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Archive - Mar 23, 2016

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DNA Molecules Directly Interact with Each Other Based on Sequence, Study Finds

Proteins play a large role in DNA regulation, but a new study finds that DNA molecules directly interact with one another in a way that's dependent on the sequence of the DNA and epigenetic factors. This could have implications for how DNA is organized in the cell and even how genes are regulated in different cell types, the researchers say. Led by Aleksei Aksimentiev, Ph.D., a professor of physics at the University of Illinois, and Taekjip Ha, Ph.D., a professor of biophysics and biophysical chemistry at Johns Hopkins University and an adjunct at the University of Illinois Center for the Physics of Living Cells along with Dr. Aksimentiev, the researchers published their work online on March 22, 2016 in the journal Nature Communications. The open-access article is titled “Direct Evidence for Sequence-Dependent Attraction Between Double-Stranded DNA Controlled by Methylation.” "We are still only starting to explore the physical properties of DNA. It's not just a string of letters," Dr. Aksimentiev said. "It's a complex molecule with unique characteristics. The prevailing hypothesis is that everything that happens inside the nucleus, the way the DNA is organized, is all the work of proteins. What we show is that direct DNA-DNA interactions may play a role in large-scale chromosome organization as well." Using the Blue Waters supercomputer at the National Center for Supercomputing Applications on the Illinois campus, Dr. Aksimentiev and postdoctoral researcher Dr. Jejoong Yoo performed detailed simulations of two DNA molecules interacting in a charged solution such as is found in the cell. The supercomputer allowed them to map each individual atom and its behavior, and to measure the forces between the molecules.

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First Evidence Found That “Cryptic Female Choice” Is Adaptive

Researchers from New Zealand's University of Otago studying chinook salmon have provided the first evidence that "cryptic female choice" (CFC) enhances fertilization success and embryo survival. CFC involves females using physical or chemical mechanisms to control which male fertilizes their eggs after mating, and is known to occur in a number of species. In 2008, Department of Anatomy researchers Dr. Patrice Rosengrave and Professor Neil Gemmell were the first to show that CFC occurred in salmon. When these fish spawn, eggs and sperm are shed simultaneously into the surrounding water with ovarian fluid being secreted with the eggs. The scientists demonstrated that ovarian fluid helped or hindered sperm swiftness depending on the male it came from. Now, after conducting a series of competitive and non-competitive fertilization experiments, the pair and colleagues have provided the first evidence that CFC contributes to reproductive success. Dr. Rosengrave says they found that not only does a particular female's ovarian fluid give a bigger boost to some male's sperm and not others, these speedier sperm have a significantly higher chance of winning the race to fertilize eggs and the resulting offspring have a better survival rate as embryos. "Additionally, after assessing the genetic quality of the males we found embryo survival was linked to being sired by higher-quality fathers," she says. The findings may have wider implications for our understanding of animal, or even human, reproduction, she adds. "There could well be equivalent mechanisms at play in environments such as mucus on vaginal or uterine walls." The research was published online on March 23, 2016 in the UK journal Proceedings of the Royal Society B.

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