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US-North Korea summit may be in danger

CNN - Mon, 2018-05-21 18:19
Administration aides have grown increasingly skeptical the summit between President Donald Trump and North Korean leader Kim Jong Un will come to fruition amid harsh rhetoric from Pyongyang and concerns over the meeting's agenda, officials and other people familiar with the matter said.

A monkey gets free at the San Antonio airport

CNN - Mon, 2018-05-21 18:18
A monkey that was being transported escaped its cage Monday afternoon and briefly ran loose at San Antonio International Airport, officials said.

Our tiny, furry genetic ancestors were bug eaters

Futurity.org - Mon, 2018-05-21 18:15

Scientists have concluded that our distant ancestors—the small, furry creatures that scurried around the feet of the dinosaurs 66 million years ago—were mostly insect eaters, based on an analysis of the genomes of 107 different species of mammals.

The scientists inferred this because the genes for the enzymes that allowed these early ancestors of all mammals to digest insects are still hanging around in nearly all mammal genomes today. Even animals like tigers and seals that would never touch an insect have non-functional pieces of these genes sitting in their chromosomes, betraying their ancient ancestors’ diet.

“One of the coolest things is, if you look at humans, at Fido your dog, Whiskers your cat, your horse, your cow; pick any animal, generally speaking, they have remnants in their genomes of a time when mammals were small, probably insectivorous and running around when dinosaurs were still roaming Earth,” says Christopher Emerling, a postdoctoral fellow at Université de Montpellier in France working on the ConvergeAnt project.

“It is a signature in your genome that says, once upon a time you were not the dominant group of organisms on Earth. By looking at our genomes, we are looking at this ancestral past and a lifestyle that we don’t even live with anymore.”

The genetic evidence independently corroborates the conclusions paleontologists reached years ago based on the shapes of fossils and teeth from early mammals.

“In essence, we are looking at genomes and they are telling the same story as the fossils: that we think these animals were insectivorous and then dinosaurs went extinct. After the demise of these large carnivorous and herbivorous reptiles, mammals started changing their diets,” he says.

The finding could shed light on other roles played by these enzymes, called chitinases, which are found not only in the gut but the salivary glands, the pancreas, and the lungs, where they may be involved in asthma.

Breaking down tough shells

Many bacteria have genes that produce an enzyme that breaks down insects’ hard, outer shells, which are composed of a tough carbohydrate called chitin. It’s not surprising that humans and mice have a chitinase gene, since many humans today include insects in their diets, as do mice.

But humans actually have remnants of three other chitinase genes in their genome, though none of them are functional. Emerling showed that these gene remnants in humans aren’t unique to humans or primates, but instead can be traced to the ancestral placental mammals.

In all, he and his colleagues found five different chitinase enzyme genes by looking through the genomes of the largest group of mammals, those that have placentas that allow longer development in the womb, which excludes marsupials like opossums and egg-laying monotremes like the platypus. These placental mammals ranged from shrews and mice to elephants and whales.

They found that the greater the percentage of insects in an animal’s diet, the more genes for chitinase it has.

“The only species that have five chitinases today are highly insectivorous, that is, 80 to 100 percent of their diet consists of insects. Since the earliest placental mammals likely had five chitinases, we think that this makes for a strong argument that they were highly insectivorous,” Emerling says.

As you would expect, ant and termite specialists such as aardvarks and certain armadillos have five functioning chitinase genes. But so do the insect-loving primates called tarsiers. They appear to be the only primates that have so many functional chitinase genes, Emerling says.

Competing in the Cretaceous Period

The story told by these chitinase genes is one of early mammals hunkering down eating insects while the big guys, the huge herbivorous dinosaurs like the brontosaurus and the big meat-eaters like T. rex gobbled up the most abundant food resources.

Only 66 million years ago at the end of the Cretaceous Period, when all non-bird dinosaurs died out, were mammals able to expand into other niches, which they quickly did. The first carnivorous and herbivorous mammals, as indicated by their teeth, arose within 10 million years of the dinosaurs’ demise.

Emerling, who compares genomes to see how mammals and humans evolved, was interested in what mammal genomes could tell us about that transition from insectivory to herbivory and carnivory since the last mass extinction.

