Life is hard. Among the many challenges is gathering and responding to information about an ever-shifting environment. One solution to this challenge is the evolution of mechanisms to convert information gathered by cellular receptors — which act like antennae to monitor the environment — into chemical signals. These chemical signals can then be translated by networks of interacting molecular factors into changes in cell growth or identity. In multicellular organisms, cellular events must be integrated into larger programs that operate at the tissue, organ or even whole organism level. We investigate how the architecture and dynamics of signaling networks allow for the effective processing and integration of information, and how plants tune these networks to optimize their morphology for a given environment.
research
Arabidopsis found in a Seattle backyard.
Our recent work has drawn from molecular genetics, genomics, physiology and synthetic biology to build new tools to study signaling dynamics and to apply these tools to a variety of fundamental questions in cell and developmental biology. Specifically, we are:
Building tools to study and reprogram signaling dynamics
Integrating metabolic status into growth control networks
Evaluating the impact of evolution on signaling networks
1. Building tools to study and reprogram signaling dynamics
Synthetic auxin-induced transcription in yeast. All of the parts of the network transferred to yeast are shown as a circuit diagram at the top. Auxin addition to the yeast culture at time 0 triggers degradation of repressors (labeled with YFP, a protein that fluoresces yellow) and activation of a reporter (CFP, a protein that fluoresces cyan).
Building dynamic networks from the ground up. Auxin is a plant hormone that plays a key role in nearly every aspect of plant biology. Direct experimental tests of signaling dynamics in this crucial pathway are confounded by the ubiquity of auxin response in plant cells. In collaboration with Eric Klavins in the UW Electrical Engineering Department, we have developed an alternative approach where we are systematically transplanting the auxin response pathway from Arabidopsis into the single-celled yeast Saccharomyces cerevisiae. An analogy to our approach is trying to understand how a radio works by removing components one by one, reconnecting each part in a simple setting, and characterizing the resulting circuits in great detail. We have successfully transferred the nuclear auxin response pathway from auxin perception through activation of transcription—a rather remarkable feat highlighting the fundamental conservation of core eukaryotic cell biology. We are currently excited to apply this system to fundamental control points of signaling, including protein degradation, transcriptional repression and transcriptional activation. We are also developing and deploying new tools to reparameterize core hormone-regulated networks (including auxin, jasmonates and gibberellins) using synthetic transcription factors.
2. Integrating metabolic status into growth control networks
Sucrose promotes rootward auxin transport. Plants grown on media supplemented with sucrose (S) showed increased rootward auxin transport compared with plants grown without sucrose supplementation (N). Transport was visualized by staining for an auxin reporter several hours after application of an auxin (IAA)-containing droplet on one cotyledon (as depicted in the schematic).
We have discovered that many facets of growth are exquisitely sensitive to developmental stage, as well as genetic and environmental perturbations. Among our most surprising findings was that carbon availability had a dramatic effect on multiple aspects of growth dynamics. Excitingly, the light-regulated transcription factors PIF4 and PIF5 were required for the growth promoting effects of elevated CO2, and the PIFs acted at least in part by regulating the amount of auxin delivered from shoots to the roots. Our results point to direct integration of the light signal downstream of both the phytochrome photoreceptors and photosynthesis. This work provides an outstanding opportunity to integrate cell signaling into an organismal framework of plant growth control. Our progress has been greatly accelerated by an on-going collaboration with Soo-Hyung Kim in UW School of Environmental and Forest Sciences.
3. Evaluating the impact of evolution on signaling networks
Brassica rapa has much to offer as a study system, including a larger seedling.
Approaches for engineering new crop varieties are remarkably crude compared to the design and implementation of non-biological technology. One strength of engineering is its ability to parse complex systems, such as a Boeing 787, into sub-networks or modules that can be analyzed in isolation. The synthetic auxin response system in yeast, developed by my lab in collaboration with Eric Klavins in the UW Electrical Engineering Department, makes it possible to interrogate the function of plant auxin signaling modules in isolation. We are currently testing the function of auxin components of Zea mays and Brassica rapa in our synthetic system. This comparative approach may help answer one of the oldest questions in auxin biology: how does such a simple molecule do so many different things?
For the most recent publications from the Nemhauser Lab, please use these links:
Lena is an undergraduate student at the University of Washington hoping to major in General Biology. She is passionate about gene editing plants, learning about plant gene expressions, and collaborating with other researchers in the lab. Lena also enjoys traveling, exercising, and doing anything involving art in her free time.
Viviana Buehrer
Undergraduate Intern
vivib393 at uw.edu
Viviana is a 3rd year undergraduate at UW studying molecular, cellular, and developmental biology and Spanish. She loves learning about molecular signaling and analytical biology, and is passionate about environmental health, equity in medicine, and music. In her free time, she loves hiking, crocheting, and spending time with her friends and family.
Ana Maria Cabral
Post-Baccalaureate Intern
acabral8 at uw.edu
Ana arrived in Seattle in 2021 with a degree in Veterinary Medicine from the University of Sao Paulo. At UW, she is pursuing a degree in Molecular and Cellular Biology with a minor in Chemistry. She is excited that plant health and immunity research may promote scientific advancements enhancing crop productivity and providing food security for vulnerable populations. She enjoys refining her multiple language proficiencies, traveling to diverse U.S. regions, wellness activities, and exploring new vegan restaurants.
Benjamin Downing
Graduate Student
downingb at uw.edu
Ben is a graduate student in the Biology program. He received his B.S. in Microbiology and Plant Biology from the University of Nebraska - Lincoln. At Nebraska his research was focused on the molecular mechanisms of antiviral immunity in plants, specifically investigating the roles of the RNA-dependent RNA polymerases in plants. Ben enjoys live music, a zesty beverage, and curating a new playlist outside the lab.
Alex joined the lab in February 2017 after finishing his Ph.D on the transcriptional network that controls pollen tube differentiation and sperm release with Mark Johnson at Brown University. Alex is interested in using synthetic biology to understand plant development, cellular differentiation and hormone signaling. In his free time, he enjoys running, hiking, and exploring the Northwest.
Cassandra is a graduate student in the Molecular Engineering (MolE) program, and joined the lab in May 2021. She received her B.S. in Chemical Engineering at UW where her undergraduate research involved decoding gene expression in methanotrophic bacteria. She also has a background in implementing CRISPR dCas9-mediated gene activation in bacteria. She is interested in synthetic biology and hopes to leverage her experience with dCas9 to develop logic circuits in plants. Her non-science hobbies include thrifting, baking cookies, and watching any and every reality competition TV show.
SRSLY?SRSLY – audio reflections on mentorship and lab culture
Jennifer has been studying plant hormones, signaling networks and development for a long time. Before coming to Seattle in 2006, Jennifer did her doctoral work on auxin and flower development at Berkeley with Pat Zambryski, followed by Postdoctoral work on hormone interactions during seedling development at the Salk Institute with Joanne Chory. When not in the lab, Jennifer loves to see great art (music, dance, visual art), eat great food, ride ferries, and have spontaneous dance parties in her living room.
Delaney Orzol
Undergraduate Intern
dorzol at uw.edu
Delaney is an undergraduate student at the University of Washington majoring in Molecular, Cellular, and Developmental Biology. After undergrad, she intends on going to medical school to pursue a career in Neuropathology. Outside of the lab, she likes to sing in the University's choir, spend time with her cat and dog, listen to new music, practice calligraphy, and raise plants of her own.
Janet is a graduate student in the Biology program. She received her B.S. in Biochemistry and Molecular Biology with a minor in Chicano/a Studies from UC Davis, where her undergraduate research involved characterizing terpenoid biochemical and regulatory pathways in Switchgrass and Maize. She is interested in using synthetic biology to understand transcriptional signaling and plant development. Outside of the lab, Janet enjoys exploring new restaurants and the Pacific Northwest.
Sarah Scallon
Undergraduate Intern
sarahs02 at uw.edu
Sarah is an undergraduate hoping to major in General Biology and minor in China Studies. Sarah enjoys learning about DNA integrases and how to use them to study cell specification events in plants. Outside of the lab, she loves playing piano, thrifting, learning languages, and discovering new local cuisine.
Sydney VanGilder
Undergraduate Intern
sydn at uw.edu
Sydney is an undergraduate at the University of Washington majoring in Biology: Physiology, and Gender, Women, and Sexuality Studies. She is interested in learning more about DNA integrases and lateral root development. Outside of the lab, Sydney enjoys exploring new creative hobbies.
Isabella Watson
Undergraduate Intern
ijw8 at uw.edu
Bella is an undergraduate at the University of Washington majoring in Biology: Physiology. She is interested in learning more about factors that influence how the hormone auxin regulates gene expression and repression. Bella enjoys attending concerts, exercising, and spending quality time with friends and family in her free time.
Cayden Weiszmann
Undergraduate Intern
caydenw at uw.edu
Cayden is an undergraduate student at the University of Washington majoring in Biochemistry and Microbiology. He is interested in studying the modulation of gene expression in plants. In his free time, Cayden enjoys supporting his favorite sports franchises as well as reading.
Art can provide an opening into abstract material and a bridge between academic and public spheres. This NSF-funded residency (IOS-1539834) brings a local artist into the Nemhauser Lab for one quarter in each of the three years of the grant. In this “immersion” experience, the artist has a desk in the lab and participates in lab meetings, department seminars and journal clubs. In the year following their residency, the artist produces at least one work inspired by their experience. These artworks will be incorporated into future classes. By collaborating with an artist in this way, we hope to discover novel ways to help students access abstract concepts and encourage a more nuanced exploration of modern biology by artists.
Deed of Gift is an art project by Matthew Offenbacher and Jennifer Nemhauser that takes the form of a collection of artworks given to the Seattle Art Museum for their permanent collection. The artworks were purchased using proceeds from the Neddy at Cornish Award in Painting, which Offenbacher received in 2013. Working closely with Catharina Manchanda, SAM’s Curator of Modern and Contemporary Art, Offenbacher and Nemhauser tailored their acquisitions to needs of the museum, with a particular emphasis on feminist and queer themes.
for information about methods, resources, positions, and other questions related to the lab contact:
jennifer nemhauser (LSB 573, jn7 at u.washington.edu)
SRSLY?SRSLY
Changing Cultures and Climates
