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In a new study in cells, University of Illinois researchers have adapted CRISPR gene-editing technology to cause the cell’s internal machinery to skip over a small portion of a gene when transcribing it into a template for protein building. This gives researchers a way not only to eliminate a mutated gene sequence, but to influence how the gene is expressed and regulated.

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Scientists at the University of Illinois at Urbana-Champaign have predicted new physics governing compression of water under a high-gradient electric field. Physics Professor Aleksei Aksimentiev and his post doctoral researcher James Wilson found that a high electric field applied to a tiny hole in a graphene membrane would compress the water molecules travelling through the pore by 3 percent. The predicted water compression may eventually prove useful in high-precision filtering of biomolecules for biomedical research.

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A new synthetic enzyme, crafted from DNA rather than protein, flips lipid molecules within the cell membrane, triggering a signal pathway that could be harnessed to induce cell death in cancer cells.   

Researchers at University of Illinois at Urbana-Champaign and the University of Cambridge say their lipid-scrambling DNA enzyme is the first in its class to outperform naturally occurring enzymes – and does so by three orders of magnitude. They published their findings in the journal Nature Communications.

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The mechanism of pattern formation in living systems is of paramount interest to bioengineers seeking to develop living tissue in the laboratory. Engineered tissues would have countless potential medical applications, but in order to synthesize living tissues, scientists need to understand the genesis of pattern formation in living systems.

A new study by researchers at the University of Illinois at Urbana-Champaign, the Massachusetts Institute of Technology, and the Applied Physics Laboratory, Johns Hopkins University has brought science one step closer to a molecular-level understanding of how patterns form in living tissue. The researchers engineered bacteria that, when incubated and grown, exhibited stochastic Turing patterns: a “lawn” of synthesized bacteria in a petri dish fluoresced an irregular pattern of red polka dots on a field of green.

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In a paper in Nano Letters ("Optical Voltage Sensing Using DNA Origami"), a research team, led by Keyser, Philip Tinnefeld from the Institute of Physical and Theoretical Chemistry at Technical University Braunschweig, and Aleksei Aksimentiev from the University of Illinois at Urbana-Champaign, has now reported for the first time, that a voltage can be read out in a nanopore with a dedicated Förster resonance energy transfer (FRET) sensor on a DNA origami.

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There is remarkable biodiversity in all but the most extreme ecosystems on Earth. When many species are competing for the same finite resource, a theory called competitive exclusion suggests one species will outperform the others and drive them to extinction, limiting biodiversity. But this isn’t what we observe in nature. Theoretical models of population dynamics have not presented a fully satisfactory explanation for what has come to be known as the diversity paradox.

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  • Condensed Matter Physics
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Quanta Magazine recently spoke with Goldenfeld about collective phenomena, expanding the Modern Synthesis model of evolution, and using quantitative and theoretical tools from physics to gain insights into mysteries surrounding early life on Earth and the interactions between cyanobacteria and predatory viruses. A condensed and edited version of that conversation follows.

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It took two years on a supercomputer to simulate 1.2 microseconds in the life of the HIV capsid, a protein cage that shuttles the HIV virus to the nucleus of a human cell. The 64-million-atom simulation offers new insights into how the virus senses its environment and completes its infective cycle.

The findings are reported in the journal Nature Communications.

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A common bacteria is furthering evidence that evolution is not entirely a blind process, subject to random changes in the genes, but that environmental stressors can also play a role. A NASA-funded team is the first group to design a method demonstrating how transposongs-DNA sequences that move positions within a genome-jump from place to place. The researchers saw that the jumping rate of these transposons, aptly-named "jumping genes" increases or decreases depending on factors in the environment, such as food supply.

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“Jumping genes” are ubiquitous. Every domain of life hosts these sequences of DNA that can “jump” from one position to another along a chromosome; in fact, nearly half the human genome is made up of jumping genes. Depending on their specific excision and insertion points, jumping genes can interrupt or trigger gene expression, driving genetic mutation and contributing to cell diversification. Since their discovery in the 1940s, researchers have been able to study the behavior of these jumping genes, generally known as transposons or transposable elements (TE), primarily through indirect methods that infer individual activity from bulk results.  However, such techniques are not sensitive enough to determine precisely how or why the transposons jump, and what factors trigger their activity.

Reporting in the Proceedings of the National Academy of Sciences, scientists at the University of Illinois at Urbana-Champaign have observed jumping gene activity in real time within living cells. The study is the collaborative effort of physics professors Thomas Kuhlman and Nigel Goldenfeld, at the Center for the Physics of Living Cells, a National Science Foundation Physics Frontiers Center.

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Researchers from the University of Illinois at Urbana-Champaign and the University of California-Davis (UC Davis) are combining in vivo experimentation with computation for highly accurate prediction of the genome-wide binding pattern of a key protein involved in brain disorders.

 “The MeCP2 gene is critical for proper brain development and expressed at near-histone levels in neurons, but the mechanism of its genomic localization remains poorly understood,” explained Jun Song, a professor of bioengineering and of physics at the University of Illinois at Urbana-Champaign. “Using high-resolution MeCP2 binding data, we show that DNA sequence features alone can predict binding with 88% accuracy.”

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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, a professor of physics at the University of Illinois, and Taekjip Ha, 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 Aksimentiev, the researchers published their work in the journal Nature Communications.

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A new study offers the first atomic-scale view of an interaction between the HIV capsid – the protein coat that shepherds HIV into the nucleus of human cells – and a host protein known as cyclophilin A. This interaction is key to HIV infection, researchers say.

A paper describing the research appears in the journal Nature Communications.

Cyclophilin A is found in most tissues of the human body, where it plays a role in the inflammatory response, immunity and the folding and trafficking of other proteins. When it fails to work properly or is overproduced in cells, cyclophilin A also can contribute to diseases such as rheumatoid arthritis, asthma, cancer and cardiovascular disease. It also facilitates some viral infections, including HIV.

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Bacterial chemotaxis, the process by which a bacterium changes direction in response to environmental cues, involves a complex array of chemical receptors (red, elongated molecules) and other sensory proteins (blue and green molecules), which work together to process sensory information. A new study offers high-resolution details of the structure and function of the chemosensory array, researchers report. 

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University of Illinois Swanlund Professor of Physics Nigel Goldenfeld, graduate student Farshid Jafarpour, and postdoctoral researcher Tommaso Biancalani have made a breakthrough in one of the most central chemical quirks of life as we know it: homochirality, the uniform “handedness” of biological molecules. Their new model addressing the emergence of this feature, published in Physical Review Letters (doi: 10.1103/PhysRevLett.115.158101) and highlighted by Physics suggests that homochirality can be used as a universal signature of life.

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Researchers, led by a team from the Beckman Institute, combined the power of two computational programs to determine the atomic structure of the abiological molecule cyanostar. This breakthrough will allow researchers to investigate the structure of more abiological molecules, which are relatively unknown.