It’s possible that I shall make an ass of myself. But in that case one can always get out of it with a little dialectic. I have, of course, so worded my proposition as to be right either way (K.Marx, Letter to F.Engels on the Indian Mutiny)
Thursday, August 14, 2025
‘Controlled evolution’ dramatically boosts pDNA production for biomedical manufacturing
FROM A POISON TO A MEDICINE; PRINCPLES OF ALCHEMY, PARACELSUS
Researchers have controlled the evolution of E. coli bacteria in the lab in order to dramatically increase the amount of plasmid DNA (pDNA) these modified bacteria produce. The advance is significant because pDNA is an essential – and expensive – ingredient in many gene therapies, and the new technique could drive down the cost of these medical treatments.
pDNA are found naturally in many bacteria and differ from other forms of DNA because the double helix shape most people are familiar with forms a circle, rather than the linear shape found in humans and most other organisms.
“pDNA is relatively easy to work with in the lab – it’s stable and easy to modify,” says Nathan Crook, corresponding author of a paper on the work and an assistant professor of chemical and biomolecular engineering at North Carolina State University. “And it is particularly good at introducing genetic information into cells. This combination of traits makes it extremely useful for many gene therapies, as well as many vaccines used in veterinary practice.”
However, obtaining pDNA for use in research and manufacturing is costly.
“pDNA is largely produced by genetically modified bacteria, and can cost as much as $100,000 per gram,” says Crook. “Our goal was to develop E. coli bacteria that are more efficient at producing pDNA, and we were surprised at how successful we were. I thought we might see some small improvement, but this was remarkable.”
“Essentially, we started with a type of E. coli that had already been modified to produce pDNA,” says Zidan Li, first author of the paper and a postdoctoral researcher at NC State. “We introduced mutations into these bacteria and tested them, one by one, to see if any of the mutations resulted in increased pDNA production. We then selected the individual bacteria that had promising characteristics and tested them further to see how well they performed at producing a variety of different pDNAs.”
Specifically, the researchers used their “evolved” line of E. coli to produce five types of pDNA. While all five types of pDNA are well-studied, three types of pDNA are well known as being easier to produce in bulk, while the other two are more difficult to produce.
“At the high end, we found our modified E. coli produced 8.7 times as much pAAV pDNA as the E. coli we started with,” Li says. “pAAV is used in gene therapies and was one of the pDNA types that is traditionally easier to produce in bulk. But even at the lowest end, we were able to increase production of p15A pDNA by a factor of 1.44. That was one of the pDNA types that is traditionally difficult to produce in bulk, and increasing production by 44% is remarkable.”
“We’re optimistic this could significantly reduce manufacturing costs for biomedical applications that rely on pDNA, and could expedite research that relies on pDNA resources,” says Crook. “We look forward to working with partners in the private sector to explore related opportunities.”
The paper, “Inducible genome-wide mutagenesis for improvement of pDNA production by E. coli,” is published open access in the journal Microbial Cell Factories. The paper was co-authored by Ibrahim Al’Abri, a former graduate student and postdoc at NC State; Yihui Zhou, a professor of biological sciences at NC State; and George Sun, a research assistant in the Zhou lab at NC State.
Li, Crook and Al’Abri have filed an invention disclosure pertaining to the engineered E. coli strains developed in this work.
This work was done with support from the North Carolina Biotechnology Center under grant 2022-TRG-6707.
A team of Caltech scientists has fabricated a superconducting qubit on a chip and connected it to a tiny device that scientists call a mechanical oscillator. Essentially a miniature tuning fork, the oscillator consists of flexible plates that are vibrated by sound waves at gigahertz frequencies. When an electric charge is placed on those plates, the plates can interact with electrical signals carrying quantum information. This allows information to be piped into the device for storage as a "memory" and be piped out, or "remembered," later. Here, a scanning electron microscope image highlighting a single mechanical oscillator from the new work. The false-colored golden lines in the image indicate the location of electrodes that transfer electrical signals between the superconducting qubit and the mechanical oscillator.
