behavior of these insects, their evolutionary relationships have never been fully clarified. In particular, it has been uncertain how ants—the world’s most successful social insects—are related to bees and wasps," Ward said. "We were able to resolve this question by employing next-generation sequencing technology and advances in bioinformatics. This phylogeny, or evolutionary tree, provides a new framework for understanding the evolution of nesting, feeding and social behavior in Hymenoptera."
“With a phylogeny or evolutionary progression that we think is reliable and robust, we can now start to understand how various morphological and/or behavioral traits evolved in these groups of insects, and even examine the genetic basis of these phenotypic changes,” Chiu said.
Johnson, whose lab studies the genetics, behavior, evolution and health of honeybees, noted that the study showed that ants and bees are more closely related than previously thought.
The scientists combined data from the transcriptome -- showing which genes are active and being transcribed from DNA into RNA-- and genomic (DNA) data from a number of species of ants, bees and wasps, including bradynobaenid wasps, a cuckoo wasp, a spider wasp, a scoliid wasp, a mud dauber wasp, a tiphiid wasp, a paper wasp and a pollen wasp; a velvet ant (wasp); a dracula ant; and a sweat bee, Lasioglossum albipes.
Of particular interest was the finding that ants are a sister group to the Apoidea, a major group within Hymenoptera that includes bees and sphecid wasps (a family of wasps that includes digger wasps and mud daubers).
The UC Davis results also provide a new perspective on lower Cretaceous fossil Cariridris bipetiolata, originally claimed to be the oldest fossil ant. Scientists later reinterpreted it to be a spheciform wasp.
“Our discovery that ants and apoids are sister taxa helps to explain difficulty in the placement of Cariridris,” the authors wrote in the paper, “and suggests that it is best treated as a lineage close to the root of the ant-apoid tree, perhaps not assignable with certainty to either branch.”
The scientists discovered that the ancestral aculeate wasp was likely an ectoparasitoid, which attacks and paralyzes a host insect and leaves its offspring nearby where they can attach to the outside of the host and feed from it.
The research drew financial support from UC Davis.
Native to Southeast Asia, Drosophilia suzukii infests soft-skinned fruits such as strawberries, raspberries, cherries, blueberries and blackberries. The insect was first detected in the United States in 2008 when scientists identified it in the central coastal region of California. It can cause an estimated $300 million in damage annually to California crops.
In pioneering research, the four-member team from the Department of Entomology and Nematology sought to find out the pest’s response to insecticide toxicity and whether it could be predicted through the integration of circadian activity and gene expression profiles.
“It is possible that if insecticides can be applied at the time when the SWD's defense system against insecticides is at its weakest state, they will be more effective,” Chiu said. “Results from our experiments turned out to be a bit more complicated than we originally envisioned, but we indeed found that at least for malathion, there is an optimal time for application to inflict maximum damage to SWD. We hope that growers will be able to use fewer insecticides, thereby decreasing damage to the environment and decreasing costs at the same time.”
“We caution growers that we still need to conduct field trials to confirm our laboratory observations,” Chiu addedf.
“SWD is becoming a big problem for growers of soft-skinned fruits such as strawberries, raspberries, blueberries, and cherries all over the world,” Chiu pointed out. “With the need to satisfy insect damage standards and to reduce crop loss, the growers generally adopt high levels of insecticide usage for SWD control and risk reduction. In the long-term, this will lead to development of insecticide resistance, not to mention the damage inflicted on beneficial insects.”
“Current Drosophila suzukii management strategies rely heavily on insecticide usage, because other pest management tactics are still being development and optimized,” wrote Chiu and fellow authors Frank Zalom, integrated pest management specialist and professor of entomology; doctoral candidate Kelly Hamby of the Zalom lab; and graduate student Rosanna Kwok of the Chiu lab.
Said Hamby: “The paper is a first look at Drosophilia suzukii daily activity rhythms under a temperature and light/dark cycle mimicking California raspberry growing conditions as well as a look at the daily cycling of insecticide susceptibility enzymes that could potentially detoxify insecticides. The next steps would be to include more temperature conditions, more insecticides, and attempt an experiment in the field.”
"For me, the importance of our research is that it allows us to move toward a more effective and efficient way of controlling this pest, which is rapidly becoming of prominent importance because of how fast Drosophila suzukii has been spreading throughout the western US since its initial introduction," said Kwok. "By recognizing temporal differences that may contribute to a difference in toxicity to certain pesticides, we may be able to move toward management programs that are tailored to target a specific species of insect. We may be able to spray less or less frequently if we can find out when these pests are most susceptible."
"As for the future," Kwok added, "I think that as we sequence and fully annotate the D. suzukii genome we can identify more genes that are implicated in toxicity and pesticide resistance."
Chiu praised the work of the graduate students. "I think Kelly and Rosanna really did a fantastic job on this project!" she said.
The study took place under laboratory conditions simulating summer and winter in Watsonville. The team found significant differences in the chronotoxicity of SWD toward malathion, with the highest susceptibility at 6 a.m., “corresponding to peak expression of cytochrome P450s that may be involved in bioactivation of malathion,” they wrote in their abstract. “Chronobiology and chronotoxicity of D. suzukii provide valuable insights for monitoring and control efforts, because insect activity as well as insecticide timing and efficacy are crucial considerations for pest management.”
