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).

The fruit fly (Drosophila melanogaster) has long been a model organism for scientists studying genetics, development, and behavior. However, despite its importance, the intricacies of the fruit fly’s nervous system have remained somewhat of a mystery – until now. Researchers at Leipzig University and other institutions have made a groundbreaking discovery, publishing a study in Nature that provides comprehensive insights into the entire nervous system of the adult fruit fly.

For the first time, scientists have mapped out the neural connections (the connectome) in a female and a male specimen, revealing differences between the two sexes. This breakthrough is a significant step forward in understanding the complex interactions within the fruit fly’s brain and nervous system.

The study, led by Dr. Katharina Eichler from Leipzig University, involved analyzing three connectomes: one female brain data set and two nerve cord data sets (one male, one female). The researchers used light microscopy to identify all neurons in the neck of the fruit fly that could be visualized using this technique.

This allowed them to analyze the circuits formed by these cells in their entirety. When comparing male and female neurons, the scientists identified sex-specific differences for the first time. They found previously unknown cells that exist only in one sex and are absent in the other.

One notable example is a descending neuron known as aSP22, which communicates with neurons present only in females. This finding provides an explanation for the behavioral differences observed when this neuron is active: female flies extend their abdomen to lay eggs, while males curl theirs forward to mate.

The study’s findings are significant not only because they provide a comprehensive overview of the fruit fly connectome but also because they offer a “roadmap” for future research. By understanding the intricate connections within the nervous system, scientists can design more intelligent experiments to investigate the function of individual neurons or entire circuits – saving time and resources.

As Eichler notes, now that the technical challenges in analyzing the fruit fly’s nervous system have been overcome, her research group is working on two new data sets covering the entire central nervous system of both a female and a male specimen. This continued research will undoubtedly shed more light on the complexities of the fruit fly brain and its implications for our understanding of nervous systems in general.

The American crocodile, a species once thought to be widespread across the Caribbean, Central America, and Mexico’s Pacific coast, has been hiding secrets. Researchers from McGill University, in collaboration with Mexican scientists, have made a groundbreaking discovery that challenges long-held assumptions about this iconic creature. Two previously unknown species of crocodiles have been found on the island of Cozumel and the atoll of Banco Chinchorro, both located off the Yucatán Peninsula.

“Biodiversity is disappearing faster than we can discover what we’re losing,” said Biology Professor Hans Larsson, the principal investigator. “Most species of crocodiles are already endangered, and rapid shoreline development threatens nearly every population. Our research aimed to uncover the true diversity of crocodiles on these isolated islands.”

Larsson and his team analyzed the genetic sequences of crocodile populations from Cozumel and Banco Chinchorro. By comparing these sequences to those of crocodiles across the Caribbean, Central America, and Mexico’s Pacific coast, they found striking levels of genetic differentiation, leading them to conclude that these populations were not simply variants of Crocodylus acutus.

“These results were totally unexpected,” former Larsson graduate student and lead author José Avila-Cervantes said. “We assumed Crocodylus acutus was a single species ranging from Baja California to Venezuela and across the Caribbean. Our study is the first to extensively explore genomic and anatomical variation in these animals.”

This discovery has significant conservation implications, as the newly identified species live in small, isolated populations, each numbering fewer than 1,000 breeding individuals. While both populations appear stable, their limited numbers and habitat restrictions make them vulnerable.

“The rapid loss of biodiversity can only be slowed if we know what species are most at risk,” said Larsson. “Now that we recognize these crocodiles as distinct species, it’s crucial to protect their habitats. Limiting land development and implementing careful conservation strategies on Cozumel and Banco Chinchorro will be key to ensuring their survival.”

The research was conducted with the help of local colleagues, including Pierre Charruau at El Colegio de la Frontera Sur in Mexico. The team captured and released crocodiles, collecting blood and scale samples for analysis. Genetic sequencing was carried out at McGill by José Avila-Cervantes during his graduate studies, with additional research on skull morphology by fellow McGill graduate student Hoai-Nam Bui.

This research was funded by the Canadian Foundation for Innovation, the Digital Research Alliance of Canada), the Comisión Nacional para el Conocimiento y Uso de la Biodiversidad, and the Natural Sciences and Engineering Research Council of Canada.