Houston scientists develop breakthrough AI-driven process to design, decode genetic circuits

biotech breakthrough

Rice University scientists Kshitij Rai, Caleb Bashor and Ronan O’Connell have developed CLASSIC, a new AI-driven process that can generate and test millions of DNA designs at the same. Photo by Jeff Fitlow. Courtesy Rice University.

Researchers at Rice University have developed an innovative process that uses artificial intelligence to better understand complex genetic circuits.

A study, published in the journal Nature, shows how the new technique, known as “Combining Long- and Short-range Sequencing to Investigate Genetic Complexity,” or CLASSIC, can generate and test millions of DNA designs at the same time, which, according to Rice.

The work was led by Rice’s Caleb Bashor, deputy director for the Rice Synthetic Biology Institute and member of the Ken Kennedy Institute. Bashor has been working with Kshitij Rai and Ronan O’Connell, co-first authors on the study, on the CLASSIC for over four years, according to a news release.

“Our work is the first demonstration that you can use AI for designing these circuits,” Bashor said in the release.

Genetic circuits program cells to perform specific functions. Finding the circuit that matches a desired function or performance "can be like looking for a needle in a haystack," Bashor explained. This work looked to find a solution to this long-standing challenge in synthetic biology.

First, the team developed a library of proof-of-concept genetic circuits. It then pooled the circuits and inserted them into human cells. Next, they used long-read and short-read DNA sequencing to create "a master map" that linked each circuit to how it performed.

The data was then used to train AI and machine learning models to analyze circuits and make accurate predictions for how untested circuits might perform.

“We end up with measurements for a lot of the possible designs but not all of them, and that is where building the (machine learning) model comes in,” O’Connell explained in the release. “We use the data to train a model that can understand this landscape and predict things we were not able to generate data on.”

Ultimately, the researchers believe the circuit characterization and AI-driven understanding can speed up synthetic biology, lead to faster development of biotechnology and potentially support more cell-based therapy breakthroughs by shedding new light on how gene circuits behave, according to Rice.

“We think AI/ML-driven design is the future of synthetic biology,” Bashor added in the release. “As we collect more data using CLASSIC, we can train more complex models to make predictions for how to design even more sophisticated and useful cellular biotechnology.”

The team at Rice also worked with Pankaj Mehta’s group in the department of physics at Boston University and Todd Treangen’s group in Rice’s computer science department. Research was supported by the National Institutes of Health, Office of Naval Research, the Robert J. Kleberg Jr. and Helen C. Kleberg Foundation, the American Heart Association, National Library of Medicine, the National Science Foundation, Rice’s Ken Kennedy Institute and the Rice Institute of Synthetic Biology.

James Collins, a biomedical engineer at MIT who helped establish synthetic biology as a field, added that CLASSIC is a new, defining milestone.

“Twenty-five years ago, those early circuits showed that we could program living cells, but they were built one at a time, each requiring months of tuning,” said Collins, who was one of the inventors of the toggle switch. “Bashor and colleagues have now delivered a transformative leap: CLASSIC brings high-throughput engineering to gene circuit design, allowing exploration of combinatorial spaces that were previously out of reach. Their platform doesn’t just accelerate the design-build-test-learn cycle; it redefines its scale, marking a new era of data-driven synthetic biology.”

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Xiaoyu Yang, a graduate student at Rice, is the lead author on a study published in the journal Science on smart cell design. Photo by Jeff Fitlow/ Courtesy Rice University

Rice research breakthrough paves the way for advanced disease therapies

study up

Bioengineers at Rice University have developed a “new construction kit” for building custom sense-and-respond circuits in human cells, representing a major breakthrough in the field of synthetic biology, which could "revolutionize" autoimmune disease and cancer therapeutics.

In a study published in the journal Science, the team focused on phosphorylation, a cellular process in the body in which a phosphate group is added to a protein, signaling a response. In multicellular organisms, phosphorylation-based signaling can involve a multistage, or a cascading-like effect. Rice’s team set out to show that each cycle in a cascade can be treated as an elementary unit, meaning that they can be reassembled in new configurations to form entirely novel pathways linking cellular inputs and outputs.

Previous research on using phosphorylation-based signaling for therapeutic purposes has focused on re-engineering pathways.

“This opens up the signaling circuit design space dramatically,” Caleb Bashor, assistant professor of bioengineering and biosciences and corresponding author on the study, said in a news release. “It turns out, phosphorylation cycles are not just interconnected but interconnectable … Our design strategy enabled us to engineer synthetic phosphorylation circuits that are not only highly tunable but that can also function in parallel with cells’ own processes without impacting their viability or growth rate.”

