nemhauser lab

introduction

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

a small weedy plant growing from between bricks at the side of a red house
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:

  1. Building tools to study and reprogram signaling dynamics
  2. Integrating metabolic status into growth control networks
  3. Evaluating the impact of evolution on signaling networks

1. Building tools to study and reprogram signaling dynamics

above: a circuit diagram show the interaction of AFB2, auxin, YFP-TPL-IAA3, ARP19 and plAA19-CFP; below: six frames from a time-lapse video of yeast cells florescing in response to auxin
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

left: a schematic of a seedling showing the application of auxin on one cotyledon; right: four images of seedlings stained to show the expression of auxin
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

a photograph showing the relative sizes of a Brassica rapa seedling (large) and an arabadopsis seedling (small)
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:

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people

  • Román Ramos Baez
  • Graduate Student
  • rramosb at uw.edu
Román is a graduate student in the Biology program. He received his B.S. in genetics and plant biology from UC Berkeley where they worked in the PBS3 node of the salicylic acid innate immune response. His curiosity surrounding phytohormone-induced complex traits has led them to his current project, which centers on the evolution of auxin receptors. In his free time, he enjoys cooking for friends, watching gaming content on Youtube, and creating drag costumes and makeup looks.
Jonah is an undergraduate student at the University of Washington and a hopeful General Biology major. He joined the Nemhauser Lab in the summer of 2019 and is assisting in the research of gene expression during lateral root development. As a native of the Pacific Northwest, he is an avid fisher and outdoorsperson who also doesn’t mind the occasional video game.
Tucker is an undergraduate student in the Molecular, Cellular, and Development Biology program. In the Nemhauser Lab, he is currently helping with research on phenotypic responses to various mutations in auxin regulated transcription factors, in an attempt to better understand how they play a role in lateral root development. In his spare time, Tucker enjoys listening to music, trying new recipes, and simply learning everything he can.
  • Dante Fisher
  • Postbac
  • dantejordanfisher at gmail.com
Dante is post-baccalaureate student at the University of Washington pursuing a degree in Neuroscience. He began working in the Nemhauser Lab in June 2019 and has been working with his mentor, Eric Yang, to test various promoters for Hormone Activated Cas9-based Repressors (HACRs) and to characterize differential lateral root expression in Arabidopsis. Dante is generally interested in the ways in which information is stored and manipulated in biological systems, and he enjoys contemplating how intelligence may manifest differentially across species. In his free time, Dante spends his time meditating, weight-lifting, and singing.
Leo is an undergraduate Biology major. He is very passionate about research and hopes to use CRISPR based techniques to gene edit plants to increase their agricultural yield and/or to aid in climate change mitigation. Leo enjoys cooking, gardening, exercising, and playing the guitar in his free time.
  • Hardik Gala
  • Postdoctoral Fellow
  • hpgala at uw.edu
Hardik joined the lab in March 2017 and is interested in understanding signaling events that confer cellular competency during developmental processes. For his doctoral work, he studied RNApol2 pausing mechanisms that control cellular quiescent cells in mouse skeletal muscle system (with Prof. Jyotsna Dhawan at CSIR-Centre for Cellular and Molecular Biology in India). He then pursued a short poslioc with Prof. Imran Siddiqi (also at CCMB), analyzing expression and DNA binding studies of meiotic-specific genes to gain insight into meiotic transition. Other than enjoying science, he likes traveling, playing board games and leisure cooking.
Wesley is pursuing a B.S. in Molecular, Cellular, and Developmental Biology. He is interested in studying how the cell cycle relates to the lateral root developmental transitions in plant roots. Outside of lab and school, he spends most of his time hiking, climbing, and playing games with his friends.
  • Sabrina Gilmour
  • Technician
  • sgilmour at uw.edu
Sabrina graduated from UW in the Spring of 2019. She received a B.S. in environmental science and resource management studying the effects of abiotic factors on plant pathology. Sabrina has been accepted to PhD programs for Fall 2020, but until then will be assisting on projects at the Nemhauser Lab as a technician to understand the evolution and pathways of auxin through transformations and synthetic biology. When she is not in the lab or the plant room, Sabrina likes to spend her time cooking, eating dessert, spending time with friends, singing, and oil painting.
  • Sarah Guiziou
  • Postdoctoral Fellow
  • guiziou.sarah at gmail.com
Sarah joined the lab in April 2019 after finishing a Ph.D. on the engineering of logic circuits in bacteria with Jérôme Bonnet in Montpellier, France. She is now interested in the development of multicellular organisms, using a synthetic biology approach to decode complex cellular circuits. In the lab, she is focusing on decoding lateral root development in A. thaliana. Outside of the lab, she enjoy running, hiking, and discovering the world.
  • Amy Lanctot
  • Graduate Student
  • alanctot at uw.edu
Amy is a graduate student in the Molecular and Cellular Biology Program. Before coming to UW, she graduated from Stanford with a B.S. in developmental and cellular biology. As an undergraduate, Amy worked on stomatal differentiation pathways. She continues to be fascinated by mechanisms of cell fate specification, and her project centers on the influence of auxin in shaping cell fate. Originally from the Bay Area, she enjoys exploring the beautiful trails and mountains around Seattle. In her free time, she enjoys reading, traveling with friends, and marathoning TV shows on Netflix.
  • Alexander Leydon
  • Postdoctoral Fellow
  • aleydon at uw.edu
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.
  • Jennifer Nemhauser
  • Professor
  • jn7 at uw.edu
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, drink lots of tea and forage in secondhand bookstores.
  • Eric Yang
  • Graduate Student
  • eriyang at uw.edu
Eric is a graduate student in the Molecular Engineering (MolE) program. He received his B.S. in Biochemistry and minors in Biology and Philosophy from Cal Poly, San Luis Obispo where he was part of a team that worked on E. coli contamination tracking through strain clustering. Before coming to Seattle, Eric also helped develop diagnostic test strips for a biotechnology company in Taiwan. Interested in synthetic biology, his current projects involve the engineering and rewiring of plant degradation machinery. In his free time, Eric enjoys learning to make noises on new instruments, hanging out with friends, and going to concerts.
  • Joey Zemke
  • Technician
  • jzemke at uw.edu
Joey graduated from the UW with a degree in Biology and will be continuing his work in the lab as a technician. In the past he has been involved in projects that explored resource allocation in Brassica rapa and helped elucidate mechanisms of auxin regulated gene expression in plants. He is extremely fascinated with the ideas and mechanisms that drive development in all organisms and will be pursuing graduate programs in the future. When he is not busy with science, he is probably cooking, reading a book, or exploring Seattle!

