Group Members

Staff:

ChunChun Tsai – Lab manager and Research Scientist
chuntsai [at] stanford [dot] edu

 

 

 

 

 

 

Alex EngelAlex Engel – Research Engineer
aengel [at] stanford [dot] edu

 

Postdocs:

RyanRyan Nett — Biosynthetic pathway discovery of medicinal plant alkaloids
rnett [at] stanford [dot] edu
Throughout history, humans have utilized plants as remedies to treat a variety of different diseases. The biological effects attributed to medicinal plants are usually due to the presence and activity of small molecules produced by the plant. One major class of bioactive plant molecules, the alkaloids, possess nitrogen atoms and are predominantly derived from amino acids. Alkaloids are not only chemically diverse, but also consist of many molecules that are used to effectively treat human disease (e.g. quinine as an anti-malarial drug, or galantamine for treating Alzheimer’s disease symptoms). However, many medicinal alkaloids are harvested from natively growing plants, making their supply non-sustainable and limited. In my research, I am focusing on discovering enzymes involved in the biosynthesis of plant alkaloids relevant to human health. My aim is to uncover novel biosynthetic pathways for medicinal alkaloids, with the hope that this will lead to the eventual reconstitution of their production in a heterologous host.

WillWill Cody – Plant cell based screens
willcody [at] stanford [dot] edu

 

ErikErik Carlson – Engineering transient gene expression in plants
erikdc [at] stanford [dot] edu

 

KevinKevin Smith – Chemistry of complex alkaloid biosynthesis in plants
kebsmith [at] stanford [dot] edu

Graduate Students:

Mathias_cropped

Mathias Voges — Plant synthetic biology
mjvoges [at] gmail [dot] com
The emerging field of synthetic biology promises exciting opportunities to improve agricultural yields while simultaneously promoting sustainability. However, the current synthetic biology toolkit for plants is limiting. Efforts in lab include 1) using multidisciplinary approaches, such as genetics, bioinformatics, transcriptomics and metabolomics, to identify and harness native parts; 2) generating design concepts for the reliable reconstruction of multicellular platforms. Designing new processes or re-designing those known will set the stage for fine-tuned regulation of plant metabolism, improved nutrient availability, and enhanced plant pathogen defenses.

RicardoRicardo De La Peña — Nicotiana benthamiana as a plant platform for discovery and engineering of terpenoid biosynthesis 
rdlp [at] stanford [dot] edu
Plant terpenoids are one of the most chemically rich and structurally diverse class of natural products. They have essential properties in plant immunity and uses in the food, health and biotechnology sectors. Although a lot is known about their structures and bioactivities, only a few examples of elucidated terpenoid pathways exist. Without complete pathways, our efforts toward engineering terpenoid biosynthesis are limited. Our goal is to develop Nicotiana benthamiana as a plant platform to (1) speed the discovery and characterization of enzymes involved in terpenoid biosynthesis and to (2) increase terpenoid yields via metabolic engineering efforts. Our platform for pathway discovery combines tools in transcriptomics, plant synthetic biology, and gas and/or liquid chromatography mass spectrometry (GC/LC-MS) metabolomics.

NikitaNikita Khlystov — Identifying a Minimal Set of Genes Required for Valorization of Lignin Biomass 
nikitak [at] stanford [dot] edu
Lignin is the second-most abundant biopolymer in the world, but previous efforts to break it down into useful carbon-based platform chemicals in a reliable and scalable manner have been thus far largely unsuccessful, rendering lignin substantially underutilized. By contrast, fungi readily degrade and metabolize this recalcitrant biopolymer using a milieu of specialized enzymes. Reconstituting this lignin-degrading machinery of white-rot fungi in a genetically-tractable model organism may therefore enable a route to efficient valorization of lignin biomass. This ​project investigates the co-expression of putative lignin-degrading enzymes in S. cerevisiae and N. benthamiana. A combinatorial approach ​is being employed to develop an enhanced understanding of the interconnected roles of putative ligninases in degrading lignin biomass.

