Posts Tagged ‘American science’

Computational Tool Offers New Insight Into Key Biological Processes

 :: Posted by American Biotechnologist on 03-06-2014

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.

Is It Time for American Scientists to Panic?

 :: Posted by American Biotechnologist on 02-06-2014

According to the Science and Engineering Indicators 2014 Report released recently by the National Science Board, spending on academic research decreased significantly in 2012 compared to the period between 2009-2011 (source: academic r&d section of the report). The good news for us life scientists is that the government seems to value life sciences over the physical sciences and has continued to provide the largest portion of the funding pot to researchers in our field.

Furthermore, besides the growth in academic life science funding, lab space for academic R&D has continued to expand, although it has done so at a somewhat slower pace in 2012 compared to prior years. While this may sound like a good indicator of growth, it should be noted that spending on research equipment fell by 1.4% in 2012 which may have a significant impact on scientists’ abilities to perform their work.

Another worrying trend, indicated in the report, is the disproportionate increase in non-faculty positions, such as post-doctoral fellows, in comparison to faculty positions. Furthermore, fewer researchers were tenured in the first decade of the century compared to the late 90s. If we are to believe the law of supply and demand, this lopsidedness will eventually lead to unhappy scientists who are dejected by their inability to obtain faculty positions due to the overpopulation of qualified candidates for very few faculty positions.

Nonetheless, according to the Washington Post, all is not lost. Here are a list of reasons that Washington Post journalist, Lydia DePillis, thinks we should keep our heads held high:

  • the US continues to fund its academic R&D at levels that are much higher than the rest of the world
  • there are more undergraduate and graduate degrees in science and technology in the US compared to other nations
  • America earns more patents than anywhere else in the world
  • American collects more royalties compared to other countries
  • Most importantly-Americans represent the largest group of scientific publishers which is the ultimate indicator of success among academic researcher

So despite some worrying trends indicated above, the Post seems to indicate that we should consider ourselves lucky that we are living in America where our chance to become successful scientists is much greater than anywhere else in the world.

Would you agree?

May the cellular force be with you

 :: Posted by American Biotechnologist on 12-09-2013

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.”

Read more…

Happy Thanksgiving America!

 :: Posted by American Biotechnologist on 11-27-2013

It’s that time of year when we relax and give thanks for our nation, our family, our friends and our HUGE turkeys. Did you know that in the time of the pilgrims, turkeys only weighed up to 6 kg, yet today, male turkeys can weigh a whopping 36 kilos! That’s enormous, and it is all thanks to science and the process of natural selection.

Yet massive size has its drawbacks. Due to their over-bearing bulk, heavy male turkeys are unable to mate which poses a challenge for continuity of the species. That is one of the main reason that all American turkeys are produced by artificial insemination. Certainly not a job for anybody.

Watch this video to learn more.

Electrical Sewage

 :: Posted by American Biotechnologist on 09-16-2013

Engineers at Stanford University have devised a new way to generate electricity from sewage using naturally-occurring “wired microbes” as mini power plants, producing electricity as they digest plant and animal waste.

In a paper published today in the Proceedings of the National Academy of Sciences, co-authors Yi Cui, a materials scientist, Craig Criddle, an environmental engineer, and Xing Xie, an interdisciplinary fellow, call their invention a microbial battery.

One day they hope it will be used in places such as sewage treatment plants, or to break down organic pollutants in the “dead zones” of lakes and coastal waters where fertilizer runoff and other organic waste can deplete oxygen levels and suffocate marine life.

Read more…