Genome stability: Intricate process of DNA repair discovered

DNA illustration (stock image).

An elaborate system of filaments, liquid droplet dynamics and protein connectors enables the repair of some damaged DNA in the nuclei of cells, researchers at the University of Toronto have found. The findings further challenge the belief that broken DNA floats aimlessly -- and highlight the value of cross-disciplinary research in biology and physics.

DNA repair helps ensure genome stability, which in turn allows cells to function and promotes health in all organisms. Double-strand DNA breaks are especially toxic to cells, and researchers had assumed for decades that these breaks floated inside cell nuclei without direction, until they trigger other cellular changes or happen on a fixer mechanism.

That thinking began to change in 2015, when Karim Mekhail and his lab showed that damaged DNA can be intentionally transported by motor protein 'ambulances' to DNA 'hospitals,' areas enriched with certain repair factors in the nuclei. The researchers later worked with U of T aerospace engineers to show that after a single double-strand break, DNA travels for repair via long 'autobahns' of thread-like microtubules, which are also moving.

In the current study, Mekhail and lead author Roxanne Oshidari looked at yeast cells with many DNA double-strand breaks, and showed that coordination between shorter types of microtubule filaments and liquid-like droplets composed of DNA repair proteins enables the creation and function of a DNA repair centre.

"The liquid droplets work with intranuclear microtubules to promote the clustering of damaged DNA sites," says Mekhail, an associate professor of laboratory medicine and pathobiology at U of T. "Repair proteins at these different sites assemble in droplets that fuse into a larger repair-centre droplet, through the action of the shorter nuclear microtubules."

This larger oil-like droplet then behaves like a spider, says Mekhail, shooting out a web of star-shaped filaments that tether to the longer autobahns along which damaged DNA can be transported to the DNA hospitals.

The journal Nature Communications published the findings today.

Mekhail turned to Nasser Ashgriz, a professor in U of T's department of mechanical and industrial engineering, to measure and understand the role of droplets in the repair process. "You couldn't ask for better expertise in fluid dynamics, and he was just across the road," Mekhail says of Ashgriz, who runs U of T's multi-phase flow and spray systems lab.

Mekhail brought a video of the droplets to Ashgriz, who projected it on a large screen in his office and confirmed that fluid dynamics appeared to be at play. But communication across the biology-physics divide was challenging. "Understanding what they do was very difficult in the beginning because our terminologies are totally different," says Ashgriz.

When he and Mekhail used plain language to describe how the droplets behaved, however, things started to make sense. "We focused on the physical aspects of the droplets," Ashgriz says. "The physics that cause their motion and dynamics became our common language."

After months of talks and experiments, computer simulations repeatedly predicted that the shorter filaments would move like pistons, lowering pressure in the nucleoplasm and creating a suction effect that leads to the fusion of droplets. Mekhail and his team confirmed that finding in their lab.

"Often when we dive deep in the specifics of a field, we get separated from one another," Ashgriz says. "Bringing together people with different views can really improve understanding, and this work was a good example -- with credit to Karim for his vision and initiative."

Mekhail and his team also uncovered further important properties of the repair droplets with U of T professors Hyun Kate Lee and Haley Wyatt in the department of biochemistry, in a process Mekhail likens to play with toys. They ran the droplets through many tests, bouncing them against each other and observing their behaviour, which turned out to be very similar in a petri dish and in cells.

The most surprising finding came after several cycles of droplet fusion, the researchers found. "It was very bizarre and totally unexpected, I still remember the day," Mekhail says. Oshidari observed that the larger droplets initiate an internal concentration of filament building blocks, forcing creation of a kind of self-interlocking brick road, which together with the spidery webs allow DNA to hook onto the longer autobahn filaments.

The complex process is easy to miss when looking at DNA damage sites, says Mekhail, largely because imaging in the field has become highly automated. Most software has been set up to see what has already been seen. "We can't rely on the old ways of observing," he says. "We need to update our software and also go back to looking with the human eye, guided by simulations when needed."

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Materials provided by University of Toronto. Original written by Jim Oldfield. Note: Content may be edited for style and length.

