Group Members

Staff:

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

Spacial organization of metabolic enzymes that coordinately function in plants. Plant natural products are a rich source of medicine and dietary nutrients, yet we know very little about their biosynthetic pathways. To advance pathway discovery, I will combine proximity-dependent biotin ligase labeling and proteomic analysis to identify biosynthetic enzymes that function together to produce metabolites of interest. We aim to apply this knowledge to engineer heterologous hosts to make plant natural products and analogs on a large scale to improve human health, and also to accelerate the discovery of biosynthetic pathways in plants. We aim to apply this knowledge to engineer heterologous hosts to make plant natural products and analogs on a large scale to improve human health. due to the presence and activity of small

Alex Engel

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

My roles include course development and instruction in the Chemical Engineering curriculum, and manuscript and grant writing support for the Sattely lab. Additionally, my interests in cell biology and genetics allow me to support a number of ongoing lab research projects.

Postdocs:

Conor

Conor McClune – Single cell analysis of plant biosynthetic pathways
mcclune [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 grr 

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

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 grr malarial drug, or galantamine for treating Alzheimer’s disease symptoms). However, many medicinal alkaloids are harvested from natively grr 

ErikErik Carlson – Engineering transient gene expression in plants
erikdc [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 grr 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.

Kevin

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

Graduate Students:

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.

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 – Discovery and engineering of metabolite-based defense mechanisms in plants
eholmes [at] stanford [dot] edu
Plants consistently face threats from fungal, bacterial, and viral pathogens. While plants lack a circulating immune system akin to ours, they still mount a robust systemic immune response via the production and movement of small molecule hormones. This response, termed systemic acquired resistance, or SAR, can lead to robust and long-lasting immunity. Despite this inherent ability, the domestication of crops and modern agricultural practices have given pathogens a distinct advantage; still today, over 20% of wheat, rice, corn, and soy grown globally are lost to pathogens every year. Reducing the proportion of crops lost to disease is essential to ensuring food security for a growing global population. In my research, I strive to better understand the underlying metabolic mechanisms that plants use to initiate and attenuate SAR. With this information, I aim to utilize metabolic and protein engineering strategies to enhance the natural immunity of essential food crops.

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 New strategies for sequencing medicinal plant genomes for biosynthetic pathway discovery
nirajm [at] stanford [dot] edu
Plants are ingenious chemists. They provide some of the most important drugs in current clinical use, which are often challenging to chemically synthesize. Understanding the biosynthesis of these drugs in plants permits their engineering into heterologous organisms for large-scale production. The first step of this process, identifying the responsible biosynthetic genes in producer plants, is challenging. The lack of availability of genome sequences for the vast majority of plant taxa is limiting in this regard – plant genomes are often large, complex and therefore, challenging to assemble. My goal is to develop new approaches that allow convenient and inexpensive access to genomic information in plants for the purpose of accelerating the identification of biosynthetic pathways for medicinal compounds.

Undergraduates:

Luis Jimenez 
luisj547 [at] stanford [dot] edu
Charlie Hoffs 
chuck99 [at] stanford [dot] edu

Group Alumni:

Nikita Khylstov – nikitak [at] stanford [dot] edu, Postdoctoral Research Associate, Cochran lab, Stanford Bioengineering
Mathias Vogesmjvoges [at] gmail [dot] com, Machine Learning Engineering, Google X
Shanon Sirk – Assistant Professor, University of Illinois Department of Bioengineering sirk [at] illinois.edu
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