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Dylan Chivian, Microbial Explorer

Floating down the Amazon River, Dylan Chivian knew that he was in the midst of an adventure. This three-day journey downstream to Manaus, a heavily populated city in the State of Amazonas, was known to be a perilous one. But it was the locals’ way to go from point A to B in one of the wildest places on the planet. So Chivian, recently graduated from a doctoral program and confirmed to start a postdoctoral position at Berkeley Lab in the fall, purchased a hammock at the dock and boarded the river boat.

Hear Chivian pronounce his name.

“I had always dreamed of seeing Brazil,” he said. As a biologist, the Amazon is a remarkable place. To a large extent, it’s the lungs of the planet.”

Chivian relaxing at the floating Uakari Lodge in the Mamirauá Reserve, Amazonas, Brazil, in 2005. (Courtesy D. Chivian)

Chivian experienced enough wonder in the natural world to make this an unforgettable experience. Now a microbial scientist and coding engineer with the Department of Energy Systems Biology Knowledgebase (KBase), he’s building software tools that aim to share microbial genomic information and promote collaboration across the broader scientific community.

From producing biofuels to cleaning up pollutants, microbes present an array of solutions to our off-balanced biosphere—and may hold the key to stabilizing our environment. “We are still at the beginning of understanding the mechanisms of ecosystems and the toolkits that nature has evolved,” Chivian said.

From Dot-com to AI

Chivian’s upbringing instilled in him the idea that one’s job in life is to help humanity. When he was in his early teens, an organization that his father co-founded won the Nobel Peace Prize. Shortly thereafter, Chivian learned to code in the C programming language. These two important events led him to pursue bioengineering at the University of California, Berkeley.

In the early 1990s, the explosive growth of computers and the internet fascinated Chivian. Initially he explored a few of the dot-com–related job avenues, but the opportunities that existed between computing technology and science proved more appealing. “I got really into bioengineering—it felt like this field was at the beginning of a burst of discovery,” he said. Putting his programming skills to use, Chivian started to explore ways that physical and statistical modeling, as well as artificial intelligence (AI), could be used to study protein structure.

By better understanding the chemical makeup and atomic structure of a protein, it’s possible to infer a plethora of functional information. The potential for discovery seemed endless to Chivian and he followed this interest to a graduate program at the University of Washington. Working with David Baker, his research there culminated in the development of a protein structure prediction tool called Robetta. “This early advancement showed me how much I enjoy making tools that are simple to use by the greater community,” Chivian said. “I realized how much they can help advance science as a whole.”

Mining for Genomic Gold

Chivian began a postdoctoral position at Berkeley Lab in 2005. He joined the team of Adam Arkin, a senior faculty scientist in the Environmental Genomics and Systems Biology Division whose lab explores how to predict, control, and design biological function in complex webs of life.

Chivian focused his research on analyzing the genomic information of a water sample from a gold mine in Africa. When mining, the workers avoid water sources, but for Chivian and the team, these fluid-filled pockets hold valuable information about the type of microorganisms that can live in belowground conditions. After removing the cells from these samples and sequencing the DNA, Chivian analyzed the information and determined which species were present.

The results of this work surprised everyone on the team. Instead of multiple organisms collaboratively living in this contained, resource-barren environment, they discovered only one. After investigating the genetic potential of that genome, the team discovered that it was capable of carrying out every one of the necessary steps to maintain life. “It was literally a single-species ecosystem,” Chivian said.

This one organism, they soon learned, could fix its own nitrogen and carbon, and used sulfate reduction for energy. Chivian dubbed the species Desulforudis audaxviator, taking the name “audax viator” (bold traveler) from a passage in Jules Verne’s “Journey to the Center of the Earth.” It was a big discovery with implications for other fields like astrobiology and led to Chivian’s first publication in a major scientific journal. “It was one of those eureka moments that all scientists work toward,” he said. “It was amazing.”

