While many nanomaterials exhibit promising electronic properties, scientists and engineers are still working to best integrate these materials together to eventually create semiconductors and circuits with them.

Northwestern Engineering researchers have created two-dimensional (2D) heterostructures from two of these materials, graphene and borophene, taking an important step toward creating intergrated circuits from these nanomaterials.

“If you were to crack open an integrated circuit inside a smartphone, you’d see many different materials integrated together,” said Mark Hersam, Walter P. Murphy Professor of Materials Science and Engineering, who led the research. “However, we’ve reached the limits of many of those traditional materials. By integrating nanomaterials like borophene and graphene together, we are opening up new possibilities in nanoelectronics.”

Supported by the Office for Naval Research and the National Science Foundation, the results were published October 11 in the journal Science Advances. In addition to Hersam, applied physics PhD student Xiaolong Liu co-authored this work.

Creating a new kind of heterostructure

Any integrated circuit contains many materials that perform different functions, like conducting electricity or keeping components electrically isolated. But while transistors within circuits have become smaller and smaller — thanks to advances in materials and manufacturing — they are close to reaching the limit of how small they can get.

Ultrathin 2D materials like graphene have the potential to bypass that problem, but integrating 2D materials together is difficult. These materials are only one atom thick, so if the two materials’ atoms do not line up perfectly, the integration is unlikely to be successful. Unfortunately, most 2D materials do not match up at the atomic scale, presenting challenges for 2D integrated circuits.

Borophene, the 2D version of boron that Hersam and coworkers first synthesized in 2015, is polymorphic, meaning it can take on many different structures and adapt itself to its environment. That makes it an ideal candidate to combine with other 2D materials, like graphene.

To test whether it was possible to integrate the two materials into a single heterostructure, Hersam’s lab grew both graphene and borophene on the same substrate. They grew the graphene first, since it grows at a higher temperature, then deposited boron on the same substrate and let it grow in regions where there was no graphene. This process resulted in lateral interfaces where, because of borophene’s accommodating nature, the two materials stitched together at the atomic scale.

Measuring electronic transitions

The lab characterized the 2D heterostructure using a scanning tunneling microscope and found that the electronic transition across the interface was exceptionally abrupt — which means it could be ideal for creating tiny electronic devices.

“These results suggest that we can create ultrahigh density devices down the road,” Hersam said. Ultimately, Hersam hopes to achieve increasingly complex 2D structures that lead to novel electronic devices and circuits. He and his team are working on creating additional heterostructures with borophene, combining it with an increasing number of the hundreds of known 2D materials.

“In the last 20 years, new materials have enabled miniaturization and correspondingly improved performance in transistor technology,” he said. “Two-dimensional materials have the potential to make the next leap.”

Numerical models have become increasingly easy to employ with advances in computer technology and software with graphical user interface (GUI). While these technologies make the models more accessible, problems can arise if they are used by inexperienced modelers, says Juan Sebastian Acero Triana, a doctoral student in the Department of Agricultural and Biological Engineering at the University of Illinois.

Acero Triana is lead author on a study that evaluates the accuracy of a commonly used numerical model in hydrology.

Findings from the research show that even when the model appears to be properly calibrated, its results can be difficult to interpret correctly. The study, published in the Journal of Hydrology, provides recommendations for how to fine-tune the process and obtain more precise results.

Model accuracy is important to ensure that policy decisions are based on realistic scenarios, says Maria Chu, a co-author of the study. Chu is an assistant professor of agricultural and biological engineering in the College of Agricultural, Consumer and Environmental Sciences and The Grainger College of Engineering at U of I.

“For example, you may want to estimate the impacts of future climate on the water availability over the next 100 years. If the model is not representing reality, you are going to draw the wrong conclusions. And wrong conclusions will lead to wrong policies, which can greatly affect communities that rely on the water supply,” Chu says.

The study focuses on the Soil and Water Assessment model (SWAT), which simulates water circulation by incorporating data on land use, soil, topography, and climate. It is a popular model used to evaluate the impacts of climate and land management practices on water resources and contaminant movement.

