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Three Botany students in the Baker Lab won merit-based awards from Miami University! Congratulations to Botany Ph.D. and M.S. students Tim Pegg (left) and Tyler Thrash (right), respectively, for receiving the Heimsch Award and Alexa Tovrea-Treft (center) for receiving the Arthur and Anna Evans Scholarship! These awards reflect years of consistent dedication, hard work, excellent performance, and high productivity – thank you for all your efforts!
The Baker Lab is proud to announce the latest product from our collaboration with Dr. Diane Wang at Purdue University in the form of an “On the Nature of Things” essay in the June issue of the American Journal of Botany. These essays are aimed at identifying new ideas and directions in Botany. Our open-access paper, “Working with longitudinal data: quantifying developmental processes using function value traits” presents some background on this technique as well as well annotated and easily reproducible R code and example data. While our examples are based on data we generated using a high-throughput phenotyping platform at Purdue University’s Controlled Environment Phenotyping Facility, the methods and code are equally applicable to data collected with an old-fashioned ruler.
Congratulations to Deannah Neupert on two grants to study Mimulus gemmiparus! The first is from Miami University’s Willard S. Turrell Herbarium and the second is a Bill Dahl Graduate Student Research Award from the Botanical Society of America! Can’t wait to see all the cool things Deannah will do with these awards!
This semester the Baker Lab welcomes back three returning undergraduates and two new undergrads have also joined the lab! Abby Kozyra and Ryan Gerbitz are working on-site while Sarah Niesen, Kathryn Sullivan, and William Gregor are assisting remotely (for now).
Two new graduate students have joined the lab! Deannah Neupert comes from Francis Marion University where she double majored in Biology and Chemistry and is starting a Ph.D. in the Ecology, Evolution, and Environmental Biology (EEEB) program studying Mimulus gemmiparus evo-devo. Alexa Tovrea-Treft is an undergraduate Botany major at Miami University who is continuing her studies in the lab as a Botany M.A. student. Alexa is examining the genetics of stomatal density in Arabidopsis.
We are proud to announce a new paper on leaf venation in Brassica! Co-first authors Eastyn Newsome and Grace Brock along with former Baker-lab undergrad Jared Lutz present fast, easy, and cheap (relatively!) methods for quantifying leaf venation and then explore intra-laminar variation in venation patterns among Brassica rapa crop types in Applications in Plant Sciences.
Congratulations to Eastyn Newsome and Grace Brock who are graduating from Miami University this semester and moving on to do exciting research in new capacities! Both Eastyn and Grace earned Young Botanist awards from the Botanical Society of America for their outstanding achievements. In the fall, Grace will be starting a position as a research technician at Miami University in Jonathan Bauer’s lab while Eastyn is off to Purdue to work on a Master’s degree in the Department of Botany and Plant Pathology. Great job!
The Baker Lab was represented by three teams of undergrads who each presented “posters” at Miami University’s first on-line Undergraduate Research Forum! A big thanks to all the undergrads (Alexa Tovrea-Treft, Parker Slaton, Grace Brock, Sarah Niesen, Abigail Kozyra, Logan Mather, Eastyn Newsome, Ryan Gerbitz, Indi Saxena, and Wolfgang Graff) who worked hard under difficulty (and constantly changing) circumstances as well as Hansol Lee and Tyler Thrash for working with them on their presentations.
The lab welcomes several new undergrads – Ryan Gerbitz, Parker Slaton, and Abby Kozyra. Logan Mather has graduated and is working on ecophysiology or Eucalyptus in Chile. Sounds exciting!
Congratulations to Tim Pegg, Botany PhD student in the Baker Lab on his first publication from his dissertation research in Frontiers in Plant Sciences! There are some phenomenal micrographs of flood-induced root aerenchyma formation in several species of Fabaceae – check it out!
The most recent Baker Lab publication in PLoS Genetics is being featured in the PLoS “Crops, Food Security & Food Systems” channel. To learn more about how we integrated transcriptomic network reconstruction, QTL, and eQTL analyses to understand the regulatory mechanisms and genetic architecture underlying plant development, read the article!
Classes started up again in September and the Baker Lab is gearing up for a large scale greenhouse experiment. To help out with the thousands of plants we will be working with, 5 new undergrads have joined the lab. Welcome Sarah Neisen, Caleb Wilkinson, Wolfgang Graff, Alexa Tovrea-Treft, and Indi Saxena!
