First crystal structure of the C. difficile surface protein Cwp84

The bacterium Clostridium difficile causes antibiotic-related diarrhea and is a growing problem in the hospital environment and elsewhere in the community. Understanding how the microbe colonises the human gut when other "healthy" microbes have been destroyed during a course of antibiotics might lead to new ways to control infection. An important clue was reported recently in an open access article published in the journal Acta Crystallographica Section D Biological Crystallography.

Ravi Acharya of the University of Bath, UK, and colleagues have reported the first crystal structure of the C. difficile surface protein Cwp84. This cysteine protease enzyme is found on the surface of the bacterium and assists with production of the microbe's surface-layer, which is likely to play an essential step in the colonisation of the gut. The enzyme cleaves a single polypeptide (surface-layer protein A; SlpA) into low- and high-molecular-weight subunits. Now, Acharya and colleagues have identified three critical regions in a mutant of the enzyme that could represent novel targets for drugs to attack C. difficile by blocking maturation of its surface layer during colonisation.

While C. difficile can be present in the normal, healthy gut (3-5% of adults), when a patient requires treatment for infection with broad-spectrum antibiotics, other protective intestinal microbes are eradicated in the process and the incidence increases to about 20%. This leaves space for the pathogenic C. difficile to grow rapidly unhindered leading to the release of toxins that cause bloating, pain and severe diarrhea. Sometimes potentially life-threatening pseudo-membranous colitis or toxic megacolon occurs (about 5 to 8% of patients). Outbreaks occur when people ingest the spores, often in contaminated medical facilities and C. difficile is known to kill tens of thousands of people every year worldwide. Mild cases are often resolved by simply halting antibiotic treatment but in more severe cases last-line antibiotics such as vancomycin and metronidazole are often needed. Worryingly, the relapse rate is 20 to 30%.

The team explains that while Cwp84 is essential for correct surface layer formation it may also break down extracellular proteins, such as fibronectin, laminin and vitronectin which are found in the body. Nevertheless, blocking its activity either genetically or chemically prevents proper growth of bacterial colonies even if this is not in itself bactericidal. Disruption of the colonization process might therefore be possible allowing healthy microbes to repopulate the gut and stifle the spread of C. difficile.

The researchers carried out X-ray crystallography at station I03 at Diamond Light Source in Didcot, UK. The resulting high-resolution (1.4 angstrom) diffraction data revealed the structure of the N-terminal propeptide, the cysteine protease domain, and a previously uncharacterized "linker" region that is 170 amino acids long. The linker lies between the cysteine protease domain and the repeat region of Cwp84 which holds it onto the cells surface. The linker region binds calcium and resembles a group of proteins known as lectins, so may have an affinity for carbohydrates which may be vital for correct cell wall processing. The same motifs are present in other types of Clostridium microbes as well as ancient single-celled organisms known as archaea.

The team suggests that the insights their research offers in terms of C. difficile surface layer growth and how this relates to gut colonization could be exploited in developing a new type of drug to treat infection-anti-colonization inhibitors.

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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.

Bacteria detected in food may cause risks to unborn children

The results of the research conducted in the ICAS Culiacán reveal that at least 10 percent of the fresh cheese, sausages and meats sold in markets and on the street may be contaminated.

Researchers at the Center for Food Research and Development (ICAS) confirmed the presence of Listeria monocytogenes in foods of animal origin, in the city of Culiacan, Sinaloa. The organism causing mainly diarrheal infections as a first symptom, but in more aggressive situations generates miscarriages and meningitis.

Because in Mexico there are no reports of cases of listeriosis by the health system, the ICAS science team, headed by Christopher Quiroz Chaidez, began working on the search for bacteria. "The only reference is a review from 1982 to 2006, a period in which only 14 cases were reported but not diagnosed because they do not associate diarrheas, miscarriages or meningitis with Listeria monocytogenes," says the researcher.

