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Archive - Jul 4, 2018

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New Tools Used to Identify Childhood Cancer Genes

Using a new computational strategy, researchers at the University of Texas (UT) Southwestern Medical Center have identified 29 genetic changes that can contribute to rhabdomyosarcoma, an aggressive childhood cancer. The group used Bayesian analysis, a method for statistical inference, in conjunction with screening using CRISPR/Cas9, the much-heralded gene-editing tool, to confirm the statistical predictions. The work helps to explain "the engine" driving formation of rhabdomyosarcoma and suggests potential treatments. Furthermore, their research method can be used to identify genetic drivers of other cancers. Nearly all genes occur in cells as pairs. This research focused on genes for which there was only one copy or for which there were three or more copies. "We came up with the idea that the altered expression of key cancer genes may be driven by genomic copy-number amplifications or losses. We then developed a new computational algorithm called iExCN to predict cancer genes based on genome-wide copy-number and gene expression data," said Dr. Stephen Skapek, Chief of the Division of Pediatric Hematology-Oncology and with the Harold C. Simmons Comprehensive Cancer Center. The work also used several new experimental tools, including CRISPR/Cas9 screening technology, to verify the function of these predicted cancer genes in rhabdomyosarcoma. "The iExCN algorithm was developed based on Bayesian statistics, which is fundamentally different from commonly used statistics methodologies, and usually provides more accurate estimation of statistical associations, though it involves more complicated computation and longer processing time," said Dr. Lin Xu, Instructor in the Departments of Clinical Sciences and Pediatrics and with the Quantitative Biomedical Research Center.

Large Spiriform Nucleus (SpM) May Be Secret to Intelligence in Parrots; Key Brain Structure Is Much Larger in Parrots Than in Other Birds

University of Alberta neuroscientists have identified the neural circuit that may underlie intelligence in birds, according to a new study. The discovery is an example of convergent evolution between the brains of birds and primates, with the potential to provide insight into the neural basis of human intelligence. "An area of the brain that plays a major role in primate intelligence is called the pontine nuclei," explained Dr. Cristian Gutierrez-Ibanez, postdoctoral fellow in the Department of Psychology. "This structure transfers information between the two largest areas of the brain, the cortex and cerebellum, which allows for higher-order processing and more sophisticated behavior. In humans and primates, the pontine nuclei are large compared to other mammals. This makes sense given our cognitive abilities." Birds have very small pontine nuclei. Instead, they have a similar structure called the medial spiriform nucleus (SpM) that has similar connectivity. Located in a different part of the brain, the SpM does the same thing as the pontine nuclei, circulating information between the cortex and the cerebellum. "This loop between the cortex and the cerebellum is important for the planning and execution of sophisticated behaviors," said Dr. Doug Wylie, Professor of Psychology and co-author on the new study. Using samples from 98 birds from the largest collection of bird brains in the world, including everything from chickens and waterfowl to parrots and owls, the scientists studied the brains of birds, comparing the relative size of the SpM to the rest of the brain. They determined that parrots have a SpM that is much larger than that of other birds. "The SpM is very large in parrots. It's actually two to five times larger in parrots than in other birds, like chickens," said Dr. Gutierrez.