While conventional computers store information in the form of bits, fundamental pieces of logic that take a value of either 0 or 1, quantum computers are based on qubits. These can have a state that is simultaneously both 0 and 1. This odd property, a quirk of quantum physics known as superposition, lies at the heart of quantum computing's promise to ultimately solve problems that are intractable for classical computers.
Many existing quantum computers are based on superconducting electronic systems in which electrons flow without resistance at extremely low temperatures. In these systems, the quantum mechanical nature of electrons flowing through carefully designed resonators creates superconducting qubits. These qubits are excellent at quickly performing the logical operations needed for computing. However, storing information—in this case quantum states, mathematical descriptors of particular quantum systems—is not their strong suit. Quantum engineers have been seeking a way to boost the storage times of quantum states by constructing so-called "quantum memories" for superconducting qubits.
Now a team of Caltech scientists has used a hybrid approach for quantum memories, effectively translating electrical information into sound so that quantum states from superconducting qubits can survive in storage for a period up to 30 times longer than in other techniques.
The new work, led by Caltech graduate students Alkim Bozkurt and Omid Golami, supervised by Mohammad Mirhosseini, assistant professor of electrical engineering and applied physics, appears in a paper published in the journal Nature Physics.
"Once you have a quantum state, you might not want to do anything with it immediately," Mirhosseini says. "You need to have a way to come back to it when you do want to do a logical operation. For that, you need a quantum memory."
Previously, Mirhosseini's group showed that sound, specifically phonons, which are individual particles of vibration (in the way that photons are individual particles of light) could provide a convenient method for storing quantum information. The devices they tested in classical experiments seemed ideal for pairing with superconducting qubits because they worked at the same extremely high gigahertz frequencies (humans hear at hertz and kilohertz frequencies that are at least a million times slower). They also performed well at the low temperatures needed to preserve quantum states with superconducting qubits and had long lifetimes.
Now Mirhosseini and his colleagues have fabricated a superconducting qubit on a chip and connected it to a tiny device that scientists call a mechanical oscillator. Essentially a miniature tuning fork, the oscillator consists of flexible plates that are vibrated by sound waves at gigahertz frequencies. When an electric charge is placed on those plates, the plates can interact with electrical signals carrying quantum information. This allows information to be piped into the device for storage as a "memory" and be piped out, or "remembered," later.
The researchers carefully measured how long it took for the oscillator to lose its valuable quantum content once information entered the device. "It turns out that these oscillators have a lifetime about 30 times longer than the best superconducting qubits out there," Mirhosseini says.
This method of constructing a quantum memory offers several advantages over previous strategies. Acoustic waves travel much slower than electromagnetic waves, enabling much more compact devices. Moreover, mechanical vibrations, unlike electromagnetic waves, do not propagate in free space, which means that energy does not leak out of the system. This allows for extended storage times and mitigates undesirable energy exchange between nearby devices. These advantages point to the possibility that many such tuning forks could be included in a single chip, providing a potentially scalable way of making quantum memories.
Mirhosseini says this work has demonstrated the minimum amount of interaction between electromagnetic and acoustic waves needed to probe the value of this hybrid system for use as a memory element. "For this platform to be truly useful for quantum computing, you need to be able to put quantum data in the system and take it out much faster. And that means that we have to find ways of increasing the interaction rate by a factor of three to 10 beyond what our current system is capable of," Mirhosseini says. Luckily, his group has ideas about how that can be done.
Additional authors of the paper, "A mechanical quantum memory for microwave photons" are Yue Yu, a former visiting undergraduate student in the Mirhosseini lab; and Hao Tian, an Institute for Quantum Information and Matter postdoctoral scholar research associate in electrical engineering at Caltech. The work was supported by funding from the Air Force Office of Scientific Research and the National Science Foundation. Bozkurt was supported by an Eddleman Graduate Fellowship.
