now e. coli has benefits?? gut biome very impressive little universe

Science | The benefits of Escherichia coli
Infection and intestinal damage can trigger severe muscle wasting and loss of fat in mice. How this happens is poorly understood. Palaferri Schieber et al. discovered a protective Escherichia coli strain in their mouse colony. Mice intestinally colonized with the E. coli and infected with the food-poisoning bug Salmonella or with the lung pathogen Burkholderia did not waste away. Without the E. coli, similarly infected mice became fatally ill. The protective E. coli stimulated an innate immune mechanism that ensured that muscle-signaling pathways were not damaged by infection. Thus, the friendly E. coli allowed its host to tolerate and survive the pathogens.

epigenetics: stressed dads == offspring with neuropsychiatric disorders

ars technica | Paternal stress given to offspring via RNA packed into sperm

The idea that parents can transmit environmentally acquired traits to their offspring has been intuitively attractive ever since Lamarck proposed it in 1801. It had to go underground as evidence continuously piled up supporting Darwin's theory of natural selection, but it seems to be enjoying a popular resurgence with the discovery of epigenetics. Epigenetics explains how information can be transmitted between generations without the involvement of DNA sequences.

A number of recent studies have suggested that stress levels and the nutritional status of parents (and even grandparents) can influence the health of their offspring. But these studies have been somewhat murky on the details on how this transmission could occur. Now scientists who had previously shown that paternal stress impacts the next generation of mice have zeroed in on how it happens: males pack their sperm with RNA that influences gene activity in their offspring.

Through the uterine environment, mothers can pass their environmental exposures on to the fetuses they are nurturing. Thus, studies looking at mechanisms of epigenetic inheritance tend to focus on fathers—pretty much all they give to the fetus is genetic material. And male mice don't need to help in rearing the young, so this genetic material can be their only contribution to the next generation.

In earlier work, these scientists exposed male mice to six weeks of alternating stressors like 36 hours of constant light, a 15-minute exposure to fox odor, exposure to a novel object (marbles) overnight, 15 minutes of restraint in a 50 mL conical tube, multiple cage changes, white noise all night long, or saturated bedding.

Poor little guys.

Then the scientists allowed the mice to breed. Adult offspring of these chronically stressed dads had reduced hypothalamic-pituitary-adrenal stress axis reactivity; when they themselves were restrained for 15 minutes, they did not make as much corticosterone as mice sired by relaxed dads. This is relevant, and problematic, because blunted stress responses in humans are associated with neuropsychiatric disorders like depression, schizophrenia, and autism.

if life came early to the universe, then it would seem to be part of the universe's purpose

phys.org | Most earth-like worlds have yet to be born, according to theoretical study

Earth came early to the party in the evolving universe. According to a new theoretical study, when our solar system was born 4.6 billion years ago only eight percent of the potentially habitable planets that will ever form in the universe existed. And, the party won't be over when the sun burns out in another 6 billion years. The bulk of those planets—92 percent—have yet to be born.

chromatin target for epigenetic changes

Science |

Epigenetic mechanisms control the combination of genes that are switched on and off in any given cell. In turn, this combination, called the transcriptional program, determines the identity and the fate of cells, which are deregulated in diseases such as cancer, inflammation, or neurological disorders. Chemical modifications (such as methylation or acetylation) of chromatin—an ensemble of nuclear factors, especially histone proteins around which DNA is wrapped—act as epigenetic signals. Enzymes that write or erase these chemical “marks,” and proteins that bind and interpret them, represent an important target class for drugs (1). On page 291 of this issue, Jiao and Liu (2) report the crystal structure of one prominent such enzyme called enhancer of zeste homolog 2 (Ezh2) in complex with obligatory protein binding partners. This structure, which has been largely elusive, provides clarity on the regulation of EZH2 catalytic activity and is an important step toward rational drug design.

specialized intelligences more effective at specific problems

phys.org | System that replaces human intuition with algorithms outperforms human teams

Big-data analysis consists of searching for buried patterns that have some kind of predictive power. But choosing which "features" of the data to analyze usually requires some human intuition. In a database containing, say, the beginning and end dates of various sales promotions and weekly profits, the crucial data may not be the dates themselves but the spans between them, or not the total profits but the averages across those spans.

MIT researchers aim to take the human element out of big-data analysis, with a new system that not only searches for patterns but designs the feature set, too. To test the first prototype of their system, they enrolled it in three data science competitions, in which it competed against human teams to find predictive patterns in unfamiliar data sets. Of the 906 teams participating in the three competitions, the researchers' "Data Science Machine" finished ahead of 615.

In two of the three competitions, the predictions made by the Data Science Machine were 94 percent and 96 percent as accurate as the winning submissions. In the third, the figure was a more modest 87 percent. But where the teams of humans typically labored over their prediction algorithms for months, the Data Science Machine took somewhere between two and 12 hours to produce each of its entries.

"We view the Data Science Machine as a natural complement to human intelligence," says Max Kanter, whose MIT master's thesis in computer science is the basis of the Data Science Machine. "There's so much data out there to be analyzed. And right now it's just sitting there not doing anything. So maybe we can come up with a solution that will at least get us started on it, at least get us moving."

alternative living arrangements

sfist | Step Inside Oakland's Illegal Dystopian Shipping Container Community, Containertopia

"It's pretty much my dream post-apocalyptic cyberpunk setup," says Luke Iseman near his 160-square-foot box home. With a camp stove and a fridge "that's a really simple hack," his miniature shipping container nightmare chamber sits alongside 11 others in a warehouse at an undisclosed location in Oakland. File under: Apartment Sadness?

Bloomberg reports that the 31-year-old cool guy Wharton graduate has been chased from two other locations by the authorities. But, like an idiot, Iseman has no plans to give up. “I’d rather ask forgiveness than ask permission,” the entrepreneur says in high Silicon Valley fashion.

Iseman rakes in $1,000 a month for each of the 11 structures docked in the 17,000-square-foot warehouse he rents for $9,100. His tenants include a Facebook engineer, a SolarCity programmer, and a bicycle messenger. This, as Iseman calls it, is "Containertopia."

fountain of youth, or where's the d*** off button!

Tech Times | Switching Off Over 200 Genes Linked To Aging Extends Lifespan By 60 Percent

A 10-year research conducted by scientists at the University of Washington and Buck Institute for Research on Aging in the United States may have found a partial chunk of the so-called Fountain of Youth. The team has identified around 238 genes which, when removed, can extend lifespan by 60 percent.

The study was conducted on 4,698 yeast strains. The research team said the results can be replicated in humans after a series of tests conducted on roundworms. By counting yeast cells and monitoring the consequences that followed when a single gene is blocked or removed, the team was able to identify the number of 'daughter cells' that a 'mother cell' can produce before it stops dividing