‘Evolutionary battle for supremacy between X & Y Chromosomes.’ By Brendan Maher

New DNA sequencing data reinforce the notion that the X and Y chromosomes, which determine biological sex in mammals, are locked in an evolutionary battle for supremacy.

David Page, a biologist who directs the Whitehead Institute in Cambridge, Massachusetts, and his colleagues explored the Y chromosomes carried by males of several species, mapping stretches of mysterious, repetitive DNA in unprecedented detail. These stretches may signal a longstanding clash of the chromosomes.

Page presented the results last week at a meeting of the Society for the Study of Reproduction in San Juan, Puerto Rico. His team’s subjects included humans and other primates, a standard laboratory mouse, and a bull named Domino.

“This idea of conflict between the chromosomes has been around for a while,” says Tony Gamble, an evolutionary biologist at the University of Minnesota in Minneapolis. But the sequencing data from the bull’s Y chromosome suggests that the phenomenon is more widespread than previously thought, he adds.

The mammalian Y chromosome has long been thought of as a sort of genomic wasteland, usually shrinking over the course of evolution and largely bereft of pertinent information. Page’s work has helped to change perceptions of the Y chromosome by revealing that it contains remarkable patterns of repeating sequences that appear dozens to hundreds of times1, 2.

But the structure of these sequences and precise measures of how often they repeat have been difficult to determine. Standard sequencing technologies often cannot distinguish between long stretches of genetic code that differ by a single DNA ‘letter’.

http://www.nature.com/news/a-battle-of-the-sexes-is-waged-in-the-genes-1.17817

Posted by f. sheikh

The Data That Threatened To Break The Physics

Ereditato is the former leader of the 160 physicists from 13 countries that compose the OPERA collaboration, whose goal is to study neutrino physics. It was first proposed in 2000, and Ereditato led it from 2008 to 2012. Then in late winter of 2011, the impossible seemed to happen. “The guy who is looking at the data calls me,” Ereditato tells me from my computer screen. “He says, ‘I see something strange.’ ” What he saw was evidence that neutrinos traveled through 454 miles of Earth’s crust, from Switzerland to Italy—which they are supposed to do—at such a high speed that they arrived 60.7 nanoseconds faster than light could travel that distance in outer space—which should have been impossible.

Over the last century, Einstein’s observation that no massive object can travel faster than the speed of light in a vacuum, enshrined in his theory of special relativity, has become a keystone of how we understand the universe. If the OPERA measurement was correct, it would mark the first-ever violation of that theory: An atom bomb in the heart of our understanding of the universe.

I ask Ereditato if he thought it must have been a mistake. “I don’t think it’s fair to say this,” Ereditato tells me. “If we say that, we bias our analysis. So when we got this indication that something was so astonishing, the first reaction was, well, let’s find why this is so.”

Wolfgang Pauli postulated the existence of neutrinos in 1930 to solve a simple problem. When nuclei undergo beta decay through the emission of an electron or a positron, the electron’s antimatter equivalent, something is missing. Either something invisible is emitted along with the electron or positron, or energy must disappear. Since no repeatable experiment of anything flying, falling, moving, colliding, decaying, or staying put had ever seen energy disappear, Pauli proposed the neutrino, an invisible particle with all the properties necessary to bring beta decay into accord with the first law of thermodynamics. By invisible, I mean that when neutrinos pass through matter they rarely leave a trace. So rarely that it took almost 30 years before an experiment (by Frederick Reines and Clyde Cowan) found physical evidence of them.

Today, neutrinos are an integral part of the Standard Model’s periodic table of particle physics. Here you’ll find the particles that make up matter listed in pairs separated into three categories: electron neutrinos are paired with electrons, muon neutrinos with muons, and tau neutrinos with, you guessed it, taus. Neutrinos can morph from one flavor into another. For example, an electron neutrino can oscillate into a muon neutrino, and a muon neutrino can flip into a tau neutrino. “Neutrino oscillations are the first indication of physics beyond the Standard Model,” Ereditato tells me. Laughing, he adds, “That’s the reason why I like neutrinos.”

http://nautil.us/issue/24/error/the-data-that-threatened-to-break-physics

posted by f. sheikh

‘Day Care And  Childhood Cancer’ By  Warren Cornwall 

For years, scientists have noticed an interesting pattern of cancer among children. Those who went to day care early in life were less likely to later develop the most common childhood cancer: acute lymphoblastic leukemia (ALL). Now, a 7-year study appears to have unraveled the molecular mechanism driving ALL. The work may explain why early exposure to infections in places such as day cares seems to protect against the disease and why unrelated vaccines help guard against this cancer.

For Mel Greaves, a cancer cell biologist at the University of London’s Institute of Cancer Research, the finding provides an explanation for the hypothesis he has long promoted: that when infants in modern societies are sheltered from routine infections, their immune systems are more likely to overreact during later infections, paving the way for ALL. “I see it as the missing link,” he says of the new research.

Most childhood ALL involves a malfunction of B cells, the scouts of the immune system that patrol the bloodstream looking for intruders like viruses and bacteria; they make antibodies that help fight infections. But with leukemia, the immune system goes haywire, churning out flawed, immature B cells at a prodigious rate and crowding out healthy blood cells.

Normal B cells are a marvel of adaptability. As they mature, they reprogram their own DNA, enabling the immune system to produce millions of different B cells programmed to recognize the vast range of potential infections. The DNA rearrangement relies on a sequence of enzymes. First, proteins known as RAGs cut and paste whole chunks of DNA. After that, another enzyme, AID, goes to work “fine-tuning” the DNA by altering single nucleotides.

But Greaves and colleagues suspected this process could go awry, introducing mutations that create flawed B cells that could cause leukemia. In a series of experiments, they found evidence that much of the problem lay with a breakdown in the orderly sequence of gene editing during infections. Rather than the RAGs doing their business and then stepping aside for the AID, the AID kicked in simultaneously, potentially increasing the risk of gene-editing errors. Click link below for full article;

http://news.sciencemag.org/biology/2015/05/study-may-explain-mysterious-cancer-day-care-connection

posted by f. sheikh