He focuses primarily on weird animals that eat insects, including anteaters and armadillos, the unrelated aardvark and the distantly related pangolin. In exploring how these animals are able to digest insects, he decided to look at chitinases, whose roles in mammals are still poorly understood. It’s not known, for example, whether the enzymes allow animals to break down chitin into its component sugars and use them for energy, or if chitinases’ sole function is to break up the exoskeleton to allow access to the soft interiors of insects.

Using databases of animal genomes, plus newly sequenced genomes of armadillos and a lesser anteater (tamandua), he searched for genes similar to the known chitinase gene and dredged up four new varieties.

Based on what is known about chitinase genes in bacteria and other animals, he was able to deduce which genes are functional and which are not, and draw conclusions about the tissues in which the genes are expressed and the enzyme active.

Among the surprises was that the insect-eating-specialist pangolin has only one functional chitinase gene, in contrast to the five in the aardvark and four in the lesser anteater. All eat ants and termites exclusively, but pangolins may have possibly evolved from carnivores that lost their chitinase genes shortly after taking over the ecological niche opened up when meat-eating dinosaurs died out.

Bison, gibbons, and the dromedary camel have only one functional chitinase. Tigers, rhinos, and polar bears have none.

Emerling has many other questions he thinks chitinases can answer about mammal evolution and physiology.

“This is suggesting that there are a lot of these enzymes that might be helping organisms digest their food. This goes from being a simple curiosity—humans have a chitinase, how cool!—to being something that can help us understand how different animals are adapted to their specialized diets.”

The findings appear in the journal Science Advances.

Additional authors of the study are from UC Berkeley and Université de Montpellier. The National Science Foundation, France-Berkeley Fund, PRESTIGE Programme, and European Research Council supported the research. Additional researchers are from the Broad Institute at MIT and Harvard University.

Source: UC Berkeley

The post Our tiny, furry genetic ancestors were bug eaters appeared first on Futurity.

Intel Discloses New 'Variant 4' Spectre-Like Vulnerability

MacRumors - Mon, 2018-05-21 18:11
Intel, Google, and Microsoft today disclosed a new variant of the Spectre design flaw and security vulnerability that impacts millions of computers and mobile devices from a range of manufacturers.

Called Variant 4, or the Speculative Store Bypass, the vulnerability is similar to Spectre, taking advantage of the speculative execution mechanism of a CPU to allow hackers to gain access to sensitive information. Variant 4 was demonstrated by researchers in a language-based runtime environment.

CVE-2018-3639 - Speculative Store Bypass (SSB) - also known as Variant 4

Systems with microprocessors utilizing speculative execution and speculative execution of memory reads before the addresses of all prior memory writes are known may allow unauthorized disclosure of information to an attacker with local user access via a side-channel analysis.According to Intel, the new vulnerability has a "moderate" severity rating because many of the exploits that it uses have already been addressed through mitigations that were first introduced by software makers and OEMs in January for Meltdown and Spectre. Intel is, however, releasing a full mitigation option that will "prevent this method from being used in other ways."

This additional mitigation for Variant 4 has been delivered in beta form to OEM system manufacturers and system software vendors, and Intel is leaving it up to its partners to decide whether or not to implement the extra measures. Intel plans to leave the mitigation set to off by default because of the potential for performance issues.This mitigation will be set to off-by-default, providing customers the choice of whether to enable it. We expect most industry software partners will likewise use the default-off option. In this configuration, we have observed no performance impact. If enabled, we've observed a performance impact of approximately 2 to 8 percent based on overall scores for benchmarks like SYSmark(R) 2014 SE and SPEC integer rate on client1 and server2 test systems.The Spectre and Meltdown family of vulnerabilities affect all modern processors from Intel, ARM, and AMD, but Intel has faced more scrutiny over the design flaw due to its high-profile position in the processor market. Apple's iOS and Mac devices are affected by these vulnerabilities, but Apple has historically been quick to patch them.

Prior to when Spectre and Meltdown were initially discovered, for example, Apple had already implemented some patches and has since addressed known Meltdown and Spectre vulnerabilities with little impact to performance on Macs or iOS devices. As mentioned above, many of the exploits in Variant 4 have been previously addressed by Apple and other manufacturers in already-existing software patches.

