Getting Teens Hooked on Stem

The Introductory College Level Experience in Microbiology (iCLEM) summer intensive is hosted and run by the Joint BioEnergy Institute (JBEI). First launched in 2008, iCLEM immerses local Bay Area students in the biological sciences – and gives them a taste of day-to-day life as a scientist – through an eight-week-long blended curriculum of instruction, hands-on basic laboratory skill training, and in-depth tours of working labs within JBEI, Lawrence Berkeley National Laboratory (which manages JBEI), and local biotech companies. The students, who receive a stipend so that they may attend the program in place of a summer job, utilize their newfound knowledge by conducting independent research projects and presenting their findings at the end of the program.

Read the story here and hear from the 2019 iCLEM cohort in this video.

 

Getting Teens Hooked on STEM

By Aliyah Kovner 

It’s 1 p.m. on a sunny afternoon in July – smack dab in the middle of summer break – and a perfect 75 degrees outside; but Jonathan Park is laser-focused. Though he could be strolling down a beach, or at home browsing social media, this 16-year-old is bent over a lab bench, intently pipetting reagents to run an Amplex Red Assay.

Park, a soon-to-be junior at Dublin High School, is part of the 2019 cohort of the Introductory College Level Experience in Microbiology (iCLEM) summer intensive, hosted and run by the Joint BioEnergy Institute (JBEI) in Emeryville. First launched in 2008, iCLEM immerses local Bay Area students in the biological sciences – and gives them a taste of day-to-day life as a scientist – through an eight-week-long blended curriculum of instruction, hands-on basic laboratory skill training, and in-depth tours of working labs within JBEI, Lawrence Berkeley National Laboratory (which manages JBEI), and local biotech companies. The students, who receive a stipend so that they may attend the program in place of a summer job, utilize their newfound knowledge by conducting independent research projects and presenting their findings at the end of the program.

“I didn’t really know what to expect, I thought maybe we would just come in and do some experiments here and there,” said Park, while on a break from the lab. He explained that he hadn’t been drawn to science until last year’s honors chemistry class challenged him in a way that got his attention. “I was like, okay, this is really interesting, I need to try this out. And iCLEM was there at just the right time. Being here has really shattered my idea of biology, chemistry and physics being these separate things – I’ve learned that they’re all just an integrated science that researchers use to do all these cool things, like making biofuels and actually saving the environment.”

Jonathan Park pipetting reagents at JBEI, in Emeryville, CA.

Jonathan Park pipetting reagents at JBEI.

The experience at iCLEM has motivated Park, who previously planned to study music, to pursue a double major with biochemistry when he attends college in 2021. If he follows through with his ambitions, Park will be in good company. According to Lauchlin Cruickshanks, iCLEM’s educational program administrator, 95% of past participants have gone on to continue their education at two or four-year colleges and universities, and 80% majored in science or engineering. Given that the program specifically recruits teens who face socioeconomic hurdles to higher education, this impressive attendance rate is a point of pride among the scientists and educators who make iCLEM happen.

Hoping to spread their prodigiously successful model beyond the confines of JBEI, a group of former and current scientific advisors have shared the iCLEM curriculum in the Journal of Microbiology & Biology Education.

“There are so many different curricula to teach basic microbiology and biochemistry already in journals, but I think one of the attractive things about this approach, and the reason it resonates with kids, is that we talk about science through the lens of sustainability,” said Jesus Barajas, the first author of the paper and a former scientific advisor for iCLEM. “Our overall goal is to teach these concepts by having students learn how to produce biofuels and bioproducts in a sustainable fashion. This is more meaningful, because if we want to think of them as the next generation of scientists, we don’t just want to train them to tackle the problems of today and tomorrow, but also for them to really understand the problems.”

The iCLEM 2019 cohort.

From the outset, iCLEM has been dedicated to nurturing budding scientists who would not otherwise have access to a college preparation scientific internship. Nearly all students are from low-income families, and many are also English language learners and/or the first generation to attend college. Clem Fortman and James Carothers, the program’s founders, came up with the premise for iCLEM during a conversation about what was lacking in STEM education. At the time, they were both postdoctoral researchers at JBEI and the Synthetic Biology Research Center (Synberc), a collaborating institution located in the same building.

“We talked about how a lot of the existing programs acted as a leg up for folks who already had a leg up. And it turned out that James and I shared the experience of having to work summers and weekends when we were teenagers,” said Fortman, who served as iCLEM’s scientific director for the first four years and is currently director of operations for the lab of Jay Keasling, JBEI’s CEO. “We didn’t have the resources or opportunities to go into the types of school camps and other stuff that can help get kids onto the STEM career track – something that is still the reality of life for many people, especially in the Bay Area.”