Growing with Berkeley Lab

In 2008, Chivian converted to a research scientist position and began working at the Joint BioEnergy Institute (JBEI), which at that time was in its initial days. Chivian’s tasks centered on developing computational tools to model protein structures, perform metagenomic analysis, and map metabolic networks. The JBEI mission, to harness the energy in plants and develop advanced biofuels, closely aligned with Chivian’s interests. He continued developing tools to explore and analyze how microbes could be used to break down the tough, lignocellulose bonds of plants and unlock their full energy potential. “At that time, microbial genomics was arguably the most exciting place to be in science, the discoveries—such as CRISPR/Cas—were just falling out,” he said.

Chivian photographed on the grounds of Berkeley Lab. (Credit: Thor Swift/Berkeley Lab)

So many discoveries and new avenues to pursue kept arising that Chivian helped to build the Department of Energy Systems Biology Knowledgebase (KBase), a new user-focused tool in 2011. It’s a high-performance computing platform with an easy-to-use interface that helps scientists analyze massive amounts of information. Chivian focuses on building solutions that help scientists analyze metagenomic samples, which contain multiple genomes of many different types of cells.

Chivian uses computer coding and an operating system called Unix to build tools that integrate users’ genomic data into a larger database and knowledge-generating framework. Ultimately, he and his KBase colleagues are working toward modeling the biological and systems interpretation of genomic information. “The foundation of life on Earth is microbial and we’re just beginning to understand how that works,” Chivian said. “The opportunities from agricultural improvements to combating climate change feel endless.”

Reconnecting to Nature

Chivian’s enjoyment of the natural world and its wonders inspires his work, as well as many of his family activities. His wife and two sons get outside often and seek out opportunities to connect with nature. Prior to the COVID-19 pandemic, the Chivians spent their Thanksgiving holiday as a family at an elephant sanctuary in Thailand. “We got to feed and help bathe the elephants, it was really special,” he said. “We called it ‘Kap khun giving’,” a playful combination of the Thai translation for “thank you” and the American holiday.

Chivian and family bathe with retired elephants in 2019 at ElephantsWorld Sanctuary, Kanchanaburi, Thailand. (Courtesy D. Chivian)

For Chivian, staying connected to nature is relevant to his work with KBase and is fundamentally important. And helping his children explore and establish a relationship with the environment is an ongoing project. “We’ve lost our connection to how life works and how we fit into that balance,” Chivian said. “We have to change our perspective in order to last.” ⬢

Written by Ashleigh Papp, a communications specialist for Berkeley Lab’s Biosciences Area.

Read other profiles in the Behind the Breakthroughs series.

May 9, 2023
Tiny Microbes Could Brew Big Benefits for Green Biomanufacturing

A research team led by Jay Keasling, Senior Faculty Scientist in the Biological Systems and Engineering Division and CEO of the Joint BioEnergy Institute (JBEI), has engineered bacteria to produce new-to-nature carbon products that could provide a powerful route to sustainable biochemicals.

The advance – which was recently announced in the journal Nature – uses bacteria to combine natural enzymatic reactions with a new-to-nature reaction called the “carbene transfer reaction.” This work could also one day help reduce industrial emissions because it offers sustainable alternatives to chemical manufacturing processes that typically rely on fossil fuels.

A team co-led by Berkeley Lab has discovered a metabolic process in bacteria that could enable sustainable alternatives to chemical manufacturing processes that typically rely on fossil fuels. (Credit: artjazz/Shutterstock)

“What we showed in this paper is that we can synthesize everything in this reaction – from natural enzymes to carbenes – inside the bacterial cell. All you need to add is sugar and the cells do the rest,” said Keasling.

Carbenes are highly reactive carbon-based chemicals that can be used in many different types of reactions. For decades, scientists have wanted to use carbene reactions in the manufacturing of fuels and chemicals, and in drug discovery and synthesis.

