nemhauser lab

DiversifyPlantSci
department of biology
university of washington

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

An illustration of a complex of proteins interacting with a DNA strand. There are circular insets. The top one shows a slightly different configuration of proteins and the DNA strand with the label: transition to activation. The middle inset shows one of the proteins with a u-shaped active part in the middle labeled: a single helix repression domain. The bottom all of the cell's nuceli are glowing green. On the righthand side, only a few nucelia are glowing green. This inset is labeled: A developmental timer.
AuxInYeast, a tool to understand and engineer cells. Auxin signaling can be ported to yeast by transfer of a few plant parts: a promoter (grey), an auxin TF (green), an auxin adaptor/substrate (orange) that binds to the TF and brings in a co-repressor (purple), and an auxin receptor F-box (not shown). Auxin induces degradation of the adaptor/substrate via interaction with the F-box, thereby activating transcription. Yeast proteins supply all other cellular functions, including the Mediator Complex (blue) that we recently discovered interacts with the plant co-repressor (highlight) and is required for repression. [Insets] We are now focused on: dissecting the transition from repression to activation; developing tools that make use of a small, conserved repression domain; and testing how degradation-driven transcriptional dynamics enable synchrony during cell fate transitions in plants. Illustration by DC SciArt.

Much of our work is inspired by insights gleaned from the recapitulation of the auxin response in Saccharomyces cerevisiae (AuxInYeast). AuxInYeast is a high-throughput assay for relief of repression of a single synthetic locus, triggered by the auxin molecule itself acting as “molecular glue” to increase affinity of F-box receptors and corepressor-linked substrates/coreceptors.

Key advantages include: the simplicity of a degradation-triggered system that does not require post-translational modification (e.g. phosphorylation) of the substrates; use of heterologous components that allow manipulation and monitoring of a single locus without disturbing endemic cell state; circumvention of genetic redundancy in auxin components in plants. These features have enabled AuxInYeast to act as a bridge between computational models and multicellular phenomena (like development), repeatedly leading us to new knowledge of conserved eukaryotic cell biology. Specifically, AuxInYeast, in combination with transgenic plant studies, led to two key discoveries:

  1. The plant TPL corepressor (and likely the mammalian ortholog TBL1) stabilizes a state similar yet distinct from the metazoan transcriptional paused state by recruiting Mediator and other components needed to initiate transcription. We call this hypothesis: corepressor priming to burst.
  2. Developmental progression in new roots is determined (and likely coordinated) by the rate of auxin-induced degradation. We call this hypothesis: the auxin timer.
On the right is a microscopic photograph showing a section of root fluorescing blue with a red floresecent strip down the middle and a green floresecent bump emerging from the red strip. On the left is a simplified cartoon of the same image, with the blue part labeled main root, the red part labeled xylem pole and xylem pericycle, and the green part labeled lateral root.
A molecular recorder. Reporters (mTurq>mScarlet>eGFP) are sequentially expressed as two different integrases are induced by a promoter expressed in xylem pole pericyle cells (pAHP6) and in lateral root initial cells (pGATA23).

Comprehensive structure-function studies of fundamental life functions (like protein degradation or transcription) can be challenging as mutant phenotypes are often hopelessly pleiotropic or lethal. We have worked hard to complement AuxInYeast assays with molecular genetic tools in Arabidopsis and mammalian cells. In plants, these tools include a number of new approaches for cell-type-specific interventions connected to the inducible and quantitative read-out of secondary root development. For example, we have built a serine integrase-based system where we can induce a switch between a wild-type and mutant form of any gene of interest with a high degree of spatiotemporal control. We have also used integrases to engineer a single cell molecular recorder of transcriptional history that can be applied in a variety of contexts.

For the most recent publications from the Nemhauser Lab, please use these links:

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people

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.
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.
Mohamed is a second-year undergraduate at the University of Washington and is planning to declare his major in Biology Physiology with a potential minor in business. He is interested in synthetic biology, gene editing, and most recently, oncology. Some of his hobbies are weightlifting, tennis, reading, and he is also a big fan of mixed martial arts.
Eddie is a second-year undergraduate at UW looking to major in Biology Physiology. He is passionate in learning about gene pathways and altered gene expression. Following undergrad, he plans to go to medical school and pursue a career in cardiology. His hobbies include lifting weights, listening to music with friends, and cooking new dishes.
  • Aaron Korenblat
  • Undergraduate Intern
  • akblat32 at uw.edu
Aaron is a third-year undergraduate at the University of Washington majoring in Molecular, Cellular, and Developmental Biology. He is interested in the role of molecular biology as it relates to plant sciences. Outside of the lab, Aaron enjoys weightlifting, playing videogames, and baking sweet treats.
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.
Tabitha is a third-year undergraduate at UW studying microbiology and chemistry. Right now, she is interested in learning more about gene expression/signaling and pharmaceuticals. In her free time, she loves hiking, reading, and is especially passionate about solitaire.
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.
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.
Linda is an undergraduate intern at the University of Washington majoring in Biochemistry. She plans on going to medical school after undergrad to become a psychiatrist. She is interested in learning about DNA integrases, and gene expression history. In her free time, Linda enjoys board games, making music, and playing copious amounts of Just Dance.
Julie arrived in Seattle with a degree in Biochemistry, Biophysics, and Structural Biology from the University of California at Berkeley. She is continuing her interest in biochemistry and genetic engineering, which she applied in her undergraduate thesis developing structured biomaterials from marine diatoms. Her work in the Nemhauser lab centers on engineering the auxin corepressor TPL and its homologues towards tunable transcriptional control. In her free time, she loves to explore trails around Seattle!
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.
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.

lab alumni

Where are they now? Click on underlined names.

Delaney Orzol
undergrad
Anny Tran
undergrad
Isabella Watson
undergrad
Lena Bae
undergrad
Ana Maria Cabral
postbac
Sarah Scallon
undergrad
Cayden Weiszmann
undergrad
Eric Yang
graduate student
Wesley George
postbac
Sarah Guiziou
post-doc
Andrew Bauer
undergrad
Román Ramos Baez
graduate student
Jonah Chu
undergrad
Khushi Tawde
undergrad
Leonel Flores
undergrad
Hardik Gala
post-doc
Joey Zemke
technician
Amy Lanctot
graduate student
Tucker Ennenga
undergrad
Dante Fisher
postbac
Sabrina Gilmour
technician
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 Gerben
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 Waite
graduate student
Kyle Havens
postdoc
Tamar Feldman
undergraduate
Julia Weisbrod
undergraduate
Anisa Noorassa
undergraduate
Andrej Arsovski
post-doc
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

community

Seriously? Seriously logoSRSLY?SRSLY – a series of audio reflections on mentorship and lab culture by Prof. Jennifer Nemhauser

Changing Cultures and Climates logoChanging Cultures and Climates – diversity, inclusivity, and equity in the international plant science community

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

where are we located?

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