Saturday, June 15, 2013

Context crucial when it comes to mutations in genetic evolution

June 13, 2013 ? With mutations, it turns out that context can be everything in determining whether or not they are beneficial to their evolutionary fate.

According to the traditional view among biologists, a central tenet of evolutionary biology has been that the evolutionary fates of new mutations depend on whether their effects are good, bad or inconsequential with respect to reproductive success. Central to this view is that "good" mutations are always good and lead to reproductive success, while "bad" mutations are always bad and will be quickly weeded out of the gene pool. However, new research led by evolutionary biologist Jay Storz of the University of Nebraska-Lincoln has found that whether a given mutation is good or bad is often determined by other mutations associated with it. In other words, genetic evolution is context-dependent.

In a study to be published in the June 14 issue of Science, Storz and colleagues at UNL and Aarhus University in Denmark report that an individual mutation can be beneficial if it occurs in combination with certain other mutations, but the same mutation can detrimental to the organism if it occurs in other combinations.

The researchers studied mutations that alter the function of hemoglobin, the protein in charge of transporting oxygen in the blood. Physiologists have long known that many high-altitude animals have evolved hemoglobins with high affinities for oxygen, which can enhance oxygen uptake in thin air. Earlier research by Storz's group on populations of North American deer mice that are native to high and low altitudes had found that the high-altitude mice had evolved hemoglobins with an increased oxygen-binding affinity -- and that this difference is attributable to the combined effects of genetic mutations at 12 different sites in the hemoglobin protein.

For the discovery reported in Science, the researchers used a technique called "protein engineering" to synthesize hemoglobin proteins that contained each of the naturally occurring mutations in all possible multi-site combinations.

"By measuring the oxygen-binding properties of these engineered hemoglobins, we discovered that the same individual mutations produced an increased oxygen-affinity in some combinations and they produced a decreased oxygen-affinity in other combinations. Their effects are completely context-dependent," said Storz, an associate professor of biological sciences.

"One of the important implications is that if there are interactions between mutations, then some mutational pathways of evolution may be more accessible than others. The evolutionary fate of a new mutation will depend critically on which other mutations have already occurred. The order in which mutations occur can determine whether evolution is more likely to follow some pathways rather than others. Evolution may follow certain pathways just because certain interactions may be negative, other interactions may be positive. These kinds of interaction effects determine what mutational pathways are open and available for evolution."

Storz's collaborators on the Science paper include Hideaki Moriyama, an associate professor of biological sciences at UNL, and two other researchers in Storz's lab, postdoctoral researcher Chandrasekhar Natarajan and graduate student Noriko Inoguchi; and Roy E. Weber and Angela Fago of Aarhus.

The research was funded by grants from the National Institutes of Health-National Heart, Lung and Blood Institute and the National Science Foundation in the United States, and the Science Faculty, Aarhus University, in Denmark.

It's the fifth time in five years that Storz's research has been published one of the major international interdisciplinary journals. Science is published by the American Association for the Advancement of Science.

Source: http://feeds.sciencedaily.com/~r/sciencedaily/top_news/top_science/~3/H970gjL5N3Y/130613142829.htm

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Tuesday, June 11, 2013

Simple theory may explain mysterious dark matter

June 10, 2013 ? Most of the matter in the universe may be made out of particles that possess an unusual, donut-shaped electromagnetic field called an anapole.

This proposal, which endows dark matter particles with a rare form of electromagnetism, has been strengthened by a detailed analysis performed by a pair of theoretical physicists at Vanderbilt University: Professor Robert Scherrer and post-doctoral fellow Chiu Man Ho. An article about the research was published online last month by the journal Physics Letters B.

"There are a great many different theories about the nature of dark matter. What I like about this theory is its simplicity, uniqueness and the fact that it can be tested," said Scherrer.

In the article, titled "Anapole Dark Matter," the physicists propose that dark matter, an invisible form of matter that makes up 85 percent of the all the matter in the universe, may be made out of a type of basic particle called the Majorana fermion. The particle's existence was predicted in the 1930's but has stubbornly resisted detection.

