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Ready, set, mutate...and may the best microbe win |
| TheAllINeed.com/NC&T/RU/ |
Rice University biologists, using an ingenious experiment that forced bacteria to compete in a head-to-head contest for evolutionary dominance, today offer the first glimpse of how individual genetic-level adaptations play out as Darwinian natural selection in large populations. The results appear in the May 19 issue of Molecular Cell.
"One of our most surprising findings is that an estimated 20 million point mutations gave rise to just six populations that were capable of vying for dominance," said lead researcher Yousif Shamoo, associate professor of biochemistry and cell biology. "This suggests that very few molecular pathways are available for a specific molecular response, and it points to the intriguing possibility of developing a system to predict the specific mutations that pathogens will use in order to become resistant to antibiotics."
Rice's study involved the heat-loving bacteria G. stearothermophilus, which thrives at up to 73 degrees Celsius (163 F). Shamoo and graduate students Rafael Couñago and undergraduate Stephen Chen used a mutant strain of the microbe that was unable to make a key protein that the bacteria needed to regulate its metabolism at high temperatures. They grew the bacteria for one month in fermentor, raising the temperature a half degree Celsius each day.
Over a span of 1,500 generations, the percentage of mutant strains inside the fermentor ebbed and flowed as the single-celled microbes competed for dominance. Eventually, one strain squeezed out almost all the competition by virtue of its ability to most efficiently metabolize food at high temperature.
The metabolic protein required to thrive at high-temperature could only be made in one genetic region of the bacteria's DNA, meaning the researchers had only to characterize that small region of the genome for each new strain in order to measure evolutionary progress.
The researchers sampled the fermentor for new strains every other day. Though millions of mutations in the target gene are believed to have occurred, only about 700 of those were capable of creating a new variant of the target gene. In all, the researchers identified 343 unique strains, each of which contained one of just six variants of the critical gene.
The first of the six, dubbed Q199R, arose almost immediately, and was the dominant strain through the 500 th generation. Around 62 degrees Celsius, the Q199R was unable to further cope with the rising temperature, and a new round of mutations occurred. Five new varieties - themselves mutant forms of Q199R - vied for final domination of the fermentor. Three of the five were driven to extinction within a couple of days, and the final two fought it out over the remaining three weeks of the test.
The research included a raft of additional experiments as well. The team characterized each of the mutant proteins to document precisely how it aided in metabolic regulation. The fermentor experiment was repeated and the same mutations - and no others - were observed to develop again. Three of the six genes - the "winner," it's closest competitor and Q199R - were spliced back into the original form of the bacteria and studied, to rule out the possibility that mutations in other genes were responsible for the competitive advantage.
Shamoo said it's significant that the mutations didn't arise where expected within the gene. Four of the six occurred in regions of the gene that are identical in both heat-resistant and non-heat-resistant forms of G. stearothermophilus. Shamoo said this strongly shows the dynamic nature of evolution at the molecular and atomic level.
Shamoo said the most promising finding is the fact that the follow-up test produced precisely the same mutant genes.
"The duplicate study suggests that the pathways of molecular adaptation are reproducible and not highly variable under identical conditions," Shamoo said.
The research was funded by the National Science Foundation, the Welch Foundation and the Keck Center for Computational and Structural Biology.
-SOURCE/ADDITIONAL INFORMATION:
http://www.media.rice.edu/media/NewsBot.asp?MODE=VIEW&ID=8562&SnID=2138348831
-CONTACT ADRESS:
Jade Boyd
USA
Ph.: 713-348-6778
E-mail: jadeboyd@rice.edu
============================================================
-REFERENCE: 0681-2006
-KEYWORD: Climatology
-TITLE: NEW CENTURY OF THIRST FOR WORLD'S MOUNTAINS
-SUMMARY: By the century's end, the Andes in South America will have less than half their current winter snowpack, mountain ranges in Europe and the U.S. West will have lost nearly half of their snow-bound water and snow on New Zealand's picturesque snowcapped peaks will all but have vanished.
-FULL TEXT:
(NC&T/PNNL) Such is the dramatic forecast from a new, full-century model that offers detail its authors call "an unprecedented picture of climate change." The decline in winter snowpack means less spring and summer runoff from snowmelt. That translates to unprecedented pressure on people worldwide who depend on summertime melting of the winter snowpack for irrigation and drinking water.
Hardest hit are mountains in temperate zones where temperatures remain freezing only at increasingly higher elevations, said Steven J. Ghan, staff scientist at the Department of Energy's Pacific Northwest National Laboratory and lead author of a study describing the model in the current Journal of Climate. PNNL scientist Timothy Shippert was co-author.
Alaska in 2100 will maintain but 64 percent of its year 2000 snowpack. In Europe, the Alps will be at 61 percent and Scandinavia 56 percent. The Sierras, Cascades and southern Rockies will be at 57 percent of current levels. The Andes will drop to 45. And Mt. Cook and its snowcapped neighbors in New Zealand will be much less scenic at 16 percent of current.
Ghan said the model, which actually simulated years 1977 to 2100 to use known data as calibration, differs from past attempts because it generates snow information for small areas – 5 kilometer grids, or about 3-miles – on mountains ranges over such a long period.
"Global climate models have never been run at 5 kilometers resolution for a period covering more than a couple of months," Ghan said, "even on the biggest computers in the world."
Ghan deployed a divide-and-conquer method to data crunching called "physically-based global downscaling" he and colleagues had used previously on mountains in the U.S. West. The world's mountain ranges are chopped into 10 different "elevation classes." For each elevation class, air circulation, moisture, temperature and other information determines snowfall to the surface. The surface snow is then distributed across the grids according to the local surface elevation.
The entire century-plus simulation, based on the National Center for Atmospheric Research Community Climate System Model funded by the National Science Foundation and DOE, can be run on a supercomputer over a few weeks. Ghan and Shippert used one at the PNNL-based W.R. Wiley Environmental Molecular Sciences Laboratory.
Ghan cautioned about "significant limitations" to the model. For example, field observations in Africa suggest the famous snows of Mt. Kilimanjaro will be gone within decades, and on Greenland signs point to accelerated snow and ice melt.
"This climate model doesn't show that," Ghan said. "That doesn't mean Kilimanjaro and Greenland aren't in trouble. But our model doesn't account for all of the snow loss that is possible. Our model neglects downward flow of snow by avalanches and snow slides, and glacial creep in places where snowfall is heavy and the snow doesn't have time to melt."
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