People in the Cooley Lab

Lab 2016

Photo of ArielleArielle Cooley. I am a broadly trained evolutionary biologist, primarily interested in the evolution of phenotypic diversity. My goal is to connect cellular, molecular and genomic processes to organismal variation in phenotype and fitness.

My research background includes a post doc in Patricia Wittkopp's lab, where I focused on two closely related fruit fly species that differ in body color. My ongoing research interest, initiated as a graduate student in John Willis' lab, involves floral diversification in a group of South American wildflowers in the "monkeyflower" genus Mimulus. I am pursuing this work at Whitman College as well as teaching Genetics; Evolution & Development; and Plant Physiology.

Current Students

Johanna AuJohanna Au '19. Johanna is building RNAi constructs to silence two genes, Myb2b and and Myb3a, that are our top candidates for causing the evolutionary gain of petal anthocyanin pigmentation in the orange-flowered Mimulus cupreus. She is using a Gateway strategy, in which fragments of each gene are directionally cloned into the pENTR entry vector and then recombined in to a destination vector that will be used for transformation.

Jessie FriedmanJessie Friedman '18. A recently-constructed Mimulus cupreus transcriptome provided coding sequence for petal pigment candidate genes Myb2b and Myb3a. To fully evaluate the functions of these genes, however, we need to know their upstream regulatory sequences so that we can build transgenic constructs driven by the native promoter of each gene. Jessie is leveraging existing genomic resources, primarily from M. luteus and M. guttatus, to design primers to "fish out" promoter sequence from M. cupreus.

Kuenzang OmKuenzang Om '18. Kuenzang is using transgenics to functionally test the necessity and sufficiency of candidate gene Myb5 to petal anthocyanin. In this photo she is transforming the purple-flowered M. l. variegatus with an RNAi construct to silence Myb5. If the offspring lack petal anthocyanin, we can conclude that Myb5 is necessary for the evolutionarily derived trait of petal anthocyanin in M. l. variegatus. Conversely, if expressing the variegatus allele of Myb5 in yellow-flowered M. l. luteus leads to the activation of petal anthocyanin, we can conclude that Myb5 is sufficient for creating this trait.

ErinErin Minus '18. Erin is continuing the work of Aaron Williams '17, using digital image analysis in ArcGIS to quantify spatially complex pigment patterns in an F2 hybrid population derived from an M. cupreus x M. l. variegatus cross. You can see the ArcGIS program running in the background of this photo. Erin will compare phenotypes she obtains to the genotypes from our first sequenced individuals (96 F2 plants) in order to genetically map some of the traits.



Taylor WilkeTaylor Wilke '18. Taylor is using the same F2 population as Erin to extract information about a different trait, yellow carotenoid pigmentation. When Mimulus cupreus gained petal anthocyanin, it kept its carotenoids; the combination of the two pigments are what creates its bright orange color. Mimulus l. variegatus, in contrast, gained anthocyanin but lost most of its floral carotenoids. Carotenoid abundance segregates in the cupreus x variegatus F2 mapping population. Suprisingly little is known about the genetics of carotenoid regulation, and we hope to discover some of the genes involved over the course of this mapping project.

Graduates

Rachel EguiaRachel Eguia '17. Rachel worked on building transgenes to test the function of candidate pigmentation gene Myb5. The eventual goal is to silence Myb5 in plants that have petal anthocyanin pigmentation, and activate Myb5 in plants that lack petal anthocyanin pigmentation, in order to test the hypothesis that Myb5 is both necessary and sufficient for the recent gain of petal anthocyanins in the purple-flowered Mimulus luteus var. variegatus.


Anne VonadaAnne Vonada '17. The recent gain of petal anthocyanins in the orange-flowered M. cupreus is controlled by a single locus that we call pla1. This region of the genome is unlinked to Myb5 (the top candidate in M. l. variegatus), but it does contain numerous Myb transcription factors that are similarly good candidates for activating petal pigmentation in M. cupreus. Anne Vonada used genomics, transcriptomics, and RT-PCR to evaluate candidate genes at pla1, and was able to narrow down the list from six genes to two: Myb2b and Myb3a.

Aaron WilliamsAaron Williams '17. Aaron helped launch a new lab project based on a striking phenotypic observation. Crossing a plant with solid purple flowers (M. l. variegatus) to a plant with solid orange flowers (M. cupreus) yields a hybrid with complex patterns of red blotches overlaid on a cream background. Little is known about the developmental regulation of "speckliness," and it is difficult to measure using traditional means. Aaron worked to develop a digital image analysis approach for extracting quantitative trait values from the complex spatial variation seen in an F2 hybrid population.

