Rice research team on quest to engineer computing systems from living cells

Rice University

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Rice University biosciences professor Matthew Bennett has received a $1.99 million grant from the National Science Foundation.

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Credit: Photo by Jeff Fitlow/Rice University.

Rice University biosciences professor Matthew Bennett has received a $1.99 million grant from the National Science Foundation to lead research on engineered bacterial consortia that could form the basis of biological computing systems. The four-year project will also involve co-principal investigators Kirstin Matthews, Caroline Ajo-Franklin and Anastasios Kyrillidis from Rice along with Krešimir Josić from the University of Houston. The research team aims to develop platforms that integrate microbial sensing and communication with electronic networks, paving the way for computing systems constructed from living cells instead of traditional silicon-based hardware.

The project highlights the growing potential of synthetic biology, where microbes are examined not just as living organisms but as processors of information. If successful, Bennett’s research could accelerate medical diagnostics, environmental monitoring and the development of next-generation computing applications.

“Microbes are remarkable information processors, and we want to understand how to connect them into networks that behave intelligently,” Bennett said. “By integrating biology with electronics, we hope to create a new class of computing platforms that can adapt, learn and respond to their environments.”

Microorganisms have the ability to sense and adapt to their surroundings naturally, often communicating chemically or electrically to produce collective responses. Bennett’s research team views each cell as a processor that, when linked with others, could function like a parallel computing system. One envisioned application is smart biosensors that can identify chemical signatures, such as disease biomarkers or environmental contaminants, and relay the results electronically.

The project aims to develop microbial consortia capable of integrating chemical and electronic signals to recognize patterns and learn through cellular memory. Continuous culture systems will maintain microbial activity while allowing electronic interfacing to refine responses over time. This approach could enable computing systems to respond to real-world chemical inputs in ways that traditional hardware cannot.

In addition, the project will also explore the ethical, legal and social implications of programmable living computers, including regulatory frameworks and public acceptance. 

“Beyond diagnostics and monitoring, living computers may one day adapt and evolve in ways that surpass the capabilities of traditional machines,” Bennett said.

Bacteria rewire digestive systems to turn plant waste into power

New study shows how bacteria juggle energy needs while digesting complex carbons

Northwestern University

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For years, scientists have marveled at bacteria’s ability to digest the seemingly indigestible, including carbon from lignin, the tough, woody material that gives plants their rigidity.

Now, a new Northwestern University study shows that Pseudomonas putida, a common soil bacterium, completely reorganizes its metabolism to thrive on these complex carbons. By slowing down some metabolic pathways while accelerating others, the bacterium manages to extract energy from lignin without exhausting itself.

The findings could have implications for the biomanufacturing industry, which has long sought to harness Pseudomonas putida to break down lignin and upcycle it into biofuels, plastics and other useful chemicals. The new information could help researchers build efficient and productive microbial factories. 

The study was published on Friday (Aug. 29) in Communications Biology. It marks the first quantitative blueprint of how bacteria coordinate carbon metabolism and energy production during digestion of lignin carbons.

“Lignin is an abundant, renewable and sustainable source of carbon that could potentially provide an alternative to petroleum in the production plastics and valuable chemicals,” said Northwestern’s Ludmilla Aristilde, who led the study. “Certain microbes naturally have an ability to make precursors to valuable chemicals that are lignin-based rather than petroleum-based. But if we want to take advantage of that natural ability to develop new biological platforms, we first need to know how it works. Now, we finally have a roadmap.”

An expert in the dynamics of organics in environmental processes, Aristilde is a professor of civil and environmental engineering at Northwestern’s McCormick School of Engineering and a member of the Center for Synthetic Biology, the International Institute of Nanotechnology and the Paula M. Trienens Institute for Sustainability and Energy.

Notoriously tough to digest

After cellulose, lignin is the second most abundant biopolymer on Earth. When broken down, it produces a mix of chemical compounds, including phenolic acids, which could be used as renewable feedstocks for valuable chemicals. But scientists have struggled to understand how bacteria manage to feed on these complex compounds. 

