Summary: A new 3D platform the simulates zebrafish behavior opens new avenues for research without the use of animals.
Source: NYU Tndon School of Engineering.
A research team headed by Professor Maurizio Porfiri has developed the first successful 3D computer modeling of the motions of zebrafish, which are increasingly the species of choice for biomedical research. NeuroscienceNews.com image is for credited to NYU Tndon School of Engineering.
Every year, approximately 20 million animals are used in scientific research. Increasingly these animals are zebrafish, which are quickly eclipsing rodents and primates as a favored species in biomedical research because of their genetic similarity to humans and their versatility. However, concerns voiced by policymakers, citizens, and scientific authorities about the number of animals used in experiments have led researchers to explore alternative, computer-based methodologies that could help reduce animal usage without compromising results.
A team of researchers led by Maurizio Porfiri, professor of mechanical and aerospace engineering at the NYU Tandon School of Engineering, has successfully developed the first data-driven modeling framework capable of simulating zebrafish swimming in three dimensions. It is rooted in real-life data and robust enough to potentially replace animals in some types of research, particularly neurobehavioral studies that are critical to understanding the brain.
The findings were published in Scientific Reports. The paper, entitled “In-silico Experiments of Zebrafish Behavior: Modeling Swimming in Three Dimensions,” was coauthored by Porfiri, NYU Tandon doctoral candidate Violet Mwaffo, and Sachit Butail, an assistant professor at Northern Illinois University.
Drawing analogies from the field of financial engineering, in which Mwaffo was trained, the group has made rapid progress in modeling the behavior of zebrafish from the 2D model first developed in 2015. The 3D model also features variables such as speed modulation, wall interaction, and the burst-and-coast swimming style of zebrafish. These technical improvements allow for in-silico experiments, or computer simulations, of zebrafish behavior that would otherwise require a large number of animal subjects and months of experiments.
“We’re proposing to use this zebrafish model during the pre-clinical stages of research,” said Porfiri. “While it can’t entirely replace animal testing, we expect using this model will lead to an overall decrease in the use of animal test subjects.”
The model was calibrated on a dataset of zebrafish swimming in 3D acquired by Porfiri’s group through a novel tracking framework, which was developed by Butail during his postdoctoral work at NYU Tandon.
To demonstrate the use of the model, the authors turned to scientific literature to collect data on the speed of zebrafish swimming in tanks of different dimensions at labs all over the world. The researchers observed that a correlation exists between increasing tank size and the speed of the zebrafish, and such a correlation is anticipated by in-silico experiments. Uncovering such a correlation from experiments would require thousands of animals, while computer-modeling requires only a few minutes of calculations.
While these initial results are promising, a more accurate model capable of reproducing all the behaviors of a zebrafish is still in the works. The next steps involve exploring social interaction and response to live and engineered stimuli.
Funding: The research was funded by the National Science Foundation.
Source: Kathleen Hamilton – NYU Tndon School of Engineering
Image Source: NeuroscienceNews.com image is credited to NYU Tndon School of Engineering.
Original Research: Full open access research for “In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions” by Violet Mwaffo, Sachit Butail & Maurizio Porfiri in Scientific Reports. Published online January 10 2017 doi:10.1038/srep39877
Abstract
In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions
Zebrafish is fast becoming a species of choice in biomedical research for the investigation of functional and dysfunctional processes coupled with their genetic and pharmacological modulation. As with mammals, experimentation with zebrafish constitutes a complicated ethical issue that calls for the exploration of alternative testing methods to reduce the number of subjects, refine experimental designs, and replace live animals. Inspired by the demonstrated advantages of computational studies in other life science domains, we establish an authentic data-driven modelling framework to simulate zebrafish swimming in three dimensions. The model encapsulates burst-and-coast swimming style, speed modulation, and wall interaction, laying the foundations for in-silico experiments of zebrafish behaviour. Through computational studies, we demonstrate the ability of the model to replicate common ethological observables such as speed and spatial preference, and anticipate experimental observations on the correlation between tank dimensions on zebrafish behaviour. Reaching to other experimental paradigms, our framework is expected to contribute to a reduction in animal use and suffering.
“In-silico experiments of zebrafish behaviour: modeling swimming in three dimensions” by Violet Mwaffo, Sachit Butail & Maurizio Porfiri in Scientific Reports. Published online January 10 2017 doi:10.1038/srep39877
http://neurosciencenews.com/simulated-zebrafish-research-5939/
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