The researchers conducted a case study at the Fort Cobb Reservoir Experimental Watershed (FCREW) in Oklahoma to assess the model’s accuracy. FCREW serves as a test site for the United States Department of Agriculture-Agricultural Research Service (USDA-ARS) and the United States Geological Survey (USGS); thus, detailed data are already available on stream flow, reservoir, groundwater, and topography.

The study coupled the SWAT model with another model called MODFLOW, or the Modular Finite-difference Flow Model, which includes more detailed information on groundwater levels and fluxes.

“Our purpose was to determine if the SWAT model by itself can appropriately represent the hydrologic system,” Acero Triana says. “We discovered that is not the case. It cannot really represent the entire hydrologic system.”

In fact, the SWAT model yielded 12 iterations of water movement that all appeared to be acceptable. However, when combined with MODFLOW it became clear that only some of these results properly accounted for groundwater flow. The researchers compared the 12 results from SWAT with 103 different groundwater iterations from MODFLOW in order to find a realistic representation of the water fluxes in the watershed.

Yielding several different results that all appear equally likely to be correct is called “equifinality.” Careful calibration of the model can reduce equifinality, Acero Triana explains. Calibration must also be able to account for inherent limitations in the way the model is designed and how parameters are defined. In technical terms, it must account for model and constraint inadequacy.

However, inexperienced modelers may not fully understand the intricacies of calibration. And because of the inherent constraints of both SWAT and MODFLOW, using metrics from just one model may not provide accurate results.

The researchers recommend using a combination model called SWATmf, which integrates the SWAT and the MODFLOW processes.

“This paper presents a case study that provides general guidelines for how to use hydrological models,” Acero Triana says. “We show that to really represent a hydrologic system you need two domain models. You need to represent both the surface and the sub-surface processes that are taking place.”

The differences in results may be small, but over time the effect could be significant, he concludes.

The discovery may help doctors stop acute pain from progressing into chronic pain, a condition in which patients experience not just pain, but a number of debilitating symptoms ranging from sensory deficits to depression and loss of motivation. The transition from acute to chronic (pathological) pain is accompanied by numerous adaptations in immune, glial, and neuronal cells, many of which are still not well understood. As a result, currently available medications for neuropathic or chronic inflammatory pain show limited efficacy and major side effects. Commonly administered opioids provide temporary alleviation of some pain symptoms, but carry serious risks like addiction in the context of long-term treatment for chronic pain. Therefore, there is an imminent need for novel approaches towards the treatment of chronic pain and for the development of medications that disrupt pain states instead of simply alleviating symptoms.

“Our research reveals that RGS4 actions contribute to the transition from acute and sub-acute pain to pathological pain states and to the maintenance of pain,” says Venetia Zachariou, PhD, Professor in the Nash Family Department of Neuroscience, the Department of Pharmacological Sciences and The Friedman Brain Institute at the Icahn School of Medicine at Mount Sinai. “Because chronic pain states affect numerous neurochemical processes and single-target drugs are unlikely to work, it’s exciting to have discovered a multifunctional protein that can be targeted to disrupt the maintenance of pain.”

RGS4 is a multifunctional protein widely expressed in brain circuits that processes pathological pain, mood, and motivation. Through this study, Mount Sinai researchers observed that RGS4 plays an important role in maintaining pain states, regardless of whether the cause of pain was nerve injury or inflammation. Using genetic mouse models to ablate the gene expressing RGS4, the team demonstrated that prevention of RGS4 action disrupts the maintenance of chronic pain states in male and female mice.

Specifically, the research team used genetically modified mice to understand the role of RGS4 in the induction, intensity, and maintenance of chronic pain symptoms. They found that while genetic inactivation of RGS4 does not affect acute pain or the induction of chronic pain, it promotes recovery from sensory hypersensitivity symptoms in preclinical models of peripheral nerve injury, chemotherapy-induced neuropathy, and peripheral inflammation. Mice lacking RGS4 developed all expected symptoms of nerve injury, but they recovered within 3 weeks. Prevention of RGS4 action was also associated with an increase in motivation-related behaviors.