But these carbene processes could only be carried out in small batches via test tubes and required expensive chemical substances to drive the reaction.

In the new study, the researchers replaced expensive chemical reactants with natural products that can be produced by an engineered strain of the bacteria Streptomyces. Because the bacteria use sugar to produce chemical products through cellular metabolism, “this work enables us to perform the carbene chemistry without toxic solvents or toxic gases typically used in chemical synthesis,” said first author Jing Huang, a Berkeley Lab postdoctoral researcher in the Keasling Lab. “This biological process is much more environmentally friendly than the way chemicals are synthesized today,” Huang said.

Read more on the Berkeley Lab News Center.

May 9, 2023
Researchers Capture Elusive Missing Step in Photosynthesis

After decades of effort, scientists have finally glimpsed a key step in the process by which nature creates the oxygen we breathe.

Researchers from Berkeley Lab – led by senior scientists Junko Yano and Vittal Yachandra, and staff scientist Jan Kern in the Molecular Biophysics and Integrated Bioimaging (MBIB) Division – SLAC National Accelerator Laboratory, and collaborators other institutions, have finally succeeded in laying bare a key secret of photosynthesis. Using SLAC’s Linac Coherent Light Source (LCLS) and the SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan, they captured in atomic detail what transpires in the final moments leading up to the release of oxygen.

In photosystem II, the water-splitting center cycles through four stable states, S0-S3. On a baseball field, S0 would be the start of the game when a batter on home base is ready to hit. S1-S3 would be players waiting on first, second, and third. The center gets bumped up to the next state every time it absorbs a photon of sunlight, just like how a player on the field advances one base every time a batter connects with a ball. When the fourth ball is hit, the player slides into home, scoring a run or, in the case of Photosystem II, releasing the oxygen we breathe. (Credit: Greg Stewart/SLAC National Accelerator Laboratory)

During photosynthesis, a protein complex called photosystem II found in plants, algae, and cyanobacteria harvests sunlight and uses it to split water, producing the oxygen we breathe. Photosystem II’s oxygen-evolving center – a cluster of four manganese atoms and one calcium atom connected by oxygen atoms – facilitates a series of challenging chemical reactions that accomplish this feat. When exposed to sunlight, the center cycles through four stable oxidation states, known as S0 through S3.

The researchers examined this center by exciting tiny samples of photosynthetic molecules from cyanobacteria with optical light. They then probed the molecules with ultrafast X-ray pulses from LCLS and SACLA, using a bespoke conveyor belt-inspired instrument designed Isabel Bogacz, a graduate student research assistant, and Philipp Simon, a postdoctoral researcher, in the Yano/Yachandra/Kern group.

Using this technique, the scientists for the first time imaged the transient S4 state, where two atoms of oxygen bond together and an oxygen molecule is released. The data, reported in the journal Nature, showed that there are additional steps in this reaction that had never been seen before.

After gathering all the data – taken over six years – the team had to analyze it and piece together structural maps of the molecules as they change during the reaction. This work was made possible by special software for data merging developed by senior scientist Nicholas Sauter and research scientist Aaron Brewster, and by programs for structure determination developed by Paul Adams, Associate Laboratory Director for Biosciences. The data analysis was performed by project scientist Asmit Bhowmick, Rana Hussein of Humboldt University, Bogacz, and Simon.

Additional MBIB researchers who contributed to this work include: Ruchira Chatterjee, Margaret Doyle, Medhanjali Dasgupta, James Holton, Corey Kaminsky, Stephen Keable, In-Sik Kim, Hiroki Makita, Nigel Moriarty, Isabela Nangca, Daniel Paley, and Miao Zhang.

Read more in the Berkeley Lab News Center.

May 5, 2023
Machine Learning Helps Link Chemical Exposure and Obesity

Obesity is a major health concern and chemical exposure is considered to contribute to this disease, along with genetic and lifestyle factors. However, real-world chemical exposure is complex and combinations of chemicals and their resulting interactions have not been studied fully.