A number of physicists have suggested that dark matter is made from Majorana particles, but Scherrer and Ho have performed detailed calculations that demonstrate that these particles are uniquely suited to possess a rare, donut-shaped type of electromagnetic field called an anapole. This field gives them properties that differ from those of particles that possess the more common fields possessing two poles (north and south, positive and negative) and explains why they are so difficult to detect.

"Most models for dark matter assume that it interacts through exotic forces that we do not encounter in everyday life. Anapole dark matter makes use of ordinary electromagnetism that you learned about in school -- the same force that makes magnets stick to your refrigerator or makes a balloon rubbed on your hair stick to the ceiling," said Scherrer. "Further, the model makes very specific predictions about the rate at which it should show up in the vast dark matter detectors that are buried underground all over the world. These predictions show that soon the existence of anapole dark matter should either be discovered or ruled out by these experiments."

Fermions are particles like the electron and quark, which are the building blocks of matter. Their existence was predicted by Paul Dirac in 1928. Ten years later, shortly before he disappeared mysteriously at sea, Italian physicist Ettore Majorana produced a variation of Dirac's formulation that predicts the existence of an electrically neutral fermion. Since then, physicists have been searching for Majorana fermions. The primary candidate has been the neutrino, but scientists have been unable to determine the basic nature of this elusive particle.

The existence of dark matter was also first proposed in the 1930's to explain discrepancies in the rotational rate of galactic clusters. Subsequently, astronomers have discovered that the rate that stars rotate around individual galaxies is similarly out of sync. Detailed observations have shown that stars far from the center of galaxies are moving at much higher velocities than can be explained by the amount of visible matter that the galaxies contain. Assuming that they contain a large amount of invisible "dark" matter is the most straightforward way to explain these discrepancies.

Scientists hypothesize that dark matter cannot be seen in telescopes because it does not interact very strongly with light and other electromagnetic radiation. In fact, astronomical observations have basically ruled out the possibility that dark matter particles carry electrical charges.

More recently, though, several physicists have examined dark matter particles that don't carry electrical charges, but have electric or magnetic dipoles. The only problem is that even these more complicated models are ruled out for Majorana particles. That is one of the reasons that Ho and Scherrer took a closer look at dark matter with an anapole magnetic moment.

"Although Majorana fermions are electrically neutral, fundamental symmetries of nature forbid them from acquiring any electromagnetic properties except the anapole," Ho said. The existence of a magnetic anapole was predicted by the Soviet physicist Yakov Zel'dovich in 1958. Since then it has been observed in the magnetic structure of the nuclei of cesium-133 and ytterbium-174 atoms.

Particles with familiar electrical and magnetic dipoles, interact with electromagnetic fields even when they are stationary. Particles with anapole fields don't. They must be moving before they interact and the faster they move the stronger the interaction. As a result, anapole particles would have been have been much more interactive during the early days of the universe and would have become less and less interactive as the universe expanded and cooled.

The anapole dark matter particles suggested by Ho and Scherrer would annihilate in the early universe just like other proposed dark matter particles, and the left-over particles from the process would form the dark matter we see today. But because dark matter is moving so much more slowly at the present day, and because the anapole interaction depends on how fast it moves, these particles would have escaped detection so far, but only just barely.

The research was funded in part by Department of Energy grant DE-FG05-85ER40226.

Source: http://feeds.sciencedaily.com/~r/sciencedaily/matter_energy/electricity/~3/Ec0tXenuxAM/130610132838.htm

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Hillary Clinton on Twitter: Welcome to the new way to reach potential voters (Washington Post)

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Monday, June 10, 2013

?Glee? Star Jane Lynch & Wife Dr. Lara Embry Divorcing!

“Glee” Star Jane Lynch & Wife Dr. Lara Embry Divorcing!

Jane Lynch & Dr. Lara Embry picsJane Lynch and wife, psychologist Dr. Lara Embry, have split after three years of marriage. The “Glee” star made the sad announcement today, asking for privacy just a day after she performed at the Tony Awards. Jane Lynch met Dr. Lara Embry at a fundraiser in 2009 in San Francisco and married on Memorial Day ...

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Wednesday, May 22, 2013

East Rutherford Sinkhole? How a forklift saved a man.

East Rutherford Sinkhole? A forklift worker narrowly escaped serious injury after a warehouse floor collapsed in East Rutherford, N.J.?

