SD-CAB Researcher Spotlight - Susan Golden, Ph.D.

By Amanda Herman

Susan Golden is a member of the Faculty of 1000 Biology, a Fellow of the American Academy of Microbiology, and a Member of the National Academy of Sciences. In addition, she runs a lab at UCSD that studies circadian rhythms of gene expression in cyanobacteria. Golden summarizes her graduate school and postdoc experiences, how cyanobacteria are useful in the production of biofuels and how SD-CAB has shaped the direction of her research in this month’s SD-CAB Researcher Spotlight.

How did you decide that studying cyanobacteria was your passion?

I grew into it. I started working on cyanobacteria as a grad student. I wanted a "recombinant DNA" project, and when I started grad school in 1978, such approaches were still new and not used in most labs. I had a chance to join a lab in which the PI (Lou Sherman) had just done a sabbatical to learn basic molecular cloning methods with the idea of capitalizing on the then-recent discovery of a transformable cyanobacterium. My job was to develop a cloning system for that species, Anacystis nidulans R2, now known as Synechococcus elongatus PCC 7942, with the idea of using it to discover new genes involved in photosynthesis. Later I chose to do my postdoc in Bob Haselkorn's lab not so much because he worked on cyanobacteria, but because he was researching transcriptional regulation. I had expected to change organisms and research directions, but when I got there I still had "one last thing" I wanted to do from a loose end of my PhD work, and I ended up finding interesting new directions with S. elongatus. Thus, I just continued my PhD work on through my postdoc and into my independent research lab. The areas of emphasis and technologies have changed over the years, but I'm still working on my favorite little bug, the Anacystis that I was among the first to work with genetically. Being at the right place at the right time is my forte. I literally walked into Sherman's lab, while he was on sabbatical, within seconds of his postdoc writing (snail mail back then) to Lou: don't overlook the contribution a graduate student could make to this project.

How do cyanobacteria fit in with the production of biofuels?

Initially cyanobacteria were dismissed as biofuel organisms because they don't naturally store carbon as neutral lipids (oil droplets) that are easily converted to biodiesel. However, cyanobacteria are easier to genetically modify than are eukaryotic algae, and they can be engineered to make designer chemicals. Many species have growth advantages as crops: filamentous forms that are easy to harvest, some fix nitrogen, and they can grow at high pH conditions that kill off a lot of invading or grazing pests. Moreover, new biomass conversion technologies are making it possible to get useful hydrocarbons from biomass without requiring neutral lipids as a starting point. Thus, cyanobacteria can contribute in many ways to the enterprise.

What advice would you give to students interested in pursing research in academia?

Do it only if you love it. The challenge is that you have to constantly raise money just to do your job (to fund your lab), and many people end up depending on you to provide their salaries. That's a lot of pressure. However, it is fantastic to have the freedom to choose what to study (within reason), and to see the transformation that occurs in a student from the time he or she enters the lab to when they leave (as a scientist!).

What do you like to do in your spare time?

I like to read good novels. I'm open to a lot of genres, but they really need to be well written, with good character development and good use of language.


If you could have one famous scientist over for dinner (living or deceased), who would it be?

I think George Washington Carver would be a fascinating dinner companion.


How has SD-CAB helped further the success of your laboratory?

Being part of SD-CAB has swept me into applied microbiology and alliances with biotech companies. I'm learning a lot, and doing more as part of the group than I would have done on my own. I'm engaging in collaborations that I wouldn't have assembled on my own. The activities and interactions, and the growing reputation of SD-CAB around the world, are all good for my research program and for forcing me to expand my scientific horizons.

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

SD-CAB Student and Postdoc Symposium this Friday

We are pleased to present this month's Student and Postdoc Symposium, chaired by Dr. Jim Golden.

Our speakers will be:
Britt Flaherty (J. Golden Lab): Cyanobacterial Heterocysts
Julie Bordowitz and Susan Cohen (S. Golden Lab): Cyanobacterial Circadian Rhythms
Joseph Boyd (S. Golden Lab): The Chlamydomonas Eye Spot

When: December 18th from 4PM to 6PM
Where: Sumner Auditorium on the SIO campus (look for the Argo bell).
Visitors should park along La Jolla Shores Dr. (please see the attached map).