Bashor is the deputy director for the Rice Synthetic Biology Institute, which launched last year.

The Rice lab's sense-and-respond cellular circuit design is also innovative because phosphorylation occurs rapidly. Thus, the new circuits could potentially be programmed to respond to physiological events in minutes, compared to other methods, which take hours to activate.

Rice’s team successfully tested the circuits for sensitivity and their ability to respond to external signals, such as inflammatory issues. The researchers then used the framework to engineer a cellular circuit that can detect certain factors, control autoimmune flare-ups and reduce immunotherapy-associated toxicity.

“This work brings us a whole lot closer to being able to build ‘smart cells’ that can detect signs of disease and immediately release customizable treatments in response,” Xiaoyu Yang, a graduate student in the Systems, Synthetic and Physical Biology Ph.D. program at Rice who is the lead author on the study, said in a news release.

Ajo-Franklin, a professor of biosciences, bioengineering, chemical and biomolecular engineering and a Cancer Prevention and Research Institute of Texas Scholar, added “the Bashor lab’s work vaults us forward to a new frontier — controlling mammalian cells’ immediate response to change.”

Cemvita aims to capitalize on Brazil’s regulatory framework around biodiesel blending and Sustainable Aviation Fuel.Photo courtesy of Cemvita

Pioneering Houston biotech startup expands to Brazil for next phase

On the Move

Houston biotech company Cemvita has expanded into Brazil. The company officially established a new subsidiary in the country under the same name.

According to an announcement made earlier this month, the expansion aims to capitalize on Brazil’s progressive regulatory framework, including Brazil’s Fuel of the Future Law, which was enacted in 2024. The company said the expansion also aims to coincide with the 2025 COP30, the UN’s climate change conference, which will be hosted in Brazil in November.

Cemvita utilizes synthetic biology to transform carbon emissions into valuable bio-based chemicals.

“For decades Brazil has pioneered the bioeconomy, and now the time has come to create the future of the circular bioeconomy,” Moji Karimi, CEO of Cemvita, said in a news release. “Our vision is to combine the innovation Cemvita is known for with Brazil’s expertise and resources to create an ecosystem where waste becomes opportunity and sustainability drives growth. By joining forces with Brazilian partners, Cemvita aims to build on Brazil’s storied history in the bioeconomy while laying the groundwork for a circular and sustainable future.”

The Fuel of the Future Law mandates an increase in the biodiesel content of diesel fuel, starting from 15 percent in March and increasing to 20 percent by 2030. It also requires the adoption of Sustainable Aviation Fuel (SAF) and for domestic flights to reduce greenhouse gas emissions by 1 percent starting in 2027, growing to 10 percent reduction by 2037.

Cemvita agreed to a 20-year contract that specified it would supply up to 50 million gallons of SAF annually to United Airlines in 2023.

"This is all made possible by our innovative technology, which transforms carbon waste into value,” Marcio Da Silva, VP of Innovation, said in a news release. “Unlike traditional methods, it requires neither a large land footprint nor clean freshwater, ensuring minimal environmental impact. At the same time, it produces high-value green chemicals—such as sustainable oils and biofuels—without competing with the critical resources needed for food production."

In 2024, Cemvita became capable of generating 500 barrels per day of sustainable oil from carbon waste at its first commercial plant. As a result, Cemvita quadrupled output at its Houston plant. The company had originally planned to reach this milestone in 2029.

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This story originally appeared on our sister site, EnergyCapitalHTX.

Thanks to technology advancements, Cemvita is now capable of generating 500 barrels per day of sustainable oil from carbon waste at its first commercial plant. Photo via cemvita.com

Houston company's sustainable oil product reaches milestone production capacity 5 years early

overachieving

Houston-based biotech company Cemvita has achieved a key production goal five years ahead of schedule.

Thanks to technology advancements, Cemvita is now capable of generating 500 barrels per day of sustainable oil from carbon waste at its first commercial plant. As a result, Cemvita has quadrupled output at the Houston plant. The company had planned to reach this milestone in 2029.

Cemvita, founded in 2017, says this achievement paves the way for increased production capacity, improved operational efficiency, and an elevated advantage in the sustainable oil market.

“What’s so amazing about synthetic biology is that humans are just scratching the surface of what’s possible,” says Moji Karimi, co-founder and CEO of Cemvita. “Our focus on the first principles has allowed us to design and create new biotech more cheaply and faster than ever before.”

