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Archive - Feb 12, 2018


Machine-Learning Algorithm Uses Time-Series Data to Reveal Underlying Gene Regulatory Networks in Cells

Biologists have long understood the various parts within the cell. But how these parts interact with and respond to each other is largely unknown. "We want to understand how cells make decisions, so we can control the decisions they make," said Northwestern University's Neda Bagheri (photo), PhD. "A cell might decide to divide uncontrollably, which is the case with cancer. If we understand how cells make that decision, then we can design strategies to intervene." To better understand the mysterious interactions that occur inside cells, Dr. Bagheri and her team have designed a new machine learning algorithm that can help connect the dots among the genes' interactions inside cellular networks. Called "Sliding Window Inference for Network Generation," or SWING, the algorithm uses time-series data to reveal the underlying structure of cellular networks. Supported by the National Science Foundation, the National Institutes of Health, and Northwestern's Biotechnology Training Program, the research was published online on February 12, 2018 in PNAS. Justin Finkle and Jia Wu, graduate students in Dr. Bagheri's laboratory, served as co-first authors of the paper, which is titled “Windowed Granger Causal Inference Strategy Improves Discovery of Gene Regulatory Networks.” In biological experiments, researchers often perturb a subject by altering its function and then measure the subject's response. For example, researchers might apply a drug that targets a gene's expression level and then observe how the gene and downstream components react. But it is difficult for those researchers to know whether the change in genetic landscape was a direct effect of the drug or the effect of other activities taking place inside the cell.

National Alliance for Hispanic Health Brings NIH's All of Us Journey to Oregon State University Feb 15

Oregon State University and the National Alliance for Hispanic Health will host the National Institutes of Health's All of Us Journey ( on Thursday, February 15, 2018. The traveling, hands-on exhibit raises awareness about the All of Us Research Program (—an ambitious effort to gather data from 1 million or more people living in the United States to accelerate precision medicine research and improve health. "We are glad the National Alliance for Hispanic Health recognizes our region as an important stop on the national tour and they are taking on a national effort to focus on the Hispanic population. If you look at most biomedical, behavioral, or social science research, it doesn't involve the Hispanic population," said Javier Nieto, Dean of the College of Public Health and Human Sciences at Oregon State. "Most clinical trials and large population health studies do not include Hispanic participants. It is our duty to figure out how we can better their lives through science." Campus and community members are invited to come learn about the NIH’s All of Us program and get information on healthy living and preventing disease. Corvallis is one stop on the All of Us Journey's 37-week national tour. "All of Us is so important to shaping the future of health in the United States," said Dr. Jane L. Delgado, President and CEO of the National Alliance for Hispanic Health, the nation's leading Hispanic health advocacy group.

Researchers in Sweden Create Gold-Treated DNA Wires 100 Times More Sensitive Than Other Biosensors

On February 12, 2018, scientists in Sweden reported a nanoengineering innovation that offers hope for treatment of cancer, infections, and other health problems –i.e., conductive wires of DNA enhanced with gold which could be used to electrically measure hundreds of biological processes simultaneously. While DNA nanowires have been in development for some time, the method developed at KTH Royal Institute of Technology and Stockholm University produces a unique three-dimensional biosensor for better effectiveness than flat, two-dimensional sensors. “Our geometry makes it much easier to measure several biomolecules simultaneously, and is also 100 times more sensitive,” says KTH Professor Wouter van der Wijngaart. “This is the first out-of-plane metallic nanowire formation based on stretching of DNA through a porous membrane,” Professor van der Wijngaart says. The DNA nanowires, treated with gold to make them conductive, are created only in the presence of specific biomarker molecules in the patient sample and transmit evidence of the biomarker presence, even when such molecules are low in concentration. The conductive wires short-circuit both sides of the membrane, which makes them easy to detect. To make the wires, the team first captured molecules, on the surface of a porous membrane, which were designed to only bind with specific biomarker molecules in the sample. Such molecular binding events then trigger the formation of long DNA wires that are drawn through the pores by vacuum drying. Then the membrane is treated with a solution of nanometer-sized gold particles, which can only bind to DNA molecules in a certain sequence, Professor van der Wijngaart says. The researchers published their results online on February 12, 2018 in Microsystems and Nanoengineering (Nature Publishing Group).