Justn Kitzes, an assistant professor in Pitt’s Biological Sciences Department, works with Pitt CRC research consultant Barry Moore II in refining OpenSoundscape – a machine learning program Kitzes developed to create dense, meaningful and applicable data on the distribution and survival of species based on a model of simple acoustic sensors acquiring vast sets of bird calls and machine learning programs making sense of the data.
“Bird calls have lots of variability between them, but also lots of similarity," Kitzes explains. "Bird calls can vary greatly within one species. Birds sing simultaneously on top of each other. It is a complex picture.” Here, Moore, left, and Kitzes show off one of the acoustic sensors.
Strengthening the marriage of computation and experimentation is a goal of Peng Liu, assistant professor in Pitt’s Department of Chemistry. The Liu lab is using Pitt CRC in refining computation models as part of a research process incorporating rapid experimental feedback.
“With only computation, we can never really reproduce reality,” explains Liu. “There can be a tremendous amount of error in computation when dealing with complex chemical systems. Experimentation works with realistic systems, but it is often based on trial and error. To advance computation to guide experiments you need new computational models that incorporate experimentation. Experimentation may be trial and error, but don’t forget the importance of intuition in trial and error.”
Computational flow cytometry offers new possibilities to researchers at Pitt with the acquisition of the Cytek Aurora model, which identifies thousands of cells with disease indicators per second, twice the capacity of existing technology. Pitt CRC customized data pipelines that automate the analysis.
At left, Lisa Borghesi, PhD, scientific director of the Unified Flow Core, points out the powerful lasers within the cytometer.
Students step into science by identifying and naming thousands of bacteriophages - viruses that attack bacteria - as part of the SEA-PHAGES program headed up by Pitt biologist Graham Hatfull. CRC powers the sequencing and analysis of a sliver of the billions-plus-strong, ever-changing population of bacteriophages. “Bacteria and phages are locked in a 3-billion year war,” Hatfull says simply. “Dynamic populations have been evolving for a long time, and they keep evolving.”
Hatfull and his team are receiving global attention for the role of SEA-PHAGES in the dramatically successful treatment of a 15-year-old girl for a rare bacterial infection. Read a small sample of of the media coverage at NOVA, Nature Medicine, NPR, The Wall Street Journal, and The Atlantic.
Left, Pitt students Aishwarya Mukundan and Daniel Zipfel hunt for phages in Pitt's SEA-PHAGE lab.