Protein secrets of Ebola virus

The current Ebola virus outbreak in West Africa, which has claimed more than 2000 lives, has highlighted the need for a deeper understanding of the molecular biology of the virus that could be critical in the development of vaccines or antiviral drugs to treat or prevent Ebola hemorrhagic fever. Now, a team at the University of Virginia (UVA), USA -- under the leadership of Dr Dan Engel, a virologist, and Dr Zygmunt Derewenda, a structural biologist -- has obtained the crystal structure of a key protein involved in Ebola virus replication, the C-terminal domain of the Zaire Ebola virus nucleoprotein (NP).

The team explains that their structure reveals a novel tertiary fold that is expected to lead to insights into how the viral nucleocapsid is assembled in infected cells. The structure could also provide a basis for the design of drugs to halt infection in humans. "The structure is unique in the RNA virus world," Derewenda explains. "It is not found in viruses that cause influenza, rabies or other diseases." It distantly resembles the β-grasp protein motif found in ubiquitin, most likely the result of convergent evolution.

Like many other related viruses, Ebola virus contains a negative-sense, single-stranded RNA that encodes seven different proteins, one of which is known as the nucleoprotein (NP) for its ability to interact with the viral RNA genome. It is the most abundant viral protein found in infected cells and also inside the viral nucleocapsid. While five of the seven viral proteins have succumbed to structural characterization by X-ray crystallography, NP so far has resisted such attempts, although analogous proteins from other viruses have had their structures analysed.

The UVA team produced the Ebola protein using an engineered form of Escherichia coli bacteria as a protein factory. This allowed them to identify the boundaries of two globular domains and to crystallize the unique C-terminal domain spanning amino-acid residues 641 to 739. The study revealed a molecular architecture unseen so far among known proteins, the team says. There is existing evidence that the newly characterized domain is involved in transcription and the self-assembly of the viral nucleocapsid. As such, the results obtained by the UVA team will be useful in deciphering precisely how these various functions are accomplished by the virus; such a detailed description offers up a potential target for the design of anti-viral drugs.

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The above story is based on materials provided by International Union of Crystallography . Note: Materials may be edited for content and length.

Minecraft Creator Explains Controversial $2.5 Billion Sale to Microsoft

Minecraft. Image courtesy Mojang

Markus “Notch” Persson has a message for Minecraft fans. “It’s not about the money. It’s about my sanity.”

On Monday morning, tech giant Microsoft announced that it has acquired Persson’s indie gaming company, Mojang, maker of Minecraft, the hit game that lets you build your own virtual worlds, and Persson took to his blog to explain his part in this highly contentious move. Rumors of such a deal first emerged last week, leaving many of Minecraft’s loyal fans wondering why Persson, who has been a vocal critic of Facebook’s acquisition of Oculus VR, would sell to a corporate giant like Microsoft.

Basically, Persson is tired. Since it launched in 2009, Persson said on his blog, Minecraft’s explosive growth and the public spotlight that came with it had become overwhelming. Persson acknowledges that as an outspoken critic of corporations, including Microsoft, he became a sort of figurehead for the indie developer community, a role he says he never really wanted in the first place. “I don’t want to be a symbol, responsible for something huge that I don’t understand,” he writes. “I’m not an entrepreneur. I’m not a CEO. I’m a nerdy computer programmer who likes to have opinions on Twitter.”

So, he explains, as soon as the deal with Microsoft is finalized, he plans to leave the company to work on “small web experiments.” And if any of those experiments should become as popular as Minecraft became, Persson writes, “I’ll probably abandon it immediately.”

Certainly, the irony of the move isn’t lost on him. “I’m aware this goes against a lot of what I’ve said in public. I have no good response to that,” he continues. “Thank you for turning Minecraft into what it has become, but there are too many of you, and I can’t be responsible for something this big.”

This decision is not likely to ease fears among Minecraft’s fan base. Many fear that their favorite game will wither under Microsoft’s leadership, or, at the very least, become inextricably linked to Microsoft’s Xbox gaming system. As WIRED pointed out last week, after Halo was acquired by Microsoft in 2000, sequels to the flagship game were launched exclusively for Microsoft platforms. Such a change could alienate a wide swath of Microsoft’s user base. And without its nonconformist leader on board, maintaining creative independence may become even more difficult for the Minecraft team.

In a blog post, Phil Spencer, Microsoft’s head of Xbox, attempted to offset that fear, writing that Microsoft plans to continue offering the game for iOS, Android, and Playstation, as well as Xbox and PC. He wrote that the company has been interested in buying Mojang ever since Minecraft became the top online game on Xbox Live. “The Minecraft community is passionate and diverse, ranging across all ages and demographics,” Spencer writes. “We respect the brand and independent spirit that has made Minecraft great, and we’ll carry on the tradition of innovation to move the franchise forward.”

Persson echoed that sentiment in his own post, noting that while Microsoft may technically own Minecraft now, “in a much bigger sense, it’s belonged to all of you for a long time, and that will never change.”

Boosting armor for nuclear-waste eating microbes

A microbe developed to clean up nuclear waste and patented by a Michigan State University researcher has just been improved.

In earlier research, Gemma Reguera, MSU microbiologist, identified that Geobacter bacteria's tiny conductive hair-like appendages, or pili, did the yeoman's share of remediation. By increasing the strength of the pili nanowires, she improved their ability to clean up uranium and other toxic wastes.

In new research, published in the current issue of Applied and Environmental Microbiology, Reguera has added an additional layer of armor to her enhanced microbes.

The microbes also use the pili to stick to each other and grow a film on just about any surface, similar to the bacterial film that forms on teeth. The Geobacter biofilm, encased by a network of nanowires and slime, gives the bacteria a shield and increases their ability to neutralize even more uranium. The improvement also allows the bacteria to survive longer even when exposed to higher concentrations of the radioactive material.

Geobacter immobilizing uranium can be described as nature's version of electroplating. The beefed-up microbes engulf the uranium and turn it into a mineral, preventing the toxic material from leaching into groundwater.

Reguera's team had previously linked the conductive pili to the ability of the microbe to mineralize the soluble uranium. As the biofilm concentrates many nanowires around the Geobacter cells, more uranium can be bound and mineralized. The pili are immersed in a matrix of slime, which surrounds the biofilm cells and boosts the Geobacter's pili armor, so the biofilm now can pull double duty by helping mineralize uranium.

The shield keeps the uranium from penetrating deep into the Geobacter biofilm. By keeping this process on the surface of the film, the bacteria are not exposed to uranium and, as a community, they are able to clean up more toxic waste.

"The results surpassed our most optimistic predictions," Reguera said. "Even thin biofilms immobilized uranium like sponges. They reduced it to a mineral, all while not suffering any damage to themselves, for prolonged periods of time."

Even when exposed to extremely high and toxic concentrations of uranium, levels that would destroy individual Geobacter cells, the biofilms didn't just survive, they thrived, she added.

Additional MSU researchers contributing to the study include Dena Cologgi, Allison Speers and Blair Bullard. Shelly Kelly with EXAFS Analysis, also contributed to the study.

Reguera's future research on this front will focus on deciphering how the biofilm matrix that encases the cells shields them so effectively and how to improve its properties further.

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The above story is based on materials provided by Michigan State University . Note: Materials may be edited for content and length.

Pterosaurs by Mark Witton [Greg Laden's Blog]

Pterosaurs: Natural History, Evolution, Anatomy by Mark P. Witton is a coffee-table size book rich in detail and lavishly illustrated. Witton is a pterosaur expert at the School of Earh and Environmental Sciences at the University of Portsmouth. He is famous for his illustrations and his work in popular media such as the film “Walking With Dinosaurs 3D.”

The first pterosaur fossil was found in the late 18th century in the Jurassic Solnhofen Limestones, in Germany, the same excellent preservational environment that would later yield Archaeopteryx. They person who first studied it thought the elongated finger bones that we now know supported a wing served as a flipper in an amphibious creature. Not long after, the famous paleontologist George Cuvier recognized the winged nature of the beast. Witton notes that at the time, and through a good part of the 19th century, it was possible to believe that many of the odd fossils being unearthed were of species that still existed but were unknown to science. This is because most of the fossils were aquatic, and who knew what mysterious forms lurked beneath the sea? But a very large flying thing like this first pterosaur was very unlikely to still exist, unseen by European and American investigators. It had to be something major that was truly extinct. So in a way the history of extinction (the study of it, that is) was significantly shaped by this find. By the early 20th century there had been enough publication and study of pterosaurs to give them a place in paleontology, but not a lot else happened until the 1970s, when a combination of factors, including advanced technology that allowed more detailed and sophisticated study of fossils, led to much more intensive study of pterosaur anatomy and behavior.

Pterosaurs are part of the large taxonomic group that includes the lizards, dinosaurs, and birds, but they branched off within that group prior to the rise of the latter two. So, they are not dinosaurs, but cousins of dinosaurs. You can call them flying lizards, but not flying dinosaurs.

Witton explores this interesting history in some detail, and then proceeds to explore various aspects of pterosaur biology, starting with the skeleton, the soft parts (of which there is some direct but mostly indirect evidence), their flight, how they got around on the ground, and their reproductive biology. These explorations into pterosaurs in general is followed by several chapters devoted to the various groups, with a treatment of the evidence for each group, reconstructions of anatomy, locomotion in the air and on the ground, and ecology.

The resemblance of this layout to a detailed field guide for birds (or some other group) is enhanced by the use of color-coded bleeds at the top of each page, separating the book’s major sections or groups of chapters. The book ends with a consideration of the origins and endings of the “Pterosaur Empire.” It turns out that we don’t actually know why they went extinct. They lasted to the end of the Cretaceous, so going extinct along with their dinosaur cousins is a reasonable hypothesis, but they had already become somewhat rare by that time.

Pterosaurs are cool. Pterosaurs: Natural History, Evolution, Anatomy is a cool book.

Of related interest:

• LOL Pterosaurs ….


• Reconsidering the Reconstruction of the Pterosaur


• Flying Dinosaurs: A New Book on the Dinosaur Bird Link


• Giant Semiaquatic Predatory Dinosaur


• Titanic Fearless Dinosaur Unearthed


• Honey, I Shrunk The Dinosaurs …

France’s Bizarre Three-Wheeled Buggies May Be the Perfect EVs

Toyota’s i-Road may be the perfect urban electric vehicle. Toyota

The streets of one French city will soon be filled with funky vehicles that resemble hulked-up mopeds. But before you make fun, consider that while they look silly, the way these things are being used may make them the perfect electric vehicles.

Next month, Toyota and Grenoble will launch a program giving residents access to two of the weirder vehicles built in recent memory. Through the Cité Lib by Ha:Mo (harmonious mobility) system, Toyota is providing 70 EVs that can be rented for short periods of time. Like bike sharing, the idea is to give people a way to get from public transit stations to their destinations, covering the “last mile” so they don’t feel the need to take their car.

The goal is to “be a part of creating a future urban mobility,” says Toyota chairman Takeshi Uchiyamada, to make getting around cities easier and reduce emissions. We’ll have to see how the Grenoblois react to the program to gauge its success, but it’s got two things going for it. The very fact that it’s a new kind of vehicle sharing service makes it worth trying out. And more importantly, Toyota has found what may be the ideal application of electric vehicles.

Anyone 18 and older with a driver’s license can sign up for the program, which uses two kinds of Toyota vehicles: the three-wheeled i-Road, which seats one, and the four-wheeled COMS, with room for two. Fees vary, but expect to pay about €3 ($3.89) for 15 minutes, or €5 ($6.50) for half an hour. Users can park at any of 27 stations around the city, where they plug in to charge before walking away.

The new program calls to mind two kinds of vehicle sharing services. The first is car sharing. A good example is Car2Go, a Daimler AG-run company that lets users in cities in Germany and the US rent Smart cars by the minute. Users can park wherever they find a space, not at set stations, which fully solves the last mile problem.

The second is bike sharing. More than 500 cities around the world have a program, and while the specifics vary, the basic premise is usually the same: Sign up for a membership, and you can borrow a bike from any station in the city, ride it for a set amount of time (usually around 30 minutes), then return it to any station where there’s an open spot. Bikes are even better than electric cars when it comes to the environment and public health, and you can pack many more bikes into a standard bike share than you get vehicles in a car share. Of course, biking is less convenient when you’re lugging around groceries or offspring. Or when you remember that humans invented automobiles because sometimes being lazy is totally fine.

The Toyota-Grenoble program is a blend of these services. The vehicles are better than Smart cars for moving around a cramped old city like Grenoble (maneuverability is an undervalued part of mobility), though you can’t just park them wherever. Using electricity instead of gasoline is good for the environment and lungs of le peuple, but not as good as making everyone pedal. In any case, these are early days for vehicle sharing services, and we don’t know what exact combination of pros and cons people want. The very fact that Ha:Mo is a new system makes it worth trying.

Toyota

But beyond that, there’s a reason we’re excited about this system: It may be the perfect application of electric vehicles. The two big downsides to the technology today are limited range and high cost. Apart from Tesla, whose vehicles can actually cross the country, automakers pitch electric cars as city vehicles with enough juice to handle most daily driving tasks. The problem is that prices are still real high, and few people are willing to pay $30,000 or more for a vehicle that’s useless when they need to hit the road for a few hours to see the in-laws. Until range goes up and prices come down, mass adoption of EVs won’t happen.

Ha:Mo solves neither problem, but sidesteps both. On a full battery, the i-Road and COMS can each drive about three hours at a presumably limited speed. That’s actually excessive for vehicles meant to be used for a few minutes at a time and charged in between. Cost isn’t an issue because people are renting the vehicles (at a reasonable rate), not buying or leasing them. EV ownership may not happen on a grand scale for years or decades. In the meantime, these vehicles fill the niche that is open to them.

One potential weakness of the Ha-Mo program is its network of just 27 parking/charging stations. The fact that the cars must be parked there limits their usefulness. Surely some residents will be too far from stations to make the vehicles worth renting.

Toyota could take a lesson here from Car2Go San Diego, one of the cities where the program uses electric instead of gas-powered cars. There, users can park wherever they want, unless the car’s battery drops below 20 percent of its range while they’re driving. In that case, they must end their journey at one of the stations around the city where they can plug in. If Ha:Mo follows suit or finds another way to solves that issue, it could finally make mass EV adoption—if not ownership—a reality.

A Brilliantly Witty Book Mined From Twitter’s Wannabe Novelists

Cory Arcangel's new book, Working on My Novel was culled from two years of tweets about the same. Cory Arcangel

Cory Arcangel's new book, Working on My Novel was culled from two years of tweets about the same.

Cory Arcangel

The artist sees the book as a meditation on the act of creation---but also a document of what life's like at our specific moment in time. Cory Arcangel

The artist sees the book as a meditation on the act of creation---but also a document of what life's like at our specific moment in time.

Cory Arcangel

Arcangel gravitated to the ones that made some comment on the world around them, even in some small, seemingly mundane way. "I didn't have a defined criteria," he says of the process. "It's a lot of a 'I know it when I see it.'" Cory Arcangel

Arcangel gravitated to the ones that made some comment on the world around them, even in some small, seemingly mundane way. "I didn't have a defined criteria," he says of the process. "It's a lot of a 'I know it when I see it.'"

Cory Arcangel

"A good tweet has to be able to stand by itself. It has paint a really good picture." Cory Arcangel

"A good tweet has to be able to stand by itself. It has paint a really good picture."

Cory Arcangel

If you’ve ever tweeted about working on a novel, there’s a good chance Cory Arcangel read it. Not your novel. Your tweet.

For the last several years, the New York artist has fastidiously tracked the phrase “working on my novel” as used on Twitter. His new book, Working On My Novel , collects hundreds of these tiny declarations of literary intent. It’s a clever conceit, but it’s also something more. Taken together, the messages make for a poignant picture of creativity—and life in general—in age of social media.

The cover. Cory Arcangel

Before the project was a book, it was a Twitter account, and before that, it was a BuzzFeed post. The earliest incarnation arrived in 2009, when Arcangel, a friend of BuzzFeed creator Jonah Peretti’s from their time running in New York’s digital arts scene, was doing a turn as a guest editor on Peretti’s then-new site. Arcangel, whose brilliant software-driven work has established him one of his generation’s most incisive artists, made a post linking to the search results for the phrase “working on my novel” on Twitter. It was a nice bit of juxtaposition: an age-old creative pursuit as it was being expressed on a frenetic new creative medium.

But the idea stuck around, and eventually, Arcangel brought it back as a Twitter account. Every morning he’d wake up, read through the previous day’s tweets that included “working on my novel,” and re-tweet the best ones. “I’d maybe Tweet one out of every four hundred,” he says. “Because they had to be right. By the time it got to the Twitter feed, I’d realized that my eye was a kind of part of it.” A while later, when Penguin asked Arcangel to pitch some ideas for a book, the “working on my novel” project emerged as an obvious fit.

Making a book full of tweets was not as straightforward as it might seem. Since Twitter doesn’t offer a way to search for messages more than a week old, Arcangel had to write a crawler that archived every usage of that exact language. Then he ran it for two years.

“It was kind of a monumental effort,” he says. “But it was really exciting to me to write a book which basically required writing a lot of software.”

When it came time for Arcangel to pick his favorites, he gravitated to the ones that made some comment on the world around them, even in some small, seemingly mundane way. “I didn’t have a defined criteria,” he says of the process. “It’s a lot of a ‘I know it when I see it.’ A good tweet has to be able to stand by itself. It has paint a really good picture. I really like ones that have references to contemporary culture.”

Though his role was largely one of curator, Arcangel thinks the book fits perfectly within his larger body of work. He compared it to his best known project, Super Mario Clouds , a modified version of the iconic game in which Arcangel stripped out the game’s visuals until it just showed a parade of pixelated clouds inching slowly across the blue sky. (Earlier this summer, when a Yahoo tech writer asked a group of respected critics what might be considered the Mona Lisa of the digital art, Super Mario Clouds was the closest they came to a consensus.)

That project, Arcangel says, was about finding the unassuming moments of beauty that often get overlooked in the digital world. “At that time, people weren’t looking at those graphics like that. Those things weren’t considered beautiful.”

In the same way, the book encourages us to look a little more closely at something we’d otherwise ignore. “On one level it’s about people dealing with what it means to be creative,” he says, “But overall, I hope when you read the book you get a sense of what life is like today. And to me, the tweets do have a beauty in them. Because they’re very human.”

Digital Literacy Is the Key to the Future, But We Still Don’t Know What It Means

Gary Waters/Getty

The entrance to GitHub is the most Instagram-able lobby in tech. It’s a recreation of the Oval Office, and the mimicry is spot-on but for the rug. Instead of the arrow-clutching eagle that graces Obama’s office rug, it shows the code-sharing site’s Octocat mascot gazing into the digital future, just above the motto: “In Collaboration We Trust.”