Some chemicals found in plastic bottles are hormone disruptors like the ones investigated in this study. (Credit: Mali Maeder/pexels.com)

Scientists at Berkeley Lab and their collaborators developed a machine learning technique to discover obesity-related mixed chemical exposure patterns associated with environmental health risk in the general U.S. population. Using this technique, the researchers assessed the relationships between the specific chemical mixture patterns and obesity indicators, such as body mass index and waist circumference. They used the National Health and Nutrition Examination Survey 2005–2012 data available from the Centers for Disease Control.

Hang Chang, a research scientist in the Biological and Systems Engineering (BSE) Division, co-led the team that found and demonstrated that mixed exposure patterns exceed the environmental risk of exposure to individual chemicals. “We studied these exposure patterns from organic chemicals that could disrupt hormones previously thought to be involved in obesity and found evidence that they could be associated with the disease. At the same time, we looked at carcinogens and didn’t find any correlation between their presence and obesity.”

The team also conducted a comprehensive evaluation of their algorithm by comparing it to existing models. “We found that our technique provides consistent and robust discoveries compared with classical models. Compared to those models, our method is better at identifying patterns of mixed exposures and improving the identification and understanding of these mixed exposure patterns on health,” said Chang.

“Our work emphasizes the importance of identifying mixed exposure patterns and adds more evidence to the association between environmental chemical exposures and obesity,” Chang said. “This model could open a new avenue for assessing health effects of environmental mixture contaminants.”

Other Berkeley Lab authors include: Kuldeep Chawla from the Information Technology Division and Bo Hang, Jian-Hua Mao, and Antoine M. Snijders from the BSE Division.

At Berkeley Lab, this work was supported by the National Institutes of Health.

May 1, 2023
The JGI Fuels Discovery in Sphagnum Sex Chromosomes

The February cover of Nature Plants highlights the role sphagnum sex chromosomes play in carbon capture. [Cover design: Erin Dewalt; Image: Blanka Aguero, featuring S. divinum (red) and S. angustifolium (green)]
Boggy peatlands, which hold much of the Earth’s carbon as well as material that can be converted to energy, are made up heavily of sphagnum mosses. New research identifies sex chromosomes in the plant and illuminates the significant role sex plays in how the moss grows, stores carbon and responds to stress.

Despite constituting less than 5% of land on Earth, peatlands store approximately one-third of the world’s soil carbon. The process to harvest energy-generating peat from these boggy wetlands produces an estimated 5% of annual greenhouse gas emissions. Understanding how sphagnum, a primary component of peatlands, processes carbon can help maximize peatlands’ potential as carbon sinks and minimize their role as carbon sources. Learn more on the JGI’s website.

April 7, 2023
How Technoeconomic Analyses Pave the Way to a Low-Carbon Future

This summary was adapted from an article written by Christina Nunez

Levels of planet-warming carbon dioxide in the air continue to rise. Cutting emissions by moving away from fossil fuels is a priority – but so is removing carbon that’s already been emitted. Of the many emerging technologies on the table, which ones will be most effective, and where? What about costs? What kinds of investments will have the most impact?

Scientists at the Department of Energy’s (DOE’s) Lawrence Berkeley National Laboratory (Berkeley Lab) are answering these kinds of questions with technoeconomic analysis, a data-driven way to predict the best routes to decarbonization.

“Berkeley Lab is building many clean energy technologies that could have an enormous impact on our path to a low carbon future. Technoeconomic analysis helps us to focus our research on those technologies that are most likely to be developed into successful and affordable products,” said Berkeley Lab Director Mike Witherell.

Technoeconomic analysis uses computer models to evaluate the cost implications and potential environmental impacts of emerging technologies. These models can build on initial research results for a technology and calculate the costs of scaling it up. This type of predictive analysis can be used to support decision-making by researchers, industry stakeholders, regulators, and policy-makers.

