We Need More Science: 06/25/14

Scientists unearth what may be secret weapon against antibiotic resistance

A fungus living in the soils of Nova Scotia could offer new hope in the pressing battle against drug-resistant germs that kill tens of thousands of people every year, including one considered a serious global threat.

A team of researchers led by McMaster University has discovered a fungus-derived molecule, known as AMA, which is able to disarm one of the most dangerous antibiotic-resistance genes: NDM-1 or New Delhi Metallo-beta-Lactamase-1, identified by the World Health Organization as a global public health threat.

"This is public enemy number one," explains Gerry Wright, director of the Michael G. DeGroote Institute for Infectious Disease Research at McMaster University.

"It came out of nowhere, it has spread everywhere and has basically killed our last resource of antibiotics, the last pill on the shelf, used to treat serious infections," he says.

Discovering the properties of the fungus-derived molecule is critical because it can provide a means to target and rapidly block the drug-resistant pathogens that render carbapenem antibiotics -- a class of drugs similar to penicillin -- ineffective.

"Simply put, the molecule knocks out NDM-1 so the antibiotics can do their job," says Wright.

Seeking an answer to the riddle of resistance in the natural environment is a far more promising approach than trying to discover new antibiotics, a challenge which has perplexed scientists for decades. No new classes of antibiotics have been discovered since the late 1980s, leaving physicians with very few tools to fight life-threatening infections.

"Not only do we have the emergence of an antibiotic resistance gene that is targeting the last drug resource we have left, but it is carried by organisms that cause all sorts of challenging diseases and are multi-drug-resistant already. It has been found not only in clinics but in the environment -- in contaminated water in South Asia -- which has contributed to its spread over the globe," explains Wright. "Our thinking was that if we could find a molecule that blocks NDM-1 then these antibiotics would be useful again."

Wright and his team from McMaster, University of British Columbia and Cardiff University in Wales created a sophisticated screening method to take the NDM-1 gene, combine it with harmless E. coli bacteria and then isolate a molecule capable of stopping NDM-1 in its tracks.

NMD-1 requires zinc to thrive but finding a way to remove zinc from it without causing a toxic effect in humans was a daunting task, until the discovery of the fungal molecule, which appears to perform the job naturally and harmlessly.

Scientists then tested the theory on mice infected with an NDM-1 expressing superbug. The mice that received a combination of the AMA molecule and a carbapenem antibiotic survived, while those that received either an antibiotic or AMA alone to fight the infection did not survive.

"This will solve one aspect of a daunting problem. AMA rescues the activity of carbapenem antibiotics, so instead of having no antibiotics, there will be some," says Wright. "This is a made-in-Canada solution for a global problem."

"Antibiotic resistance may be the most urgent and perplexing challenge facing health-care researchers today," says Dr. John Kelton, dean of the Michael G. DeGroote School of Medicine and vice-president of the Faculty of Health Sciences at McMaster. "This research provides new hope by showing us a completely new way to approach this problem, and none too soon, given the growing risk that superbugs pose to all of us. "

The findings are published online in the current edition of the journal Nature.

"Antibiotic resistance is one of the top public health concerns in Canada and internationally and it represents a research priority for the Canadian Institutes of Health Research (CIHR). It is exciting to see Canadian researchers finding innovative strategies to overcome antimicrobial resistance," says Dr. Marc Ouellette, scientific director of the CIHR Institute of Infection and Immunity.

Story Source:

The above story is based on materials provided by McMaster University . The original article was written by Michelle Donovan. Note: Materials may be edited for content and length.

Previously 'hidden diversity' of mouth bacteria revealed in study

A new computational method for analyzing bacterial communities has uncovered closely related, previously indistinguishable bacteria living in different parts of the human mouth. The technique, developed by Marine Biological Laboratory (MBL) scientists, provides high taxonomic resolution of bacterial communities and has the capacity to improve the understanding of microbial communities in health and disease. The study will be published in PNAS Online Early Edition.

An important step in understanding the role of oral bacteria in health and disease is to discover how many different kinds live in the mouths of healthy people, and exactly where in the mouth they normally live.

Using a novel computational method called oligotyping, developed by MBL Assistant Research Scientist A. Murat Eren, scientists analyzed gene sequence data from nine sites in the oral cavity. The data was provided by The Human Microbiome Project (HMP), an effort of the National Institutes of Health that produced a census of bacterial populations from 18 body sites in more than 200 healthy individuals. DNA in these samples was sequenced from the gene in bacteria that encodes ribosomal RNA, called the 16S rRNA gene, or 16S.