A poster for this event is below.  Please feel free to share it with your friends, co-workers and post it in your buildings to help us spread the word.

KPBS Says: 2012 Could Determine Future of Algae as Fuel

Recently, KPBS covered a story on SD-CAB labs and algae fuels in San Diego. Watch the video below or read the article at the KPBS website.

Grants Available for Biofuels Training

KPBS covered the new biofuels training program at UCSD. It's a must read! Follow this link to the article.

Biologists Use Algae-Produced Protein in Global Health Initiative

A research team in the Division of Biological Sciences headed by Stephen Mayfield will produce a mammary gland protein called MAA from algae to determine if has the potential to significantly reduce infectious diarrheal diseases, a major cause of infant mortality in the developing world.

The UC San Diego biologists will supply their algae-produced MAA to researchers at the University of Nebraska Medical Center as part of a newly funded initiative from the Bill & Melinda Gates Foundation to enable researchers worldwide to test unorthodox ideas that address persistent health and development challenges.

Mayfield, a professor of biology and director of the San Diego Center for Algae Biotechnology, is also one of the founders of Sapphire Energy, a San Diego company known for its development of a crude oil replacement produced from algae.

Mayfield’s research team engineered edible algae to produce high levels of bovine colostrum MAA using Sapphire Energy’s algae biotechnology platform. The MAA will be used by researchers at Nebraska headed by Thomas McDonald, a professor of pathology and microbiology there. His team of scientists has demonstrated that the protein increases the production of a natural protective barrier in the intestine against organisms such as Salmonella that can cause diarrhea.

For more on the research project and the grant received by the research team go to: http://app1.unmc.edu/publicaffairs/todaysite/sitefiles/today_full.cfm?match=8735

SD-CAB Student and Postdoc Symposiums

We are pleased to present this month's Student and Postdoc Symposium; chaired by SD-CAB Director, Dr. Stephen Mayfield.

Our speakers will be:
Javier Gimple: "Synthetic Biology Engineering of Phototosystem II"
William Ansari: "Metabolic engineering of algal strains for OMEGA-3 production"
Beth Rasala: "Stable heterologous expression and secretion of xylanase1 in Chlamydomonas reinhardtii"

When: November 18th from 4PM to 6PM
Where: Sumner Auditorium on the SIO campus (look for the Argo bell).
Visitors should park along La Jolla Shores Dr.

A poster for this event is attached. Please feel free to share it with your friends, co-workers and post it in your buildings to help us spread the word.

The reception will be organized by the wonderful Ms. Mary Anderson, from the Mitchell Lab, following the talks. Please join us for some stimulating conversation followed by frosty beverages and tasty snacks
on the patio.

SD-CAB Researcher Spotlight - Steve Mayfield, Ph.D.

By Britt Flaherty

Steve Mayfield
image courtesy of Mayfield Lab Website

  Steve Mayfield is the director of the San Diego Center of Algae Biotechnology, but he also runs a lab studying algal biofuels and spends his days teaching the public about the importance of our future in green energy. In this SD-CAB Researcher Spotlight, Mayfield tells us about how he became interested in algae, what he tells young scientists, and where he sees SD-CAB in the future.  


How did you decide that algal biofuels were your passion?
It kind of snuck up on me. I was happily working away on molecular genetics in algae and expressing recombinant proteins, and life was good. It was obvious that algae had the potential to scale up at very low cost. Even today we continue to work on therapeutic proteins, industrial enzymes and vaccines, all of these can be made in algae for a fraction of the cost to produce them in the systems they are presently made in.
We were working on algal genetic engineering in earnest since 1999. Back then oil was less than $20/barrel and climate change was something that people were talking about, but with no real urgency. That all began to change about 5 or 6 years ago, and by 2007 it had become the perfect storm: the cost of oil was going up fast and at the same time it was obvious that climate change was not only real but happening much faster then we thought possible. We either had to figure out how to generate renewable energy, or we would suffer some pretty severe consequences, both environmental and economic. Given algae's ability to turn sunlight and CO2 into liquid fuels, I decided we better give this a serious try.