Recent international reports relate the emergence of a strong outbreak of listeriosis in the United States due to consumption of Chinese melon from Mexico.

However, research in different markets were visited for sampling dairy products, sausages and meats, which are taken to the laboratory for analysis by culture media and molecular methods.

After the tests, the five serotypes of Listeria monocytogenes, mainly 4B, which is the most aggressive were found. "We found it in greater amounts in the chicken, with a percentage of 23 percent; sausages by 11 percent; cheeses with nine percent and eight percent meat, "says Quiroz Chaidez.

Therefore, these results suggest that "at least 10 percent of the fresh cheese, sausages and meats sold in markets and on the street may be contaminated with the bacteria."

Human listeriosis is a disease with a high mortality rate (20 to 30 percent) leading to severe diseases such as meningitis, septicemia, and miscarriages. It usually affects immunocompromised individuals, pregnant women, elderly and children.

While the infection is spread by fecal-oral route of animal to human and from mother to fetus, the main source of infection is by eating contaminated food because of poor hygiene practices. "Upon entering the body, the bacteria travels through the bloodstream, making it easy to reach the meninges, in addition to having the ability to cross the placenta and harm the unborn product," warns Quiroz Chaidez.

The implementation of a preventive programs is required, define the legal framework to ensure food safety, and enforce the reporting of outbreaks. In the latter case, the participation of the health sector is of great importance, since the presence of clinical symptoms suggesting the involvement of bacteria, such as diarrhea, must apply for the necessary studies leading to confirm or exclude the diagnosis.

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The above story is based on materials provided by Investigación y Desarrollo . Note: Materials may be edited for content and length.

Why Uber Just Hired Obama’s Campaign Guru

David Plouffe, (L) chats with President Barack Obama backstage at BankUnited Center at the University of Miami in Coral Gables, Florida, on Thursday, October 11, 2012. Nikki Kahn/The Washington Post via Getty Images

Getting any startup off the ground is difficult, but things are particularly dicey when governments across the globe are working to make your app illegal.

Such is the challenge facing Uber. Each time it spreads to a new city, it faces a new front in its politically charged battle to undermine local taxi monopolies in favor of app-powered, on-demand rides. And at the middle of these myriad controversies, Uber remains a technology company racing against competitors to solve a deeply complicated engineering problem: how to bring time, space, supply, and demand into delicate alignment so that you can push a button and bring a car to your door.

It’s a bit like, say, running a campaign for President, and that’s why Uber just hired David Plouffe, who managed Barack Obama’s successful election in 2008. The logistics, economics, and politics of orchestrating a large group of people toward a common goal takes a rare expertise, and Plouffe has certainly shown he has it. As Uber’s senior vice president of policy and strategy, he is almost uniquely qualified to tackle the company’s enormously complex problems.

With $1.4 billion in financing to date, the only serious obstacle to Uber’s radical growth is the threat of regulation. To reach its goals, Uber needs a feat of political engineering that its code geniuses—including CEO Travis Kalanick—have not been able to hack. But in Plouffe—credited with spearheading the first serious application of modern analytics and e-mail outreach to presidential campaigning—Uber now has a bone fide politico that suits its data-driven culture. The hope is that he can turn out political support in the the same way its algorithms funnel drivers to the streets where they’re needed most.

“Uber has been in a campaign but hasn’t been running one,” Kalanick said in announcing Plouffe’s hiring. “That is changing now.”

The Field General Arrives

From its first days in San Francisco nearly a half-decade ago, Uber has always faced attempts to shut it down. New York, Washington, London, Paris, Berlin, Seoul. Name a world capital, and chances are, you’ll name a city where Uber has faced regulatory resistance, often underwritten by the politically connected players in the existing taxi industry.

That Uber is still operating and growing in most of those places is due mainly to Kalanick’s aggressively unapologetic willingness to defy local authorities. To date, Uber’s political strategy has mainly hinged on getting enough users to embrace the app that politicians fear alienating constituents or looking like they’re “anti-innovation.”