The spotted-wing drosophila was first observed in Japan as early as 1916. The females lay their eggs in ripe and ripening fruit, unlike other Drosophila species known to infest overripe and blemished fruit. The larvae feed on the fruit. “The adult is the only stage that can be targeted for control by conventional pesticides,” the UC Davis scientists wrote. The most commonly used insecticides are organophosphates, pyrethroids and spinosyns.
In announcing the awards, Provost Ralph Hexter noted (1) that Tatiossian’s research on the walnut twig beetle makes a significant contribution to establishing an integrated pest management plan; (2) that her manuscript, “Flight Response of the Walnut Twig Beetle, Pityophthorus juglandis, to Aggregation Pheromones Produced by Low Densities of Males”; is in preparation for submission to the Journal of Chemical Ecology; and (3) that her poster received attention at a national entomology conference for the ceramic bark beetle she sculpted.
Hexter presented awards of excellence to Brenda Marin-Rodriguez and L. Carolina Tavarez. In addition to Tatiossian, honorable mentions went to Amanda Steele, biomedical engineering; Rachel Borthwell, biological sciences and art history; and Lindsey Black, history.
A photo of Tatiossian and Black appears as the cover photo on the UC Davis Undergraduate Facebook site at https://www.facebook.com/UCDavisUndergraduateEducation. Her poster, including the ceramic bark beetle she crafted, is mounted on the third floor of Briggs Hall, next to the administration office of the UC Davis Department of Entomology and Nematology.
Tatiossian, who joined the Research Scholars Program in September 2011, graduated from UC Davis in three years (she achieved the top grade point average in entomology) and is currently working in the laboratory of Diane Ullman, professor of entomology and associate dean for undergraduate academic programs in the College of Agricultural and Environmental Sciences.
Among those nominating her or supporting her nomination were her mentor, chemical ecologist and forest entomologist Steve Seybold of the Davis-based Pacific Southwest Research Station, USDA Forest Service, and an affiliate of the UC Davis Department of Entomology; professor Jay Rosenheim who co-founded and co-directs the Research Scholars Program in Insect Biology; and Diane Ullman.
Rosenheim noted that Tatiossian was a member of the first cohort of undergraduates recruited to the program. “I witnessed her tremendous determination to develop independent research skills” and she “succeeded in all phases of the project, from design, data collection, data analysis and manuscript preparation.”
Among the 30 students who have entered the program since 2011, “Kristina is absolutely the standout in terms of motivation and enthusiasm for research,” Rosenheim said. “She leaped at the opportunity to learn how to become an independent researcher. Kristina will generate the first-lead authored publication for any student in our program—hopefully, the first of many. In this sense, she has already been a trailblazer for our program.”
Seybold noted that Tatiossian “worked on the host-finding behavior of a major pest of walnut trees, the walnut twig beetle. This is a nationally significant pest that spreads a disease of live trees called thousand cankers disease (TCD). The condition threatens not only the English walnuts that form the basis of the California nut industry, but also the black walnuts that represent over $500 billion in growing stock value of fine wood products in the eastern U.S.
“Kristina formulated her research project in fall 2011 and spring 2012 and then carried it out in spring and summer 2012. As she developed the project, she also applied to the Department of Entomology for a McBeth Scholarship, which she was awarded in summer 2012. The award helped her offset the costs of her research supplies and funded her travel to several scientific meetings.”
“Kristina collected a live population of the walnut twig beetle from a traditional orchard habitat in the southern Central Valley, reared the insects to the adult stage, and re-introduced the adults into freshly cut black walnut branch sections. Once the male beetles had begun producing their aggregation pheromones (attractants) in the branch sections, Kristina used the branch sections as lures to attract new males and females into flight traps. Using this basic technique she was able to establish that as few as 1 to 5 male beetles would provide a threshold of flight behavioral attraction in the field. This finding has ramifications for establishing an integrated pest management program for the walnut twig beetle nationwide.”
Tatiossian developed and displayed her poster at the 60th Annual Meeting of the Entomological Society (ESA), held Nov. 11-14, 2012 in Knoxville, Tenn. “Her poster reached a very interested target audience because Knoxville is in the heart of the distribution of eastern black walnut trees and in the center of the current distribution of TCD in the eastern U.S.,” Seybold said. “In a very creative touch, Kristina sculpted a replica of the female walnut twig beetle (through her participation in the UC Davis Art/Science Fusion Program) and attached the sculpture directly to her poster. This elicited quite a response at the national meeting and led to a news story released by UC Davis.”
The poster also drew attention at the arts exhibit at the 24th Annual UC Davis Undergraduate Research, Scholarship and Creative Activities Conference, held April 26, 2013.
In addition, Tatiossian delivered an oral presentation on her research at the 97th Annual Meeting of the Pacific Branch of the ESA in South Lake Tahoe, Nev.
Her poster, now on permanent display at Briggs Hall, credits Seybold; Extension entomologist Mary Louise Flint, associate director for Urban and Community IPM, UC Statewide Integrated Pest Program; entomology graduate student Stacy Hishinuma, and postdoctoral researcher Yigen Chen of the UC Davis Department of Entomology. Robin Schmidt of UC Davis Molecular and Cellular Biology mounted the unusual poster with the ceramic beetle.