Lucas Hartsough Landing Page & Portfolio

Bio

I believe that engineering biology as a computational and metabolic machine constitutes the future of bioscience, and that synthetic biology will revolutionize how we approach our most pressing scientific pursuits, both here on earth and among the stars.

Contact

Skills

I am passionate about creating tools that lower the barrier for others to adopt traditionally complex techniques and to accelerate their research.

Wetware

Optogenetic & chemical manipulation of bacterial gene expression using custom hardware, both in liquid culture and with microscopy
Proficient in design and assembly of bacterial gene circuits, especially sense-respond systems.
Highly experienced with measurement & analysis of single-cell fluorescence via flow cytometry as well as time-lapse, single-cell fluorescence microscopy
Comfortable with a range of model systems, including: E. coli, S. cerevisiae & C. elegans worms.

Software

Proficient with Python. Created a custom package, PyHMMER, that enables high-throughput analysis of all NCBI genomes to mine co-localized proteins matching arbitrary hidden Markov models.
Comfortable with JavaScript and AngularJS. Co-developed a webapp, Iris, used to program and simulate dynamic optogenetic time courses for use with our lab's open-source hardware platform.
Familiar with C, Java, LaTeX, SolidWorks, Inkscape & Linux, and comfortable with version control (Git, GitHub)

Hardware

Comfortable with basic circuit design: PCB design & routing, surface-mount soldering, assembly, and debugging. Used these skills to adapt our optogenetic hardware to be compatible with a CubeSat form factor.
Highly experienced with programmable microcontrollers (Arduino, RaspberryPi) for use in automating optogenetic apparatus and other hardware.
Comfortable with basic 3D design in SolidWorks and 3D printing (PLA extrusion)
Experience with sub-milliliter fluidic devices and metered flow systems

Publications

Info

Optogenetic control of C. elegans gut bacterial gene expression

Hartsough, Kotlajich, Lin, Han, Wang & Tabor

Info

PyHMMER: a high-throughput tool for identifying protein clusters and domain architectures using Python and HMMER

Hartsough & Tabor

Info

PDF

An open hardware platform for optogenetics and photobiology

Gerhardt, Olson, Castillo-Hair, Hartsough, Landry, Ekness, Yokoo, Gomez, Ramakrishnan, Suh, Savage & Tabor

Info

Link

How Synthetic Biology Will Solve Biological Mysteries and Make Humans Safer in Space

Hartsough

Optogenetic function generator for characterizing gene circuits

Info

PDF

Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals

Olson, Hartsough, Landry, Shroff & Tabor

Software

Info

Link

Iris

Iris is a visual programming interface for the Tabor Lab optogenetic hardware platform.

Info

PyHMMER

PyHMMER enables high-throughput genome searches using HMMER.

Experience

May 2018

PhD Candidate & NSTRF Fellow

Dept. of Bioengineering, Rice University

Created quantitative models of the Tabor Lab bacterial optogenetic tools and used them to investigate the relationship betwen gut microbiome and host in C. elegans.
Summers 2012-2015

NASA Summer Research Intern

NASA Ames Research Center, Moffett Field, CA

As a recipient of the NASA Space Technology Research Fellowship, I was able to spend summers with fantastic bioengieers at NASA Ames. I was also awarded a $25k grant to adapt optogenetic hardware to a CubeSat (OptoGeneSat).
June 2011

BS Bioengineering with Honors

California Institute of Technology, Pasadena, CA

I was a member of the first cohort of Bioengineers and President of Lloyd House, one of the 8 undergraduate houses and hubs of student life. I also assessed student Honor Code violations as Secretary of the Board of Control and served as a student counselor & certified First Responder.
Jan - Nov 2010

Caltech iGEM Team Captain

International Genetically Engineered Machine Competition, Boston, MA

I was awarded a $45k grant to restart the Caltech iGEM team. Along with 5 others, we earned a gold medal for our optogenetic 3D printer concept.

For Fun!

EMS

I recently earned my national EMT Basic certification and am licensed to practice in the state of Texas. Stressful, but rewarding!

Lucas attempting to BBQ a turkey for Thanksgiving

Texas BBQ

My favorite Texas tradition. While not a Texan myself, I've studied this arcane art under their tutelage.

Horseback Riding

I'm no expert, but enjoy the relaxing experience of getting the chance to ride when I visit home.

Bartending

I volunteer an hour of my week at Rice's dive bar, Valhalla, where we serve the best beer on campus! Perhaps one day I'll graduate to cocktails...