Dogs process numerical quantities in similar brain region as humans

Dog and chalkboard addition (stock image).

Dogs spontaneously process basic numerical quantities, using a distinct part of their brains that corresponds closely to number-responsive neural regions in humans, finds a study at Emory University.

Biology Letters published the results, which suggest that a common neural mechanism has been deeply conserved across mammalian evolution.

"Our work not only shows that dogs use a similar part of their brain to process numbers of objects as humans do -- it shows that they don't need to be trained to do it," says Gregory Berns, Emory professor of psychology and senior author of the study.

"Understanding neural mechanisms -- both in humans and across species -- gives us insights into both how our brains evolved over time and how they function now," says co-author Stella Lourenco, an associate professor of psychology at Emory.

Such insights, Lourenco adds, may one day lead to practical applications such as treating brain abnormalities and improving artificial intelligence systems.

Lauren Aulet, a PhD candidate in Lourenco's lab, is first author of the study.

The study used functional magnetic resonance imaging (fMRI) to scan dogs' brains as they viewed varying numbers of dots flashed on a screen. The results showed that the dogs' parietotemporal cortex responded to differences in the number of the dots. The researchers held the total area of the dots constant, demonstrating that it was the number of the dots, not the size, that generated the response.

The approximate number system supports the ability to rapidly estimate a quantity of objects in a scene, such as the number of predators approaching or the amount of food available for foraging. Evidence suggests that humans primarily draw on their parietal cortex for this ability, which is present even in infancy.

This basic sensitivity to numerical information, known as numerosity, does not rely on symbolic thought or training and appears to be widespread throughout the animal kingdom. Much of the research in non-humans, however, has involved intensive training of the subjects.

Previous research, for example, has found that particular neurons in the parietal cortex of monkeys are attuned to numerical values. Such studies had not clarified whether numerosity is a spontaneous system in non-human primates, because the subjects underwent many trials and received rewards for selecting scenes with greater numbers of dots in preparation for the experiments.

Behavioral studies in dogs that were trained in the task of discriminating between different quantities of objects have also indicated that dogs are sensitive to numerosity.

The Emory researchers wanted to delve further into the neural underpinnings of canine number perception using fMRI.

Berns is founder of the Dog Project, which is researching evolutionary questions surrounding man's best, and oldest friend. The project was the first to train dogs to voluntarily enter an fMRI scanner and remain motionless during scanning, without restraint or sedation.

Lourenco primarily researches human visual perception, cognition and development.

Eleven dogs of varying breeds were involved in the current fMRI experiments. The dogs did not receive advance training in numerosity. After entering the fMRI, they passively viewed dot arrays that varied in numerical value. Eight of the 11 dogs showed greater activation in the parietotemporal cortex when the ratio between alternating dot arrays was more dissimilar than when the numerical values were constant.

"We went right to the source, observing the dogs' brains, to get a direct understanding of what their neurons were doing when the dogs viewed varying quantities of dots," Aulet says. "That allowed us to bypass the weaknesses of previous behavioral studies of dogs and some other species."

Humans and dogs are separated by 80 million years of evolution, Berns notes. "Our results provide some of the strongest evidence yet that numerosity is a shared neural mechanism that goes back at least that far," he says.

Unlike dogs and other animals, humans are able to build on basic numerosity in order to do more complex math, drawing primarily on the prefrontal cortex. "Part of the reason that we are able to do calculus and algebra is because we have this fundamental ability for numerosity that we share with other animals," Aulet says. "I'm interested in learning how we evolved that higher math ability and how these skills develop over time in individuals, starting with basic numerosity in infancy."

Additional authors of the study include Veronica Chiu and Ashley Prichard, Emory graduate students in psychology, and Mark Spivak, CEO of Comprehensive Pet Therapy. Spivak and Berns co-founded Dog Star Technologies to develop techniques to study how dogs perceive the world.

The work was supported by the National Institutes of Health, the John Merck Fund and the Office of Naval Research.

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Story Source:

Materials provided by Emory Health Sciences. Original written by Carol Clark. Note: Content may be edited for style and length.

