New regulatory component in infectious bacterium discovered

The discovery of a new regulatory component in an infectious bacterium could aid efforts to explain its ability to survive in the human body, report microbiologists at The University of Texas Health Science Center at Houston (UTHealth) and University of Maryland, College Park, in the journal Science.

The scientists analyzed a bacterium called Enterococcus faecalis that is found in the gut of most adults. While in healthy people this bacterium is normally benign, certain strains can cause severe disease when they contaminate non-intestinal sites. It is a leading cause of health care-associated infection.

"We are trying to learn more about the interaction between E. faecalis and the host," said Danielle Garsin, Ph.D., co-senior author and associate professor in the Department of Microbiology and Molecular Genetics at the UTHealth Medical School. "Our goal is to understand how key genes and processes are regulated in this pathogen."

She added, "This information may lead to the development of novel therapeutics."

Garsin's research focused on a compound called ethanolamine (EA) that is potentially used by E. faecalis to survive in the human body. While the ability of E. faecalis to utilize EA was known, how the bug regulates the genes involved was not completely understood.

The scientists identified a novel regulatory component that was key to turning on the genes involved in EA metabolism under the right conditions. When researchers blocked the regulatory component, the molecular machinery was produced inappropriately.

"Not only does this regulatory component help explain how this particular process is controlled in E. faecalis, its discovery and elucidation increases our understanding of the variety and diversity of regulatory mechanisms in bacteria," Garsin said.

Story Source:

The above story is based on materials provided by University of Texas Health Science Center at Houston . Note: Materials may be edited for content and length.

It turns out that coffee is special [Greg Laden's Blog]

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But you knew that already.

The Coffea canephora Genome has been sequenced. This is probably more important than the Human Genome project because humans are completely useless first thing in the morning, but coffee is very important first thing in the morning.

Some important plant evolution involves wholesale duplication of large parts of the genome. This does not appear to be the case with coffee. Rather, diversification of single genes characterizes the genome, so, according to the paper reporting these results in Science, “…the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis.”

Also of great interest is the apparent fact that caffeine related genes either evolved separately from, or engaged in the important work of making caffeine separately from similarly functioning sets of genes in tea and cacao (chocolate). I had always suspected tea was … different.

So, not at all unexpectedly, the most important molecule on earth evolved more than once!

Elizabeth Pennisi also has a writeup here.

The FBI Finally Says How It ‘Legally’ Pinpointed Silk Road’s Server

Ross Ulbricht.

Ross Ulbricht. Courtesy The Ulbricht Family

As the trial of alleged Silk Road drug market creator Ross Ulbricht approaches, the defense has highlighted the mystery of how law enforcement first located the main Silk Road server in an Icelandic data center, despite the computer being hidden by the formidable anonymity software Tor. Was the FBI tipped off to the server’s location by the NSA, who used a secret and possibly illegal Tor-cracking technique?

The answer, according to a new filing by the case’s prosecution, is far more mundane: The FBI claims to have found the server’s location without the NSA’s help, simply by fiddling with the Silk Road’s login page until it leaked its true location.

In a rebuttal filed Friday to a New York court Friday and accompanied by a letter from the FBI, the prosecution in Ulbricht’s case laid out an argument dismissing a series of privacy concerns Ulbricht’s lawyers had expressed in a motion submitted to a New York court last month. That earlier motion had accused the government of illegal searches in violation of the Fourth Amendment, including a warrantless search of the Silk Road server, and argued that those privacy violations could render inadmissible virtually all of the prosecution’s evidence. The defense motion also demanded that the government explain how it tracked down the Silk Road’s server, and reveal whether the NSA had participated in that hunt.

If the judge accepts the prosecution’s explanation, it could represent a major blow to Ulbricht’s chances of beating the seven charges against him.

In the latest filing, however, former FBI agent Christopher Tarbell counter’s Ulbricht’s defense by describing just how he and another FBI agent located the Silk Road server in June of last year without any sophisticated intrusion: Instead, he says, they found a misconfiguration in an element of the Silk Road login page, which revealed its Internet Protocol (IP) address and thus its physical location.

As they typed “miscellaneous” strings of characters into the login page’s entry fields, Tarbell writes that they noticed an IP address associated with some data returned by the site didn’t match any known Tor “nodes,” the computers that bounce information through Tor’s anonymity network to obscure its true source. And when they entered that IP address directly into a browser, the Silk Road’s CAPTCHA prompt appeared, the garbled-letter image designed to prevent spam bots from entering the site.