August was a busy month full of meetings and presentations in the Baker Lab! Undergrads Eastyn Newsome and Grace Brock presented their updated poster on Brassica leaf venation and stomatal density at the Ecology Society of America meeting in Louisville, Kentucky while doctoral student Tim Pegg won first place in the Biological Sciences category for his poster on aerenchyma formation in Fabaceae at the Microscopy and Microanalysis meeting in Portland, Oregon. Congrats to all!
Meanwhile, Rob escaped to Colorado to visit some new populations of Mimulus gemmiparus, collect tissue, and start in on logistics for next summer’s field experiments. The Baker Lab is still actively recruiting grad students to join the lab and work on this project. Email Rob for more information.
Rob and Hansol Lee are headed to Li-Cor in Lincoln, Nebraska for a week-long workshop and training session using the lab’s new Li-Cor 6800! We are excited to continue integrating plant physiology with developmental genetics, evolution, and ecology. Upgrading from the Li-Cor 6400 to 6800 will make this faster and easier than ever – can’t wait to get started!
We are moving! Goodbye old lab in Pearson 367 and hello new collaborative research space in Pearson 351! The Baker Lab is excited to join forces with the Tomoyasu and Fernandes research groups.
The Baker Lab welcomes Vada Bowen, a summer undergraduate research assistant to the lab!
The Baker Lab welcomes Hansol Lee, the first PhD student to the lab! Hansol is off to a great start collecting data on stomatal density and working in the greenhouse in addition to teaching and coursework.
The Baker Lab and the Biology Department at Miami University were featured in LumiGrow’s annual news letter, which highlighted the work we are currently doing on the developmental genetics of Brassica. Check it out!
We are up and running with a new group of diverse Brassica rapa genotypes! Thanks to the Biology Department at Miami University, we have new LED lights to extend day length and increase the amount of light energy the plants receive. These LEDs are designed to be super energy efficient. Because plants primarily absorb light energy in red and blue wavelengths, they emit primarily red and blue wavelengths – and don’t waste energy on wavelengths plants don’t use. The result? Shockingly pink lights! We can also manipulate the ratio of red:blue light as well as other aspects of the light environment to test the effects of these abiotic inputs on plant growth and development. Check out the “highlights” on the Miami U campus news website!
The Baker Lab welcomes two new additions! Casey Albarran is an undergraduate from Humboldt State University who joins the lab as a summer REU student participating in the Miami University Research Experience for Undergraduates program focused on ecology in human dominated landscapes. Asuman Inan is an undergraduate intern from Bogazici University in Istanbul, Turkey. It’s going to be a busy summer in the Baker Lab!
Congratulations to Eastyn Newsome and Jared Lutz, undergrads in the Baker Lab, who presented their first poster today at Miami University’s Undergraduate Research Forum! Eastyn Newsome spent an hour an a half explaining all the cool work she and Jared have been doing including quantifying stomatal density and leaf venation patterns in Brassica.
We are excited to announce that our latest paper on predicting non-linear developmental phenotypes based on genotypic data is out at G3: Genes|Genomes|Genetics and is featured on the journal website! We argue that predicting phenotypes based on genotypes is a central objective of evolutionary developmental biology and a key component of breeding programs, but that predictive models require understanding the genetic architecture of phenotypes throughout ontogeny. Using Brassica rapa genotypes grown in multiple density settings and seasons, we statistically factor out genotype-specific differences in carbon availability (estimated by Amax) to more precisely examine the core genetic mechanisms underlying leaf development. We then constructed QTL-based models that predict leaf growth dynamics based on genotypic data. Our models successfully predicted non-linear developmental phenotypes for genotypes not used in model construction.
Rob Baker, alongside co-first-author Leong Wen Fun, have had a new paper published in Theoretical And Applied Genetics, the international journal of plant breeding research. The paper describes the growth trajectory of leaves using Bayesian function-valued trait models that isolate the genetic architecture underlying leaf developmental by factoring out genotype-specific differences in photosynthesis. They also demonstrate that high throughput remote sensing data can be used as a proxy for of leaf-level physiological measurements. This is the first paper Rob has had published in affiliation with Miami University, the new home of the Baker Lab!
The Baker Lab has recently moved from the University of Wyoming to the Biology Department at Miami University in Oxford, Ohio. The move took place earlier this year and Rob Baker has been building a team to continued research on the genomics of structure-function relationships for improved agricultural sustainability and evolution and development of structure-function relationships in Brassica rapa, as well as evo-devo in locally adapted populations of Mimulus guttatus (monkey flower).