The group also used genetic tools to reduce the expression of RGS4 in the ventral-posterior lateral nucleus of the thalamus, a pain processing center that receives input from the spinal cord and relays this information to several cortical areas. Ultimately, inhibition of RGS4 actions in brain region resulted in recovery from mechanical and cold allodynia. Additionally, the research team used next-generation sequencing to gain insight on the genes and intracellular pathways affected by RGS4. The lab is further investigating the actions of RGS4 in the spinal cord and in mood-regulating areas of the brain to better understand the mechanism by which this protein affects sensory and affective pain symptoms.

Dr. Zachariou’s laboratory is conducting further investigation into the actions of RGS4 in the spinal cord and mood-regulating areas of the brain to better understand the mechanism by which this protein affects sensory and affective pain symptoms. They are also testing the therapeutic potential of RGS4 inhibitors.

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Materials provided by The Mount Sinai Hospital / Mount Sinai School of Medicine. Note: Content may be edited for style and length.

A new study from the University of Illinois, published in the Journal of Engineering, Design and Technology, takes a look at the biases that may influence the effectiveness of international engineering efforts implemented by development organizations such as Engineers Without Borders.

The study’s author Ann-Perry Witmer conducted an in-depth analysis of the motivations and beliefs of engineers working on international projects. She says her research is unique because it combines technology with anthropological insights.

“As engineers we think we’ve got all the technical solutions, but we tend to neglect where the project is being done, and the people we’re working with,” says Witmer, a lecturer in the Department of Agricultural and Biological Engineering in the College of Agricultural, Consumer and Environmental Sciences and The Grainger College of Engineering at U of I.

Contextual engineering is a new approach that can help overcome those hurdles, Witmer says, by merging technical knowledge with a place-based understanding of conditions that inform the process.

Witmer’s research grew out of her experiences as a practicing engineer, specializing in the design of water systems for communities. She has worked on numerous projects in Central America, South America, Asia and Africa, and she advised Engineers Without Borders at the U of I for the past five years.

“For this paper the core of the research comes from my decade of working on projects around the world,” she says. She kept detailed journals of each project, which formed the basis of a qualitative data analysis, using social science software that scans content for themes and patterns. She also developed a detailed questionnaire and conducted in-depth interviews with engineers, engineering students, and international project practitioners.

Witmer observed how projects were often derailed by limited understanding of local conditions. For example, she says, a water pump manufactured in the U.S. was transported to Guatemala for use in a community water system. However, seals in the pump housing frequently wore out and needed to be replaced. Getting replacement parts turned out to be difficult and time-consuming, leaving the community without a functioning water pump for much of the time.

Witmer’s research identified a number of dimensions that are important for the outcome of a project. These include:

• The engineers’ confidence in industrialized technology. Witmer says the experts often are so certain of the superiority of the technology they bring in that they overlook whether it’s appropriate for the local context.
• Uniqueness of the context. Engineers may be aware of obvious differences in climate and topography, but they may not consider social and cultural dimension that are unique to each location.
• Power dynamics. Each society will have its own structure of politics and power that can significantly influence the outcome of a project but that can be hard for an outsider to grasp.
• Innovative self-sufficiency. Local constituents may be able to craft solutions based on available materials and conditions, and engineers are not always willing to consider whether these solutions are appropriate for the project.

Witmer concludes that by ignoring the complexity of the context, there is a risk that international aid projects may not function as intended; the efforts and money will be wasted; and the local population will not be helped. Chances of project success are much greater if the factors listed above are considered.

“The ultimate conclusion of this paper and the work I’ve done is that every place is so different it doesn’t matter what kind of brilliant technology you come up with, there are places it’s not going to work. It’s not appropriate. So the idea of creating this silver bullet that’s going to solve the world’s problems, it simply doesn’t exist,” she says.

However, engineers working on international projects can take steps to ensure greater success. They can aim to develop a high degree of self-reflection and awareness of their own motivations and implicit biases; assimilate into the local culture and identify unique contextual influences; and employ rigorous design in close partnership with local people and conditions.