How Synthetic Biology Will Solve Biological Mysteries and Make Humans Safer in Space

Hartsough

Blog: PLoS Synthetic Biology

Year: 2016

An opinion article explaining the status and future of synthetic biology in space.

One of the challenging aspects of human spaceflight is that many biological systems, including humans and the commensal bacteria living inside us, are physiologically perturbed in microgravity. At the large scale, humans develop issues in many organ systems, including the eyes, musculature, and bones. Worse, at even smaller scales bacteria also experience dramaitc changes in space that can make pathogens more virulent and resistant to antibiotics.

To learn how to address these problems, and perhaps even engineer organisms resistant to microgravity stress, we will have to turn to synthetic biology. It will give engineers the tools to investigate the biological mechanism of this phenomenon and, more excitingly, to develop engineered organisms that can help humans expand into long-duration space missions, aiding with tasks from food production, to pathogen protection and resource mining.
Link

Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals

Olson, Hartsough, Landry, Shroff & Tabor

Journal: Nature Methods

Year: 2014

DOI: 10.1038/nmeth.2884

We demonstrated the ability to program arbitrarily complex gene expression profiles in E. coli using optogenetics.

We set out to characterize the previously-published Tabor Lab optogenetic sensor proteins (Cph8/OmpR & CcaS/R), which convert light inputs to gene expression outputs. Using custom optogenetic hardware, we used a series of step-responses to assess the dynamic response of each of these sensors to light input. This was then used to parameterize a quantitative model that allowed us to predict the output of each sensor for any series of light inputs.

With this predictive power, we realized that we could use such a model in reverse to calculate the exact series of light inputs (green dashed line) required to achieve a specified output, like the arbitrary curve to the left (black line), which we were able to do with over 95% accuracy (green dots).

The ability to remotely program arbitrarily complex gene expression patterns in cells has never before been achieved with such precision. This capability enables the light sensors to act as the biological analogs of electronic function generators, which are used to debug and characterize other downstream circuits (right). We applied this analogy to the CcaS/R light sensor by connecting its output to both a reporter gene (sfGFP) and a simple downstream gene circuit (TetR). We then used light to program various dynamic output signals from the CcaS/R system, through the TetR inverter circuit, and finally to TetR's output with another reporter gene (mCherry).

In this way, we used the CcaS/R light sensor to dynamically characterize the input-output characteristics of the TetR gene circuit, which serves as a proof of principle for more complex circuits. As circuit characterization is a crucial method for electrical engineers to debug and engineer electronic circuits, so too do we believe our method will enable bioengineers to better construct and debug novel biological circuits.

PDF

Iris

Hartsough, Landry & Ekness

URL: http://iris.taborlab.rice.edu

Language: JavaScript+AngularJS

GitHub

A simple web-based programming interface for the Tabor Lab optogenetic hardware

The Tabor Lab has developed an open-source hardware platform for standardizing optogentic and photobiology experiments and to help more people apply optogenetics in their own labs. To facilitate programming the LEDs in this device for use in exposing cells to dynamic light patterns, we have also developed a web-based visual programming interface, called Iris.

Iris allows anyone to quickly and easily get their hardware up and running by helping users specify each aspect of their light program in the left panel, and immediately seeing its effect in the simulation panel on the right. Users can check how their light program behaves accross the entire plate (shown) or full time traces for individual LEDs in a well. Once the desired program is complete, the user simply downloads the compiled binary file to an SD card and inserts it into their LPA device to start the program.
Publication

Skills

I am passionate about creating tools that lower the barrier for others to adopt traditionally complex techniques and to accelerate their research.

Wetware

Software

Hardware

Publications

Optogenetic control of C. elegans gut bacterial gene expression

PyHMMER: a high-throughput tool for identifying protein clusters and domain architectures using Python and HMMER

An open hardware platform for optogenetics and photobiology

How Synthetic Biology Will Solve Biological Mysteries and Make Humans Safer in Space

Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals

Software

Iris

PyHMMER

Experience

May 2018

PhD Candidate & NSTRF Fellow

Dept. of Bioengineering, Rice University

Summers 2012-2015

NASA Summer Research Intern

NASA Ames Research Center, Moffett Field, CA

June 2011

BS Bioengineering with Honors

California Institute of Technology, Pasadena, CA

Jan - Nov 2010

Caltech iGEM Team Captain

International Genetically Engineered Machine Competition, Boston, MA

For Fun!

EMS

Texas BBQ

Horseback Riding

Bartending