Dr. Laura Vietti, the Geological Museum and Collections Manager at the University of Wyoming Department of Geology and Geophysics, and I had a poster accepted to the Sci-Art Symposium “Re-envisioning the laboratory”. The goal of the symposium is to catalyze collaboration, scholarship, and community through interdisciplinary conversations and presentations. Laura and I used a variety of specialized microscopes to investigate the natural world at different scales. Because these objects of our investigations are not visible to the naked eye, observing new phenomena with the aid of technology has an air of discovery. The excitement of seeing and understanding our world in a new way is not limited to the quantifiable, scientific realm. The images we produced are often visually compelling and, we hope, address the underlying goals of both art and science: a deeper understanding and appreciation of who we are and the world we inhabit.
Sub-epidermal laser scanning confocal image of a Brassica leaf
“The Macro/Microscopic Life of Plants: An exploration of art from the scientific perspective”: Marc Brock (a postdoc in the Botany Department at the University of Wyoming) and I were awarded a grant from the University of Wyoming Biodiversity Institute to produce art based on science. Specifically, we were interested in exploring plant biology across a broad spectrum of physical scales – from traditional landscape photography all the way to scanning electron microscopy. Our goal was to produce aesthetically pleasing art that starts conversations about science by bridging the gap between familiar and relatively foreign plant imagery. We wanted to encourage people to think of science from a different perspective, and perhaps to remind ourselves how fun and exciting science can be. Although each piece is designed to be appreciated with little or no scientific context, we’ve integrated a web site into the exhibit so that people can learn more if they’d like; the exhibit was also featured in our local paper. Drop on by the Berry Center (10th & Lewis St) at the University of Wyoming to see our exhibit. The opening reception is Friday, October 16th at 7pm (free refreshments & a botanical surprise!). The exhibit will be on display until December. And if you can’t make it, check out the website with examples of the work we have on display: www.macromicroscopic.com
Listen to a interview I did with Ryan Haupt for the podcast “Science . . . sort of“. We go on a rambling journey that covers topics such as evolutionary developmental biology, the modern synthesis, modeling leaf development, the movie E.T. & taxonomy, the evolution and development of shoot architecture, plant anatomy & meristems, a discussion of the geography and beer brewing including a tasting of a local Oatmeal IPA, the ecological and economic impacts of Genetically Modified Organisms, and the possibility of colonizing mars. Not necessarily in that order.
A recent commentary by Kyle Hernandez, “Understanding the genetic architecture of complex traits using the function-valued approach” in New Phytologist highlights our recent paper (Baker et al., 2015) in the same issue. Hernandez clearly and concisely explains how function-valued traits (FVT) modeling can be used to examine complex traits, such as those that involve continuous change during ontogeny:
Despite their biological relevance and statistical advantages, FVTs are frequently discussed but rarely implemented in practice. In this issue of New Phytologist, Baker et al. (pp. 257–268) put the FVT approach into practice through an exploration of the genetic architecture of leaf development in Brassica rapa and its relationships with organism-level performance. . . Beyond providing an excellent framework for studying FVTs, Baker et al.’s study has implications for breeding of sustainable crop cultivars. For example, by modeling FVTs Baker et al. found that leaf allometry was genetically independent from leaf length and width and is associated with features that affect desiccation resistance. . . Some of the most compelling results in Baker et al.’s work are the genetic differences between function-valued and STP (single time point) measurements. . .
Check out the Science Café talk I’m presenting as part of a series of public science talks hosted by the University of Wyoming Biodiversity Institute, “Cabbages and turnips and oilseeds, oh my!”. I’ll be discussing my approach to basic research on the anatomy and genomics underlying water use efficiency in Brassica rapa. I’ll also talk about how modern DNA sequencing techniques and analyses can be used to make traditional breeding programs more flexible, intelligent, customizable, and agile in the face of a rapidly changing global environment.
Come by Altitude Brewery and Chophouse on April 16th 5:30-7:30 in Laramie, Wyoming – free dinner for the first 30 or so people!
In 2012, a paper I published in the New Phytologist along with Drs. Hileman and Diggle (“Patterns of shoot architecture in locally adapted populations are linked to intraspecific differences in gene regulation”, Baker et al.) was featured on the cover of the journal. This false-color scanning electron micrograph depicts an axillary bud in an early stage of developing into a branch. Two prophylls (the first set of leaves on a branch) are poking straight out at you, covered in a dense forest of spikey trichomes (plant hairs, which may function in herbivore deterrence).
Our recent paper in the New Phytologist (“Patterns of shoot architecture in locally adapted populations are linked to intraspecific differences in gene expression”, Baker et al., 2012) was recommended in Faculty of 1000!
This study shows that gene function information deduced from model organisms can be used to test the genetic basis of adaptive variation in non-model species. The non-model in this case is monkey flower, Mimulus guttatus. . .