TimTim Schnabel – Rhizosphere and plant pathway discovery and metabolic engineering
tims2015 [at] stanford [dot] edu
Nitrogen is the most limiting agricultural nutrient on earth. Without synthetic fertilizer, we would feed 3 billion fewer people than our world population today. However, our current way of supplying nitrogen to plants is unsustainable and is leading to increasing environmental problems such as leaching, fresh water poisoning, and reactive volatiles emission. For these reasons, managing the nitrogen cycle has been named an Academy of Engineering Grand Challenge. I am working toward a biological solution for this challenge by engineering bacteria that already symbiotically colonize plant roots in nature, to take nitrogen out of the atmosphere, and make it available to plants as ammonia or other nitrogen rich small molecules.

EricEric Holmes – Characterization of Plant 2-ODDs and Active Transporters
eholmes [at] stanford [dot] edu
Because of their sessile lifestyle, plants have evolved a complex secondary metabolism to produce chemicals that are important for defense against pathogens and responses to environmental stressors. By using a combination of transcriptomics, metabolomics, and molecular biology, I seek to elucidate the function of putative secondary metabolic enzymes in the model plant Arabidopsis thaliana and discover novel metabolites important for plant fitness. In addition to enzymes involved in secondary metabolism, plants have evolved a wide array of active transporters that have been implicated in development, hormone signaling, pathogen defense, nutrient uptake, and chemical production. Despite the inherent utility of these proteins for engineering plant fitness and isolation of plant natural products, the vast majority have not been characterized. My goal is to identify plant active transporters involved in stress responses, characterize their function, and utilize them for engineering applications.

CatherineCatherine Liou – Effect of dietary context on phytonutrient action
csliou [at] stanford [dot] edu
Glucosinolates, found in cruciferous plants like broccoli and cabbage, have been shown to benefit human health; isothiocyanates produced from glucosinolate metabolism exhibit effective chemopreventive activity. While the mechanism of action of these isothiocyanates has been well-studied, the observed physiological effects are sensitive to the dietary context surrounding the consumed glucosinolates. Other metabolites found in the dietary plant, as well as the plant matrix itself, can play a deciding role in glucosinolate absorption and isothiocyanate action. My goal is to increase understanding of the relationship between nutritional context provided by the dietary plant and the physiological action of the consumed glucosinolates.

StacieStacie Kim— Biosynthesis of non-natural etoposide derivatives in Nicotiana benthamiana
staciek [at] stanford [dot] edu

 

NirajNiraj Mehta — Sequencing of medicinal plants for biosynthetic pathway discovery
nirajm [at] stanford [dot] edu

Undergraduates:

Luis Jimenez 
luisj547 [at] stanford [dot] edu

Group Alumni:

Bailey Schultz - Graduate student at Harvard Chemistry
Amy Calgaro-Kozinaacalgaro [at] alumni [dot] stanford [dot] edu
Jeremy Huntjeremy_hunt [at] alumni [dot] stanford [dot] edu – Product Support Engineer at OSIsoft
Warren Lauwarlau [at] stanford [dot] edu – Scientist I at Zymergen
Russell Jingxian Lijingxian [at] stanford [dot] edu – Senior Member of Technical Staff at DSO National Laboraties, Singapore
Jakub Rajniakjrajniak [at] stanford [dot] edu – Postdoctoral Associate, Fischbach Lab, Stanford University Bioengineering Department
Andrew Kleinapklein [at] stanford [dot] edu – Scientist at Amyris (Emeryville, CA)
Yi-Lin Chungyilinc [at] stanford [dot] edu
Gulbenk Anarat Cappillinogulbenk.cappillino [at] thermofisher [dot] com – Staff Scientist, Research & Development Chromatography and Mass Spectrometry at Thermo Fisher Scientific Sanofi/Genzyme, Waltham, MA
Ben Baradbbarad [at] stanford [dot] edu – Graduate Student studying Biophysics in James Fraser’s lab at UCSF
Camil Diazcacdiaz [at] udel [dot] edu – PhD student in Antoniewicz Lab of Metabolic Engineering and Systems Biology at the University of Delaware
Ellie Oatesehoates [at] udel [dot] edu – Graduate Student at the University of Delaware
Evelyn Changechang11 [at] stanford [dot] edu – law student at Harvard Law School, studying for the J.D. degree