Dwarf galaxies are small galaxies that contain between 100 million to a few billion stars. In contrast, the Milky Way has 200-400 billion stars. Dwarf galaxies are the most abundant galaxy type in the universe and often orbit larger galaxies.

The team of three astronomers was surprised by the strength of the detected winds.

“We expected we would need observations with much higher resolution and sensitivity, and we had planned on obtaining these as a follow-up to our initial observations,” said Gabriela Canalizo, a professor of physics and astronomy at UC Riverside, who led the research team. “But we could see the signs strongly and clearly in the initial observations. The winds were stronger than we had anticipated.”

Canalizo explained that astronomers have suspected for the past couple of decades that supermassive black holes at the centers of large galaxies can have a profound influence on the way large galaxies grow and age.

“Our findings now indicate that their effect can be just as dramatic, if not more dramatic, in dwarf galaxies in the universe,” she said.

Study results appear in The Astrophysical Journal.

The researchers, who also include Laura V. Sales, an assistant professor of physics and astronomy; and Christina M. Manzano-King, a doctoral student in Canalizo’s lab, used a portion of the data from the Sloan Digital Sky Survey, which maps more than 35% of the sky, to identify 50 dwarf galaxies, 29 of which showed signs of being associated with black holes in their centers. Six of these 29 galaxies showed evidence of winds — specifically, high-velocity ionized gas outflows — emanating from their active black holes.

“Using the Keck telescopes in Hawaii, we were able to not only detect, but also measure specific properties of these winds, such as their kinematics, distribution, and power source — the first time this has been done,” Canalizo said. “We found some evidence that these winds may be changing the rate at which the galaxies are able to form stars.”

Manzano-King, the first author of the research paper, explained that many unanswered questions about galaxy evolution can be understood by studying dwarf galaxies.

“Larger galaxies often form when dwarf galaxies merge together,” she said. “Dwarf galaxies are, therefore, useful in understanding how galaxies evolve. Dwarf galaxies are small because after they formed, they somehow avoided merging with other galaxies. Thus, they serve as fossils by revealing what the environment of the early universe was like. Dwarf galaxies are the smallest galaxies in which we are directly seeing winds — gas flows up to 1,000 kilometers per second — for the first time.”

Manzano-King explained that as material falls into a black hole, it heats up due to friction and strong gravitational fields and releases radiative energy. This energy pushes ambient gas outward from the center of the galaxy into intergalactic space.

“What’s interesting is that these winds are being pushed out by active black holes in the six dwarf galaxies rather than by stellar processes such as supernovae,” she said. “Typically, winds driven by stellar processes are common in dwarf galaxies and constitute the dominant process for regulating the amount of gas available in dwarf galaxies for forming stars.”

Astronomers suspect that when wind emanating from a black hole is pushed out, it compresses the gas ahead of the wind, which can increase star formation. But if all the wind gets expelled from the galaxy’s center, gas becomes unavailable and star formation could decrease. The latter appears to be what is occurring in the six dwarf galaxies the researchers identified.

“In these six cases, the wind has a negative impact on star formation,” Sales said. “Theoretical models for the formation and evolution of galaxies have not included the impact of black holes in dwarf galaxies. We are seeing evidence, however, of a suppression of star formation in these galaxies. Our findings show that galaxy formation models must include black holes as important, if not dominant, regulators of star formation in dwarf galaxies.”

Next, the researchers plan to study the mass and momentum of gas outflows in dwarf galaxies.

“This would better inform theorists who rely on such data to build models,” Manzano-King said. “These models, in turn, teach observational astronomers just how the winds affect dwarf galaxies. We also plan to do a systematic search in a larger sample of the Sloan Digital Sky Survey to identify dwarf galaxies with outflows originating in active black holes.”

The research was funded by the National Science Foundation, NASA, and the Hellman Foundation. Data was obtained at the W. M. Keck Observatory, and made possible by financial support from the W. M. Keck Foundation.

Hannele Ruohola-Baker, professor of biochemistry at the University of Washington School of Medicine, headed the multi-institutional study. The findings are published in the Oct. 11 edition of Nature Communications. The research focused on mitochondrial tri-functional protein deficiency, a potentially fatal cardiac metabolic disorder caused by a genetic mutation in the gene HADHA.