A combination of robust computing power and more sophisticated techniques have made technoeconomic analysis an increasingly powerful approach. Accordingly, Berkeley Lab’s team, centered in the Lab’s Energy Technologies Area with staff across the Earth & Environmental Sciences and Biosciences Areas, has expanded to include 20 scientists from a broad range of disciplines who work in partnership with teams across Berkeley Lab and with other institutions. The research often requires a blend of engineering design, process design and simulation, cash flow analysis, life-cycle assessment, and geospatial analysis.

“When technologies are so nascent and they are being commercialized rapidly, we are getting data from all directions,” said Corinne Scown, a Biosciences Area staff scientist and Vice President of the Life-Cycle, Economics and Agronomy Division (LEAD) at the Joint BioEnergy Institute (JBEI) and “So we have to get a handle on what the major drivers are for costs, energy balances, and emissions really quickly. That requires the kind of technological expertise and abilities that we’ve been building.”

Public-private partnerships are also an important way to strengthen technoeconomic analysis and help move technologies forward. “It works best if you’re able to partner with companies and make sure that you are incorporating some of their lessons learned back into the modeling,” Scown said.

Berkeley Lab’s Technoeconomic Analysis Team provides analytical insight into ways to balance economic realities with sustainability goals. (Credit: Thor Swift/Berkeley Lab)

TEA and the Biosciences Area

Biosciences Area researchers apply technoeconomic analysis to a variety of research topics, however, JBEI has an entire division, led by Scown, devoted to the discipline. The LEAD division partners with all of JBEI’s divisions to determine which research approaches might lead to technologies that can be competitive in industry.

Technoeconomic analysis helps in assembling a road map that spans the near- and long-term opportunities. The results can build a strong case for moving ahead with the “low hanging fruit,” Scown says, of solutions like biomass for carbon removal that are ready to deploy today. On the other end of the spectrum, technoeconomic analysis can play a central role in charting the path forward for early-stage technologies like those for direct air capture and hydrogen.

In the case of biofuels, a technoeconomic analysis could tell you the minimum price a particular biofuel would need to deliver a solid return on investment. Or it could predict how the cost and emissions impact would change at an ethanol biorefinery if the facility were also to make biogas from manure and food waste. The carbon intensity of bio-based products and fuels is the most critical metric for securing tax incentives, but requires careful life-cycle assessment and carbon accounting of supply chains and processes that can be highly spatially and temporally heterogeneous.

An infinitely recyclable plastic called poly(diketoenamine), or PDK was invented at Berkeley Lab’s Molecular Foundry a few years ago. Now researchers including Baishakhi Bose, a postdoctoral scholar at JBEI and the Biosciences Area, are conducting analyses to zero in on the most cost-effective versions of the material, as well as where the material might work best (mattresses and automotive parts are two candidates).

“With technoeconomic analysis, we can generate scenarios that can help us determine whether PDK compounds being explored in the lab would be cost-competitive with plastic compounds currently in the market,” Bose said. “The technoeconomic analysis studies are also helping us understand which stages of the PDK production process need improvement.”

Learn more about TEA research at the Berkeley Lab News Center

April 6, 2023
Gemini Beamline Banks First Protein Structure

First Gemini structure deposited in the PDB.

A protein structure obtained at Beamline 2.0.1 (“Gemini”) at the Advanced Light Source (ALS) has recently been published in the literature and deposited into the Protein Data Bank—two significant firsts for this beamline. The structure helped provide new insights into the molecular mechanisms involved in triggering certain inflammatory diseases. This milestone, which utilized Gemini’s capacity to target crystals smaller than 20 microns, was almost a decade in the making. Simon Morton, now a semi-retired staff scientist at ALS, and Corie Ralston, facility director at the Molecular Foundry and a staff scientist in the Molecular Biophysics and Integrated Bioimaging Division (MBIB), helped bring the microfocus beamline to the Berkeley Center for Structural Biology (BCSB) in 2014. Beamline operations are now led by Marc Allaire, a biophysicist staff scientist in MBIB and head of the BCSB.