These complex compounds are made up of a ring of six carbons with chains of carbons attached to the ring. Few organisms can process these compounds efficiently. In other words, it simply takes too much energy to digest.

“Before we eat food, we have to shop for it, cook it and eventually chew it up,” Aristilde explains. “That whole process uses energy but consuming the food also gives us energy. There is a balance between the energy we exert to make the food versus the energy we derive from the food. It’s the same for soil microbes.”

Shifting from a major highway to back roads

To probe how bacteria strike this balance, Aristilde and her team grew Pseudomonas putida on four common, lignin-derived compounds. Then, they used a suite of “multi-omics” tools — including proteomics, metabolomics and advanced carbon-tracing techniques — to map exactly how the bacteria move carbon through their metabolism.

Aristilde likened this metabolic network to a collection of roads in a busy urban area.

“We wanted to see what happens on every street at very high resolution,” she said. “We wanted to know where every ‘stoplight’ and ‘traffic jam’ might occur. That allowed us to determine which pathways are important to balance the energy in a way that is optimal for the cell.”

The team discovered that, when faced with lignin, the bacterium rewires its metabolism into a high-energy mode. It ramps up the level of enzymes for certain metabolic reactions — sometimes by hundreds- to thousands-fold — to reroute digestive pathways, shifting carbon away from the “main highway” to backup metabolic “roads” to avoid bottlenecks. Due to this metabolic remodeling, the bacteria produced six times more ATP — a molecule that provides energy — compared to when it consumes easier-to-digest compounds.

A delicate balance

While these strategies keep Pseudomonas putida balanced and functioning, the researchers also found the system is fragile. When they tried to relieve bottlenecks by overexpressing certain enzymes, the approach backfired, and the bacteria’s metabolism fell out of its careful balance.

“Engineering strategies can often result in negative effects on the metabolism in a completely unexpected way,” Aristilde said. “By speeding up the flow of one pathway, it can introduce an imbalance in energy that is detrimental to the operation of the cell.”

This finding is especially important for biotechnology applications, where engineers often tweak bacteria’s metabolism to produce bio-based fuels and chemicals. Aristilde says it’s important to understand bacteria’s natural energy rules before trying to push them to work harder. By revealing which pathways are speed bumps or energy boosters, the biotech industry can develop smarter strategies for harnessing bacteria to produce sustainable products from plant waste.

“Before this study, we could not explain exactly the coordination of carbon metabolism and energy fluxes important in the rational design of bacterial platforms for lignin carbon processing,” Aristilde said. “We just had to figure it out as we went along. Now that we have an actual roadmap, we know how to navigate the network.”

The study, “Quantitative decoding of coupled carbon and energy metabolism in Pseudomonas putida for lignin carbon utilization,” was supported by the U.S. Department of Energy (award number DE-SC0022181).

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Journal

Communications Biology

DOI

10.1038/s42003-025-08723-3 

Method of Research

Experimental study

Subject of Research

Cells

Article Title

Quantitative decoding of coupled carbon and energy metabolism in Pseudomonas putida for lignin carbon utilization

 

Climate change may contribute to new snakebite hotspots in India

As snake species’ geographic distribution shifts, new regions are at risk of exposure

PLOS

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Russell's viper (Daboia russelii)

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Credit: Dhritiman Mukherjee (CC-BY 4.0, https://creativecommons.org/licenses/by/4.0/)

India records the highest number of snakebite fatalities worldwide, between 46,000-60,000 annually. A study published in PLOS Neglected Tropical Diseases by Imon Abedin at Dibru-Saikhowa Conservation Society, Tinsukia, India and colleagues suggests that climate change-related shifts in the geographic distribution of venomous snakes will increase the risk of snakebites in certain regions.

The Big Four refers to four venomous snake species responsible for the greatest number of medically significant human snakebite cases on the Indian subcontinent. However, how changing geographic distribution of these species due to climate change may affect envenomation risk across India has not been assessed. In order to better understand how climate change might change different regions’ exposure to venomous snakes, researchers analyzed predictive models visualizing current and future geographic distribution of the Big Four species under different climate scenarios. The researchers then analyzed regional socioeconomic and public health data to develop a snakebite risk index for Indian districts and states over the next 50 years.