Newborns with this genetic anomaly can’t metabolize the lipids found in milk, and die suddenly of cardiac arrest when they are a couple months old. Lipids are a category of molecules that include fats, cholesterol and fatty acids.

“There are multiple causes for sudden infant death syndrome,” said Ruohola-Baker, who is also associate director of the UW Medicine Institute for Stem Cell and Regenerative Medicine, where the lab she heads is located. “There are some causes which are environmental. But what we’re studying here is really a genetic cause of SIDS. In this particular case, it involves defect in the enzyme that breaks down fat.”

Jason Miklas, who earned his Ph.D. at the UW and is now a postdoctoral fellow at Stanford University, was the lead author on the paper. He said he first came up with the idea while researching heart disease. He noticed a small study that had examined children who couldn’t process fats and who had cardiac disease that could not be readily explained.

So Miklas, along with Ruohola-Baker, started looking into why heart cells, grown to mimic infant cells, were dying in the petri dish where they were being grown.

“If a child has a mutation, depending on the mutation the first few months of life can be very scary as the child may die suddenly,” he noted. “An autopsy wouldn’t necessarily pick up why the child passed but we think it might be due to the infant’s heart stopping to beat.”

“We’re no longer just trying to treat the symptoms of the disease,” Miklas added. “We’re trying find ways to treat the root problem. It’s very gratifying to see that we can make real progress in the lab toward interventions that could one day make their way to the clinic.”

In MTP deficiency, the heart cells of affected infants do not convert fats into nutrients properly, This results in a build-up of unprocessed fatty material that can disrupt heart functions. More technically, the breakdown occurs when enzymes fail to complete a process known as fatty acid oxidation. It is possible to screen for the genetic markers of MTP deficiency; but effective treatments are still a ways off.

Ruohola-Baker sees the latest laboratory discovery as a big step towards finding ways to overcome SIDS.

“There is no cure for this,” she said. “But there is now hope, because we’ve found a new aspect of this disease that will innovate generations of novel small molecules and designed proteins, which might help these patients in the future.”

One drug the group is focusing on now is Elamipretide. It is used to stimulate hearts and organs that have oxygen deficiency, but was barely considered for helping infant hearts, until now. In addition, prospective parents can be screened to see if there is a chance that they could have a child who might carry this genetic mutation.

Ruohola-Baker has a personal interest in this research, as one of her friends in her home country of Finland had a baby who died of SIDS.

“It was absolutely devastating for that couple,” she said. “Since then, I’ve been very interested in the causes for Sudden Infant Death Syndrome. It’s very exciting to think that our work may contribute to future treatments, and help for the heartbreak for the parents who find their children have these mutations.”

A new study describes how spheres can be transformed into twisted spindles thanks to insights from 16th century navigational tools. Researchers show how polymers can contract into spiral structures, known as loxodromes, that have complex patterning ten times smaller than the width of a human hair. Published in Physical Review Letters, the research was conducted by University of Pennsylvania graduate student Helen Ansell, postdoc Daeseok Kim, and professors Randall Kamien and Eleni Katifori in the School of Arts and Sciences, in collaboration with Teresa Lopez-Leon of the École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI).

Kim, who worked on this project at ESPCI before coming to Penn, was inspired by other studies showing that a mixture of polymer and liquid crystal took on a new shape when placed in a different solvent. It was a change that was also reversible and reproducible, with little to no energy required to cause the change in shape.

To understand the interesting conformational changes that Kim had seen in the lab, he sought out theorists who could help make sense of how the polymer’s geometry caused it to twist and contract. After seeing the microscopic images and data that was collected and analyzed by Kim, Ansell had an initial idea of what the spindle’s structure might be: a loxodrome.

More commonly referred to as rhumb lines, a loxodrome is an arc that follows a constant angle as it cuts across a sphere. Sailors throughout the 16th-19th centuries used these lines to navigate, allowing them to set their compasses to a constant bearing so that their ship did not have to change its bearing.