Read More in the ALS News Feature.

April 3, 2023
Anthony Rozales, Beamline Runner

For scientific engineering associate Anthony Rozales, the workday begins before the sun rises. His shift overseeing the protein crystallography beamlines at the Advanced Light Source (ALS), a user facility at Berkeley Lab, is from 5 AM to 1 PM. It’s critical for many of the ALS users to run their experiments around the clock, so the team divides the day into three shifts.

Hear Rozales pronounce his name.

While some people might find Rozales’s early morning shift grueling, for him it’s ideal. His drive home takes less than half the time than it would during normal commuting hours, and he’s left with an open afternoon to do what he loves most. Years ago, Rozales began running as a hobby after he ran in a race with a few friends. So most days of the week, after his shift ends and he makes it home, Rozales usually turns right around and leaves again, this time on foot.

Rozales on a run in the Berkeley Hills. (Courtesy of A. Rozales)

“There are so many stresses that we deal with at work and with family,” Rozales said. “When I’m running, I really can’t think of anything except my breathing. It becomes meditative.”

The Power of Light

A member of the Berkeley Center for Structural Biology (BCSB) team, Rozales works with scientists from around the world to provide technical support for their experiments, which are designed to help them better understand the molecular structure of proteins. Proteins are known as macromolecules because, in the grand scheme of things, they’re much larger and more complex than smaller molecules, like hormones or water.

Through understanding the arrangement of atoms in a sample, protein crystallography provides scientists insight into its function and how it interacts with other molecules. This information is critically important to solve a vast array of challenges that range from human health to environmental. “It’s exciting to work on these projects,” Rozales said. “I know that this work is helping society, it just feels good.”

In the early days of the COVID-19 pandemic, Rozales and his team worked with academia and pharmaceutical companies to decode the structure of the SARS-CoV-2 virus. Samples were processed around the clock and, over time, the data generated by the BCSB team contributed to structural information about the virus that was critical to drug development and therapy breakthroughs.

At the ALS, bright beams of X-ray energy are directed to about 40 beamlines, six of which are managed by the BCSB team. On these beamlines, protein crystal samples are maintained at cryogenic temperatures. Powerful electromagnetic radiation hits the crystal and, while most of the energy passes through, some intercepts parts of the crystal and scatters in a different way depending on its contents. The resulting spots of X-ray light are collected and analyzed with computer software. Like a human fingerprint, every protein has a unique structure so this scatter map provides scientists with a more precise understanding of its unique molecular makeup.

Rozales helps to both set up experiments and ensure that things run smoothly on the beamline. Once a user is scheduled for beamtime, samples are sent to the ALS where Rozales and his team receive them and then walk the user through how to use the beamline from afar.

In recent years, many aspects of the BCSB beamlines have been automated or configured to operate remotely. So instead of manually arranging the samples for experiments as users had to do in the past, Rozales and the team use a graphical user interface (GUI) that controls the robot that, once programmed, takes care of this step automatically. “But things don’t always work right,” Rozales said. “That’s why I’m here.”

In Motion

Using his hands to make and repair things is something that Rozales has always enjoyed. Growing up in Southern California, and later the Bay Area, he spent time with his father tinkering away in the garage on various projects. This led Rozales to an industrial technology program at San Francisco State University and a role with a semiconductor company immediately following graduation. After a few years working in the hardware industry, Rozales pivoted to his role at Berkeley Lab in 2003.

When not working on the beamline, Rozales still finds plenty of projects around the house to keep his hands busy. One of his sons is approaching legal driving age and recently they’ve been working together to repair a car that will be his to use, pending a passing score on the driving test. And when his hands need a break, Rozales laces up his running shoes.