Spectre and Meltdown-related vulnerabilities are hardware-based and therefore must be mitigated rather than outright fixed, but future Intel chips will not be as vulnerable. Intel has said that its next-generation Xeon Scalable processors (Cascade Lake) and its 8th-generation Intel Core processors will feature redesigned components to protect against some Spectre and Meltdown flaws.

Tags: Intel, Meltdown-Spectre
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Understanding bacteria ‘switch’ could lead to new antibiotics

Futurity.org - Mon, 2018-05-21 18:06

Scientists have deciphered the workings of a common but little-understood bacterial switch that cuts off protein production before it begins. The discover points to potential new antibiotics.

Many gram-positive bacteria use T-box riboswitches to regulate production of proteins that utilize amino acids, the basic building blocks of all proteins.

A study in Nature Communications describes how one of these switches, a glycine regulator in Bacillus subtilis, flips and locks into the “on” position via a snap-lock mechanism. Engaging the lock increases production of proteins that utilize glycine, the simplest amino acid. Researchers also detailed the switch’s “off” position: A single glycine at the tip of the locking arm blocks protein production.

“T-box riboswitches are intriguing because they are regulated—turned on or off—by molecules central to protein production,” says study coauthor Edward Nikonowicz, professor of biosciences at Rice University. “While they were discovered a quarter century ago, it’s not been entirely clear how they operate. By highlighting their structural and kinetic details, we hope to spur interest in these switches as potential targets for new antibiotics.”

New antibiotics could help avert a looming health crisis, Nikonowicz says. The Centers for Disease Control and Prevention expects antibiotic-resistant bacteria to kill at least 23,000 people in the US this year, and if current trends go unchecked, the World Health Organization estimates that by 2050, drug-resistant pathogens will kill 10 million people per year worldwide.

T-box riboswitches like the one the new study highlights are vital to many gram-positive bacteria, a broad class that includes pathogens that cause tuberculosis, gangrene, botulism, anthrax, inflammation of the inner heart lining, and other diseases.

T-box riboswitches are located on strands of messenger RNA (mRNA), blueprints for proteins that are copied directly from a cell’s DNA. In complex organisms such as animals and plants, the writing, or “transcription,” of mRNA takes place in a vault-like DNA storage facility called the nucleus. Only after mRNA leaves the vault can its message be used, or “translated,” into a new protein. Because bacteria have no nucleus, “transcription” of mRNA and “translation,” decoding of mRNA by ribosomes to make new proteins, happen in close proximity.

“Riboswitches are common in many bacteria, but not in humans, making them such attractive targets for new drugs,” says study coauthor Nils Walter, professor of chemistry, biophysics, and biological chemistry at the University of Michigan. “T-box riboswitches regulate transcription, the writing of the messenger RNA itself, but use a locking arm borrowed from the translation machinery, making it a unique jack-of-all-trades.”

The mRNA blueprints help build proteins, the workhorses of biology. Cells employ millions of proteins at a given time, but each of these is made from the same 20 building blocks, the amino acids that T-box riboswitches help regulate in gram-positive bacteria. To make a protein, cells string amino acids end to end, like beads on a necklace, based on the order specified in mRNA instructions.

The locking arm trigger in the glycine T-box riboswitch is part of another molecule called transfer RNA (tRNA). There are many types of tRNA in cells, but each acts like a kind of car, shuttling payloads to the ribosome, where proteins are strung together. Each type of tRNA can only carry one type of amino acid.

Antibiotics can goad ‘superbugs’ into ganging up on us

In the new study, Walter and Nikonowicz designed an experiment in which glycine-specific tRNA molecules, some loaded with glycine and others unloaded, would pass by and randomly attach to a T-box riboswitch.

“Ed’s team was able to attach a fluorescent marker to the tRNA in a such a way that it wouldn’t interfere with their binding,” Walter says. “My lab employed a technique called ‘single molecule fluorescence microscopy’ to probe the dynamic associations of single T-box riboswitches with the tRNA, either when the glycine cargo was attached or not.”