“We tried to figure out if this was the case,” Ansell says about investigating if her hypothesis was correct. “We think we found these loxodromes, so we had to go about comparing what does it look like versus the data.”

Ansell then developed a mathematical model that describes how the spheres become elongated and twisted using the geometry of the loxodrome as a starting point. By comparing the results of her theory to the data generated by Kim, she was able to show that changing the solvent caused the polymers to shrink, which caused its shape to twist as the polymer chains along the sphere’s lines of longitude became shorter.

At the top of the spindles are one micron spirals, nearly one hundred times smaller than the width of a human hair. Creating humanmade patterns that small usually requires costly methods and equipment, but this method of making self-assembled small-scale structures using course-scale starting materials is much simpler.

The polymer loxodrome is the latest finding that delves into the Kamien group’s interests in the crossover between chemistry and geometry. Kamien says that many interactions in biology, like protein folding, immune responses, and even smell, is usually depicted as a chemical bond, but emphasizes that geometry also drives much of what happens in biology.

“Think about proteins,” says Kamien, “You have these different amino acids, and they attract in different ways, but when you’re all done, you have this giant glob, and there’s this little pocket that grabs the residues, so you think of it geometrically. Helen’s explanation is completely geometrical: It doesn’t involve anything specific about how the binding works.”

For Kim, this research is an exciting first step for studying unique structures in other biological systems. By designing new types of polymer particles and testing them out in different conditions, he hopes to learn more about how shape drives function, especially in systems that twist and contract. “We could study some biological matter in nature by mimicking a similar topological model,” he says, “And we may solve or study some complex problem in nature.”

Now, entirely coincidentally, Ansell’s efforts have laid the groundwork for another unrelated project she had been stuck on for some time which also appears to have a loxodrome solution.

“They just appear,” she says about the twisted spindle shape.

“As Pasteur said, luck favors the prepared mind,” adds Kamien. “Now, we’re primed to look for them.”

This research was supported by National Science Foundation Materials Research Science and Engineering Center grants DMR-1720530 and DMR-1720530, NSF CAREER Award PHY-1554887, a Simons Investigator Grant from the Simons Foundation, and Engineering and Physical Sciences Research Council Grant EP/R014604/1.

Now, a new tool created by researchers at the Wyss Institute for Biologically Inspired Engineering at Harvard University and Harvard Medical School (HMS) provides a solution to this problem in the form of a set of bacterial genes that have been engineered to detect and record changes in the growth of different populations of bacteria over time in the guts of living mice with single-cell precision, and can serve as a platform for complex, synthetic-biology-based diagnostics and therapeutics for a variety of applications in the gut. The study is published in Nature Communications.

Keeping time

The system uses an oscillating gene circuit, called a repressilator, as a kind of genetic clock to measure bacterial growth. The repressilator consists of three bacterial genes that code for three proteins (tetR, cl, and lacI), each of which blocks the expression of one of the other proteins. The genes are linked into a negative feedback loop, so that when the concentration of one of the repressor proteins falls below a certain level, the protein it had been repressing is expressed, which blocks the expression of the third protein, and the process repeats in a cyclical fashion.

When all three genes are inserted into a plasmid and introduced into bacteria, the number of negative feedback loop cycles completed can serve as a record of how many cell divisions the bacteria have undergone. Every time the bacteria divide, any repressor proteins present in their cytoplasm are diluted, so their concentration gradually falls and triggers the expression of the next protein in the repressilator cycle. Crucially, the repressilator cycle repeats after 15.5 bacterial generations regardless of how quickly or slowly the bacteria are growing. This allows it to act as an objective measurement of time, much like a clock or a watch.

“Imagine if you had two people wearing two different watches, and the second hand on one person’s watch was moving twice as fast as the other person’s,” explained first author David Riglar, Ph.D., a former postdoc at the Wyss Institute and HMS who now leads a research group as a Sir Henry Dale Fellow at Imperial College London. “If you stopped both watches after one hour, they wouldn’t agree on what time it was, because their measurement of time varies based on the rate of the second hand’s movement. In contrast, our repressilator is like a watch that always moves at the same speed, so no matter how many different people are wearing one, they will all give a consistent measurement of time. This quality allows us to more precisely study the behavior of bacteria in the gut.”