By Eoin O'Carroll,?Staff / May 21, 2013

A forklift operator found himself suddenly waist-deep in a viscid and aromatic pool of cooking oil and soy sauce, following the collapse of a warehouse floor in East Rutherford, N.J., on Monday.

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Shortly after noon, Danny Rodriguez was moving pallets near the loading dock of a warehouse unit rented by the trucking company?AM Express Freight, when the floor gave way. Mr. Rodriguez, his forklift, and several containers of oil and soy sauce plunged into a hole that witnesses described as six to 10-feet deep and 30 to 40-feet wide. Rodriguez escaped from the warehouse unit ? which at this point resembled the world's largest wok ? ?with only minor injuries.

"Fortunately for the operator, the forklift went straight down and didn?t tip to the side because then he could have really been hurt," said borough Police Chief Larry Minda, in an interview with The Record, a North Jersey daily newspaper.

Authorities declared the warehouse unit and two adjacent ones unsafe and ordered them evacuated.

It is not clear what caused the collapse. The Record quotes property manager, Bruce Jordan, who said that the unit's reinforced concrete floor sat atop a forgotten basement. "We had no idea it was hollow under there,? he said. ?We thought the floor was built over dirt."

The news aggregator site New Jersey Online attributes the collapse to a sinkhole, an underground hollow caused by the erosion of sedimentary rock, such as limestone or dolomite, by groundwater or, in some instances, burst water mains.

In recent years, sinkholes have appeared in?Florida;?California;?Illinois;?Washington, D.C.;?Pennsylvania;?Guangzhou, China;?Guatemala City;?Quebec;?Milwaukee;?Germany; and Chicago.

Source: http://rss.csmonitor.com/~r/feeds/csm/~3/IJufGL56n50/East-Rutherford-Sinkhole-How-a-forklift-saved-a-man

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Viruses and mucus team up to ward off bacteria

Phages may play unforeseen role in immune protection

By Tina Hesman Saey

Web edition: May 20, 2013

The last thing most people would want in their bodies is mucus laden with viruses. But a new study suggests that viruses called bacteriophages, or phages, grab onto mucus and then infect and kill invasive bacteria. The finding, reported May 20 in the Proceedings of the National Academy of Sciences by Forest Rohwer of San Diego State University and colleagues, could mean that some viruses partner with animals and humans to stave off bacterial infections and control the composition of friendly microbes in the body.

Bacteriophages are viruses that break open bacteria, killing them. Researchers have studied bacteriophages for decades, and some disease therapies take advantage of the viruses? bacteria-slaying abilities, says microbiologist Frederic Bushman of the University of Pennsylvania medical school. But the study provides what Bushman says is a revelation that should have been obvious; phage may be a natural part of the immune system. ?It?s new in a way that is sort of common-sensey,? he says.

Previously, researchers thought of mucus mainly as a physical barrier to keep invading organisms from entering the body. The slimy substance made by our noses, intestines and other organs also fights invaders with antimicrobial molecules. ?Some researchers had found bacteriophages stuck in mucus, but they figured that the mucus had stopped or slowed the viruses. No one realized that the viruses are part of the body?s defense, says study coauthor Jeremy Barr, who works in Rohwer?s lab. ?This is a natural use of phage therapy that has probably been around since mucosal surfaces evolved,? Barr says.

Rohwer, who studies corals, had noticed that phages tend to concentrate in mucus. To find out why, the researchers collected mucus from human gums, sea anemones, fish, corals and mouse intestines. Mucus layers had more phages and fewer bacteria than the surrounding environment, suggesting that the viruses helped to limit the number of bacteria allowed into the mucus.

Phages are coated in proteins that latch onto sugars called glycans, anchoring the viruses in the mucus, the team discovered. From there the phages can ambush encroaching bacteria.

So far, the researchers have demonstrated that mucus and phages can work together to protect cells in a dish. The next step, Bushman says, would be determining what happens inside an organism, an experiment the researchers are already planning.

Source: http://www.sciencenews.org/view/generic/id/350573/title/Viruses_and_mucus_team_up_to_ward_off_bacteria

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Tuesday at 11:00 p.m., John White has a special report on California prison over...

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