The researchers found that climate change may shift geographic distribution of the Big Four into the Northern and Northeastern states increasing snakebite risks in India. The study had several limitations, however, and future studies attempting replication are needed. The accuracy of the prediction models is contingent on data quality and snake occurrence is difficult to document in large, rural regions, leading to potential undercounting. Additionally, the compounded effects of land use change, urbanization, and habitat degradation may limit the value of predictive models on snake distribution.

According to the authors, “Climate change is altering snake species' geographic ranges, resulting in expansions, contractions, or shifting ranges. Such changes may increase human-snake interactions across rural and urban areas, presenting new challenges for public health and medical management. Consequentially, to mitigate snakebite risk in affected regions, it is essential to implement strategies that enhance decision-making in healthcare delivery, antivenom research, and production capabilities.”

“This is the first study in India to integrate climate-based species distribution models with socioeconomic vulnerability and healthcare capacity,” the authors noted. “It shows that climate change is not just an environmental crisis but it’s also a looming public health crisis.”

 

In your coverage, please use this URL to provide access to the freely available paper in PLOS Neglected Tropical Diseases: https://plos.io/4oFE251

Citation: Abedin I, Kang H-E, Saikia H, Jung W-K, Kim H-W, Kundu S (2025) Future of snakebite risk in India: Consequence of climate change and the shifting habitats of the big four species in next five decades. PLoS Negl Trop Dis 19(9): e0013464. https://doi.org/10.1371/journal.pntd.0013464

Author countries: India, Republic of Korea

Funding: This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (RS-2021-NR060118). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Journal

PLOS Neglected Tropical Diseases

DOI

10.1371/journal.pntd.0013464 

Method of Research

Computational simulation/modeling

 

Wildfire ‘char’ may help suppress methane

University of Delaware researcher studies how these chars positively impact the environment after devastation brought by fires

University of Delaware

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It's hard to believe that there is anything positive that could come out of wildfires. They have devastated homes, taken lives, erased memories, leveled cities and destroyed our forests and wildlands. But a University of Delaware professor has found that there is something of value to be learned from what’s left behind in the remnants.

The charred debris left in the wake of wildfires, such as those currently burning in Colorado, Canada and Arizona’s Grand Canyon National Park, is known as wildfire char. UD’s Pei Chiu, professor of civil, construction and environmental engineering, studies wildfire chars and the ways they just might prove useful in reducing methane, a powerful gas that traps heat in the atmosphere. Methane emissions come from many different sources, ranging from livestock manure to landfills and wastewater treatment plants.  

This work also informs his research on biochar — man-made chars created from leftover wood chips, rice husks, corn stover and other agricultural biomass — that can be used in soil amendments, stormwater treatment and other applications.

Below, Chiu shares five important facts about char — both natural (wildfire char) and manmade (biochar). He also discusses his team’s recently published research in Environmental Science and Technology, a peer-reviewed journal of the American Chemical Society, detailing the potential of wildfire chars to suppress methane produced by microorganisms. Co-authors on the paper include UD doctoral student Jiwon Choi and Danhui Xin, a former graduate student in Chiu’s lab, now at Southern California Coastal Water Research Project.

What is char and where is it found?

Chiu: Char is a carbon-rich material formed at high temperature. In nature, chars are produced through wildfires (i.e., wildfire chars). Biochar, or manmade char, can be produced in a laboratory or commercially by heating surplus biomass, such as wood chips, leftover corn stalks or other crop residues at high temperatures in an oxygen-limited environment, through a process called pyrolysis. In agriculture, biochar is commonly used as a soil amendment to improve soil quality and productivity. It also can be incorporated into compost and filtration systems, among other uses. 

Why are you studying char?