A soybean looper (Chrysodeixis includens) caterpillar feeds on the leaf of a soybean plant as part of Arkansas Agricultural Experiment Station research on the impacts of drought-stress and herbivory.
Credit: U of A System Division of Agriculture photo by Manish Gautam
By John Lovett
University of Arkansas System Division of Agriculture
Arkansas Agricultural Experiment Station
FAYETTEVILLE, Ark. — When soybean plants survive attacks from insects and periods of drought, they remember.
While plants don’t remember in the way animals do, research out of the Arkansas Agricultural Experiment Station shows that soybean plants can pass on adaptive responses to stress — like those hungry insects — across generations without changing their DNA.
Scientists call this kind of adaptation across generations “transgenerational plasticity,” and the consensus has been the independent stressors of drought and herbivory, or animals feeding on plants, can induce gene expression — possibly through epigenetics. Unlike genetic changes, or mutations, epigenetic changes are reversible and don’t change the DNA sequence, but rather how an organism read its DNA sequence.
Implications for agriculture
In soybean — one of the world’s most important crops — researchers with the experiment station, the research arm of the University of Arkansas System Division of Agriculture, have found the first evidence that drought and insect herbivory can create lasting, transgenerational effects. These stressors not only affect the parent plants but alter the traits and defenses of their offspring.
The research demonstrates some of the positive and negative impacts the stressors have on a plant’s progeny and could be used to develop more resilient crops in the same season.
As a vaccine can build immunity, techniques such as “priming” and “hardening” in the early vegetative stages might enable the plants to withstand future setbacks with minimum reduction in yield, according to Rupesh Kariyat, associate professor of crop entomology in the entomology and plant pathology department for the Division of Agriculture and the Dale Bumpers College of Agricultural, Food and Life Sciences.
“This gives us the opportunity where we can manipulate the degree of stress of soybean to bolster defenses early in the season without compromising the final yield of the crop,” Kariyat said. “But there is a catch — we have yet to quantify the threshold under drought and herbivory stress that may cause more harm than good to the plants.”
For the past two years, Kariyat and doctoral students Manish Gautam and Insha Shafi have looked at how the caterpillars of two insects — soybean looper and fall armyworm — interact with soybean plants, and their effects on parent and progeny plants in a variety of situations including the coincidence of drought and sequential herbivory.
Ecology and economics
Kariyat, who holds the Clyde H. Sites Endowed Professorship in International Crop Physiology, notes that climate change is already making insect threats worse.
“Insects are getting bigger, and they’re going through multiple generations each year,” he said. “That leads to increased pesticide use, which isn’t sustainable.”
Improving soybean resilience through stress memory could reduce pesticide dependence, with significant ecological and economic benefits. While U.S. farmers typically purchase fresh seed annually, in Brazil and Kenya, many farmers rely on saved seeds to avoid the high cost of commercial varieties. In such systems, traits passed from parent plants to offspring become especially relevant.
Pros and cons of stress memory
Kariyat and his doctoral candidates conducted multi-layered experiments to test if soybean plants under drought stress are more vulnerable to insects, and how much of the parental plant’s memory — its response to stress — is passed on to its progeny to cope with specific kinds of herbivory.
Progeny of stressed plants had seeds with higher nitrogen and protein content, key markers of plant fitness. Offspring also produced more flowers and had a greater density of trichomes, the tiny hair-like structures that defend against pests. Kariyat noted that these positive effects were strongest when parent plants experience both drought and herbivory pressure.
Despite these advantages, the stress memory came at a cost — strong defenses but weaker growth. Stressed progeny showed reduced yield, including a higher rate of empty pods.
Defensive trichomes also declined with maturity, suggesting that the enhanced defenses may be short-lived or age-dependent. The research suggests that there is a costly trade-off between survival and productivity, Kariyat said.
Kariyat concluded that their research so far points tostress memory in soybeans being a double-edged sword. While it can improve defense and early vigor, it also leads physiological trade-offs that ultimately reduce fitness and yield.