What part of your career has gotten easier with time? What's harder?
I think the part that has gotten easier is convincing people that what we are doing in lab really matters to the world. I always knew it did, and so did some great post-docs and students that worked with me in the past, but I think many people dismissed algae as a kind of fringe scientific organisms that was maybe interesting, but not really something that mattered in their life. Now everyone agrees that bioenergy is THE science of the next decade, and it will matter in everyone's life.
I think what has really gotten harder is my ability to stay connected directly with research. It seems I spend more and more time talking to politicians and reporters and students, and less time in lab talking research. I honestly believe that my time spent educating students and politicians and the public is time well spent so no complaints on what I do, I just wish I had more time to do research.


What's the best part about your job? The worst?
The best part is still discovery. When someone from lab runs in with a great new result that is just exciting. For some reason knowing something that no one else in the world knows, at least until you tell them, is just a great feeling, I loved that when I started in science 25 year sago, and love it just as much today!
The worst part of my job is watching science get reduced to slogans and op-ed opinions, like it has become in the press and by many politicians. I now consider it one of my main jobs to call people on this behavior.


It sounds like you're pretty busy, but what's your favorite hobby?
Surfing and golf for sports and tuna fishing when time allows.


What do you tell young people interested in science?
First if you love science you WILL be successful, because when you love something you work hard on it and when you work hard you are almost always successful. The second I tell them is that the future is energy, in any form, fossil fuel, renewable you name it in the next decade anyone that makes energy will have something to sell, so if you want a job, work on energy.

How do you see SD-CAB shaping the future of algae fuels? What's the big picture?
SD-CAB has become one of the premiere algal research centers in the country and, perhaps, the world. Our plan is to make sure we stay that way, and to expand our research, education and training programs on every front.


Britt Flaherty is a graduate student at UC San Diego and a volunteer writer and educator with SD-CAB. You can contact her at blflaher@ucsd.edu.

EDGE Interns get Hands on Experience in Green Biotech

By Britt Flaherty

Pearson Fuels at the Pump

Brett Schwemmer packs his surfboard into a diesel-fueled blazer when the waves roll in, and since hitting the beach in an eco-friendly way is important to this San Diego lover, he is interested in new fuels that don't pollute our oceans. Schwemmer is part of the Educating and Developing Workers for the Green Economy (EDGE) Initiative's internship program, which places EDGE-certified graduates in local biotech companies for hands-on experience and training. Schwemmer is working at Pearson Fuels, which is currently developing biodiesel and ethanol-based fuels in San Diego. A marketing major from CSU San Marcos, Schwemmer is interested in applying his advertising skills to help sell biofuels. "Biodiesel was something that I always wanted to use in my blazer, but never had the chance," he says. Schwemmer's internship is giving him the skills necessary to join his background in advertising with his passion for green technology. "The best part of the EDGE program has been the job experience for me. I was able to have a lot of freedom while working at Pearson Fuels in their marketing department. The challenges and opportunities took my skills to the next level."

EDGE Intern Emily E. Effner
working at her microscope

The EDGE internships aren't all marketing and business, though – most EDGE interns are at the bench learning valuable lab skills to develop green fuel themselves. Emily E. Effner and Bharath Bharadwaj spent their two-month internships in industry. Effner worked at General Atomics, collecting and analyzing biological samples from photosynthetic microbes. "I enjoyed taking an experiment from cradle (setting up, research) to grave (writing reports), and can't wait to continue studying photosynthetic organisms in industry or graduate school," she says. Bharadwaj worked for SG Biofuels using next generation sequencing technology to analyze larger photosynthetic organisms like plants. Bharadwaj isolated DNA from a plant species and prepared this DNA for genome sequencing, thus adding to our knowledge of how photosynthetic organisms grow and develop.

