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New Study: Funding Science is Good for the US Economy

 :: Posted by American Biotechnologist on 04-04-2014

University research is a key component of the US economic ecosystem, returning the investment through enormous public value and impact on employment, business, and manufacturing nationwide.

Using new data available to examine the short-term economic activity generated by science funding, researchers have for the first time been able to illuminate the breadth of the scientific workforce and the national impact of the research supply chain that is funded by federal grants.

Most of the workers supported by federal research funding are not university faculty members. In fact, fewer than one in five workers supported by federal funding are faculty researchers. The study, published this week in the journal Science, provides the first detailed information about the short-term economic impacts of federal research spending, the researchers said.

Using a new data set, the researchers also found that each university that receives funding spends those dollars throughout the United States – about 70 percent spent outside their home states – supporting companies both large and small.

The researchers conclude that federal funding has a wider impact than is often assumed. “The process of scientific research supports organizations and jobs in many of the high skill sectors of our economy,” the researchers wrote in Science.

The study was conducted by researchers from the American Institute of Research, the Committee on Institutional Cooperation, University of Michigan, University of Chicago, and the Ohio State University. The data came from the STAR METRICS project, which is a partnership between federal science agencies and research institutions to document the outcomes of science investments to the public.

In this study, the researchers examined STAR METRICS data from nine universities – Michigan, Wisconsin-Madison, Minnesota, Ohio State, Northwestern, Purdue, Michigan State, Chicago and Indiana (all members of the Committee on Institutional Cooperation consortium).

The universities in this study received about $7 billion in total research and development funding in 2012, and about 56 percent of that came from the federal government.

One key insight from the study was whose jobs were supported by federal funding. “Workers with many different skill levels are employed, and these are not primarily faculty,” the authors said.

Faculty members accounted for fewer than 20 percent of the people supported by federal funding. About one in three workers is either a graduate student or an undergraduate. One in three is either research staff or a staff scientist, and about one in ten is a post-doctoral fellow.

The study also sheds light on where universities spend the federal funding they receive. In 2012, almost $1 billion of research expenditures were spent with U.S. vendors and subcontractors.

Of those expenditures, 15 percent went to vendors in the university’s home county, 15 percent in the rest of the home state and the balance to vendors across the United States.

The researchers noted that universities bought goods and services from a wide range of contractors in a variety of industries: everything from test tubes to telescopes and microscopes to gene sequencing machines.

Many of the purchases came from large U.S companies. But as the researchers examined the websites of some of the tens of thousands of vendors, “we were struck by how many are small, niche, high-technology companies…” they wrote.

Noting the scope of the impact of scientific work being done across universities, co-author Roy Weiss, Deputy Provost for Research at the University of Chicago, said, “Research universities are dedicated to the discovery of new knowledge. This study reports the first cooperative endeavor by multiple universities to evaluate the benefit of government investment in research. In addition to making the world a better place by virtue of these discoveries, we now have data to support the overall benefits to society.”

“The main purpose of science funding isn’t as a jobs or stimulus program, but this study shows there are also major short-term economic benefits to science funding,” said Bruce Weinberg, co-author and professor of economics at Ohio State.

As Julia Lane, Senior Managing Economist at the American Institutes for Research and a lead researcher on the project, summarized, “This study provides evidence that while science is complicated, it is not magic. It is productive work. Scientific endeavors employ people. They use capital inputs. Related economic activity occurs immediately. Policy makers need to have an understanding of how science is produced when making resource allocation decisions, and this study provides that information in a reliable and current fashion.”

Thanks to the Committee on Institutional Cooperation for contributing this story.

Suprise! mRNA and Protein Levels Do Not Always Correspond!

 :: Posted by American Biotechnologist on 03-27-2014

The central dogma of molecular biology states that DNA codes for RNA and RNA codes for protein. It was widely understood that because protein is translated from mRNA, the amount of mRNA in a cell would somewhat correspond to the quantity of cellular protein. In a new study out of Notre Dame, scientists have shown that this theory is not always correct. While in many cases mRNA and protein levels do correspond, there are a surprisingly high number of exceptions, demonstrating that the amounts of a particular protein can be controlled by multiple mechanisms.

Bioanalytical chemist Norman Dovichi and molecular biologist Paul Huber identified and measured the levels of about 4,000 proteins, which exhibited patterns of expression that reflect key events during early Xenopus development resulting in the largest data set on developmental proteomics for any organism.

The study was conducted in Xenopus laevis embryos, which is a favored model for this type of research. In Xenopus, development takes place in well-defined stages outside the mother, thereby allowing embryogenesis to be monitored in real time. Additionally, embryos develop rapidly, achieving a nearly fully developed nervous system within four days.

Their results are available open access in Scientific Reports.

Dissecting a Two-Faced Calf

 :: Posted by American Biotechnologist on 03-25-2014

What’s the strangest thing you have ever dissected?

Powerful New Tool for Studying DNA Elements that Regulate Genes

 :: Posted by American Biotechnologist on 03-24-2014

An international team led by researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) has developed a new technique for identifying gene enhancers – sequences of DNA that act to amplify the expression of a specific gene – in the genomes of humans and other mammals. Called SIF-seq, for site-specific integration fluorescence-activated cell sorting followed by sequencing, this new technique complements existing genomic tools, such as ChIP-seq (chromatin immunoprecipitation followed by sequencing), and offers some additional benefits.

“While ChIP-seq is very powerful in that it can query an entire genome for characteristics associated with enhancer activity in a single experiment, it can fail to identify some enhancers and identify some sites as being enhancers when they really aren’t,” says Diane Dickel, a geneticist with Berkeley Lab’s Genomics Division and member of the SIF-seq development team. “SIF-seq is currently capable of testing only hundreds to a few thousand sites for enhancer activity in a single experiment, but can determine enhancer activity more accurately than ChIP-seq and is therefore a very good validation assay for assessing ChIP-seq results.”

Dickel is the lead author of a paper in Nature Methods describing this new technique. The paper is titled “Function-based identification of mammalian enhancers using site-specific integration.”

Read more…

Going Beyond the Central Dogma of Molecular Biology

 :: Posted by American Biotechnologist on 03-18-2014

Our genome, we are taught, operates by sending instructions for the manufacture of proteins from DNA in the nucleus of the cell to the protein-synthesizing machinery in the cytoplasm. These instructions are conveyed by a type of molecule called messenger RNA (mRNA).

Francis Crick , co-discoverer of the structure of the DNA molecule, called the one-way flow of information from DNA to mRNA to protein the “central dogma of molecular biology.”

Yehuda Ben-Shahar and his team at Washington University in St. Louis have discovered that some mRNAs have a side job unrelated to making the protein they encode. They act as regulatory molecules as well, preventing other genes from making protein by marking their mRNA molecules for destruction.

“Our findings show that mRNAS, which are typically thought to act solely as the template for protein translation, can also serve as regulatory RNAs, independent of their protein-coding capacity,” Ben-Shahar said. “They’re not just messengers but also actors in their own right.” The finding was published in the March 18 issue of the new open-access journal eLife.

Although Ben-Shahar’s team, which included neuroscience graduate student Xingguo Zheng and collaborators Aaron DiAntonio and his graduate student Vera Valakh, was studying heat stress in fruit flies when they made this discovery, he suspects this regulatory mechanism is more general than that.

Many other mRNAs, including ones important to human health, will be found to be regulating the levels of proteins other than the ones they encode. Understanding mRNA regulation may provide new purchase on health problems that haven’t yielded to approaches based on Crick’s central dogma.

Read the full story A novel mechanism for fast regulation of gene expression.