The researchers coupled each of the three repressor proteins to a differently colored fluorescent molecule, and developed an imaging workflow called RINGS (Repressilator-based Inference of Growth at Single-cell level) to track which protein is expressed at different time points during the bacteria’s growth. “As a bacterial colony grows outwards, the repressilator circuit creates these different fluorescent, tree-ring-like signatures based on which repressor protein was active in the single bacterium that started the colony,” said Riglar. “The pattern of the fluorescent rings records how many repressilator cycles have occurred since growth began, and we can analyze that pattern to study how growth rates vary between different bacteria and in different environments.”

Using RINGS, the team was able to successfully track cell divisions in several different bacterial species grown in vitro, and observed that the length of the bacteria’s repressilator cycle remained consistent when they were grown on extracted samples of mouse intestine (to simulate a complex microenvironment) or exposed to an antibiotic (to simulate stress conditions and inconsistent growth patterns).

Tracking change

To evaluate the repressilator’s performance in vivo, the team administered E. coli containing the repressilator circuit to mice orally, then analyzed bacteria extracted from fecal samples. The repressilator remained active for up to 16 days after introduction, showing that long-term oscillatory gene expression could be maintained in gut bacteria in living mammals. The RINGS analysis successfully detected changes in bacterial growth patterns, and bacteria whose repressilator circuits were in different stages could be “synchronized” by giving the mice a compound in their drinking water that arrested the repressilator cycle at a given stage.

Finally, the researchers tested the repressilator’s ability to detect differences in bacterial growth rates that have been observed as a result of gut inflammation. Mice were given an inflammation-inducing compound, followed by repressilator-loaded bacteria. After 15 hours, RINGS analysis showed that the bacteria from mice with inflammation had repressilators in a wider range of phases compared to bacteria from control mice, suggesting that inflammation produces an environment that drives inconsistencies in bacterial growth, potentially leading to imbalances in the gut microbiome.

“This repressilator allows us to really probe the intricacies of bacterial behavior in the living gut, not only in both healthy and diseased states, but also spatially and temporally,” said corresponding author Pamela Silver, Ph.D., who is a Core Faculty member at the Wyss Institute and the Elliot T. and Onie H. Adams Professor of Biochemistry and Systems Biology at HMS. “The fact that we can re-synchronize the repressilator when it’s already in the gut, as well as maintain it without the need to administer selective antibiotics, also means that we can study the microbiome in a more natural state with minimal disruption.”

In addition to understanding the dynamics of the microbiome, the repressilator unlocks the potential for complex, synthetic-biology-based diagnostics and therapeutics for the human gut. Potential applications include the creation of a system that is programmed to initiate a gene transcription cascade at a certain point in the circadian rhythm, or a diagnostic that records how much time has elapsed following the detection of a given biomarker.

“Not only does this research solve a specific problem related to monitoring dynamic changes in microbiome physiology within the living gut, it provides a platform that could lead to entirely new types of diagnostics and even time-dependent therapeutics.” said Wyss Founding Director Donald Ingber, M.D., Ph.D., who is also the Judah Folkman Professor of Vascular Biology at HMS and the Vascular Biology Program at Boston Children’s Hospital, as well as Professor of Bioengineering at Harvard’s John A. Paulson School of Engineering and Applied Sciences.

Additional authors of the paper include David Richmond, Laurent Potvin-Trottier, Andrew Verdegaal, Somenath Bakshi, Emanuele Leoncini, Lorena Lyon, and Johan Paulsson from HMS, and Alexander Naydich from the Wyss Institute, HMS, and Harvard’s John A. Paulson School of Engineering and Applied Sciences. This research was supported by a Human Frontier Science Program Long-Term Fellowship, the Menzies Foundation, the Wellcome Trust, the National Science Foundation, the Defense Advanced Research Projects Agency, Harvard Medical School, and the Wyss Institute for Biologically Inspired Engineering.