Rozales wearing two of his running-related medals and a Berkeley Lab Runaround t-shirt. (Credit: Thor Swift/Berkeley Lab)

About 10 years ago, a group of friends decided to run in a local race that involved training beforehand. Although Rozales had never been into running as a hobby before, he decided to sign up. What started for Rozales as an excuse to get active and be social evolved into a full-blown obsession. “I was never a runner before that first race, but afterward, I realized that it was a great way to be active and just kept going,” he said.

The group signed up for their next race together, another 5K which equates to just over 3 miles. They continued signing up for opportunities to run together, graduating to a 10K, a half-marathon, and eventually, a marathon (26.2 miles). “We just kept saying, let’s see if we can go a little further,” Rozales remembered with a laugh.

Work-Life Optimization

Most of the time, Rozales goes out for a run five days a week, with the other two intentionally reserved as recovery days. He’s noticed how much this hobby helps his mental health and ability to focus at home and on the job. “When I’m running, I think about how to optimize everything, from my body movements to my breathing,” Rozales said.

With the ALS in the background, Rozales poses with a few marathon mementos. (Credit: Thor Swift/Berkeley Lab)

And he’s applying that awareness and perspective to his role on the beamline. Receiving samples and executing the users’ experiments is a process that Rozales is continually looking to optimize and improve. One of the steps in his routine for shipping samples back to the user after they’ve been analyzed involves removing reagents that were added for the experiment.

The samples are sent in a dewar, a container about the size of a barbeque’s propane tank, which must be picked up and emptied of its liquid nitrogen before being sent back to the user. Previously, the team used a rope and pulley system to tip the dewar, a time-consuming process that often held up the line on busier days. Rozales realized that instead, he could lift the container on his own in an ergonomically-safe way that was much faster. “It’s not for everyone, but because I’ve become so fit from running, I can do it,” he said. He has since taught his technique to others at several ALS beamlines. “I always find myself thinking about how my job can be done better and faster,” he said.

Rozales and his two sons after a race. (Courtesy of A. Rozales)

At home, running permeates into Rozales’ family life too. His two teenage children recently joined their school track teams and, after finishing his daily post-work run, Rozales stops by their practices to volunteer as an assistant coach. Despite the impressive distances that he’s already covered, Rozales is feeling ready to go for the next level: later this year, he will be running a 100K race in hopes to qualify for a 100-mile ultramarathon race.

Out of the group of friends that he began running with, only one continues to run with Rozales at these longer distances. But he’s made plenty of new friends along the way. “It feels so healthy,” Rozales said. “I’m going to keep doing it until I can’t.” ⬢

Written by Ashleigh Papp, a communications specialist for Berkeley Lab’s Biosciences Area.

Read other profiles in the Behind the Breakthroughs series.

March 22, 2023
A Biofuel Breakthrough, Courtesy of Fungi

Credit: Bianca Susara/Berkeley Lab

It’s a tough job, but someone’s got to do it. In this case, the “job” is the breakdown of lignin, the structural molecule that gives plants strength and rigidity. One of the most abundant terrestrial polymers (large molecules made of repeating subunits called monomers) on Earth, lignin surrounds valuable plant fibers and other molecules that could be converted into biofuels and other commodity chemicals – if we could only get past that rigid plant cell wall.

Fortunately, the rather laborious process already occurs in the guts of large herbivores through the actions of anaerobic microbes that cows, goats, and sheep rely on to release the nutrients trapped behind the biopolymer. In a paper published in the journal Nature Microbiology, UC Santa Barbara chemical engineering and biological engineering professor Michelle O’Malley and collaborators prove that a group of anaerobic fungi – Neocallimastigomycetes – are up to the task. O’Malley is part of the Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) where she serves as the Deputy Director for Microbial and Enzyme Discovery. The mission of this group is to explore targeted ecosystems and discover novel microbes and enzymes that break down plant cell walls, and in particular the lignin within them.

