The Future of Fat - an SD-CAB Researcher Spotlight

by Britt Flaherty

Christine Shulse working in Puerto Rico while
collecting rare microbial samples

Christine Shulse loves fat. While I spend my day avoiding it at all costs, Christine looks for fat in new places, studies how it's made, and even thinks about engineering ways to make more fat. But Christine isn't studying the fat in my french fries – she's studying polyunsaturated fatty acids, or PUFAs, the heart-healthy fats found in expensive fish oil supplements. PUFAs are powerhouse lipids that are good for our cholesterol and have been the focus of medical studies on everything from weight loss to cancer. They can be found in fish, eggs, chicken, and healthy oils, but Christine is looking for a new and inexpensive source of heart-healthy lipids, and her work may even help us understand how to make biofuels, such as fatty-acid derived hydrocarbons.

Christine is a graduate student in Dr. Eric Allen's lab at The Scripps Institute of Oceanography, and she's discovering a source of PUFAs, a form of secondary lipids, in bacteria: "Generally I'm interested in the production of secondary lipids by microbes," she says. "Similar to secondary metabolites, secondary lipids are lipids that have not been shown to be necessary for the normal growth, development, and reproduction of these microbes under laboratory conditions. Therefore these pathways can hopefully be messed with without upsetting the cell's primary metabolism." This would allow Christine to artificially produce more or less secondary lipids in a microbe without affecting its health, which is important for engineering bugs in industrial settings. 

Christine in the Lab in San Diego

Christine studies both hydrocarbons and PUFA secondary lipids, and the synergy between the two is key: "The hydrocarbons could be used as fuel, while the fatty acids are important in human nutrition and are used as nutraceuticals. So with the knowledge of how to make that switch industry could decide which product they're interested in and then have the knowledge to optimize production of that product."

Christine's work utilizes cutting edge DNA sequencing technology and bioinformatics as well as environmental samples from all over the world, including bacteria from Lake Tyrell in Australia and even samples from 6000 meters below the ocean surface in the Puerto Rico Trench. She hopes to discover and understand energy-containing molecules that are already being made in nature and is searching for these molecules in extreme environments. "I have surveyed various environments for the genetic signatures ultimately responsible for the production of secondary lipids so that we can get an idea of the diversity and distribution of secondary lipid production in nature," she says.  She has also scanned every sequenced genome (millions of genes worth of information) from algae to cyanobacteria to protists, looking for genetic signatures of PUFA and hydrocarbon production.

 Christine analyzes every gene expressed by microbes that produce secondary lipids through high-throughput transcriptomics, or the study of gene expression in the entire organism. She looks at changes in gene expression when you change the microbe's environment, trying to decipher the triggers of lipid production. "I'm quantifying the trade-off between hydrocarbon and fatty acid production in a group of marine bacteria called Shewanella," she says.

The view from the boat in Puerto Rico

As a graduate student in an SD-CAB lab, Christine had the opportunity to present her work at the monthly SD-CAB symposium this past spring. "I love SD-CAB!" she says. "The Student and Post-Doc symposium is a great venue to polish a research presentation and also to connect with colleagues interested in the same problems." Being in SD-CAB helps her to interact with some of the best algal biotech minds in San Diego: "The feedback and questions I got when I presented at the SD-CAB symposium in January helped me publish a paper on that work in May and then present it in a more polished form at the American Society for Microbiology General Meeting in New Orleans." 

This summer, the Allen lab is even hosting an SD-CAB summer undergraduate intern, Michael Mayfield. Michael is working closely with Dr. Allen on a project that compliments Christine's work, scanning new microbes for secondary metabolite production and trying to find strains that make these important molecules. 

Christine's work and the work of the Allen group may one day leave the lab in pill or gasoline form, and while it won't make my french fries healthy, it may replace expensive fish oil supplements or help reduce the environmental impact of our energy needs.

Britt Flaherty is Ph.D. candidate at UCSD and a volunteer writer and outreach coordinator with SD-CAB. You can contact her at blflaher@ucsd.edu.

Sapphire Energy

by Amanda Herman

Tim Zenk, VP of Corporate 
Affairs at Sapphire Energy

Sapphire Energy is a local biotech with a bold mission statement:  “To change the world by developing a domestic, renewable source of energy that benefits the environment and hastens America’s energy independence.”  While all startup companies boast unique visions and lofty expectations in paragraph form, only a small number actually meet their goals in real time, and Sapphire is undoubtedly a gem among these few (pun intended).  It was established in 2007 with only a handful of employees and an ambitious desire to manufacture direct replacement fuels for the current gasoline, diesel, and jet distillates.  Since then it has grown exponentially, with a work force of over 100 and facilities in San Diego, Orange County, and Las Cruces and Columbus, New Mexico.  After talking with Tim Zenk, the Vice President of Corporate Affairs at Sapphire, it is clear that this burgeoning company is well on its way to solving the nation’s most pressing energy issues today for a greener tomorrow.  Read on for my short question and answer session with Zenk to learn more about Sapphire.

Q:  Why is there a necessity for a company like Sapphire?

Sapphire's planned Algae Plant 

A:  Sapphire Energy was founded based on the concept that there had to be a better way to do biofuels.  There had to be (1) a biological source of materials that could be converted into hydrocarbons (organic compounds naturally found in crude oil), (2) these biological materials needed to be easily scalable in accordance with a growing demand, and (3) have no impact on existing agriculture.  Sapphire applies viable technology in a sustainable manner.  The use of algae-based oils eliminates the need for additional transportation and refining systems in addition to reducing greenhouse gas emissions.  Algae are also one of the most scalable things on the planet, so large-scale production (over 1 billion gallons a year) is a feasible goal.

Q:  How is the green crude produced by Sapphire different from the biodiesel fuel made by other companies?

Mills at the outdoor 
field station

Sapphire manufactures renewable crude oil from algae, using a proprietary procedure of converting direct sunlight and carbon dioxide to generate high-value hydrocarbons.  Green crude produced in this manner uses the same industrial, refining, and distribution methods as the existing petroleum infrastructure and can be used as a drop-in fuel replacement.  This makes it a superior alternative to companies that use algae to make biofuels, which are not compatible with the same industrial refining processes.

Educating a Green Workforce

by Britt Flaherty

Green algae may soon be what powers our cars, planes, and light bulbs, but only if a workforce of smart professionals learns how to grow and process the energy stored in photosynthetic bugs. That's where Educating and Developing Workers for the Green Economy, or EDGE, comes in. EDGE is a collaborative effort on behalf of San Diego powerhouses such as UCSD, SDSU, CleanTECH San Diego, BIOCOM, and the San Diego Workforce Partnership, focused on educating a next-generation workforce in green technology. In this second entry of SD-CAB's new blog on all things green in San Diego, I'll profile a few students from an EDGE course on Biofuels this past quarter, taught by Professor John Buchner, Ph.D. Buchner, like many EDGE instructors, is a post-doctoral scholar in an SD-CAB lab and is focused on a career in educating the next generation of scientists and researchers.

These are the men and women who will power the green economy: