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Biochemistry Research

A More Realistic Look at DNA in Action: Researchers Shed Light on the Mechanical Forces Behind Strand Separation

By creating a more true-to-life representation of DNA’s environment, researchers have discovered that strand separation may take more mechanical force than the field previously believed.

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The way we study DNA has long been a topic of discussion among researchers. Traditionally, biochemistry labs isolate DNA within a water-based solution that allows scientists to manipulate it without interacting with other molecules. However, this approach can be misleading, as it doesn’t reflect the true environment of a living cell. In fact, the interior of a cell is “super crowded” with molecules, which can significantly impact the behavior of DNA.

Researchers at Northwestern University have taken a more realistic approach to studying DNA by creating an environment that mimics the conditions within a living cell. Led by Professor John Marko, the team used microscopic magnetic tweezers to separate DNA and then carefully attach strands of it to surfaces on one end, and tiny magnetic particles on the other. This allowed them to conduct high-tech imaging and investigate how different types of molecules interact with DNA.

The researchers found that strand separation, a crucial process for initiating replication or making repairs, may require more mechanical force than previously believed. They introduced three types of molecules to the solution holding DNA, mimicking proteins and investigating interactions among glycerol, ethylene glycol, and polyethylene glycol (each approximately the size of one DNA double helix, two or three nanometers).

“We wanted to have a wide variety of molecules where some cause dehydration, destabilizing DNA mechanically, and then others that stabilize DNA,” said Northwestern post-doctoral researcher Parth Desai. “It’s not exactly analogous to things found in cells, but you could imagine that other competing proteins in cells will have a similar effect.”
The team wrote a paper on their findings, which will be published on June 17 in the Biophysical Journal. Marko and Desai hope to run more experiments that incorporate multiple crowding agents and move closer to a true representation of a cell.

“If this affects DNA strand separation, all protein interactions with DNA are also going to be affected,” said Marko. “For example, the tendency for proteins to stick to specific sites on DNA and to control specific processes — this is also going to be altered by crowding.”

Their research has significant implications for understanding fundamental biochemical processes and may lead to new medical advances. The team hopes to study how interactions between enzymes and DNA are impacted by crowding in a living cell, which could have far-reaching consequences for our understanding of cellular biology.

This work was supported by the National Institutes of Health (grant R01-GM105847) and by subcontract to the University of Massachusetts Center for 3D Structure and Physics of the Genome (under NIH grant UM1-HG011536).

Biochemistry Research

The Double Edge of Love and War: How Female Earwigs Evolved Deadly Claws for Mate Competition

Female earwigs may be evolving exaggerated weaponry just like males. A study from Toho University found that female forceps, once assumed to be passive tools, show the same kind of outsized growth linked to sexual selection as the male’s iconic pincers. This means that female earwigs might be fighting for mates too specifically for access to non-aggressive males challenging long-standing assumptions in evolutionary biology.

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In a groundbreaking study published in the Biological Journal of the Linnean Society on June 12, 2025, researchers from Toho University have shed new light on the evolution of deadly claws in female earwigs. For decades, it was believed that these pincer-like appendages were exclusive to males and evolved solely as weapons in battles with rivals. However, the findings of Tomoki Matsuzawa (then an undergraduate) and Associate Professor Junji Konuma have challenged this notion, revealing a surprising parallel between male and female earwigs.

The researchers conducted a quantitative study on the maritime earwig Anisolabis maritima, analyzing the morphometric data of both sexes. They found that not only do females possess forceps, but they also exhibit positive allometry – a phenomenon where certain body parts grow disproportionately large relative to body size. This is strikingly similar to the pattern observed in males, suggesting that female earwigs may have evolved these traits through sexual selection.

In their study, the team measured various dimensions of the head, thorax, abdomen, and bilateral forceps, as well as shape differences between sexes. They discovered that males possess thick, short, and curved forceps, while females have thin, long, and straight ones – a clear example of sexual dimorphism. When they plotted body size against forceps width and length on a log-log scale, the results revealed positive allometry in both males (in forceps width) and females (in forceps length).

Associate Professor Konuma explained that this finding suggests female earwigs may have evolved their forceps as effective weapons in competing for mates. A previous behavioral study had shown that female earwigs engage in competition with each other for small, non-aggressive males. This new research highlights the importance of considering female traits when studying the evolution of insect morphologies.

These groundbreaking findings demonstrate how the complex and fascinating world of insects can continue to surprise us, revealing the intricacies of natural selection and mate competition.

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Biochemistry Research

Unlocking Nature’s Secrets: Scientists Discover Natural Cancer-Fighting Sugar in Sea Cucumbers

Sea cucumbers, long known for cleaning the ocean floor, may also harbor a powerful cancer-fighting secret. Scientists discovered a unique sugar in these marine creatures that can block Sulf-2, an enzyme that cancer cells use to spread. Unlike traditional medications, this compound doesn t cause dangerous blood clotting issues and offers a cleaner, potentially more sustainable way to develop carbohydrate-based drugs if scientists can find a way to synthesize it in the lab.

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Unlocking Nature’s Secrets: Scientists Discover Natural Cancer-Fighting Sugar in Sea Cucumbers

In a groundbreaking study, researchers from the University of Mississippi and Georgetown University have discovered a natural sugar compound found in sea cucumbers that can effectively block Sulf-2, an enzyme crucial for cancer growth. This breakthrough has significant implications for the development of new cancer therapies.

The research team, led by Marwa Farrag, a fourth-year doctoral candidate in the UM Department of BioMolecular Sciences, worked tirelessly to isolate and study the sugar compound, fucosylated chondroitin sulfate, from the sea cucumber Holothuria floridana. This unique sugar is not commonly found in other organisms, making it an exciting area of research.

Human cells are covered in tiny, hairlike structures called glycans that help with cell communication, immune responses, and the recognition of threats such as pathogens. Cancer cells alter the expression of certain enzymes, including Sulf-2, which modifies the structure of glycans, helping cancer spread. By inhibiting this enzyme, researchers believe they can effectively fight against the spread of cancer.

Using both computer modeling and laboratory testing, the research team found that the sugar compound from sea cucumbers can effectively inhibit Sulf-2, a promising step towards developing new cancer therapies. This natural source is particularly appealing as it does not carry the risk of transferring viruses and other harmful agents, unlike extracting carbohydrate-based drugs from pigs or other land mammals.

While this discovery holds great promise, the researchers acknowledge that further study is needed to develop a viable treatment. One of the challenges lies in finding a way to synthesize the sugar compound for future testing. The interdisciplinary nature of the scientific study highlights the importance of cross-disciplinary collaboration in tackling complex diseases like cancer.

This groundbreaking research has far-reaching implications for the medical field and demonstrates the power of scientific discovery in unlocking nature’s secrets. As researchers continue to explore this area, they may uncover new therapies that can effectively combat cancer, ultimately saving lives and improving patient outcomes.

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Air Quality

Unlocking the Secrets of Environmental DNA: A Powerful Tool for Wildlife and Human Surveillance

Environmental DNA from the air, captured with simple air filters, can track everything from illegal drugs to the wildlife it was originally designed to study.

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Dublin, a city known for its warm welcome and lively traditional music, has an unsuspecting secret – the air is teeming with DNA from various species. From cannabis to bobcats, even magic mushrooms – at least their DNA – are floating on the breeze. A new study reveals that this phenomenon can be leveraged to track wildlife, viruses, and other substances in unprecedented ways.

David Duffy, Ph.D., a professor of wildlife disease genomics at the University of Florida, has developed innovative methods for deciphering environmental DNA (eDNA). His lab has been studying sea turtle genetics using eDNA from water samples. Expanding on this research, they’ve created tools to study every species – including humans – from DNA captured in environmental samples like air filters.

“What we’re finding is that you can get intact large fragments of DNA from the air,” Duffy said. “That means you can study species without directly having to disturb them.” This approach opens up vast possibilities for tracking all species in an area simultaneously, from microbes and viruses to vertebrates like bobcats and humans.

A proof-of-concept experiment demonstrated that researchers could pick up signs of hundreds of different human pathogens from the Dublin air, including viruses and bacteria. This surveillance method can aid scientists in tracking emerging diseases. Additionally, it can track common allergens, such as peanut or pollen, more precisely than current methods allow.

In another test, Duffy’s lab identified the origin of bobcats and spiders whose DNA was collected from air filters in a Florida forest. This technique allows researchers to track endangered species without having to lay eyes on them or gather scat samples – all while knowing their exact origin is crucial for conservation efforts.

This powerful analysis is paired with impressive speed and efficiency, as demonstrated by the team’s ability to process DNA for every species in as little as a day using compact, affordable equipment, and software hosted in the cloud. This quick turnaround is orders of magnitude faster than was possible just a few years ago, making advanced environmental studies more accessible to scientists worldwide.

However, Duffy and his collaborators have called for ethical guardrails due to the potential for sensitive human genetic data to be identified using these tools.

“It seems like science fiction, but it’s becoming science fact,” Duffy said. “The technology is finally matching the scale of environmental problems.” As researchers continue to explore the capabilities of eDNA, they must also address the challenges and implications of this rapidly developing field.

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