Read more on the Berkeley Lab News Center.

March 22, 2023
DOE Renews Funding for Joint BioEnergy Institute

The Department of Energy’s Joint BioEnergy Institute (JBEI), led by Lawrence Berkeley National Laboratory (Berkeley Lab), was selected as one of four Department of Energy (DOE) Bioenergy Research Centers (BRC) to be awarded a combined total of $590 million to support innovative research on biofuels and bioproducts.

These new BRC awards, announced today by the U.S. Department of Energy, will kick off JBEI’s fourth five-year funding phase. “To meet our future energy needs, we will need versatile renewables like bioenergy as a low-carbon fuel for some parts of our transportation sector,” said Secretary of Energy Jennifer M. Granholm. “Continuing to fund the important scientific work conducted at our Bioenergy Research Centers is critical to ensuring these sustainable resources can be an efficient and affordable part of our clean energy future.”

Each center will initially receive $27.5 million for fiscal year 2023 with the possibility of additional funding for the next four years of the program cycle. JBEI and the other centers conduct basic science research to create biofuels and bioproducts from non-food plants. Each BRC has their own distinct research mission and programmatic goals, however, this new funding also specifically earmarks funds for all four BRCs to collaborate together on shared strategic goals.

“We are very excited that the Department of Energy has awarded us with another five years of funding to continue our path-breaking research,” said Jay Keasling, JBEI’s chief executive officer. “This work will enable the cost-effective production of carbon neutral biofuels and carbon negative bioproducts from lignocellulosic biomass. Usage of these fuels and products will reduce the nation’s dependence on fossil fuels while significantly reducing the amount of carbon added to the atmosphere and contamination of the environment.”

Read more on the Berkeley Lab News Center

March 19, 2023
Dub-seq Used to Screen Phage Proteins for Antibiotic Properties

As conventional antibiotics continue to lose effectiveness against evolving pathogens, scientists are keen to employ the bacteria-killing techniques perfected by bacteriophages (phages), the viruses that infect bacteria. One major challenge is the difficulty of studying individual phage proteins and determining precisely how the virus wields these tools to kill their host bacteria.

A rendering of bacteriophage viruses attacking a bacteria (Credit: nobeastsofierce/Adobe Stock)

Even some of the smallest known phages code for single-gene lysis proteins (Sgls), also known as protein antibiotics, that inhibit key components of bacterial cell wall production, consistently killing the cell. A team of researchers from Berkeley Lab, UC Berkeley, and Texas A&M University worked together on a high-throughput genetic screen to identify which part of the bacteria the phage Sgls were targeting.

They used Dual-Barcoded Shotgun Expression Library Sequencing (Dub-seq), a technology previously invented by Environmental Genomics and Systems Biology (EGSB) Division researchers Adam Arkin, Adam Deutschbauer, and Vivek Mutalik. This work showed that the Sgls target pathways for cell wall building that arose very early in bacteria’s evolutionary history and are highly conserved.

Read more in the Berkeley Lab News Center.

March 14, 2023
ABPDU Hosts 2023 Industry Listening Day
The Advanced Biofuels and Bioproducts Process Development Unit (ABPDU) hosted its 2023 Industry Listening Day on March 7, 2023. Representatives from 41 entities, including 28 companies, participated in the event.

The event allowed ABPDU to provide updates on action items from its last Industry Listening Day in 2019. These action items included generating equipment video SOPs to train affiliates, developing case studies, deploying new gas fermentation and analytical capabilities, and improving the project onboarding process.

The majority of the event was dedicated to gathering feedback from attendees on equipment needs and collaboration processes.

“We are very grateful for the time our collaborators take out of their schedules to provide very essential feedback to us,” said Deepti Tanjore, Director of ABPDU. “We are now very excited to have the action items needed to make our capabilities and expertise more accessible to our collaborators.”

Presentations from the event can be found below and on ABPDU’s resources page.
March 13, 2023