This study marks the first time researchers have accurately predicted a cell’s dynamics at the genome scale (for most of the thousands of components in the cell). The findings, which are based on a study of Halobacterium salinarum, a free-living microbe that lives in hyper-extreme environments, appear in the latest issue of the journal Cell.
The study’s lead authors are New York University Assistant Biology Professor Richard Bonneau, who holds appointments at NYU’s Center for Genomics & Systems Biology and the university’s Courant Institute for Mathematical Sciences, and Nitin Baliga of the Institute for Systems Biology in Seattle, WA. The study also included researchers at the University of Maryland, Vanderbilt University, and the University of Washington.
The researchers focused on a little studied organism that can survive high salt, radiation, and other stresses that would be deadly to most other organisms. By focusing on such an organism the researchers were able to show definitively that they could understand and model the circuit controlling the cell directly from experiments designed to measure all genes in the genome simultaneously. These are called systems-biology experiments. This scholarship is part of a new scientific field, systems biology, which examines how genes influence each other via extremely large networks of interaction and how these networks respond to stimuli, adapting over time to new environments and cell states. The field has blossomed over the past 10 years, spurred by successful mapping of genomic systems.
By a combination of experimental and algorithmic advances studies in this area have shown that scientific knowledge can go from genome to a functional and dynamical draft-model of the whole organism in a relatively short time. Important previous studies in this area identified cell components (genome sequencing) and how cell components are connected. But the study in Cell went beyond previous scholarship and accurately modeled how Halobacterium, an important organism in high-salt environments such as the Dead Sea or Utah’s Great Salt Lake, functioned over time and responded to changing environmental conditions. The researchers were, for the first time, able to predict how over 80 percent of the total genome (several thousand genes) responded to stimuli over time, dynamically rearranging the cell’s makeup to meet environmental stresses.
“This organism is amazingly versatile and tolerates lots of different extreme environmental stresses,” said Bonneau. “It does this by making decisions and dynamically changing the levels of genes and proteins; if it makes incorrect decisions it dies. Our model shows how these decisions get made, how the bug responds.”
“This is also a good model to explain how, in general, cells make stable decisions as they move through time scales,” added Bonneau, who is part of an NYU research group that handled the analysis of this genome. “If you want to understand how cells respond to their environments, the model offers a clearer window than previously existed for this domain of life.”
The collaboration between Baliga’s and Bonneau’s research groups represents a type of partnership becoming more essential to biological and biomedical research: biologists and computer scientists teaming up to design experiments and analysis that synergize to decipher living systems, resulting in ever more complex and accurate models of the cell. The result is more comprehensive, reaching genome-scale levels, more accurate, and more relevant to biologists and biomedical researchers hoping to understand the whole system.
Bonneau added that by understanding how biological systems function, researchers can then turn their attention to engineering the biosynthesis of biofuels and pharmaceuticals.
“We are now gearing up to try this sort of analysis on several other organisms,” he noted. “In addition, because this study examined the dynamics of a key environmental microbe it offers a window into understanding life in extreme environments, in some cases created by human activities, such as the concentration of pollution by evaporation or high salt marine environments.”
James Devitt | EurekAlert!
Smart Data Transformation – Surfing the Big Wave
02.12.2016 | Fraunhofer-Institut für Angewandte Informationstechnik FIT
Climate change could outpace EPA Lake Champlain protections
18.11.2016 | University of Vermont
A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.
Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...
In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.
“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...
The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.
The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...
Broadband rotational spectroscopy unravels structural reshaping of isolated molecules in the gas phase to accommodate water
In two recent publications in the Journal of Chemical Physics and in the Journal of Physical Chemistry Letters, researchers around Melanie Schnell from the Max...
The efficiency of power electronic systems is not solely dependent on electrical efficiency but also on weight, for example, in mobile systems. When the weight of relevant components and devices in airplanes, for instance, is reduced, fuel savings can be achieved and correspondingly greenhouse gas emissions decreased. New materials and components based on gallium nitride (GaN) can help to reduce weight and increase the efficiency. With these new materials, power electronic switches can be operated at higher switching frequency, resulting in higher power density and lower material costs.
Researchers at the Fraunhofer Institute for Solar Energy Systems ISE together with partners have investigated how these materials can be used to make power...
16.11.2016 | Event News
01.11.2016 | Event News
14.10.2016 | Event News
02.12.2016 | Medical Engineering
02.12.2016 | Agricultural and Forestry Science
02.12.2016 | Physics and Astronomy