We discovered a few years ago that heating up plant biomass through pyrolysis can create a large capacity in biochar to reversibly accept and donate electrons. This capacity, called electron storage capacity, plays a key role in biological metabolism. When you run, for example, electrons are exchanged between sugar molecules in the body and the oxygen you breathe to create energy. If you need energy faster than you can take oxygen in, the body ferments the sugars for energy instead.

Microbes do the same thing. When there is no oxygen for microbes to breathe (exchange electrons with), fermenting microbes take over. This often leads to products we don’t want, like methane, in landfills, cattle, wetlands, rice paddies, waste digesters, swamps and other oxygen-depleted environments. Our recent work shows that all chars can serve as oxygen for microbes to breathe and grow, allowing good bacteria to outcompete fermenting microbes called methanogens that produce over 50% of the global methane, and suppressing methane formation in the process.

What does this have to do with wildfires?

Wildfire chars have been part of the global carbon cycle for millions of years. We hypothesized that microorganisms must have evolved the ability to metabolize, or process, chars. If true, this novel biological role of chars would have many important implications and applications in biogeochemistry, global climate, contaminant fate and environmental cleanup. While this benefit will never outweigh the detrimental effects of wildfires, both human and environmental, it is something we can learn from and leverage in our effort to mitigate the impact of greenhouse gases.

What has your latest work shown?

My group recently published a paper, showing that all chars have a significant electron storage capacity (ESC). For example, wildfire chars and biochars can store a few billion trillion electrons in a gram (about a quarter teaspoon) of char. Agriculture in the United States generates approximately 140 million dry tons of crop residues every year. Corn stover and wheat straw are the main contributors. In addition, forestry generates between 60-70 million dry tons of biomass annually. So, that’s a lot of storage capacity. Meanwhile, common soil microbes can grow by respiring or "breathing" char for energy, something they have likely been doing for eons without us knowing.

Why is this important?

All wildfire chars and plant-based biochars can suppress methane. By supporting the growth of char-breathing bacteria, wildfire chars enable these microbes to outcompete methanogens. This is important because methanogens produce over 50% of the global methane today, a major greenhouse gas that is 85 times more potent than carbon dioxide and contributes to over 30% of the current warming. Enlisting microbes with the ability to breathe chars to help us combat this challenge is both smart and sustainable — since these microbes are common in nature and can use the same char repeatedly to suppress methane production again and again. Microbes with the ability to use char for energy can do other things, too, like prevent arsenic from entering drinking water and food crops, and remove pollutants such as nitrate and perchlorate, from stormwater and groundwater.

What keeps you passionate about this research?

What really motivates me is the science. Chars collectively represent an enormous rechargeable and bioavailable reservoir of nearly a trillion-trillion-trillion electrons that we inject into the global biogeochemical cycle every single year. Never heard of a trillion-trillion-trillion? It’s a one, followed by 36 zeros. We did not know this until now, but microbes have been eating and breathing chars for hundreds of millions of years. But how? How do they eat or breathe a piece of solid — repeatedly? 

Globally, the research community has focused for a long time on reducing carbon dioxide from the environment. Carbon dioxide stays in the environment for anywhere from 50 to 200 years, so if today’s solutions are successful, my great-great-grandchildren will benefit. Methane is 85 times more potent than carbon dioxide, and its lifespan in the environment is only 11.8 years. If we can find ways to reduce methane in the environment, I could live to see the impact in my lifetime.

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Journal

Environmental Science & Technology

DOI

10.1021/acs.est.5c05709 

AI-equipped aerial robots help to track and model wildfire smoke

Understanding wildfire smoke dispersion could lead to more accurate air quality models

University of Minnesota

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In this video, we present a new method that uses a swarm of drones to reconstruct the 3D structure of smoke plumes in outdoor environments. This approach enables high-resolution, volumetric tracking of plume dynamics, offering powerful insights for wildfire response, air quality modeling, and environmental forecasting.

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Credit: Jiarong Hong Lab

MINNEAPOLIS / ST. PAUL (09/02/2025) — Researchers at the University of Minnesota Twin Cities have developed aerial robots equipped with artificial intelligence (AI) to detect, track and analyze wildfire smoke plumes. This innovation could lead to more accurate computer models that will improve air quality predictions for a wide range of pollutants.