To this point, an understanding of the biomedical significance of HMP data has been hindered by limited taxonomic resolution. "Different species of bacteria can have very similar 16S gene sequences, sometimes differing by only a single DNA base in the region that was sequenced, and errors in DNA sequencing can also create differences of one or a few DNA bases," says the study's co-author Jessica Mark Welch, an Assistant Research Scientist at the MBL.

While the HMP data set has been used to identify bacteria broadly, to genus-level groups, it has never been used to identify bacteria more precisely, to the species level. "This genus-level grouping meant that many bacteria with similar DNA, but very different roles in the human microbiome, were lumped together, limiting the usefulness of the data," says Mark Welch.

Using oligotyping, Eren, Mark Welch and their colleagues Gary Borisy of the Forsyth Institute and Susan Huse of Brown University re-analyzed the HMP 16S gene data from dental plaque, saliva, and the surfaces of the tongue, cheek, gums, hard palate, tonsils, and throat. They found closely related, but distinct, bacteria living on the tongue, on the gums, and in plaque. For example, bacteria in saliva and in hard palate, tonsils, and throat resembled the tongue bacteria, while bacteria on the cheek were similar to bacteria on the gums. Bacteria from plaque below the gum-line also were detected on the tonsils, suggesting that the tonsils provide an oxygen-free environment where these bacteria can grow and come into contact with the human immune system.

Oligotyping detected kinds of bacteria that differed by as little as a single DNA base in the sequence tag. These differences in the 16S gene did not change the properties of the bacteria, but acted as markers for larger changes elsewhere in the bacterial genome which, the researchers believe, lead to different bacterial properties that make the bacteria prefer one part of the mouth over another.

"These distinct bacteria were present in the data all along, but were indistinguishable because they were so similar to each other -- hidden in plain sight, and revealed by oligotyping," says Mark Welch. "This method offers a better understanding of the distribution of precisely defined taxa within the mouth, and demonstrates a level of ecological and functional biodiversity not previously recognized. The ability to extract maximum information from sequencing data opens up new possibilities for the analysis of the dynamics of the human oral microbiome."

Eren has applied the oligotyping method to improve taxonomic resolution in other bacterial communities, including those from wastewater, from marine sponges, and from ocean water. The researchers say the technique has the capacity to analyze entire microbiomes, discriminate between closely related but distinct taxa and, in combination with habitat analysis, provide deeper insights into the microbial communities in health and disease. "The diversity of naturally occurring bacteria continues to impress us, and our study demonstrates that a comprehensive understanding in microbial ecology through marker genes requires our attention to subtle nucleotide variations," says Eren. "I anticipate that the ecologically important information oligotyping helped us recover from the human oral microbiome will intrigue other investigators to take a second look from their microbiome data sets."

Story Source:

The above story is based on materials provided by Marine Biological Laboratory . The original article was written by Gina Hebert. Note: Materials may be edited for content and length.

Jerry Seinfeld Answers Your Pressing Etiquette Questions

Illustrations by Mark Nerys

Illustrations by Mark Nerys

Is it OK to video a concert with my iPad? Can I spy on my neighbor with a drone? How should I deal with my annoying friend who texts too much? Seinfeld enlightens you on what to do and how to behave in the digital age.

Google Splits Up Your Android Phone for Work and Play

Ariel Zambelich/WIRED

Google wants to split the personality of your Android phone.

On Tuesday, at its Google I/O conference in San Francisco, the company said that the latest version of its Android mobile operating system will let you run both business and personal apps on the same phone while at same time keeping them separate from each other. “We provide underlying data separation,” said Google senior vice president Sundar Pichai, “so your personal data is isolated from your corporate stuff–and vice versa.”

According to Amit Singh–who oversees business sales at Google–the software used to separate apps is based on technology Google acquired with its recent purchase of a company called Divide. The idea is that, by placing corporate apps in secure software “containers,” Google can allow businesses to manage and monitor them without messing with all the personal stuff on your phone. For instance, if you leave your job at a particular company, Singh told us after Pichai’s keynote speech, the company can erase all your corporate data and apps without touching, say, your personal Gmail account or Twitter app.

For Google, the ultimate aim is to make Android more appealing to businesses that are concerned about securing corporate data on employee phones. Singh calls it the company’s “first major effort” to push Android into the corporate world. As Google stretches into new consumer markets with things like the Android Wear OS for smartwatches and Android Auto for cars, it continues to woo businesses and schools as well. The company has long offered a suite of online applications for corporate users–Google Apps–and it has actively pitched Google Chromebook notebooks at the business the world. Now, it’s doing much the same with Android.