As the duo continued discussing the unmet needs in science education, Fortman excitedly realized that much of the fundamental laboratory work supporting JBEI and Synberc’s biofuels research, i.e., the tasks typically done by undergraduate students, could be used as a real-world foundation for teaching basic microbiology and biochemistry. With that conversation, the concept for iCLEM was born. Fortman and Carothers soon pitched their idea to Keasling, drawing upon their own career journeys as they emphasized that providing “opportunities to those who don’t have an easy pipeline into science” means small class sizes, providing financial assistance, and offering college preparation support. Their proposal was approved on the spot. 

Zoe Siman-Tov. (Credit: Marilyn Chung/Berkeley Lab)

“I had some really high expectations for iCLEM and [it has] surpassed them all. I love this program. It’s the highlight of my summer,” said participant Zoe Siman-Tov. “The things we got to do are things that you’d never be able to get to do in high school. And being able to do it myself has really cemented it in, and I’m very sure that I’d like to work in a lab.”

Over the next several years, iCLEM’s curriculum evolved organically, as the founding scientists and a rotating roster of advisors, enthusiastic mentors, and high-school teachers – who help lead the instruction-based portions of the program – refined and enriched their approach.

Raymundo Sanchez, a past student in the 2015 cohort, notes that iCLEM’s behind-the-scenes instructional model helped guide him toward his current interest in biological anthropology. He will soon begin his senior year at UC Santa Barbara as a double-major in the field, alongside Chicano/a studies. “I really love my majors and feel like they blend perfectly what I strive to do in the future, which is help out underrepresented communities by helping them gain better access to healthcare and education,” said Sanchez. “But I would have not even thought of all the different careers that are possible within STEM if it wasn’t for my internships, which were hard to find and only a handful of them were out there for underrepresented individuals. For STEM fields to become more diverse, I think it would be helpful to have more experiences, like iCLEM, that bring awareness and exposure to the many possibilities out there.”

Now that the details of iCLEM are widely available, Fortman and the rest of the team are optimistic that other programs with the same core tenets will indeed develop, and that more teens than could ever fit at the JBEI lab benches will soon be able to participate.

Looking back, the group regards the many hours of volunteered time spent developing the curriculum and building iCLEM into the experience it is today as a necessary contribution toward the long-overdue, large-scale shift that is happening throughout the education framework. “I believe that the STEM fields are trying to be more inclusive than they were,” said Fortman. “But there needs to be educational equality much earlier than when we’re intervening, starting at day one.”

iCLEM is currently funded by JBEI, which is supported by the DOE Office of Science; the Amgen Foundation, administered through UC Berkeley; and the Heising-Simons Fund.

Keasling Featured in NHK World, Japan’s Public TV Station

Jay Keasling, JBEI’s Chief Executive Officer, was featured in NHK World’s interview program “Direct Talk”. Keasling, a pioneer of synthetic biology, talks about the impact that this interdisciplinary technology can have in people’s lives as well as addresses its safety concerns.

Direct Talk is a program that interviews leaders, visionaries and pioneers who shape the world and is broadcast to 300-million households in 160 countries in six different language subtitles.

Watch the interview

More Investment Needed for Machine Learning for Bioengineering

In an opinion piece published July 19 in ACS Synthetic Biology, Hector Garcia Martin and Tijana Radivojevic of the Joint BioEnergy Institute collaborated with Pablo Carbonell of the Manchester Institute of Biotechnology’s SynBioChem Centre, to highlight the opportunities in a radical new approach to bioengineering that leverages the latest disruptive advances in machine learning.

The opinion piece entitled “Opportunities at the intersection of Synthetic Biology, Machine Learning, and Automation” puts forward a new approach to bioengineering that may significantly accelerate metabolic engineering for the creation of all types of bioproducts: from biofuels to biomaterials and medical drugs. According to the authors sustained investment in the intersection of the three domains and strong multidisciplinary collaboration are key to drive forward predictive biology and produce improved machine learning algorithms.

Machine learning methods make inferences from raw data using sophisticated algorithms and powerful computers. In order to be trained, machine learning techniques need large amounts of data. Yet challenges remain on how to acquire large-scale high-quality biological data. The authors see automation as the best way to produce the quantity and quality of data needed for effective machine learning. In the long run the intersection of synthetic biology, machine learning, and automation will helps us better design biological systems for a renewable bioeconomy, and it sets the base for a better understanding of biology in general.

Related Information:

New Machine Learning Approach Could Accelerate Bioengineering

Garcia Martin Lab Website

Could Synthetic Biology Stop Global Warming?, Latino USA

Héctor García Martín, Deputy Vice President of JBEI’s Biofuels and Bioproducts Division spoke to Latino USA about the emerging field of synthetic biology and how it allows scientists to re-engineer biological systems for new purposes, namely how it could lead to new biofuels which would reduce the release of carbon dioxide—the main cause of global warming. Listen here

Blue Pigment from Engineered Fungi Could Help Turn the Textile Industry Green

By Aliyah Kovner

Often, the findings of fundamental scientific research are many steps away from a product that can be immediately brought to the public. But every once in a while, opportunity makes an early appearance.