EDGE Intern Baharath
Bharadwaj working in lab

Both Effner and Bharadwaj's internships are the first step in their careers in biotech. "The internship gave me the opportunity to get my 'foot in the door' at a company," Effner says. "Not only did I learn everything that is fundamental to working in a lab, but I had the opportunity to demonstrate a strong work ethic and passion for learning. I have no doubt the experience and friends I made will help me secure a position with an innovative biofuel company." This kind of hands-on experience is even more vital in a slower economy. "We all know how difficult it is to obtain the first work experience in a field we are interested in." Baharadwaj points out. "I think the EDGE program makes it easier for both industry as well as candidates seeking jobs to find people with shared interests."

            A new class of EDGE students will start taking courses next Spring for certification and internship placement. To find out more, you can check out the Biocom website or read the previous SD-CAB blog on EDGE certification.


Britt Flaherty is a graduate student at UC San Diego and a volunteer writer and educator with SD-CAB. You can contact her at blflaher@ucsd.edu.

SD-CAB Student and Postdoc Symposium this Friday

We would like to welcome you to the October SD-CAB Student and Postdoc Symposium.  Drs. Greg Mitchell and Dominick Mendola, the chairmen for October's symposium, have three great speakers lined up.  Please note the adjusted time.


Jeff McQuaid: Transcriptional analyses of sea ice diatom communities
Nathan Schoepp: SD-CAB Greenhouse and Wetlab Virtual Tour
Jamie Rhodes: The Blind Date Between Algal Biofuels and Public Policy

Time: 4:30pm - 5:30pm Friday October 21st
Location: Sumner Auditorium on the SIO Campus (look for the Argo Bell)
Parking: Visitors should park on La Jolla Shores Drive between Naga Way and Paseo Grande Dr.

Presentations will, as usual, be followed by some lovely light refreshments, courtesy of Ms. Mary Anderson.

SD-CAB Hits the Beach

By Spencer Diamond

If you happened to stop by my office on the 17^th or 18^th of September you may have seen a sign that said “Gone Surfing”. However, this was no ordinary surf session, as the SD-CAB was invited for the first time to participate in the annual Cardiff Surf Classic and Rerip Green Fest. This annual event put on by the Cardiff chamber of commerce strives to bring environmental awareness to costal communities, and showcased a number of sustainable initiatives and products. Over 60 different organizations were present at the event ranging from organic food vendors to local water and power authorities (for a full list see here). The surfing itself featured a square off between the Cardiff and the Solana Beach sponsored businesses, which really seemed to get people excited about all of the different vendors present at the event. Even the surfing had gone green with many surfers riding used boards from the Rerip Board Swap, which included over 100 used surfboards for purchase or trade.

In the midst of all of the excitement the SD-CAB booth was showcasing some of the tools, programs, and research that are helping us develop sustainable energy solutions. One notable piece of work that was presented at the event was research conducted by UCSD graduate student Will Ansari. In his research Will is utilizing high-throughput methods, such as flow cytometry, to screen thousands of mutant algal strains for individuals with increased oil content. In addition to the cutting edge research

preformed by SD-CAB scientists, common laboratory hardware such as pipettes and shakers drew a lot of interest from both young and old visitors. Getting hands on with the tools of the trade seemed to help a lot of people understand what our researchers do on a daily basis. One young boy staring at flasks of the cyanobacterium Synechococcus elongatus declared, “You’re going to make gas out of that!” The SD-CAB booth also attracted the attention of a number of corporate representatives including individuals from Mo Bio Laboratories, Community Fuels, and the San Elijo Joint Powers Authority. With the wealth of biotechnology companies and green initiatives in San Diego, you never know who you will meet down by the beach!

Overall the Cardiff Surf Classic and Rerip Green Fest was a great time and brought out hundreds of people of all ages and walks of life. The wide variety of people at the event provided an excellent atmosphere for both public education and professional interaction. If you get a chance to check it out next September I would highly recommend it!

Spencer Diamond is a graduate student at UCSD and a guest blogger and volunteer with SD-CAB. You can contact him at sdiamond@ucsd.edu.

