Yesterday we told you about how mRNA plays a role in protein expression that goes well beyond protein synthesis. In the video below, principal investigator Yehuda Ben-Shahar explains his lab’s findings.
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Researchers from North Carolina State University have developed a computational tool designed to guide future research on biochemical pathways by identifying which components in a biological system are related to specific biochemical processes, including those processes responsible for gene expression, cell signaling, stress response, and metabolism.
“Our goal was to identify modules, or functional units, which are critical to the performance of the biochemical pathways that govern a host of biological processes,” says Dr. Cranos Williams, an assistant professor of electrical and computer engineering at NC State and senior author of a paper describing the work.
“For example, a car has lots of modules – the parts that make it go, the parts that make it stop, the parts that let you steer, etc. If you understand those modules, you understand how the car works. But if you just have a list of parts, that’s not very helpful.
“And what we have right now for many biochemical pathways is essentially just a list of parts – metabolites, biochemical reactions and enzymes that facilitate those reactions – and, in some cases, how those parts change over time. What we need is a clear understanding of which parts work together. That’s where our new algorithm comes in.”
The researchers developed an algorithm that allows them to identify which parts – the metabolites, reactions and enzymes – are related to each other and can be grouped into functional modules. The algorithm also identifies whether an individual component plays a role in multiple modules. For example, an enzyme may play a primary role in critical stress response pathways and a secondary role in processes associated with programmed cell maintenance or death.
The algorithm also characterizes how the relationships between different modules and individual components may change over time and under different internal and external conditions.
The input for the algorithm comes from using well-established dynamic models to observe changes in concentrations of metabolites, reactions and enzymes under various conditions. The algorithm then processes that data to establish primary and secondary relationships between all of the constituent parts.
“When modifying biological processes, there are thousands of possible combinations of metabolites, reactions and enzymes for any given biochemical pathway,” Williams says. “Our work should help life scientists narrow down the list of key players in order to target their research efforts on functional groups that are most likely to improve our ability to understand and control important biological processes. This has applications in everything from biomedical research to agriculture to biofuels.”
The paper, “Hierarchical Modularization Of Biochemical Pathways Using Fuzzy-C Means Clustering,” is forthcoming from IEEE Transactions on Cybernetics. Lead author of the paper is Dr. Maria de Luis Balaguer, a former Ph.D. student at NC State.
Thanks to North Carolina State University for contributing this story.
Like tiny construction workers, cells sculpt embryonic tissues and organs in 3D space. This task is complicated and requires constant communication between cells to coordinate their actions and generate the forces that will shape their environment into complex tissue morphologies.
Biologists have long studied the communication between cells and their behavior while building these structures, but until now, it had not been possible to see the forces cells generate to shape them. A new method to quantify the mechanical forces that cells exert while building tissues and organs can help answer long unresolved questions in biology and provide new diagnostic tools for medicine.
Developed initially in the Wyss Institute at Harvard University by Otger Campàs and Donald Ingber, this technique is the first of its kind to measure the mechanical forces that cells generate in living embryos. Now an assistant professor who holds the Mellichamp Chair in Systems Biology at UC Santa Barbara, Campàs leads a lab that is developing this droplet technique in several new directions, and applying it to discover the patterns of cellular forces that shape embryonic structures in fish and chicken.
“There is a lot of interest in understanding how genetics and mechanics interplay to shape embryonic tissues,” said Campàs. “I believe this technique will help many scientists explore the role that mechanical forces play in morphogenesis and, more generally, in biology.”
Very funny piece from a very funny man. Listener’s discretion is advised.
The following videos help explain:
1. What is the Nogoya Protocol
2. Why is the Nogoya Protocol necessary?