The research was recently published in Science of the Total Environment, a peer-reviewed scientific journal.

According to a 2024 Associated Press report, 43 wildfires resulted from 50,000 prescribed burns between 2012 and 2021, creating the need for better smoke management tools. 

Previous simulation tools have worked to model fire and smoke particle behavior, but there were still limitations in accurate collection of data, modeling and the current field tools to observe these smoke plumes. In this paper, the researchers addressed the challenges in accurately modeling how smoke particles behave and spread during wildfires and prescribed burns.

“A key step is understanding the composition of smoke particles and how they disperse,” said Jiarong Hong, a professor in the University of Minnesota’s Department of Mechanical Engineering and senior author on the paper. “Smaller particles can travel farther and stay suspended longer, impacting regions far from the original fire.”

Using a swarm of AI-guided aerial robots, they were able to capture multiple angles of the smoke plumes to create 3D reconstructions of smoke plumes and analyze flow patterns. Unlike traditional drones, these aerial robots can identify smoke and navigate into it to collect data. 

“This approach allows for high-resolution data collection across large areas—at a lower cost than satellite-based tools,” said Nikil Nrishnakumar, a graduate research assistant with the Minnesota Robotics Institute at the University of Minnesota and first author of the paper. “It provides critical data for improving simulations and informing hazard response.”

The cost-effective technology has potential beyond wildfires and could be adapted for sandstorms, volcanic eruptions, and other airborne hazards. The team’s next goal is to translate the research into practical tools for early fire detection and mitigation.

“Early identification is key,” Hong said. “The sooner you can see the fire, the faster you can respond.”

Previously, the team developed an autonomous drone system, equipped with onboard computer vision and sensors to detect and track wildfire smoke plumes in real time. Building on this, they will now be focusing on efficient plume tracking and particle characterization using Digital Inline Holography with coordinated multi-drone systems. They are also working on integrating a type of drone, called a fixed-wing VTOL (Vertical Takeoff and Landing), that can take off without a runway and can fly for more than an hour for extended-range surveillance missions. 

In addition to Hong and Nrishnakumar, the team included Shashank Sharma and Srijan Kumar Pal from the Minnesota Robotics Institute. The paper was supported by the National Science Foundation Major Research Instrumentation program. This work was done with the help of the St. Anthony Falls Laboratory.

Read the full paper entitled, “3D characterization of smoke plume dispersion using multi-view drone swarm,” go to the ScienceDirect website.

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Journal

Science of The Total Environment

DOI

10.1016/j.scitotenv.2025.179466 

Article Title

3D characterization of smoke plume dispersion using multi-view drone swarm

Using autonomous drones, researchers are able to create a 3D reconstruction of the smoke plume and improve analysis of flow patterns. 

Credit

Jiarong Hong Lab

Dad’s childhood passive smoking may confer lifelong poor lung health onto his kids

They run risk of COPD, heightened further if they are childhood passive smokers themselves Findings highlight intergenerational harms of smoking, say researchers

BMJ Group

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A father’s exposure to passive smoking as a child may impair the lifelong lung function of his children, putting them at risk of COPD—a risk that is heightened further if they are childhood passive smokers themselves—finds research published online in the respiratory journal Thorax.

The findings highlight the intergenerational harms of smoking, say the researchers, who urge fathers to intercept this harmful legacy by avoiding smoking around their children.

Chronic obstructive pulmonary disease, more usually known by its acronym of COPD, includes chronic bronchitis and emphysema. Now the third leading cause of death around the world, COPD kills around 3 million people every year, say the researchers.

Several factors throughout the lifespan may increase the risk of poor lung function and subsequent COPD, and attention is now beginning to focus on the potential role of intergenerational factors, they explain.

While previously published research showed that passive smoking during a father’s childhood may be linked to a heightened risk of asthma in his children by the time they are 7, it’s not clear if compromised lung function may extend into middle age and beyond, they add. 