Algae Industry Magazine Interviews Dr. Stephen Mayfield

Algae Industry Magazine recently interviewed Dr. Stephen Mayfield about the EDGE Initiative, a 4 million dollar project that prepares the future workers of the bioenergy sector through certificate classes and hands-on industry internships. In this article, Dr. Mayfield describes the origins of EDGE, what the green work force looks like, how some of San Diego’s local biotechs and nonprofits contribute to the training process, and what the future holds for the program. Check out the full story here. Stay tuned in the next few weeks for exciting blog entries from EDGE participants who recently completed internships this past summer!

SD-CAB Student and Postdoc Symposiums

We would like to welcome you to the first SD-CAB Student and Postdoc Symposium of the 2011/2012 academic year. Dr. Steven Briggs, the chairman for September's symposium, has two great speakers lined up:

Ying Lin: Nitrogen starvation induces post-translational modifications
Arnaud Taton: Gene transfer in Leptolyngbya sp. strain BL0902, a cyanobacterium suitable for biomass and biofuel production

Time: 4pm - 5pm
Location: Sumner Auditorium on the SIO Campus (look for the Argo Bell)
Parking: Visitors should park on La Jolla Shores Drive between Naga Way and Paseo Grande Dr.

Algal Biotechnology in the Gerwick Lab: From Pharmacy to Fuel

By R. Cameron Coates

 

Drs. Bill and Lena Gerwick

Dr. Bill and Dr. Lena Gerwick lead the Gerwick lab and have developed an effective style that builds on their respective strengths in chemistry, molecular biology, innate immunity and microbiology.  Bill describes himself as “incredibly lucky” to be working with Lena everyday, because despite the complexities it can sometimes create, they “get the chance to interact on such a multi-dimensional way.”  It is, however, the interdisciplinary nature of the Gerwick lab as a whole that makes them a unique group of scientists.  Dr. Bill Gerwick sees the lab’s interdisciplinary qualities as valuable because “it is at the confluence of a variety of disciplines where one finds a rich interface that is ripe with opportunity and innovation.  We consciously try to create that interface in the context of a lab through the basic application of biology, analytical and organic chemistry, pharmaceutical sciences, molecular biology and biosynthesis.” By bringing together an expertise in these varied disciplines the lab has been able to explore the unique chemical adaptation of marine algae and cyanobacteria and how those adaptations might be useful in a variety of biomedical or biotechnological applications.

To explore the unique chemical adaptations of marine life one needs to travel to unique habitats.   Dr. Bill Gerwick and his students make regular collection trips to distant locations to find novel strains of algae and cyanobacteria.  “Each collection trip takes us to new parts of the world at different times of the year and we find different organisms.  Those organisms are the engine that drives the downstream chemistry and biology pursuits of our lab.” The lab has accumulated samples from 16 different countries including remote places like Papua New Guinea, Panama, Madagascar and even Palmyra Atoll in the middle of the Pacific.  From these trips Gerwick and his students bring back live samples as well as larger collections preserved for chemical investigations and DNA isolation.  It is from this treasure trove of samples that the lab has amassed a collection of over 100 live cyanobacterial strains in culture, over 18,000 extracts and purified fractions and 129 pure compounds.  Maintaining a culture collection of so many strains is no small task and Tara Byrum (a multi-talented biologist/lab manager) is the one who keeps it all running.  “It’s exciting to see all of the samples coming into the lab from collection trips and having seen what happens with the samples afterwards I really like how we use chemistry and molecular biology for such a multi-disciplinary approach “

Dr. Bill Gerwick and the author, graduate student Cameron Coates, on a collection trip in Papua New Guinea

            The isolation and identification of natural products from marine algae and cyanobacteria has been a major focus of the lab over the last 25 years.  This effort has yielded compounds like Curacin A, an anti-cancer drug candidate that is active against colon, kidney and breast cancer cell lines.   The compound was isolated from a filamentous marine cyanobacterium from Curacao in the late 90’s and the unique structural characteristics and activity it possesses has driven the lab to investigate the biosynthesis of this molecule and learn more about its activity against cancer cells.  Moorea producta, the cyanobacterium that produces Curacin A, also produces a variety of other novel secondary metabolites.  The lab recently sequenced the genome of this cyanobacterium to investigate the pathways involved in producing Curacin A and these other secondary metabolites.  The results of this sequencing project were recently published in PNAS and can be found here.