Experiment spotlight: Caterpillars on a bridge
To see whether insects could detect past drought stress in soybeans, the researchers built tiny bridges between previously drought-stressed plants and plants that had consistently received enough water. They observed soybean looper caterpillars pausing, rotating their heads and often reversing course back to the healthier plants, the study noted.
The scale of damage by the caterpillars on consistently watered plants was significantly higher than the plants that had recovered from drought stress, supporting the “plant vigor hypothesis” that pests prefer robust hosts.
First contact matters
Most previous studies focus on a single stressor, but real farm conditions often involve multiple. Kariyat’s team tested what happens when soybean looper and fall armyworm attack in sequence. What they found was surprising.
When soybean looper came first, soybean plant progeny had 40 percent higher nitrogen content, more flowers and pods, and better protein levels than when the order was reversed.
While this might suggest herbivory can prime soybeans for better performance, Kariyat cautions the effect depends on the type, timing and severity of stressors.
“It’s not that herbivory always improves the plant performance, but the type, severity and combination of stressors determine whether the responses would be beneficial or detrimental,” Kariyat said. “From the research so far, while moderate or minimum biotic stress may induce resilience in soybeans — and this is also found in other systems — the combined abiotic and biotic stress may lead to exhaustive performance, triggering expensive defensive responses that often compromise yield and fitness.”
For example, the hair-like structures on plants called trichomes increased in the progeny of plants that had been exposed to drought and herbivory treatments more so than those just for drought. However, when sequential herbivory was tested, there was no difference in trichome density, which suggested the plants were investing in physiology and fitness traits over physical defenses when coping with just herbivory.
This indicates that drought may play a major role in tipping the balance from beneficial stress to harmful overload.
The University of Arkansas System Division of Agriculture’s mission is to strengthen agriculture, communities, and families by connecting trusted research to the adoption of best practices. Through the Agricultural Experiment Station and the Cooperative Extension Service, the Division of Agriculture conducts research and extension work within the nation’s historic land grant education system.
The Division of Agriculture is one of 20 entities within the University of Arkansas System. It has offices in all 75 counties in Arkansas and faculty on three system campuses.
Pursuant to 7 CFR § 15.3, the University of Arkansas System Division of Agriculture offers all its Extension and Research programs and services (including employment) without regard to race, color, sex, national origin, religion, age, disability, marital or veteran status, genetic information, sexual preference, pregnancy or any other legally protected status, and is an equal opportunity institution.
Background: Ancient events in plant evolution have left behind large, duplicated regions in their genomes.
New discovery: Salk Institute scientists found that deleting these large blocks of DNA can still lead to normal plants.
The findings demonstrate that large chromosomal deletions are a viable strategy in plant genetic engineering, which could now accelerate the development of streamlined, minimal plant genomes—a major goal in industries looking to create new plant-based biotechnologies.
The new study, led by Salk Research Professor Todd Michael and computational scientist Ashot Papikian, was published in Proceedings of the National Academy of Sciences on August 11, 2025.
More details: The researchers used CRISPR-Cas9 to delete four large, duplicated blocks in Arabidopsis thaliana, a model plant commonly used in plant biology research. The deletions were then verified using whole-genome sequencing, which revealed minimal off-target effects.
While two deletion lines showed distinct phenotypes resulting from the loss of many genes, two others displayed no obvious defects. RNA-sequencing revealed that expression compensation, where deletions of duplicated genes led to the upregulation of intact duplicates, was not a general response to the deleted regions under these conditions.
The results suggest that it is possible to obtain viable plants when deleting large fragments that may be redundant or that contain non-essential genes.
Why this is important: These findings challenge the assumption that these duplicated regions are essential and highlight the potential redundancy or modularity within plant genomes. The scientists’ approach of removing entire duplicated blocks now offers a powerful strategy to functionally dissect conserved genomic regions, investigate gene linkage and dosage effects, and accelerate the development of streamlined, minimal plant genomes with broad implications for plant biology, synthetic genomics, and biotechnology.