With his keynote speech, Pichai also introduced new technology that will let you run Android smartphone and tablet applications on Chromebooks, and Singh says this too could help push Android into businesses, where Chromebooks are already used–at least to a certain extent. “It’s a very interesting opportunity that could eventually lead to enterprises,” he told us.

In order to separate business and personal apps on phones, Google is releasing new developer tools–application programming interfaces, or APIs–that let companies wrap applications inside protective containers. These tools, Pichai said, will be available with the new version of Android–”Android L”–but he also said the company is working on a way of using the similar tools on previous versions of Android.

Samsung, a company that builds Android phones, has offered similar technology via something it calls Knox, and during his keynote, Pichai said that the phone maker was contributing Knox as open source software to Google’s OS project. “So,” he said, “we can have a consistent story across Android.”

Google Unleashes More Big-Data Genius With a New Cloud Service

Ariel Zambelich/WIRED

Google continues to share the wealth of the uniquely powerful software systems it erected to run its enormous online empire.

On Tuesday morning, at its Google I/O developer conference in San Francisco, the tech giant introduced a cloud computing service it calls Google Cloud Dataflow. Based on two software systems that have helped Google drive its own online operation for years–Flume and MillWheel–the service is a way of more easily moving, processing, and analyzing massive amounts of digital information. As he unveiled the service, Google’s Urs Hölzle–the man who oversaw the creation of Google’s global network of data centers–said it’s designed to help companies deal with petabytes of data–aka millions of gigabytes.

“Cloud DataFlow is the result of over a decade of experience in data analytics,” he said. During the conference keynote, one Googler showed how the system could be used to analyze reactions to World Cup matches posted to Twitter.

This is just the latest way that Google is sharing its unprecedented online infrastructure with the world at large through its cloud services. Google Compute Engine and Google App Engine–cloud services that let companies and independent developers build and run large software applications–are based on internal Google infrastructure, as is BigQuery, a way of almost instantly asking questions of massive datasets. Following the lead of Amazon–the company that pioneering modern cloud computing–Google sees cloud computing as a potentially enormous market, one that might even eclipse the market for online ads, its primary business today.

Long ago, with a sweeping software system called MapReduce, Google set the standard for processing “big data.” A tool that ran across hundreds of servers, MapReduce is what the company used to build the enormous index of webpages that underpins its search engine. Thanks to an open source clone of MapReduce–Hadoop–the rest of the world now crunches data in similar ways. But Hölzle says that Google not longer uses MapReduce. It now uses other Flume, aka FlumeJava, for this kind of massive “batch processing.”

After Hölzle’s keynote, Google director of product management Greg DeMichillie told us that Flume essentially removes much of the pain that came with MapReduce. It lets the company more easily build complex “data pipelines,” meaning the entire processor of ingesting, cleaning, and analyzing data.

Ariel Zambelich/WIRED

Now, DeMichillie says, Google is not only sharing this system with the rest of the world. In doing so, it’s also combining Flume with MillWheel, a similar system that handles “stream processing.” Whereas batch processing is a way of crunching data that has already been collected, stream processing involves analyzing data in near real-time as it comes off the net. Many companies require both types of data analysis, and Cloud Dataflow brings both under one umbrella.

Others have built similar tools. Twitter, for instance, has created an open source contraption it calls Summingbird. But Dataflow is a little different in that Google is offering it solely as a cloud service, something that anyone can access over the internet. The company is not distributing software that you could install on your own machines.

At today’s conference, Google also introduced new tools for monitoring and debugging applications that you build and run on Compute Engine and App Engine. DeMichillie showed off a tool called Google Cloud Trace, which helps you find particular performance bottlenecks that may plagues your applications. He tells uses it uses the same concepts as DTrace, a tool originally developed at Sun Microsystems, but he says that the Cloud Trace technology was developed entirely at Google.

High doses of antibiotics may have potential to promote increased cross-resistance

Antibiotic resistance has become an increasing public health concern, with MRSA infections and last lines of antibiotic drug treatments having to be increasingly deployed in hospitals and clinics.

In the advanced online edition of Molecular Biology and Evolution, Oz, et. al., utilized an experimental evolution approach to evolve 88 different E. coli populations against 22 antibiotics, under "strong" and "mild" selection conditions. After 21 days, they isolated bacterial clones, measured the resistance to each antibiotic, and performed whole-genome sequencing of resistance clones to tease out the genetic changes that could be responsible for antibiotic resistance.