Such was the case for a team from the Department of Energy’s Joint BioEnergy Institute (JBEI), whose outside-the-box thinking when investigating microbe-based biomanufacturing led straight to an eco-friendly production platform for a blue pigment called indigoidine. With a similar vividly saturated hue as synthetic indigo, a dye used around the world to color denim and many other items, the team’s fungi-produced indigoidine could provide an alternative to a largely environmentally unfriendly process.

Lead researcher Aindrila Mukhopadhyay holds a vial of purified indigoidine powder. (Credit: Marilyn Chung/Berkeley Lab)

“Originally extracted from plants, most indigo used today is synthesized,” said lead researcher Aindrila Mukhopadhyay, who directs the Host Engineering team at JBEI. “These processes are efficient and inexpensive, but they often require toxic chemicals and generate a lot of dangerous waste. With our work we now have a way to efficiently produce a blue pigment that uses inexpensive, sustainable carbon sources instead of harsh precursors. And so far, the platform checks many of the boxes in its promise to be scaled-up for commercial markets.”

Importantly, these commercial markets already have considerable demand for what the scientists hope to supply. After meeting with many key stakeholders in the textile industry, the team found that many companies are eager for more sustainably sourced pigments because customers are increasingly aware of the impacts of conventional dyes. “There seems to be a shift in society toward wanting better processes for creating everyday products,” said Maren Wehrs, a graduate student at JBEI and first author of the paper describing the discovery, now published in Green Chemistry. “That’s exactly what JBEI is trying to do, using tools derived from biological systems – it just so happens that our engineered biological platform worked very well.”

Droplets of purified indigoidine, produced by bioengineered fungi, are added to water to showcase the pigment’s rich, saturated hue. (Marilyn Chung/Berkeley Lab)

The story began when the team set out to test how well a hardy fungi species called Rhodosporidium toruloides could express nonribosomal peptide synthetases (NRPSs) – large enzymes that bacteria and fungi use to assemble important compounds. The scientists examined this fungi’s NRPS expression capability by inserting a bacterial NRPS into its genome. They chose an NRPS that converts two amino acid molecules into indigoidine – a blue pigment – to make it easy to tell if the strain engineering had worked. Quite simply, when it did, the culture would turn blue.

Going into this experiment, indigoidine itself was not the main interest for the team. Instead, they were focused on the larger picture: exploring how the assembly line functionality of these enzymes could be harnessed to create biosynthetic manufacturing pathways for valuable organic compounds, such as biofuels, and assessing whether or not the fungi represented a good host species for the production of these compounds. But when they cultivated their engineered strain, and saw just how blue the culture was, they knew something incredible had happened.

Aindrila Mukhopadhyay and Maren Wehrs inspect a bioreactor full of their Bluebelle strain at JBEI. (Credit: Marilyn Chung/Berkeley Lab)

With an average titer of 86 grams of indigoidine per liter of bioreactor culture, the yield of the strain – which they named Bluebelle – is by far the highest that has ever been reported. (Other research groups, including the JBEI team, have synthesized indigoidine using different host  microbes.) Adding to the weight of the achievement, the record-breaking yield was obtained from a culture process that uses nutrient and precursor inputs sourced from sustainable plant material. Previous pathways required considerably more expensive inputs yet made about one-tenth the amount of indigoidine.

Beyond the potential applications of indigoidine, the study succeeded in its original goal of providing a potential production pathway for other NRPSs – something that is much more valuable than any single product. These complex enzymes have multiple subunits that each perform a distinct and predictable action in assembling a compound out of smaller molecules. Scientists at JBEI and beyond are keen to engineer enzymes that use NRPSs’ Lego block-like features to produce advanced bioproducts that are currently hard to make.

“A big challenge is to get a microbe to efficiently express such enzymes. This host has huge potential to fulfill that need,” said Mukhopadhyay.

The team’s next steps will be to characterize how indigoidine could be used as a dye and to dig deeper into the capabilities of R. toruloides.

This work was made possible by the expertise of multiple JBEI groups including John Gladden from Sandia National Laboratories, who leads JBEI’s Fungal Biotechnology team, as well as Berkeley Lab’s Advanced Biofuels and Bioproducts Process Development Unit (ABPDU). The other researchers included Yuzhong Liu, Lukas Platz, Jan-Philip Prahl, Jadie Moon, Gabriella Papa, Eric Sundstrom, Gina Geiselman, Deepti Tanjore, Todd Pray, Jay Keasling, and Blake Simmons. JBEI is funded by the Department of Energy Office of Science. ABPDU is funded by the DOE Office of Energy Efficiency and Renewable Energy.