“This indicated that the Subject IP Address was the IP address of the SR Server,” writes Tarbell in his letter, “and that it was ‘leaking’ from the SR Server because the computer code underlying the login interface was not properly configured at the time to work on Tor.”

That discovery by the FBI, the prosecuting attorneys in Ulbricht’s case argue, means that no illegal spying techniques were needed to pinpoint the world’s largest anonymous bazaar for narcotics. In fact, they write, the evidence revealing its physical location was left in plain sight.

“Ulbricht conjures up a bogeyman—the National Security Agency (‘NSA’)—which Ulbricht suspects, without any proof whatsoever, was responsible for locating the Silk Road server, in a manner that he simply assumes somehow violated the Fourth Amendment,” the 58-page motion reads. “The facts are not at all what Ulbricht imagines them to be…The Silk Road server was located not by the NSA but by the Federal Bureau of Investigation (“FBI”), using perfectly lawful means.”

Ulbricht’s defense attorneys didn’t immediately respond to a request for comment on the prosecution’s motion.

After the initial revelation of the Silk Road server’s location in a data center in Reykjavik, Iceland, the motion explains that Reykjavik police accessed and secretly copied the server’s data. As agents of a foreign government, the prosecution argues, they weren’t required to seek a warrant from any US authority. And the prosecution writes that Ulbricht didn’t himself even own the server: He had allegedly rented it through a third-party service, which in turn rented space in the Icelandic data center. The motion goes on to quote the web host’s terms of service, which warned that “systems may be monitored for all lawful purposes, including to ensure that use is authorized.”

If the judge in Ulbricht’s case accepts the prosecution’s explanation of that breakthrough in the Silk Road investigation, it could represent a major blow to Ulbricht’s chances of beating the seven charges against him, which include conspiracy to traffic in narcotics, money laundering conspiracy, and a “kingpin” charge usually reserved for leaders of drug cartels and mafia organizations. Ulbricht’s lawyers have previously outlined a defense against those charges they refer to as the “fruit of the poisonous tree” doctrine, an argument that an initial illegal search taints the rest of the evidence resulting from that violation. On Friday, Ulbricht appeared in court to plead not guilty to new charges that included selling counterfeit IDs and directly trafficking in narcotics rather than merely leading a conspiracy to do so.

“The Silk Road server was located not by the NSA but by the Federal Bureau of Investigation (“FBI”), using perfectly lawful means.”

But the prosecution’s motion goes on to request that all of Ulbricht’s claims of illegal evidence collection be dismissed. The defense had argued that a surveillance technique known as a pen register applied to Ulbricht’s Comcast internet connection without a warrant had also violated his privacy; the prosecution responds that it merely collected metadata rather than the actual content of his communications, and thus didn’t require proving probable cause to a judge. The defense’s earlier motion argues that when the FBI did get a warrant to seize and search Ulbricht’s Samsung laptop, it used an illegal “general” warrant rather than specifying the data it sought. The prosecution claims that it needed to see all data on the machine to establish Ulbricht’s alleged identity as the so-called “Dread Pirate Roberts” who had created and managed the Silk Road’s billion-dollar drug trade.

“That identification was the fundamental objective of the Government’s investigation,” the prosecution’s motion reads. “The criminality of the conduct of the Silk Road user ‘Dread Pirate Roberts’ was manifest throughout the operation of Silk Road. The mystery was his true identity. And the Government sought to analyze Ulbricht’s writings and his travel patterns in order to confirm that ‘Dread Pirate Roberts’ was indeed Ulbricht.”

In last month’s motion, Ulbricht’s defense hadn’t only addressed issues of privacy and potentially illegal searches. It had also requested that the government strike from its indictment accusations that Ulbricht paid for the murder of six people. Ulbricht’s defense and his family have protested that grisly element of the indictment, which has yet to result in any actual criminal charges, has been used to scare off support for the 30-year-old despite a lack of necessary evidence to press those charges of violence.

But the prosecution counters that the uncharged murder accusations show Ulbricht’s character and motivations. “The use of violence and threatened violence to protect one’s drug empire are relevant to proving the intentional operation of a narcotics conspiracy, and such conduct may be alleged as overt acts in furtherance of such a charge,” the prosecution writes.

Finally, the prosecution dismisses a request from Ulbricht’s defense for more information on a series of facts in the case, including all agencies and contractors involved in the Silk Road investigation, and the names of all software tools used to scan for potential vulnerabilities in its infrastructure.

