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:

Search PubMed

Search Google Scholar

people

  • Andrej Arsovski
  • Visiting Scientist
  • arsovski at uw.edu
  • 206 543 4845
Andrej did his doctoral work at McGill University in Montreal with Tamara Western, identifying novel genes involved in the synthesis and modification of cell wall components using cells in the Arabidopsis seed coat. In his Postdoctoral studies, he investigated regulatory DNA in Arabidopsis, the evolution of gene regulatory networks, engineering approaches to improving the Pawpaw fruit, and virus resistance in peach and soybean. Currently, he is spearheading the Nemhauser Lab’s effort to understand the molecular mechanisms underlying resource allocation in Brassica rapa. Outside of the lab, Andrej enjoys playing with his kids, skiing, playing hockey, and watching as many movies as possible.
  • Román Ramos Baez
  • Graduate Student
  • rramosb at uw.edu
  • 206 543 4845
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.
  • Hardik Gala
  • Postdoctoral Fellow
  • hpgala at uw.edu
  • 206 543 4845
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.
  • Morgan Hamm
  • Volunteer
  • morganohamm at gmail.com
  • 206 543 4845
Morgan received a BS in mechanical engineering from UW in 2012 and has been working in the medical device industry. He has come back to UW to explore interests in biology as well as data science, and is contributing to software tools used to analyze natural variation in the Arabidopsis genome. In his free time he enjoys reading, hiking, and a variety of hobbies from flying RC planes to making coffee tables.
  • Lauren Houston
  • Undergraduate Intern
  • lahoust at uw.edu
  • 206 543 4845
Lauren is pursuing bachelor‘s degrees in General Biology and Japanese. In the Nemhauser lab she is helping to characterize molecular mechanisms of resource allocation and seed development in Brassica rapa. Her favorite protein is Phytochrome B. Outside of lab the lab, Lauren can be found studying, practicing taekwondo, playing D&D with friends, and encouraging her long-suffering garden along.
  • Arjun Khakhar
  • Graduate Student
  • arjunkhakhar at gmail.com
  • 206 543 4845
Arjun is an honorary member of the Nemhauser Lab. He is a graduate student in the Bioengineering department at the University of Washington, jointly advised by Prof. Eric Klavins and Prof. Georg Seelig. He has a background in microbial synthetic biology with previous experience in metabolic engineering, protein engineering using directed evolution and synthetic signal transduction systems. He is currently working on engineering organism level behaviors, specifically how plants interpret and respond to internal and external signals, with the end goal of designing more productive crops.
  • Amy Lanctot
  • Graduate Student
  • alanctot at uw.edu
  • 206 543 4845
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.
  • Orlando de Lange
  • Postdoctoral Fellow
  • odl at uw.edu
  • 206 543 4845
Orlando is an honorary member of the Nemhauser Lab. His primary appointment is with Prof. Eric Klavins, UW Electrical Engineering. Orlando arrived in Seattle in February 2016 after completing his PhD with Thomas Lahaye at the University of Tuebingen in Germany. During his PhD, he worked on TAL-effector-like DNA binding proteins and their potential roles in crop diseases. He is interested in the role of immune-system transcription networks in cellular decision making, as well as how these networks can be engineered to develop pathogen resistant crops. When in the lab or out of it Orlando is likely singing to himself.
  • Andrew Lemmex
  • Undergraduate Intern
  • alemmex at uw.edu
  • 206 543 4845
Andrew is pursuing a bachelor’s degree in molecular biology. In the Nemhauser Lab, he is characterizing synthetic transcription factors that are degradable in the presence of different plant hormones. The end goal is to develop new tools to control plant development. In his free time you can find Andrew reading, taking his dog for a walk, or swimming.
  • Alexander Leydon
  • Postdoctoral Fellow
  • aleydon at uw.edu
  • 206 543 4845
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
  • office: 206 543 0753
  • lab: 206 543 4845
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.
  • Oghenemega Okoloko
  • Undergraduate Intern
  • okoloo at uw.edu
  • 206 543 4845
I am currently pursuing a B.S. in Biology (Molecular, Cell, Developmental Biology) and a B.A in Political Science. In the Nemhauser lab, I am working on the auxin signaling pathway. I am very excited about learning more about physiological and developmental implications of gene repression in Arabidopsis. In my spare time I play football (the real football) and producing music on my computer.
  • Manraj Sahota
  • Undergraduate Intern
  • manraj34 at uw.edu
  • 206 543 4845
Manraj is working towards her Bachelor’s degree in Molecular, Cellular, & Developmental Biology. What she loves most about working in the Nemhauser Lab is learning something new every day. When not in the lab or busy studying, Manraj is likely enjoying a good movie with ice cream or visiting home up in Bellingham and spending time with her family and friends.
  • Mrunmayee Shete
  • Undergraduate Intern
  • mrun2217 at uw.edu
  • 206 543 4845
Mrunmayee is pursuing a BS in Molecular, Cellular and Developmental Biology. She is interested in the field of synthetic biology, especially modulation of plant response using engineered transcription factors. She enjoys learning more about various research techniques to solve biological problems, reading scientific literature, and hearing about research projects of other lab members. In her free time, Mrunmayee enjoys traveling, dancing, swimming and cooking new recipes.
  • Mallorie Taylor-Teeples
  • Postdoctoral Fellow
  • mmtt at uw.edu
  • 206 543 4845
Mallorie joined the lab in June 2015 after completing a PhD on the transcriptional network surrounding Arabidopsis root xylem development in Siobhan Brady’s lab at University of California, Davis. Mallorie is interested in studying how biological networks and signaling pathways can be changed or “tweaked” to lead to new developmental patterns. When not in lab, Mallorie enjoys drinking tea, meditating, playing board games, and sewing Victorian and steampunk-inspired costumes.
  • Clay Wright
  • Postdoctoral Fellow
  • wrightrc at uw.edu
  • 206 543 4845
Clay joined the lab in April 2014 after finishing his Ph.D. on the directed evolution of cancer therapeutic switchable enzymes with Marc Ostermeier at Johns Hopkins University. Clay is interested in using directed evolution and synthetic biology to study the evolution of plant hormone receptors. In his free time he enjoys cooking, running, fermenting and exploring the Pacific Northwest. Clay’s website.
  • Mollye Zahler
  • Undergraduate Intern
  • mzahler at uw.edu
  • 206 543 4845
Mollye is pursuing a B.S. in biology. She is currently studying receptor and repressor proteins involved in the auxin response pathway. She is excited about exploring the different avenues of biology research and taking classes in her major. In her free time, she enjoys exploring Seattle on her bike, spending time oulioors, and making art.
  • Joey Zemke
  • Undergraduate Intern
  • jzemke at uw.edu
  • 206 543 4845
Joey is pursuing a B.S. in Microbiology. He is interested in phototropism in plants, as well as exploring the ideas and mechanisms behind cellular communication across biological systems. He is excited to learn more about the research process as a whole as well as learning more about Nemhauser Lab’s integration of art and science. When he is not working in lab or studying, Joey is most likely spending time with family and friends, taking pictures, or exploring his new hometown of Seattle.

lab alumni

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 (hck 507, jn7 at u.washington.edu)

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

lab contact:
hck 507 & 543, p 206 543 4845, f 206 685 1728

lab instagram

where are we located?

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