Other authors include: Rachel J. Rattner, Jenni Kao, Neil Hauser, Nicholas Allsing, Allen Mamerto, Nolan T. Hartwick, and Kelly Colt at Salk.
Funding: This work was supported by the Harnessing Plants Initiative at the Salk Institute, with funding from TED Audacious and the Bezos Earth Fund.
About the Salk Institute for Biological Studies:
Unlocking the secrets of life itself is the driving force behind the Salk Institute. Our team of world-class, award-winning scientists pushes the boundaries of knowledge in areas such as neuroscience, cancer research, aging, immunobiology, plant biology, computational biology, and more. Founded by Jonas Salk, developer of the first safe and effective polio vaccine, the Institute is an independent, nonprofit research organization and architectural landmark: small by choice, intimate by nature, and fearless in the face of any challenge. Learn more at www.salk.edu.
New York, NY | August 12, 2025 – On July 31, more than 200 New York City teens, 20 partner organizations, and numerous community advocates came together at the CUNY Graduate School of Public Health and Health Policy (CUNY SPH) for the second annual Menstrual Equity Summit: PERIODT POWER!
Hosted by Teens PACT, the Harlem Health Initiative, and GorjusDoc, the event marked a powerful milestone for the menstrual equity movement in the city, putting youth voices front and center. The day-long event combined education, advocacy, art, and community building to challenge stigma, expand access to menstrual products, and celebrate gender equity.
Hosted for the first time at CUNY SPH, the summit embraced a fully youth-centered approach. Teen leaders facilitated workshops, moderated panel discussions, and led interactive sessions on topics such as menstrual health literacy, advocacy strategies, and the intersection of menstrual justice with racial and economic equity.
The event also featured a marketplace of resources, where participants connected directly with local organizations championing reproductive justice, public health, and youth empowerment.
“Too often, people think distributing period products to those in need is enough but it's time we move away from period poverty and towards menstrual equity,” said Dr. Natasha Ramsey, adolescent medicine doctor and founder of GorjusDoc. “Menstrual equity goes beyond that because menstrual equity and reproductive justice are intrinsically linked. It's ensuring that we meet people where they are, not only with products, but with knowledge and policies that empower them.”
“Period poverty affects us all, regardless of whether we menstruate or not,” said peer leader Shalena Brown. “It’s crucial to show up and advocate for those with limited access, because an injustice to one is an injustice to all.”
"Everything about the day was truly inspiring, from the exhilarating keynote to the motivating panel,” said Teens PACT Program Manager Natasha Sutherland. “I even shed a little tear watching the youth-led panel and hosting team, who created a powerful space where young people could see themselves represented in leadership, advocacy, and wellness. The youth are the real MVPs for showing up for a cause that truly matters."
“I’m honored to work with Teens PACT and its great team,” said Harlem Health Initiative Director Deborah Levine. “Helping to create a safe space for young adults to learn and expand their advocacy skills is at the heart of our mission. Congratulations to all who made this year’s summit a success.”
With momentum growing from this year's summit, event organizers and community partners are already planning for expanded programs, citywide advocacy campaigns, and a broader coalition for menstrual justice in 2026.
Stay connected and view highlights on Instagram: @teenspact
The CUNY Graduate School of Public Health and Health Policy (CUNY SPH) is committed to promoting and sustaining healthier populations in New York City and around the world through excellence in education, research, and service in public health and by advocating for sound policy and practice to advance social justice and improve health outcomes for all.
About Teens PACT
Teens PACT is a youth-led program dedicated to empowering young people with the knowledge, skills, and resources to make informed decisions about their health.
About Harlem Health Initiative
The Harlem Health Initiative works to reduce health inequities in Northern Manhattan through grassroots outreach, education, and advocacy.
About GorjusDoc
GorjusDoc is a health equity advocate and media creator using storytelling to bring attention to urgent public health issues affecting marginalized communities.