Lab Technician Tara Byrum

            The lab plans to maintain their effort in drug discovery while joining forces with SD-CAB and applying their expertise in organic chemistry and molecular biology to biofuel applications.  Growing interest in developing algae as a source of biofuels has opened up many opportunities for the lab to explore new projects that connect their work in natural products to biofuels.  For example, the biomass that remains after the algae has been extracted for fuels may contain compounds that could be used for other biotechnology applications like a pharmaceutical.  These compounds are commonly referred to as “co-products” and members of the Gerwick lab are actively working on identifying potential co-products.   Separately, the lab is working more directly on biofuel applications using cyanobacteria and diatoms.  Emily Trentacoste, a 3^rd year PhD student in the lab is investigating lipid pathways in diatoms with hopes to identify ways to increase yields of triglycerides that could be converted to biodiesel.   

Cameron Coates, a 4^th year PhD student in the lab is investigating hydrocarbon biosynthesis in cyanobacteria.  Cyanobacteria naturally produce hydrocarbons that could be used as a jet fuel directly at about 1-2% of their dry biomass and it appears that they are making these hydrocarbons from fatty acids.  He is investigating the unique enzymes that cyanobacteria use to produce these hydrocarbons and hopes to engineer these enzymes into microbes that would eventually produce a large yield of high quality fuel that could avoid the costly and energy intensive steps of converting fatty acids and triglycerides into diesel or gasoline.  Interestingly, one of these hydrocarbon producing enzymes was discovered as a direct result of the investigations into the biosynthetic pathway for Curacin A, thus creating a direct connection between the labs work on natural products and biofuels.  It is just this type of finding that reinforces the interdisciplinary approach of the Gerwick Lab and will continue to fuel their future research for years to come.

Marine cyanobacterium Moorea producta

 

Cameron Coates is Ph.D. candidate at UCSD and a volunteer writer for SD-CAB. You can contact him at rccoates@ucsd.edu.

SD-CAB Summer Interns Video Blog

This summer, SD-CAB labs hosted undergraduate interns for 10 weeks of science, field trips, and course work. Here's a glimpse into the life of a summer intern, made for the SD-CAB blog by UCSD undergraduate Neil Raina.

Posted and edited by Britt Flaherty

Code Green For US Biofuels

By Spencer Diamond


The name “Green Hornet” may conjure up images of superhero crime fighters riding around in a souped up Chrystler Imperial, but Hollywood may have been taking a page out of the US Navy’s secret playbook. Only a year earlier of the aforementioned movie, the Navy made a public demonstration of an F/A-18 Super Hornet with the ability to fly on a 50-50 blend of standard jet fuel and camelina derived biofuel. This F/A-18, dubbed the “Green Hornet”, is just one example of the Navy’s mission to half its consumption of fossil fuels by 2020. The Navy, which uses 1.5 billion gallons of fuel annually, has become increasingly concerned about obtaining oil from foreign sources, and has called on both industry and academia to develop biofuel solutions for its fleet.


In its call to arms the Navy has directly reached out to the SD-CAB and its partners as pioneers in the areas of algal and bacterial derived biofuels. A speech by Richard A. Kamin of the Navy Fuels Team at the annual SD-CAB symposium this past April highlighted the importance of algae and bacteria in the Department of Defense (DoD) strategy to produce more fuel domestically. Specifically there is hope that technologies can be developed in time to fuel their “green” strike group that will operate completely without conventional fuel by 2016. One of the major challenges involved in this transition is the difference in chemical properties between petroleum and algal derived fuels. The lower density and a lack of aromatic compounds characteristic of algal derived fuels can have an adverse effect on systems not designed for their use. Currently the Navy compensates for these issues by using mixtures of renewable and petroleum derived fuels, but complete independence from petroleum may require specialized engineering of fuel producing microbes.