One recent morning, just past this presidential decor, representatives of the tech industry (Google, Palantir, Mozilla, Github) and academia (UC Berkeley and digital education nonprofit Project Lead the Way) sat on massive leather couches trying to figure out how to give more people the means to participate in that future. The theme in play was “digital literacy,” the idea that the world’s citizens, and kids in particular, will benefit if they’re skilled in the ways of information technology.

“The amount of potential unlocked by the industrial revolution is dwarfed in information terms by what you can do with computers,” said Ari Geshner, a senior software engineer at Palantir, a much-discussed data analysis startup whose customers include US intelligence and defense agencies. “Digital literacy is about learning to use the most powerful tools we’ve ever built.”

The tricky part comes in defining what exactly is meant by “use.” Most people who use computers don’t know how to build software. Does that mean they’re digitally illiterate?

For some, it does. It’s become commonplace to argue that everyone is better off learning at least basic programming skills—that coding itself is the new, necessary literacy. We’ve seen online courses, games, new programming languages, and even children’s books pushing kids and their parents in this direction.

But “learning to code” is an exceedingly broad concept, and one which without more specifics risks oversimplifying conversations about what digital literacy really means. And how digital literacy is defined is important. This isn’t just about filling Silicon Valley jobs. It’s about educators, policy makers, and parents understanding how to give the rising generations of digital natives the tools they need to define the future of technology for themselves.

Can’t Just Code a Solution

For Carol Smith, who oversees Google’s Summer of Code program, learning to program is about more than learning to program. “It’s more about giving people the skills and the tools they learn in the act of coding,” she said during the roundtable at GitHub. “It gives them the critical thinking skills that are important whether or not they go into computer science as a profession.” Among other things, it helps people understand the power of algorithms.

Armando Fox, a U.C. Berkeley professor who teaches an introductory software engineering course, describes the algorithmic mindset as applying “structured linear thinking” to a seemingly open-ended problem. An excessive faith in the power of the algorithm has bred its own kind of uncritical thinking in some corners of Silicon Valley. But that may because few people outside Silicon Valley have the kind of literacy needed to apply algorithms informed by the sophistication of deep knowledge in a non-tech field.

For most of the time computer science has existed, Fox said, its practitioners have focused attention inward, on making computers faster and getting them “not to suck.” Only recently, he said, has that suckiness been overcome to the extent that computer scientists can start looking outward toward figuring out how to apply computational thinking to problems beyond computing.

“It’s difficult for me to think of a professional career path that’s not data-driven or on its way to becoming data driven,” he said . “Our tools have become good enough that we can become outward-facing.”

Make It Do What You Want

Moving beyond improving career prospects, the conversation then turned repeatedly to the idea that literacy means more than using digital technology as a means of consuming things other people make. Digital literacy, Smith said, also is about “how to make it do what you want.” Or as Geshner put it: “Are you an iPad or are you a laptop? An iPad is designed for consumption.” Literacy, as he described it, means moving beyond a passive relationship with technology. “When you get down to coding, you’re creating your own tools.”

Perhaps surprisingly for a group of technologists, the group largely agreed that getting computers in schools was a far lower priority than teaching computing as an intellectual discipline. “It’s more about introducing early on how to work collaboratively,” said Kaitlin Thaney, director of the Mozilla Science Lab, who said even “paper prototyping” with small children can be a valuable first step.

One serious concern is putting devices in kids’ hands can give the appearance of teaching digital literacy without providing the actual substance. Even if the computers are there, teachers often aren’t. Of 37,000 U.S. public high schools, fewer than 10 percent offer college-level courses in computing, says Bennett Brown, director of curriculum at Project Lead The Way, which is developing a K-12 computer science program. The problem, he said, is lack of professional development, and the consequence is lack of equal opportunity for students: “We need a teacher who’s comfortable at teaching coding in every school in the United States.”