Each time a tRNA with a fluorescent tag attached took up a position on the T-box riboswitch, a bright signal appeared in the microscope. By measuring exactly how long the signal lasted, and thus how long the molecules stayed in position, the team was able to reconstruct the binding speed and ultimately the locking mechanism for the switch.

Nikonowicz says he and Walter began the glycine T-box riboswitch project about 2 1/2 years ago.

“Glycine was the simplest case, in part because there’s an additional domain in the T-box sensing other amino acids,” he says. “There are questions about what this domain does and how it operates. Given what we’ve already learned about the glycine T-box riboswitch, I’d like to extend this work to see what we can learn from other types of T-boxes.”

Walter adds that the findings could also pay off in the emerging field of RNA nanotechnology, in which scientists are attempting to use RNA templates for precision engineering of complex structures.

The way T cells attack may inspire new antibiotics

“In the active, locked position, the T-box-tRNA complex has a very stable three-dimensional shape,” he says. “It’s possible these could be exploited for ultra-stable ring-like complexes in novel biomimetic architectures.”

The National Institutes of Health supported the research. Additional coauthors are from Rice University and the University of Michigan.

Source: Rice University

The post Understanding bacteria ‘switch’ could lead to new antibiotics appeared first on Futurity.

Trump aides skeptical Kim summit will happen

CNN - Mon, 2018-05-21 18:01
Trump administration aides are growing increasingly skeptical that the summit between President Trump and North Korean leader Kim Jong Un will come to fruition. CNN's Jeremy Diamond reports.

Trump the dealmaker should understand Trump the president's North Korea problem

Washington Post - Mon, 2018-05-21 18:00
It may be time to reread “The Art of the Comeback” on North Korea.

Oliver North Blames ‘Culture of Violence’ for Mass Shootings

NY Times - Mon, 2018-05-21 17:58
The incoming president of the National Rifle Association said shootings are tied to violent television shows and movies and a dependence on medications like Ritalin.

We’re messing up the way hippo poo keeps rivers healthy

Futurity.org - Mon, 2018-05-21 17:55

Drying rivers due to deforestation, human agriculture, and climate change are redefining the way hippos—and their dung—shape the ecology of freshwater ecosystems in sub-Saharan Africa, according to new research.

The average hippo weighs more than 3,000 pounds and consumes about 100 pounds of vegetation daily. This naturally results in large quantities of dung being deposited into the rivers and lakes where hippos spend their days.

“Global change has turned productive hippo pools, once teeming with fish and life, into fetid black cesspools.”

In general, the nutrients delivered via hippo dung to such aquatic ecosystems are thought to be beneficial. For millennia, they provided a natural source of fertilizer that appears to fuel life in aquatic food webs. That may be changing.

“This work explores how hippo dung shapes freshwater chemistry and links these changes to associated patterns of aquatic biodiversity change,” says Keenan Stears, a postdoctoral researcher in the ecology, evolution, marine biology department at the University of California, Santa Barbara.

“It also illustrates that the net impact of hippos on river ecosystems is dynamically controlled by river hydrology and reveals the capacity of human disturbances on river flow to drastically alter the role of ecosystem-linking species,” he says.

Stears and his team studied river flow and hippo density in the Great Ruaha River in Tanzania’s Ruaha National Park, which protects an area about the size of Connecticut and is home to large populations of some of Africa’s most iconic species. The Great Ruaha River is the backbone of life in this dry region. Since 1993, however, the once constantly flowing river has ceased to flow during the dry season.

Hippo pool during wet season with clean water. (Credit: Keenan Stears)

The researchers tested nearly a dozen attributes of water quality and measured the diversity and abundance of aquatic life in hippo pools over multiple years, both when river flow was high and during dry periods when the river stopped flowing.

“During the dry season when there was no flow, the pools were completely separated,” Stears explains. “We found a huge buildup of hippo dung, and therefore nutrient concentrations within high-density hippo pools. The high influx of nutrients caused the dissolved oxygen concentration to decline to sublethal levels for most fish species.”

Douglas McCauley, a senior researcher on the project from the University of California, Santa Barbara, called these results an alarm bell for African wildlife.