“There is therefore no basis—especially at this late juncture, six months after discovery was originally produced—for Ulbricht to go on a ‘blind and broad fishing expedition’ for proof of some darker, alternative storyline, somehow involving violations of his Fourth Amendment rights, when there isn’t a shred of evidence that any such violations actually happened,” the motion concludes.

Read the full motion from the prosecution in the Silk Road case below.

Silk Road Prosecution 4th Amendment Rebuttall

Tech Time Warp of the Week: Watch Steve Ballmer Laugh at the Original iPhone

When Apple unveils some sort of computerized mega watch in Cupertino next week—inside the same venue where Steve Jobs unveiled the original Macintosh 30 years ago—most of the world will ooh and ahh. Over and over again. Those with a more nuanced view of the universe will question whether a smartwatch is really what the people want. And, certainly, various Apple competitors will carefully explain why their wearables make more sense than the one flaunted by Tim Cook.

But no reaction will compare with the one that emerged from Microsoft CEO Steve Ballmer when Apple unveiled the original iPhone in 2007. As you can see from the video above—yet another gem in the seemingly endless list of wonderfully entertaining Ballmer videos from years past—the big man’s response to the original iPhone, one of the most important devices in the history of computing, was to laugh at it.

“Five hundred dollars? Fully subsidized? With a plan?” Ballmer chuckles in the way that only Ballmer chuckles. “That is the most expensive phone in the world. And it doesn’t appeal to business customers because it doesn’t have a keyboard, which makes it not a very good email machine.”

Yes, with more than seven years of hindsight, it’s easy to make fun of him. But it was nearly as easy without any hindsight.

Certainly, he does says that the iPhone may “sell very well.” But then he says Microsoft can hold its own. As he explains, Microsoft’s $99 Zune phone “will do music. It will do internet. It will do email. It will do instant messaging. I kinda look at that and I say: ‘I like our strategy.’”

On the one hand, you could argue that this is merely what he had to say, that he had no choice but to talk up his own business. But history shows that Microsoft, unlike Google, took far too long to follow Apple’s lead, and now, it’s still struggling to play catchup. Plus, Larry Page and Sergey Brin never chuckled at the iPhone. At least not like that.

Superstar Designer Marc Newson Is Joining Apple

Marc Newson, the renowned industrial designer, is joining Apple.

The news, first reported by Vanity Fair , is about as big of a deal as it gets in the design world. It means that Apple will now officially have two of the world’s best-known and most influential designers working together on future products.

The collaboration is not an entirely new one. Newson—probably best known for his furniture, though his work has included cars, cameras, and (yes) watches—has been close friends with Apple’s design master, Jony Ive, for a number of years. Recently, the pair co-curated a charity auction for Sotheby’s, for which they collaborated on two wholly new designs: a 2,600 pound aluminum desk and a limited-edition-of-one Leica camera.

In a statement to Vanity Fair, Ive had this to say about the announcement:

“Marc is without question one of the most influential designers of this generation…He is extraordinarily talented. We are particularly excited to formalize our collaboration as we enjoy working together so much and have found our partnership so effective.”

The announcement is an unexpected one, to say the least. Newson is a celebrity designer in his own right, having worked for companies like Ford, Pentax, Nike and Qantas, the Australian airline. His furniture, with curvy “biomorphic” forms that have the designer’s signature style, sells for hundreds of thousands of dollars. (Jony Ive reportedly sits in a Newson-designed chair in Apple’s design shop.) His work’s in MOMA’s permanent collection. In 2005, he was one of Time magazine’s 100 most influential people of the year.

So what does Apple want with him? It could simply be a response to Jony Ive’s expanded role in the company. Now that Ive’s in charge of the company’s software products, Newson’s addition could relieve some of the burden on the hardware side.

But it’s hard to imagine Newson being content to play second-fiddle to Ive, toiling away on the iPhones 7, 8 and 9. Instead, it seems more likely that Newson will be something like a high-powered consultant, helping shape Apple’s product pipeline as the company continues its transition into a true lifestyle brand. Indeed, Vanity Fair’s report suggests that the two have already collaborated on some Apple products, perhaps even Apple’s wearable, which is expected to be unveiled next week. Intriguingly, Newson has designed several timepieces for his own watch company, Ikepod.

Newson will reportedly continue to live in the UK and do his own design work, though he’ll visit Cupertino regularly. Not that working remotely should be a big deal. “It’s very very easy for us to talk on the phone and design something more or less verbally,” Newson told WIRED last year, commenting on his collaboration with Ive for the charity auction. “We’ve both been doing our jobs for more than 20 years—it’s what we do day in and day out. We speak each other’s language completely fluently.”