The production achievement follows Cemvita’s recent breakthrough in development of a solvent-free extraction bioprocess.

In 2023, United Airlines agreed to buy up to one billion gallons of sustainable aviation fuel from Cemvita’s first full-scale plant over the course of 20 years.

Cemvita’s investors include the UAV Sustainable Flight Fund, an investment arm of Chicago-based United; Oxy Low Carbon Ventures, an investment arm of Houston-based energy company Occidental Petroleum; and Japanese equipment and machinery manufacturer Mitsubishi Heavy Industries.

The new collaborative hub will foster research into cell therapies, artificial intelligence, nanotechnologies, and more. Photo via tmc.edu

Houston health care leaders announce new hub for cancer-fighting bioengineering

team work

Two Houston organizations recently announced a new hub that will focus on developing cell therapies, nanotechnologies, cancer vaccines, artificial intelligence, and molecular imaging.

Rice University and The University of Texas MD Anderson Cancer Center have teamed up to “drive industry growth and advance life-saving technologies” through the newly established Cancer Bioengineering Collaborative, according to a news release announcing the initiative.

The collaboration between the two institutions includes fundamental and translational cancer research, developing new technologies for cancer detection and therapy, and securing external funding in support of further research and training.

Leading the hub will be Rice researcher and Cancer Prevention and Research Institute of Texas (CPRIT) scholar Gang Bao and MD Anderson’s Dr. Jeffrey Molldrem.

“There is tremendous potential in bringing together experts in engineering and cancer as part of this focused, collaborative framework that is truly unique, not only owing to the complementary nature of the respective strengths but also because this is the first formal joint research initiative of its kind between the two institutions,” says Bao, department chair and Foyt Family Professor of Bioengineering, professor of chemistry, materials science and nanoengineering and mechanical engineering, in the release.

The joint effort will also host monthly seminars focused on cancer bioengineering, annual retreats to highlight research and international leaders in cancer and bioengineering, and also a seed grant program to fund research projects in the early stages of development.

“From fundamental discoveries in cancer science, tumor immunology and patient care to innovative engineering advances in drug delivery systems, nanostructures and synthetic biology, there is great potential for enabling cross-disciplinary collaboration to develop new technologies and approaches for detecting, monitoring and treating cancer,” Molldrem, chair of Hematopoietic Biology & Malignancy at MD Anderson, says in the release. “Our goal is to bridge the gap between bioengineering and cancer research to create transformative solutions that significantly improve patient outcomes.”

Dr. Jeff Molldrem (left) and Gang Bao will lead the new collaborative hub. Photo via MD Anderson

The new Rice Synthetic Biology Institute is part of an $82 million investment the university put toward synthetic biology, neuroengineering, and physical biology in 2018. Photo via Rice.edu

Houston university launches new institute for synthetic biology

new to Hou

Rice University announced this month that it has officially launched the new Rice Synthetic Biology Institute.

The institute aims to strengthen the synthetic biology community across disciplines at the university, according to an announcement from Rice. It is part of an $82 million investment the university put toward synthetic biology, neuroengineering, and physical biology in 2018.

RSBI will be led by Caroline Ajo-Franklin, professor of biosciences, bioengineering, and chemical and biomolecular engineering, with support from a faculty steering committee.

Caroline Ajo-Franklin, professor of biosciences, bioengineering, and chemical and biomolecular engineering, will lead the new institute. Photo via Rice.edu

“At Rice, we have such deep expertise in synthetic biology,” Ajo-Franklin said in the announcement. “Connecting that deep expertise through this institute will lead to better science and more innovation.”

Synthetic biology is a discipline in which "researchers design living systems with new properties to address societal needs," according to Rice, with applications in medicine, manufacturing and environmental sustainability.

The university says that there are currently 18 faculty and more than 100 students and postdoctoral scholars at Rice working in this field within the schools of engineering and natural sciences.

The institute will initially focus on four research themes:

  1. Controlling the biological synthesis and patterning of proteins and cells into living materials that self-replicate and self-repair across a range of length scales
  2. Understanding cells as natural sensors and repurposing them into living therapeutics to detect and treat diseases, maintain health and prevent infections
  3. Developing living electronics to convert biochemical information into information-dense electronic signals in real-time at the cell-material interface
  4. Supporting cross-cutting scholarship aimed at accelerating the Design-Build-Test-Learn cycle and understanding the ethical, legal and social implications of translating these technologies into the public domain.