But consumer sentiment alone isn’t enough of a political guarantee when a billion dollars of other people’s money is on the line. As popular as Uber has become, it isn’t so much a part of the urban fabric yet that the company can depend on bottom-up citizen backlash alone to counteract the regulatory forces allied against it. By hiring Plouffe to manage what he describes as the campaign for “Uber the Candidate,” Kalanick is seeking to turn enthusiastic users of Uber’s product into a politically potent force that will rally on behalf of Uber’s existence.

“David’s background needs little introduction,” Kalanick said of Plouffe on Uber’s blog. “He is a proven field general and strategist who built the startup that elected a President.”

From Campaign to Cars

The Obama 2008 campaign is an object lesson in turning sentiment into success. Obama the candidate had a natural charisma and a compelling message that inspired excitement and optimism, two qualities in short supply in recent presidential campaigns. But Obama’s electoral success against two better-known quantities—Hillary Clinton in the Democratic primary and John McCain in the general election—was only partly due to the candidate himself.

In a discussion at Harvard’s Kennedy School just a few weeks after Obama’s successful first election, Plouffe described an approach to campaigning that would make any Silicon Valley geek’s heart melt. “Obviously, a campaign’s about message delivery at the candidate level,” Ploufee said, “but at the campaign level, it is about numbers.”

Plouffe goes on to describe how the campaign on the ground would work to identify voters and collect data to game out its chances on a weekly basis. “We’d say, okay, if the election were held this week based on all our data, put it all in a blender, where are we? And obviously, with technology today, we could measure this very carefully.”

Based on that intelligence, the campaign would engage in the kinds of micro-targeting that have become the common currency of marketing in the Facebook and Google era. Replace campaign workers with drivers, and voters with riders, and Plouffe describing the way he ran the Obama campaign sounds a lot like how Uber runs its own operation. “You’ve got real-time data, and that makes you make scheduling decisions and resource-allocation decisions and where to send surrogates and you’re adjusting those by the end multiple times a day.”

Turning Out the Base

If he can use that same expertise to turn out support for Uber like he did for Obama, Plouffe can likely get Uber over the last significant hurdle to becoming the pervasive medium for transportation in the 21st century that Silicon Valley is banking it will become. The grassroots, in some sense are there: Riders who love the service but have no idea that it might be threatened by regulation. Plouffe’s resume seems perfectly geared towards bending that sentiment into, say, signing petitions and lobbying congress.

“I look forward to doing what I can right now to ensure drivers and riders are not denied their opportunity for choice in transportation due to those who want to maintain a monopoly and play the inside game to deny opportunity to those on the outside,” Plouffe said yesterday, taking a shot at the taxi industry in a statement that rode the razor’s edge between Democratic populism and Silicon Valley libertarianism.

Whatever the underlying politics, Plouffe’s arrival at Uber signals a new chapter in the company’s ground game. To survive, Uber is now about more than rides. It’s about turning out the base.

Regime Change: Steve Ballmer Has Finally Resigned From Microsoft’s Board

WIRED

When Steve Ballmer resigned as CEO of Microsoft last February, he didn’t leave the company entirely. The 58-year-old executive retained his seat on the Microsoft board. But now, after 34 years with the company, Ballmer is finally moving on.

“Microsoft has been my life’s work and I am proud of that and excited by what I see in front of the company and this leadership team,” Ballmer wrote in an open letter to new CEO Satya Nadella announcing his resignation from the board, published on the company website today. “There are challenges ahead but the opportunities are even larger.”

Steve Ballmer. Microsoft

The move is yet another sign that Nadella, who has been CEO for just under six months now, is well and truly in charge of a new Microsoft, a Microsoft that is quickly moving away from the attitudes and strategies it fostered for more than 10 years under Ballmer.