To explore this further, the researchers drew on 8022 child participants in the Tasmanian Longitudinal Health Study (TAHS), all of whom had tests to assess their lung function (spirometry).

Their parents completed an initial comprehensive survey on their and their children’s respiratory health. Further check-ups ensued when those children were 13, 18, 43, 50 and 53. These included spirometry to assess 2 measures of lung function (FEV1 and FVC) as well as questionnaires on demographics and respiratory symptoms/disease. 

Of the 7243 parents who were alive and could be traced in 2010, 5111 were re-surveyed about whether either of their own parents had smoked when they were under the age of 5 and/or up to when they were 15.

Among the 5097 respondents with complete data, 2096 were fathers. The final analysis included 890 father-child pairs with data on the father’s passive smoke exposure before puberty and lung function data for their children up to the age of 53.

More than two thirds of the fathers (nearly 69%) and more than half of their children (56.5%) had been exposed to passive smoking during their childhoods.

Around half of the children (49%) had a history of active smoking by middle age, and just over 5% of them had developed COPD by this time point, as assessed by spirometry.

After adjusting for potentially influential factors, including the father’s lifetime history of asthma/wheeze and his age, his passive smoke exposure as a child was associated with 56% higher odds of below average FEV1, but not FVC, across the lifespan of  his children. 

Similarly, fathers’ childhood passive smoke exposure was also associated with a doubling in the odds of an early low-rapid decline in FEV1/FVC in their children. This was statistically significant even after adjusting for potentially influential factors.

And paternal exposure to passive smoking as a child was also associated with a doubling in the risk of COPD by the age of 53 in his children, although this was no longer statistically significant after adjusting for potentially influential factors. 

But children whose fathers had been exposed to passive smoking as a child were twice as likely to have below average FEV1 if they, too, had been exposed to passive smoking during their childhood.

The observed associations were only partly mediated through smoking and respiratory illnesses in fathers and their children (each contributing less than 15%).

This is an observational study, and as such, no firm conclusions can be drawn about cause and effect. And the researchers acknowledge that TAHS lacks data on paternal lung function and genetics, preventing assessment of familial aggregation as a potential mechanism. 

And their children’s childhood passive smoke exposure was defined as at least one parent smoking 6 days a week, which might have misclassified moderate/light smokers as non-smokers, they add.

But the period before puberty is especially critical for boys, when exposure to harmful substances may change gene expression and modify repair mechanisms, which may then become heritable, say the researchers by way of an explanation for their findings. 

“Our findings are novel as this is the first study to investigate and provide evidence for an adverse association of paternal prepubertal passive smoke exposure, rather than just active smoking, on impaired lung function of offspring by middle age,” they write. 

“This is of importance from a public health perspective, as passive smoke exposure affects about 63% of adolescents, which is significantly higher than the approximately 7% affected by active smoking.” 

They conclude:  “These findings suggest that smoking may adversely affect lung function not only in smokers but also in their children and grandchildren…Fathers exposed to tobacco smoke during prepuberty may still reduce risk for future generations by avoiding smoking around their children.” 

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Journal

Thorax

Method of Research

Observational study

Subject of Research

People

Article Title

Paternal prepubertal passive smoke exposure is related to impaired lung function trajectories from childhood to middle age in their offspring

Article Publication Date

2-Sep-2025

COI Statement

s JLP, CJL, AJL, MJA and SCD have received an investigatorinitiated grant from GlaxoSmithKline (GSK) for unrelated research. JLP and SCD also hold a similar grant from AstraZeneca. AJL has received an investigational product (EpiCeram) free of charge from Primus Pharmaceuticals for use in unrelated research. AJL and SCD have also received grant funding from Sanofi Regeneron for unrelated research. MJA holds investigator-initiated grants from Pfizer, Boehringer-Ingelheim and Sanofi for unrelated research. He has undertaken an unrelated consultancy for Sanofi and received a speaker’s fee from GSK. The rest of the authors declare that they have no conflicts of interest.