Dogs process numerical quantities in similar brain region as humans

Dog and chalkboard addition

Dogs spontaneously process basic numerical quantities, using a distinct part of their brains that corresponds closely to number-responsive neural regions in humans, finds a study at Emory University.

Biology Letters published the results, which suggest that a common neural mechanism has been deeply conserved across mammalian evolution.

"Our work not only shows that dogs use a similar part of their brain to process numbers of objects as humans do -- it shows that they don't need to be trained to do it," says Gregory Berns, Emory professor of psychology and senior author of the study.

"Understanding neural mechanisms -- both in humans and across species -- gives us insights into both how our brains evolved over time and how they function now," says co-author Stella Lourenco, an associate professor of psychology at Emory.

Such insights, Lourenco adds, may one day lead to practical applications such as treating brain abnormalities and improving artificial intelligence systems.

Lauren Aulet, a PhD candidate in Lourenco's lab, is first author of the study.

The study used functional magnetic resonance imaging (fMRI) to scan dogs' brains as they viewed varying numbers of dots flashed on a screen. The results showed that the dogs' parietotemporal cortex responded to differences in the number of the dots. The researchers held the total area of the dots constant, demonstrating that it was the number of the dots, not the size, that generated the response.

The approximate number system supports the ability to rapidly estimate a quantity of objects in a scene, such as the number of predators approaching or the amount of food available for foraging. Evidence suggests that humans primarily draw on their parietal cortex for this ability, which is present even in infancy.

This basic sensitivity to numerical information, known as numerosity, does not rely on symbolic thought or training and appears to be widespread throughout the animal kingdom. Much of the research in non-humans, however, has involved intensive training of the subjects.

Previous research, for example, has found that particular neurons in the parietal cortex of monkeys are attuned to numerical values. Such studies had not clarified whether numerosity is a spontaneous system in non-human primates, because the subjects underwent many trials and received rewards for selecting scenes with greater numbers of dots in preparation for the experiments.

Behavioral studies in dogs that were trained in the task of discriminating between different quantities of objects have also indicated that dogs are sensitive to numerosity.

The Emory researchers wanted to delve further into the neural underpinnings of canine number perception using fMRI.

Berns is founder of the Dog Project, which is researching evolutionary questions surrounding man's best, and oldest friend. The project was the first to train dogs to voluntarily enter an fMRI scanner and remain motionless during scanning, without restraint or sedation.

Lourenco primarily researches human visual perception, cognition and development.

Eleven dogs of varying breeds were involved in the current fMRI experiments. The dogs did not receive advance training in numerosity. After entering the fMRI, they passively viewed dot arrays that varied in numerical value. Eight of the 11 dogs showed greater activation in the parietotemporal cortex when the ratio between alternating dot arrays was more dissimilar than when the numerical values were constant.

"We went right to the source, observing the dogs' brains, to get a direct understanding of what their neurons were doing when the dogs viewed varying quantities of dots," Aulet says. "That allowed us to bypass the weaknesses of previous behavioral studies of dogs and some other species."

Humans and dogs are separated by 80 million years of evolution, Berns notes. "Our results provide some of the strongest evidence yet that numerosity is a shared neural mechanism that goes back at least that far," he says.

Unlike dogs and other animals, humans are able to build on basic numerosity in order to do more complex math, drawing primarily on the prefrontal cortex. "Part of the reason that we are able to do calculus and algebra is because we have this fundamental ability for numerosity that we share with other animals," Aulet says. "I'm interested in learning how we evolved that higher math ability and how these skills develop over time in individuals, starting with basic numerosity in infancy."

Additional authors of the study include Veronica Chiu and Ashley Prichard, Emory graduate students in psychology, and Mark Spivak, CEO of Comprehensive Pet Therapy. Spivak and Berns co-founded Dog Star Technologies to develop techniques to study how dogs perceive the world.

The work was supported by the National Institutes of Health, the John Merck Fund and the Office of Naval Research.

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Story Source:

Materials provided by Emory Health Sciences. Original written by Carol Clark. Note: Content may be edited for style and length.