Microsoft has been rebranding itself under Nadella’s leadership, starting with initiatives that would have been unthinkable on Ballmer’s watch, such as releasing Microsoft Office for iPad and, even more radically, announcing a free version of Windows for devices with screens smaller than nine inches and open sourcing the bulk of its developer tools.

Nadella has also jettisoned Ballmer’s “devices and services” tagline, rebranding Microsoft as the “productivity and platform company for the mobile-first and cloud-first world,” in a somewhat muddled memo last month.

Many of these changes were likely begun months ago, when Ballmer was still CEO, but as ex-employees point out, it’s no coincidence that they came to a head under Nadella’s watch. Now, more than ever, Nadella will have the freedom to move forward with his new strategy. He’ll also have to carry the weight of Microsoft’s massive layoffs on his own.

As for Ballmer, he’ll be busy teaching classes this fall, and just last week, he completed his much-discussed acquisition of the Los Angeles Clippers NBA basketball franchise. We’ll all miss the rather unique antics Ballmer brought to Microsoft, but you can bet that much of this will resurface in the NBA.

Month-Long Tournament Celebrates End of Oakland’s 80-Year Pinball Ban

Pinball enthusiast TJ Beyer sets up an Iron Man machine at a Radio Shack in Oakland to mark the beginning of a month-long tournament. Ariel Zambelich/WIRED

OAKLAND, California—Can you believe there was a time when the game of pinball was illegal in this town?

Can you believe that time was this year?

Residents of this Bay Area city probably couldn’t possibly imagine they were breaking the law every time they sidled up to a Bally table and played the silver ball. But it was only last month that the Oakland city council finally passed a measure lifting an 80-year ban on the public operation of pinball machines. To celebrate this occasion, a local RadioShack is holding a month-long pinball tournament. The chain, a key resource for pinball owners, has purchased and installed an Iron Man machine in the store in the city’s Fruitvale Station, and invited players to test their skills. Anyone who tops 50 million points will be invited back to compete for the grand prize—the table itself.

Pinball, Scourge of the Nation’s Youth

Oakland’s absurd ban dates to the 1930′s, when the machines were considered a form of gambling. Before the addition of flippers, which allowed the player to bounce the ball and more accurately affect the game’s outcome, pinball machines simply rolled the ball down the playfield. The only way of controlling the outcome was to imprecisely nudge the table. This was not particularly effective, making pinball largely a game of chance. You might get a payout for achieving a high score.

“There was this stigma for what pinball was,” said Josh Sharpe, president of the International Flipper Pinball Association, “which stuck around as it evolved into an amusement machine, with electricity and the opportunity to control the ball via flippers.”

The Iron Man pinball game, ready to be played. Ariel Zambelich/WIRED

Roger Sharpe, the Association’s co-founder and Josh’s father, was a driving force behind destigmatizing pinball in the 1970s. In 1976, the elder Sharpe appeared before the New York city council to demonstrate that pinball as practiced was a game of skill, not chance. His testimony (and supple wrist) helped reverse New York’s ban on pinball. But the bans, like other ridiculous or outdated laws, remained on the books in other cities across America, including Oakland.

That said, the law went largely unenforced and it wasn’t until an Association tournament was shut down that the organization knew it must fight to see the statute reversed.

“It might have even been about the noise of the business, just based on the machines and the people there,” Sharpe said of the complaint that led to the enforcement of the anti-pinball law. “If you want to shut someone down, find a way to make what they’re doing illegal. So they found this old rule that didn’t allow people to operate pinball machines that way.”

Managing to stack 4 balls on one flipper — something that rarely, if ever, happens in real game play. Ariel Zambelich/WIRED

Instead of backing down, the group fought the law as many other communities have done over the last 40 years. The result was Oakland lifting its pinball ban, as a part of a larger measure looking at modern gambling establishments in the Bay Area city.

“We’ve had a really big pinball renaissance and resurgence in the past five years,” said Jody Dankberg, director of marketing for Stern, the only company in America currently manufacturing pinball machines.

“We’re seeing a huge growth in location pinball, a huge growth in league play, tournaments, and things like that,” Dankberg said. “Organizations like the IFPA, these competitive players, they’ve really been the driving force behind getting some of these bans lifted.”

Pinball bans still exist, like in Oakland’s neighboring city Alameda—the location of the Pacific Pinball Museum, which had to remove all the coin slots off of its machines to comply with the law. But pinball can finally emerge from out of the shadows in Oakland.

“It opens the door for so many more cool things,” Dankberg said. “Across the country we’re seeing a huge trend in the barcade business: bars that sell craft beer and have classic videogames and pinball machines.”

“With a law on the books, like it was in Oakland, it prevents that type of venue. So now this is pretty exciting—hopefully we’ll see more pinball in Oakland.”

Terminal Velocity

Much of high-end auto racing has always been about squeezing a bit more kinetic energy out of each drop of gasoline. But improvements in electric car technology mean racing can ditch the fossil fuels. Starting in September, the new FORMULA E series will bring teams from around the world to compete on the streets of Beijing, Monte Carlo, Buenos Aires, Miami, and six other cities. And they'll all be driving a version of the same car: the Spark-Renault SRT_01E. Built using systems from several storied automotive firms, the 1,764-pound electrorocket represents the thinking of the best minds in the sport. Carmakers hope that new ideas will emerge from the crucible of racing to zoom all electric vehicles forward.

The battery-powered rocket that could transform formula 1 racing. WILSON HENNESSY | BRYAN CHRISTIE DESIGN

1. Chassis Built by the Italian firm Dallara, which also makes the chassis for Indy cars, the Formula E chassis is made of a strong, lightweight carbon-fiber composite. As in a typical F1 car, the driver sits in an aluminum tub for better crash protection.

2. Steering Wheel This is the command center. Many of the controls are what you'd find on a typical race car: paddle shifters for flicking between the SRT's six gears, a speed limiter for driving in the pit lane, a radio button so the driver can talk to his team. Here, though, there's also a knob for adjusting the motor's power and a button that engages a temporary boost for passing. And, of course, a screen displays how much juice is left in the battery.

3. Tires Formula E tires must be both efficient and versatile, since the cars will be racing not on dedicated racetracks but on city streets. Michelin designed an 18-inch tire that's treaded for all-weather performance—a first for an international race series—with low rolling resistance to extend battery life. The're so rugged that they won't need to be changed mid-race, which makes the series more sustainable and also saves the teams some cash—a single tire gun (the tool that removes a lug nut in a split second) can cost thousands of dollars.

4. Battery Pack In a normal F1 car, the engine and gas tank are right behind the driver. Here that space is occupied by a roughly 772-pound cube containing 164 lithium-ion batteries. Designed by the British firm Williams F1, the power pack has a capacity of 30 kilowatt-hours—enough for 20 to 30 minutes of hard driving. The races will last twice that, so when the driver makes a pit stop with an almost-dead battery, he'll hop into a different, fully charged car. Right now all the battery packs are the same, but to encourage innovation, this stricture may eventually be relaxed, allowing teams to experiment with different suppliers to gain an edge.

5. Battery Management System In any electric car, the BMS is a bundle of hardware and software that keeps the battery pack operating safely and reliably by balancing the charges in the cells and tracking temperature, voltage, and current. Here it's even more crucial, because racing demands more of each cell, draining them much more rapidly than in an electric passenger car and recharging them constantly through the regeneration system. Williams crammed the BMS with many more sensors than usual, allowing it to monitor conditions at a greater level of detail; each second, the unit captures some 350,000 inputs that help the software maximize the health and performance of the battery pack.