“Hippos are to Africa what polar bears are to the Arctic,” he says. “Everything we thought we knew about how African ecosystems worked appears to be changing. Global change has turned productive hippo pools, once teeming with fish and life, into fetid black cesspools.”

Only a few species of fish and insects are able to survive in the hippo pools when the river dries, because of extreme losses of dissolved oxygen in these pools. Stears and his colleagues noted large reductions in fish diversity and abundance inside the pools that were overfueled by dung when river flow ceased.

Hippo pool during peak dry season with dirty water. (Credit: Keenan Stears)

When the rains returned and the river resumed its flow, the researchers saw a reset in many impacts of hippo dung on water quality and biodiversity detected during the dry season.

“This suggests some kind of resilience within the system that allows it to recover after the hydrological disturbance every dry season,” Stears says. “This resilience signifies that there is hope for this system, but without intervention soon, the chronic stress caused by river drying and overfertilizing of hippo dung may cause long-term species loss in this river system.”

According to Stears, the findings from this study highlight the value of accelerating more efficient water-management policies and land-management practices not only for the conservation of hippos but also to ensure the sustained health and functioning of African watersheds in a changing environment.

How shark poo keeps coral reefs healthy

“A lot of our results directly assess how changing river flow alters the hippos’ influence on the ecological diversity and functioning of watersheds,” Stears says.

“However, these findings also call attention to the profound ways in which the dry-season impacts of hippos may influence local communities that rely on rivers as a food source. Tilapia are a commonly consumed fish throughout Africa and, during the dry season, we found that the presence of hippos reduced tilapia abundance by 41 percent across the watershed. That’s not only bound to have ecological consequences but will also impact the human populations that rely on these rivers.”

Researchers from the University of California, Berkeley, and Sokoine University of Agriculture in Tanzania contributed to the work.

Source: UC Santa Barbara

The post We’re messing up the way hippo poo keeps rivers healthy appeared first on Futurity.

Opinion: Pompeo speech is complete fantasy

CNN - Mon, 2018-05-21 17:54
On Monday morning, Secretary of State Mike Pompeo gave a speech at the Heritage Foundation in Washington: "After the Deal: A New Iran Strategy." Over 26 minutes, Pompeo articulated a strategy that can best be summarized as, "Do everything we say, or we will crush you." This speech was the first clear articulation of American Iran policy since President Donald Trump effectively withdrew from the Joint Comprehensive Plan of Action (a.k.a. "the Iran deal") on May 12.

Trump v. the Department of Justice

NY Times - Mon, 2018-05-21 17:54
President Trump and his enablers in Congress and the right-wing media are engaged in a dangerous campaign to undermine the foundations of American justice.

5 Women Sue U.S.C., Alleging Sexual Abuse by Campus Doctor

NY Times - Mon, 2018-05-21 17:46
Lawsuits against U.S.C. in the case of a former gynecologist raised the possibility of hefty financial settlements as the university tried to contain the growing scandal.

In Jersey City, It’s Kushner vs. Kushner in a Race to Develop

NY Times - Mon, 2018-05-21 17:46
Charles and Murray Kushner, famously estranged brothers, are each betting they can transform a gritty neighborhood. Can both win?

Can Parents Be Charged for Failing to Keep Their Guns Locked Up?

NY Times - Mon, 2018-05-21 17:44
Texas is one of 14 states with a “negligent storage law,” which can make parents liable for crimes committed with their firearms by their children.

In Hard-Line Speech, Pompeo Criticizes Iran’s Behavior

NY Times - Mon, 2018-05-21 17:30
Secretary of State Mike Pompeo delivered a remarkably hard-line speech about Iran, offering no concessions to European leaders who want to do business with Tehran.

An egg a day could cut risk of heart disease

CNN - Mon, 2018-05-21 17:30
Eating an egg a day may lower your risk of cardiovascular disease, a study of more than 400,000 adults in China suggests.

Trump warns China to stay ‘strong & tight’ on North Korea border

Washington Post - Mon, 2018-05-21 17:30
The president’s tweet comes amid continuing uncertainty about whether his summit with Kim Jong Un will take place next month.
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