One SD-CAB investigator, Prof. Steven Briggs, has been applying a proteomics approach to figure out how microalgae regulate their production of lipids under stress. Comparing the proteins found in cells producing and not-producing lipids will give researchers a clue as to which proteins are responsible for controlling various aspects of lipid production. Knowing what proteins control the production of lipids will allow SD-CAB researchers to engineer algal strains to produce both more oil as well as oil with different properties. For the Navy, the development of this technology would mean the ability to manipulate the type of oil they are producing to better suit the needs of their ships and aircrafts. It seems our nation’s air support is going to be calling in the scientist support.





Spencer Diamond is a graduate student at UCSD and a guest blogger and volunteer with SD-CAB. You can contact him at sdiamond@ucsd.edu.

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:

One Barrel For Baja

Kristian Gustavson (right) and 
Nathan Schoepp (left

by Amanda Herman

The Biology Field Station at the University of California San Diego (UCSD) is home to a thriving center for cutting-edge experiments made possible by the San Diego Center for Algal Biotechnology (SD-CAB) in support of research aimed towards understanding and developing eco-friendly energy solutions, like the 1 Barrel for Baja (1BFB) project.  1BFB is a student-based undertaking, which started and quickly gained momentum based on scientific collaborations between laboratories at UCSD, the Salk Institute, the Scripps Institution of Oceanography (SIO), and San Diego State University with funding from the US Department of Energy and local private industries.  Kristian Gustavson is a former Master’s student from Dr. Jim Leichter’s Laboratory at SIO.  He is the visionary behind the 1BFB initiative, and continues volunteering at the Field Station to further the progress of the project.  Gustavson, along with Nathan Schoepp, a Chemistry graduate student in Dr. Michael Burkart’s Laboratory at UCSD and five undergraduate volunteers from the Biofuels Action and Awareness Network (BAAN) helped construct the greenhouse and the wet laboratory.  Both facilities function as factories for growing algae and are rapidly expanding to accommodate the demands of the 1BFB endeavor.

The greenhouse contains large bags 
of algae in various stages of growth.

Algae are a broad and diverse group of organisms that make complex organic compounds. They grow significantly faster than conventional food crops such as maize and soybeans.  They also thrive in warm, arid, and salty climates, making them an attractive alternative to other crop-based biofuels and the greater San Diego area a prime location for their cultivation.  Schoepp summarizes the process of taking algae from the greenhouse to the barrel: first, large bags that hold 50 to 100 liters of freshwater algae are inoculated with one of three algal production strains that have been specially engineered for better growth.  A continuous supply of both air and CO2 is pumped through the bags for four days.  After this incubation period, the algae are harvested and their biomass, the biological material containing important fuel precursor molecules, is isolated by centrifugation.  The biomass is then sent to Dr. Skip Pomeroy’s Laboratory at UCSD, where the lipids and fats and are extracted and further converted into usable diesel fuel.

Gustavson’s goal is to obtain enough biomass to fill one 42-gallon barrel with biofuel (also known as B100 biodiesel).  In an effort to scale up the production by the end of the summer, Gustavson and Schoepp plan to grow 300 to 500 liter algal cultures in large plastic pools of saline water.  They hope to eventually build an in-ground circulating pond where bulk volumes of algae can be cultured.  Optimizing the growth of one algal strain and promoting its use as a renewable form of energy to local companies is the next step for Gustavson. “This is a good opportunity for UCSD to lead the way in applied algal biotechnology,” he says.  The Baja 1000 is a series of off-road desert races that will take place on November 17^th, 2011 in the Baja California Peninsula.  The race is sanctioned by SCORE International and often showcases new technologies in motor vehicles.  Gustavson will race one of three diesel enduro motorcycles from Holland using the fuel that he and his team have produced from start to finish.

The success of the One Barrel for Baja project has also been made possible with the help of Drs. Steve Mayfield, Greg Mitchell, Michael Burkhart, Skip Pomeroy, and Dominick Mendola. 

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