lab alumni

Mallorie Taylor-Teeples
post-doc
Morgan Hamm
research scientist
Samuel Juarez-Solis
undergraduate
Alex Koriath
undergraduate
Meghan Wedeking
undergraduate
Deepthi Sathyanarayana
undergraduate
Erika Oki
undergraduate
Orlando de Lange
post-doc
Lauren Houston
undergraduate
Jennifer Jones
undergraduate
Mollye Zahler
undergraduate
Clay Wright
post-doc
Mrunmayee Shete
undergraduate
Manraj Sahota
undergraduate
Oghenemega Okoloko
undergraduate
Andrew Lemmex
undergraduate
Andrej Arsovski
visiting scientist
Arjun Khakhar
graduate student
Benjamin Haagen
undergraduate
Stacey Lowman
technician
Josephine D'Angelo
undergraduate
Amber Hageman
technician
Edith Pierre-Jerome
graduate student
Britney Moss
post-doc
Maia Sebek
undergraduate
Anahit Galstyan
post-doc
Jessica Gusema
graduate student
Tamar Feldman
undergraduate
Julia Weisbrod
undergraduate
Anisa Noorassa
undergraduate
Jodi Stewart Lilley
graduate student
Autumn
undergraduate
Chris Gee
technician
Danny Liang
undergraduate
Yingying Li
undergraduate
Vincent Wei Liu
undergraduate
Morgan Matz
undergraduate
Cristy Walcher
graduate student
Zachary Mccauley
undergraduate
Andy Chen
technician
Rachel Denney
undergraduate
Edison Calaunan
undergraduate
Alec Nielsen
undergraduate
Selma Alkafeef
undergraduate
Cameron Gomez
undergraduate
Liz Hulphers
undergraduate
Kavitha Kuppusamy
post-doc
Kris Lawerence
undergraduate
Karen Regan
technician
Jesse Session
undergraduate
Brian Watson
technician
Moham Ansari
undergraduate
Navia Nguyen
undergraduate

outreach

instagram logofollow our education and outreach activities

host, artist residency

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

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.

other projects

lab pictures

members of the nemhauser lab enjoying themselves on the beach
lab pictures
close-up of beautiful orchid flowers in a tropical greenhouse
greenhouse pictures

contact

for information about methods, resources, positions, and other questions related to the lab contact:
jennifer nemhauser (LSB 573, jn7 at u.washington.edu)

shipping address:
department of biology, university of washington, box 351800, seattle, wa 98195-1800

lab location:
LSB 5W

lab instagram

where are we located?

flowering cherry trees in a quad at the university of washington
spring at uw. photo by peter repetti