JessicaJessica Palacios '16. Previous work in the luteus complex of Mimulus has utilized a single inbred line as the representative of the species. But just how representative is that line? Jessica launched an exploration of the wider range of diversity within several species, which revealed consistent trends as well as important differences between our inbred lines and a panel of wild-collected accessions.


JeremyJeremy Nolan '16. Jeremy is interested in the physiological consequences of environmental pollution. He modified a plant incubator to serve as a CO2 chamber, in order to test the effects of elevated CO2 on plant growth and photosynthesis across a diverse collection of Mimulus accessions from Chile.



Allison EggertAllison Eggert '16. The luteus group of Mimulus is tetraploid, and contains two "homeologous" (genome-duplicated) copies of the Myb5 gene. Myb5a is tightly linked to the gain of petal pigmentation in M. l. variegatus, while Myb5b is unlinked. Surprisingly, the two copies are 100% identical from start codon through 3'UTR. Divergence in the 5'UTR allowed Allison to design copy-specific primers to investigate expression divergence between the homeologs. She found that Myb5a has high expression in anthocyanin-pigmented petals, while Myb5b has uniformly low expression across tissues and species.

Kimmy Stanton prepares to transform MimulusKimberly Stanton. Kimmy, a Reed College ('14) graduate, worked as a technician in the Cooley lab before going on to graduate school in evolutionary biology at Duke University. She developed a transcriptome-supported approach to identifying qPCR reference genes for Mimulus, and worked towards transgenic transformation in M. cupreus. In this photo, Kimmy prepares plants for a vacuum infiltration to help drive Agrobacteria into the floral bud tissue, as part of the plant transformation process. (Photo Credit: Larry North)

PhilipPhilip Cheng '15. Philip used quantitative RT-PCR to carry out sensitive assays of the expression patterns of candidate pigmentation genes Myb4 and Myb5 in M. l. luteus and M. l. variegatus.Here he is setting up a run on the qPCR machine. He also used our new M. l. luteus genome sequence to design primers to amplify the complete cDNA sequence of each gene. This will facilitate building transgenic plasmids. Philip discovered that Myb4 has almost no expression in leaf, petal, or nectar guide tissue; in contrast, Myb5 expression is high in anthocyanin-pigmented tissues. This strongly supports Myb5 as the causal gene for pigment gain in M. l. variegatus.

MarijkeMarijke Wijnen '15. Celine's research revealed an anthocyanin-producing stress response following an (unplanned!) heat wave that imposed both heat and drought. Marijke followed up on this work, using controlled treatments to disentangle the effects of these two environmental stressors. She found that drought, but not heat, induced vegetative anthocyanin pigments. Interestingly, the heat treatment resulted in an increased proportion of deformed flowers - possibly a Heat Shock Protein effect..? Here she measures photosynthesis in the greenhouse.

Celine in the greenhouseCeline Valentin '14. Celine studied stress tolerance in two Mimulus species. She found that the yellow-flowered M. l. luteus and the orange-flowered, more anthocyanin-rich M. cupreus responded differently to an intense week-long heat wave: the former produced significantly more vegetative anthocyanin pigments. Such environmentally-induced vegetative anthocyanins are considered a sign of plant stress. M. l. luteus therefore appears to have been more stressed during the heat wave. We hypothesize that M. cupreus, in contrast, may be "pre-protected" by its higher constitutive levels of anthocyanin pigments.

Photo of Leah and JanaeLeah Mohtes-Chan '14 (left) and Janae Edelson '14 (right). Leah and Janae launched the molecular lab - Step 1, unpack a LOT of boxes! They extracted DNA from M. l. luteus and prepared it for genomic sequencing at Duke University, which led to the sequencing of the first ever Chilean Mimulus genome. They also used semi-quantitative RT-PCR to discover that two tandemly duplicated candidate pigmentation genes, Myb4 and Myb5, have diverged in function: Myb5 is expressed in both petal and leaf tissue, while Myb4 is not.


Photo of SageSage Stutsman '13. Founding member of the Cooley lab, Sage planted and tended the very first monkeyflower population at Whitman. She is especially interested in hydroponics and developed a hydroponics system to study the effects of different nutrient treatments on plant growth and development.