Microbes harvest electrons: Novel process discovered

Bacteria illustration

Ever since scientists discovered that certain microbes can get their energy from electrical charges, researchers have wondered how they do it.

Bacteria don't have mouths, so they need another way to bring their fuel into their bodies. New research from Washington University in St. Louis reveals how one such bacteria pulls in electrons straight from an electrode source. The work from the laboratory of Arpita Bose, assistant professor of biology in Arts & Sciences, was published Nov. 5 in the scientific journal mBio.

"The molecular underpinning of this process has been difficult to unravel until our work," Bose said. "This is mostly due to the complex nature of the proteins involved in this process. But now, for the first time, we understand how phototrophic microbes can accept electrons from solid and soluble substances."

Dinesh Gupta, a PhD candidate in the Bose laboratory, is the first author on this new study. "I was excited when we found that these phototrophic bacteria use a novel processing step to regulate the production of key electron transfer protein involved in this process," Gupta said. "This study will aid in designing a bacterial platform where bacteria can feed on electricity and carbon dioxide to produce value-added compounds such as biofuels."

Getting the electricity across the outer layer of the bacteria is the key challenge. This barrier is both nonconductive and impermeable to insoluble iron minerals and/or electrodes.

Bose and her collaborators, including Robert Kranz, professor of biology, showed that the naturally occurring strain of Rhodopseudomonas palustris TIE-1 builds a conduit to accept electrons across its outer membrane. The bacteria relies on an iron-containing helper molecule called a deca-heme cytochrome c. By processing this protein, TIE-1 can form an essential bridge to its electron source.

Extracellular electron uptake, or EEU, can help microbes to survive under nutrient-scarce conditions.

Now that Bose has documented these mechanisms behind EEU, she hopes to use it as a biological marker to identify other electricity-eating bacteria in the wild. The findings will help researchers to understand the importance of this functionality in metabolic evolution and microbial ecology.

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Story Source:

Materials provided by Washington University in St. Louis. Original written by Talia Ogliore. Note: Content may be edited for style and length.

Microbes harvest electrons: Novel process discovered

Bacteria illustration

Ever since scientists discovered that certain microbes can get their energy from electrical charges, researchers have wondered how they do it.

Bacteria don't have mouths, so they need another way to bring their fuel into their bodies. New research from Washington University in St. Louis reveals how one such bacteria pulls in electrons straight from an electrode source. The work from the laboratory of Arpita Bose, assistant professor of biology in Arts & Sciences, was published Nov. 5 in the scientific journal mBio.

"The molecular underpinning of this process has been difficult to unravel until our work," Bose said. "This is mostly due to the complex nature of the proteins involved in this process. But now, for the first time, we understand how phototrophic microbes can accept electrons from solid and soluble substances."

Dinesh Gupta, a PhD candidate in the Bose laboratory, is the first author on this new study. "I was excited when we found that these phototrophic bacteria use a novel processing step to regulate the production of key electron transfer protein involved in this process," Gupta said. "This study will aid in designing a bacterial platform where bacteria can feed on electricity and carbon dioxide to produce value-added compounds such as biofuels."

Getting the electricity across the outer layer of the bacteria is the key challenge. This barrier is both nonconductive and impermeable to insoluble iron minerals and/or electrodes.

Bose and her collaborators, including Robert Kranz, professor of biology, showed that the naturally occurring strain of Rhodopseudomonas palustris TIE-1 builds a conduit to accept electrons across its outer membrane. The bacteria relies on an iron-containing helper molecule called a deca-heme cytochrome c. By processing this protein, TIE-1 can form an essential bridge to its electron source.

Extracellular electron uptake, or EEU, can help microbes to survive under nutrient-scarce conditions.

Now that Bose has documented these mechanisms behind EEU, she hopes to use it as a biological marker to identify other electricity-eating bacteria in the wild. The findings will help researchers to understand the importance of this functionality in metabolic evolution and microbial ecology.

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Story Source:

Materials provided by Washington University in St. Louis. Original written by Talia Ogliore. Note: Content may be edited for style and length.