Gizmorama - August 24, 2015

Good Morning,

When I read headlines like "Computerized 'fishing expedition' hooks 12,500 virus genomes" it makes me wish I knew more about computers because none of that made any sense to me. I'm confused, but I'm still interested in the science and technology of it all.

Learn about this and more interesting stories from the scientific community in today's issue.

Until Next Time,
Erin

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*-- Computerized 'fishing expedition' hooks 12,500 virus genomes --*
COLUMBUS, Ohio - Researchers at Ohio State University have increased the number of sequenced virus genomes almost tenfold with a new computer analysis tool that mines genetic code from public databases.

The computerized 'fishing expedition' netted the sequenced genomes of 12,500 previously uncharacterized viruses, doubling the number of known virus genera.

Viruses play an important role in the lives of bacteria and archaea, single-cell microorganisms that are similar but evolved separately from bacteria. Because of the intertwined nature of their existence, virus genes can be located within microbial genomes.

The fishing program mined public databases of sequenced bacteria and archaea genomes for fragments unique to viruses.

All viruses have a set of genes that produce a protein shell called a capsid. This ubiquitous set of genetic coding helped the tool fish out virus genomes.

"The idea is that bacteria don't use capsids or produce them, so any capsid gene should come from a virus," Matthew Sullivan, an assistant professor of microbiology at Ohio State, explained in a press release.

Sullivan is the lead author of a new paper on the analysis, published this week in the journal eLife.

Once capsid coding was located, the program keyed in on attached segments that were unique and unlikely to belong to bacteria.

"None of these genomic features is really a smoking gun per se, but combining them led to a robust detection of 'new' viruses -- viruses we did not have in the database, but can identify because they have capsid genes and a viral organization," Sullivan said.

Sullivan says viruses are a missing component of the growing field of microbiota research, the study of microbial communities in humans (their gut and lungs, for example) and natural environments (in soils and aquatic habitats).

"Virus-bacteria and virus-archaea interactions are probably quite important to the dynamics of that microbe, so if researchers are studying a microbe in a specific environment, they've been missing a big chunk of its interaction dynamics by ignoring the viruses," Sullivan said. "This work will help researchers recognize the importance of viruses in a lot of different microbes."

Most viruses studied -- ones associated with disease -- are lytic in nature, meaning they replicate themselves and essentially take over their host, destroying their host cells in the process. But there are other types of virus that seem to have a more reciprocal relationship with their hosts, producing genes that help their host cells thrive.

These viruses are called prophages, and Sullivan's research suggest they're likely more abundant that scientists realize. Many of them, the new analysis suggests, keep their genetic material separate from their host cells.

"The extrachromosomal form of this virus type appears quite widespread, and virtually nobody is studying these kinds of viruses," he said. "That is a really different and largely unexplored phenomenon, and it's important to understand those viruses' ability to interact and tie into the function of those cells."

Sullivan hopes his new study will inspire researchers to further explore these little-understood virus-bacteria relationships.


*-- Better-tasting grocery store tomatoes coming soon, scientists say --*
BOSTON - After decades of complaints, scientists have finally decided to solve the problem of the watery, flavorless mass-market tomatoes found in grocery stores.

As most cooks know, the only way to procure a consistently tasty tomato is to pick it from a backyard garden or buy it from a farm stand. But consumers want tomatoes 365 days a year, which means the ruby red fruit must be stored for several days and sometimes shipped thousands of miles across the country.

To get tomatoes on the shelves of stores in Northern Michigan in the middle of February, growers in California, Florida, Mexico and elsewhere pick the fruit before its ripe and then blast it with ethylene to trigger ripening. The ripening fruit is then shipped and stored at very low temperatures until it reaches its point of sale.

This process degrades flavor, researchers explained on Wednesday at the American Chemical Society 250th National Meeting & Exposition, held this week in Boston.

"To produce a better tasting tomato, we added a hot water pre-treatment step to the usual protocol that growers follow," Jinhe Bai, a plant physiologist with the USDA and researcher at the U. S. Horticultural Research Laboratory, said in a press release. "We found that this pre-treatment step prevents flavor loss due to chilling."

Bai teamed up with researchers at the University of Florida to test their process. First, green tomatoes are picked, sprayed and dipped in hot water for five minutes, soaking at a temperature of approximately 125 degrees Fahrenheit. Next, the tomatoes are chilled to a temperature between 41 and 55 degrees Fahrenheit.

The process produced tomatoes that, once ripe, boasted higher concentrations of flavor compounds, including 6-methyl-5-hepten-2-one, 2-methylbutanal and 2-phenylethanol.

"Chilling suppresses production of oxygen, nitrogen and sulfur-containing heterocyclic compounds, ketones, alcohols and aldehydes, including 13 important aroma components of tomato flavor," Bai explained. "But hot water-treated fruit actually produced higher concentrations of these important aroma contributors, even with subsequent chilling."

Researchers say the process could be easily implemented by current commercial producers and processors -- without new technology and without sacrificing food safety or protection against spoilage.

Bai and his colleagues also tested another promising technique, whereby tomatoes are picked when they are slightly riper (half-green, half-pink) and then sprayed with an EPA-approved gas called 1-methylcyclopropene.

These tomatoes also showed higher concentration of important flavor and aroma compounds. Researchers are hoping to compare and contrast the flavors preserved by these two methods.

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