6. Electric Motor The 57-pound cylindrical motor comes from McLaren, the British company famous for supercars that cost more than a nice house in a good school district. This is the same motor that McLaren uses in its $1.5 million P1 hybrid. Although the P1 has a higher top speed (217 mph as opposed to the Spark-Renault's 140 mph), electric motors have a lot of low-end torque, so the SRT_01E and the P1 both catapult from 0 to 60 in less than three seconds. One important feature is the motor's regeneration system: Whenever the driver takes his foot off the throttle, the spinning rotor charges the battery pack. The motor also helps produce the car's unique, pod-racer-esque sound; at top speed, the car hums at 80 decibels, compared with the 130-decibel scream of its gas-fueled Formula 1 brethren.

WILSON HENNESSY

How Agriculture’s Growth Promoters Might Work: A Mouse Study Sheds Some Light

Rama (CC), Flickr

The farm practice that underlies most agricultural use of antibiotics is known as “growth promotion”: It calls for giving very small doses of antibiotics routinely to meat animals because those doses cause them to gain fat and muscle more quickly than they would otherwise. Growth promotion dates back to the early days of the antibiotic era, and has always been somewhat mysterious. Though there were attempts to pick apart its mechanisms in the 1950s and 1960s (I’ve been reading some fascinating old accounts), for the most part, people simply accepted that it worked. It’s only in the past decade or so, as interest has increased in the microbes that reside everywhere in our and animals’ bodies (a vast community generally known as the microbiome), that researchers have begun trying to dissect what is going on.

The scientific team that has probably pursued this most intensely is the NYU Langone Medical Center lab led by Martin J. Blaser. Blaser published a popular account of their research into antibiotics’ effect on obesity, asthma, diabetes, and other disorders in Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues , published in April. (Disclosure: I reviewed the book for Nature .) Two years ago, the team showed that giving small doses of antibiotics to very young mice affected genes controlling metabolism of nutrients, and caused the mice to gain weight. Now they have followed up that research with detailed work exploring how much the timing and length of antibiotics affects weight gain. Though the work is still in mice, it leads to provocative conclusions about how growth promoters work in livestock, and what early-life antibiotics might do to humans as well.

In the new study, published last week, Blaser’s colleague Laura Cox and additional researchers from both NYU and other institutions gave both long and short-term regimens of low doses of penicillin to rat pups and also to rat mothers before they gave birth. In all cases, the mice that received the low-dose penicillin, or their offspring, grew up to be heavier than undrugged mice. In the mice that received the low doses continuously, the balance of microbes in their guts was permanently altered. In the ones that received the short regimens, their microbiomes returned to normal after the drug doses ceased — but they continued to gain weight faster than they should have. And finally, when mice that had not been dosed received transplants of gut bacteria from dosed mice, they gained weight abnormally as well, even though they had not received any antibiotics themselves.

Granted that mice are not cattle, pigs, chickens or other meat animals, this is still illuminating of what may be going on when growth promoters are administered. (Something that, even today, is dismissed with “it just works” hand-waving.) It also sheds light on what may happen in humans when young children receive antibiotics. Children don’t get antibiotics as a routine thing the way livestock do, but they do very commonly receive short courses for common childhood infections such as ear infections. It’s possible, as Blaser has suggested elsewhere, that those early-life prescriptions may be an unacknowledged cause of the worldwide rise in obesity.

In the paper, Blaser’s team is careful to call this work a model; and, again, the work is only conducted in mice. But to me the results provide one more clause in the long argument of why antibiotic overuse — which we know contributes to antibiotic resistance, and may contribute to obesity — should be scaled back.

Note: I am a few days late in writing about this because I was traveling. Faster and more thorough responses appeared at The Scientist and the Genetic Literacy Project, and Ed Yong’s take at Phenomena is especially good.

Cite: Cox, Laura M. et al. Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences. Cell , Volume 158 , Issue 4 , 705 – 721. DOI: http://ift.tt/1oxrkE9