“Rice University is an amazing place to learn, teach, research and innovate,” Ramamoorthy Ramesh, executive vice president for research, added. “The Rice Synthetic Biology Institute will ensure that our researchers are recognized on the international stage for the life-changing work they are doing in Houston and around the world.”

Last year, Rice also launched the new Center for Human Performance with Houston Methodist inside Rice’s Tudor Fieldhouse. The interdisciplinary space aims to advance the study of exercise physiology, injury prevention, and rehabilitation while serving Rice student-athletes.

The university also unveiled another massive, collaborative space this academic year: The 250,000-square-foot Ralph S. O’Connor Building for Engineering and Science. Click here to read more about the state-of-the-art building.

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Houston lab explores how AI bots can help the elderly

AI for aging

The University of Houston’s Empathetic Lifespan AI & Robotics for Aging (ELARA) Lab is currently conducting research into how AI bots may be able to help the elderly live more social and independent lives through several ongoing initiatives.

The lab officially launched last month as part of the Gerald D. Hines College of Architecture & Design under the leadership of Assistant Professor Chorong Park. Part of the lab’s mission is tackling ongoing problems with aging, such as dealing with disabilities and social isolation. Researchers’ current work is focused on designing a new AI companion bot specifically tailored to the needs of older people.

“We need to take all the needs of older adults seriously,” Park said in a news release. “They won't use the robot if they don't feel at ease or if they feel they are being constantly watched.”

The field testing of new AI bots in this population hopes to overcome several traditional obstacles in technology use among the elderly. A study by Park shows that many older people have a fear of overt surveillance when using advanced AI. There is also ageism to consider. Most new technologies are designed with younger and employed buyers in mind, not retirees who may need help remembering daily tasks or accessing important information.

“The more older adults are excluded from technology development, the worse those technology gaps will become,” Park said. “AI and the majority of technologies are created for younger people, so my research method integrates older adults directly into the design process.”

ELARA recently collaborated with the Mamie George Community Center in Richmond, Texas, to track seniors’ response to desktop AI bots like Emo and Cupboo. Researchers also had participants use air-dry modeling clay to create their ideal robotic companion.

While the eventual AI bot may be able to help the elderly feel less isolated and more supported, there are concerns to consider. A study published in the Asian Journal of Psychology charted the development of delusional thinking in a 72-year-old woman who became convinced the empathic-response bot was in love with her. The rise of “AI psychosis” has the potential to exacerbate mental health problems, particularly in socially isolated people, which a quarter of Americans over the age of 65 are.

ELARA’s research is focused on creating “pet-like” AI models with enhanced trust cues. If it can overcome the dangers of socially isolated people relying on AI for companionship, it could be a big step forward for independent aging.

SpaceX IPO set to be biggest ever and could make Elon Musk a trillionaire

IPO News

SpaceX says it plans to raise up to $75 billion when it goes public this month, setting the stage for the largest-ever stock market debut and putting Elon Musk on course to becoming the world's first trillionaire.

The company, formally known as Space Exploration Technologies Corp., said Wednesday it will sell 555.6 million shares at $135 a piece in an initial public offering. The estimated proceeds would easily top the $26 billion raised by oil giant Saudi Aramco in 2019. The offering would also give SpaceX a market value of $1.77 trillion. Only six companies in the S&P 500 are currently worth more, with Nvidia tops at $5.2 trillion.

Besides the size of the offering and the expected proceeds, SpaceX's amended prospectus updates details about how much control of the company Musk will have. As SpaceX's CEO, chief technical officer and chairman, Musk's voting power will come primarily through his ownership of 5.22 billion Class B shares, which give the holder 10 votes for every share held. According to the filing, Musk would have 82.4% of the voting power in the company.

Forbes currently values Musk's net worth at $826 billion and his stake in SpaceX at $542 billion. The estimated value of his SpaceX holdings was based on an overall value for the company of $1.25 trillion. Based on those numbers, a $1.77 trillion valuation for SpaceX would boost Musk's net worth by $223 billion, making him a trillionaire. However, much of Musk's worth is in stock that he has yet to cash in.

Even as it makes a bid for a blockbuster market debut, SpaceX is currently losing billions of dollars a year. The filing shows that the company lost $2.6 billion from operations last year on $18.7 billion in revenue, and the losses kept piling up at the start of this year, too.

Fantastical plans

Time will tell how SpaceX fares on the market. Musk's plans for the company are as fantastical as the money he hopes raise in the sale.