Turning the Switch on Biofuels

-By Anne M. Stark

Plant cell walls contain a renewable, nearly-limitless supply of sugar that can be used in the production of chemicals and biofuels. However, retrieving these sugars isn’t all that easy.

Imidazolium ionic liquid (IIL) solvents are one of the best sources for extracting sugars from plants. But the sugars from IIL-treated biomass are inevitably contaminated with residual IILs that inhibit growth in bacteria and yeast, blocking biochemical production by these organisms.

Lawrence Livermore National Laboratory (LLNL) scientists and collaborators at the Joint BioEnergy Institute have identified a molecular mechanism in bacteria that can be manipulated to promote IIL tolerance, and therefore overcome a key gap in biofuel and biochemical production processes. The research appears in the Journal of Bacteriology.

“Ionic liquid toxicity is a critical roadblock in many industrial biosynthetic pathways,” said LLNL biologist Michael Thelen, lead author of a paper appearing in the June 10 edition of the Journal of Bacteriology. “We were able to find microbes that are resistant to the cytotoxic effects.”

The team used four bacillus strains that were isolated from compost (and a mutant E. coli bacterium) and found that two of the strains and the E. coli mutant can withstand high levels of two widely used IILs.

Douglas Higgins, a postdoc working with Thelen at the time, dived into how exactly the bacteria do this. In each of the bacteria, he identified a membrane transporter, or pump, that is responsible for exporting the toxic IIL. He also found two cases in which the pump gene contained alterations in the RNA sequence of a regulatory guanidine riboswitch. Guanidine is a toxic byproduct of normal biological processes; however, cells need to get rid of it before it accumulates.

The normal, unmodified riboswitch interacts with guanidine and undergoes a conformational change, causing the pump to switch on and make the bacterial cells resistant to IILs.

“Our results demonstrate the critical roles that transporter genes and their genetic controls play in IIL tolerance in their native bacterial hosts,” Thelen said. “This is just another step in engineering IIL tolerance into industrial strains and overcoming this key gap in biofuel production.”

The results could help identify genetic engineering strategies that improve conversion of cellulosic sugars into biofuels and biochemicals in processes where a low concentration of ionic liquids surpass bacterial tolerance.

Scientists from Sandia National Laboratories and Lawrence Berkeley National Laboratory also contributed to this research.

The work is funded by the Department of Energy, Office of Science.

JBEI participates at 2019 East Bay STEM Career Awareness Day

East Bay STEM Career Awareness Day took place on May 16 in Emeryville. At this annual event, local businesses and organizations collaborated to provide activities that provided insight into potential careers in STEM to 200 students from schools in Berkeley, Emeryville, Richmond, and Oakland. The event was hosted by the Institute for STEM Education at California State University, East Bay in partnership with Bayer, Wareham Development, the East Bay EDA, the City of Emeryville, and the City of Berkeley. We thank the JBEI volunteers  that participated at this event: Deepika Awasthi, Irina Silva, Nicole Ing, Peter Otoupal, and Tina Wang.

2019 Undergraduate Poster Presentation

Undergraduates who have interned at Emery Station East (ESE), where JBEI is located, participated at an on-site poster presentation and celebration on May 10. The students who interned at JBEI and other research programs hosted at ESE presented results of their research. Twelve posters and two talks were presented to the JBEI community.

The undergraduates were judged for their presentation and poster making skills. This year, there was a tie in both categories. Julie Lake and Allison Pearson won for “Best Poster Design” and Kenneth Workman and Isabel Honda won for “Best Poster Presentation”.

The following students presented seminar talks:

  • Marian-Joy Baluyot (Mentor: Sam Curran)
  • Will Sharpless (Mentor: Mitch Thompson)

And the students below presented posters:

  • Alex Cardia (Mentor: Luis Valencia)
  • Allison Pearson (Mentor: Mitch Thompson)
  • Amanda Hernandez, Samantha Chang (Mentor: Amin Zargar)
  • Isabel Honda (Mentor: Laure Leynaud-Kieffer)
  • Jasmine Cisneros, Jennifer Zhang (Mentor: Paul Opgenorth)
  • Julie Lake (Mentor: Sam Curran)
  • Kenneth Workman (Mentor: Henrique De Paoli)
  • Marty Ng (Mentor: Ankita Kothari)
  • Maya Ramamurthy (Mentors: Connie Bailey, Luis Valencia)
  • Shania Tedja (Mentor: Deepika Awasthi)
  • Silver Alkhafaji (Mentor: Laure Leynaud-Kieffer)
  • Suneil Acharya (Mentor: Pablo Cruz-Morales)
Allison Pearson, one of the “Best Poster Design” winners seen here presenting her poster.
Kenneth Workman (on the right), one of the “Best Poster Presentation” winners, with his mentor Henrique De Paoli.