Colorful, even frightening in parts, the IPO document strikes a contrast with the typically dry, technical prose in IPO documents, detailing plans to use proceeds from the sale to help put men on the moon again and perhaps even Mars. In one section, it talks of a need to build "a permanent human colony" on the red planet with "at least one million inhabitants" as existential threats loom that could consign man to "the same fate as the dinosaurs."

Musk has almost equally ambitious plans for his other publicly traded company, Tesla. His goal is to transform the maker of electric vehicles into a producer of robotaxis and humanoid robots. Dan Ives of Wedbush Securities wrote in a research note that he expects Tesla and SpaceX to merge next year.

AI plays a key role

Key to the success of both companies — and any merged entity — is artificial intelligence. In its IPO filing, SpaceX says it sees potential revenue from AI of up to $26.5 trillion. But that depends on another lofty Musk ambition — putting data centers in space, which is not technologically possible at the moment.

Transforming his space company into a primarily AI-focused company will be a challenge for Musk, who started xAI in 2023 with 11 other co-founders who have all since left. Some were recruited away by rivals.

Its main AI product, the chatbot Grok, is "less impressive than anything that we see from any other major player in the space, whether that's OpenAI, or Anthropic, or (Google's) Gemini," said IDC analyst Arnal Dayaratna.

Dayaratna said that doesn't mean SpaceX doesn't have potential as a major AI player, thanks in part to its computing partnership with Anthropic and Musk's recent deal that gave SpaceX the rights to buy AI coding tool Cursor for $60 billion later this year. Folding in Cursor's capabilities would give SpaceX access to the coveted business customers now using Anthropic's Claude or OpenAI's ChatGPT.

SpaceX plans to use the net proceeds from the IPO to fund the expansion of infrastructure for its AI and rocket businesses, and to beef up the constellation of satellites that power Starlink Mobile, among other investments.

The company plans to list on the Nasdaq under the symbol "SPCX" and could begin trading as soon as the end of next week.

And SpaceX isn't the only colossal market debut investors are now bracing for. Earlier this week, Anthropic submitted a confidential filing with the U.S. Securities and Exchange Commission to officially start its own IPO clock.

OpenAI has not yet reported filing the initial SEC paperwork, but an IPO from the ChatGPT maker is widely expected.

"This listing represents the first major test for public markets after years of muted IPO activity with SpaceX paving the way for AI giants Anthropic and OpenAI to follow soon after," Ives wrote.

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Associated Press Technology Writer Matt O'Brien contributed.

New UH survey reveals concerns over AI data center growth in Houston

data findings

A new report out of the University of Houston shows that area residents remain wary of the long-term effects of operating data centers.

The recent survey from the University of Houston’s latest SPACE City Panel, conducted by the Center for Public Policy at the Hobby School of Public Affairs, shows that while 85 percent of Houston-area residents use AI, nearly 63 percent oppose the construction of AI data centers within 1 mile of their homes.

Respondents’ concerns centered around data centers’ high energy demand and the area’s power grid reliability. According to the survey, 32 percent of residents who oppose local data center projects would be more likely to support the centers if they relied on renewable energy over fossil fuels.

“Respondents understand that AI can bring economic and educational benefits, but they are also concerned about the physical infrastructure needed to fuel AI, especially data centers,” Soran Mohtadi, post-doctoral fellow at the Hobby School and a researcher on the report, said in a news release. “This physical infrastructure demands more electricity and water, leading to environmental impacts.”

Experts estimate that 6.5 gigawatts of data center capacity will be added to the Texas grid by 2030. And Houston’s data center capacity is predicted to more than double by 2028.

The Electric Reliability Council of Texas also projects electricity demand could reach 218 gigawatts by 2031, which would be more than double the record peak set in August 2023. Data centers are expected to account for 86 gigawatts of that new demand.

Survey respondents also said they are concerned about the state's future water supply, given the large amounts of water that data centers need to stay cool.

In terms of who’s responsible for that issue, 57.6 percent of respondents said they put the onus on Texas lawmakers, while 31.5 percent say tech companies should be responsible.

Additionally, more than 75 percent of respondents believed that data center developers and technology companies—not residents—should bear the cost of infrastructure upgrades to support data centers.

“Every decision legislators make has implications on residents’ everyday lives and local infrastructure now and in the future,” Maria P. Perez Arguelles, lead researcher on the report and research assistant professor at the Hobby School, added in the news release. “This issue is going to become more important in years to come, so this is just the beginning.”

Read the full report here.

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