Their results demonstrate that the evolution of cross-resistance depends on selection strength. Overall, they found evidence for higher cross-resistance in the strongly selected strains and higher numbers of pathway-specific mutations. The study yielded important new insights into the increased emergence of drug resistance with the use of high doses of antibiotics, as well as hypersensitivities to exploit for new antibiotic therapies.

Story Source:

The above story is based on materials provided by Molecular Biology and Evolution (Oxford University Press) . Note: Materials may be edited for content and length.

Google Announces Its Answer to Apple’s CarPlay: Android Auto

Ariel Zambelich/WIRED

At today’s I/O conference, Android director of engineering Patrick Brady kicked the tires on Android Auto, the company’s long-awaited in-car infotainment system. Android Auto will be featured in cars from partners that are members of the Open Automotive Alliance—40 carmakers around the world in all—and the first cars compatible with the system will be available by the end of the year.

Android Auto looks and run similar to Apple’s CarPlay system, which was announced earlier this year. It’s not an operating system installed in the car itself; instead, you physically plug an Android phone into a car’s console, and the car’s center display becomes a larger-screened interface for the phone. According to Google, the entire Android Auto experience is voice-enabled; you can also use steering-wheel-mounted controls and the console touchscreen.

Android Product Manager Andy Brenner performed the test drive of Android Auto in a faux Kia.

“All of the apps we see here are running on Andy’s phone, which means the experience gets better when he updates his apps or gets a newer, faster phone,” explained Brady. The on-stage demo offered a quick tour of audio, messaging, and navigation applications.

Android Auto will offer a big-screen experience for Google Maps, a potentially huge advantage over the Apple Maps-powered CarPlay system. The in-car Google Maps features include live traffic information and local search. As you’d expect, the navigation system can look up and provide turn-by-turn directions for spoken-word locations, but the voice-dictated features go deeper than that.

During the demo, the system was able to respond to queries about what time certain businesses opened and closed, and simply saying “navigate there” brought up directions without having to repeat the full name of the destination.

The music demo was a quick spin around Google Play Music. The in-car version of the app has “simple, glanceable controls for the car,” according to Brady, and supports access to albums, playlists, and radio stations.

Messaging features also look similar to CarPlay. The voice-enabled system will read out messages you receive and also let you dictate messages to send.

To help independent developers create in-car apps, Google also announced the Android Auto SDK. At first, it will offer APIs for messaging and music apps only. Big-name audio apps available for the Android Auto platform will include Spotify, MLB At Bat, Pandora, Pocket Casts, Joyride, iHeart Radio, and Songza.

Of the 40 Open Auto Alliance members that will support the Android Auto system, there are a few interesting overlaps: Honda, Hyundai, and Volvo, which are all carmakers that will also offer Apple’s CarPlay system in future cars.

Boring 3-Minute Video Dares You to Overcome Your Attention Span

The latest video from CollegeHumor asks a piercing and fateful question of each internet user who watches it: Can you be bored for three minutes?

Much like the Saltine cracker challenge, it’s harder than it sounds. And what makes this video wonderful—and terrible—is that the longer it goes on, the more you start to realize that deep down, the obnoxious man in the suit is right. Much like the literal video for Aha’s “Take on Me,” he is describing something that is happening right in front of you, and like it or not, he is telling the truth. It’s a truth you can feel growing second by second in the itch behind your eyeballs and in your fingers, the almost automatic impulse to turn your attention to another tab the moment when your interest wavers, even slightly.

Hell, most people can’t even finish an article. After all, with the panoply of screens, feeds, and apps available to us, we don’t ever have to be bored. But can we? Can you? Has the internet made us weak and soft, like little mollusks shucked from our protective shells? Does a slightly uninteresting three-minute video make us want to scuttle back into the warm, infinitely stimulating embrace of the internet, and its endless buffet of information where each tiny slice of content is both delicious and ultimately unsatisfying? If we continue to flit from plate to plate and tab to tab, can we ever truly be full? Or, as the man in the suit suggests, will the fitful, restless hunger of our hearts and minds consume us forever?

Watch and learn—if you dare.

Google’s New TV Play: Android TV

Photo: Google

Following reports and rumors, Google announced its new push into the set top box space: Android TV.

Google’s no stranger to the space. Google TV, Google’s first attempt at a set top box, failed to gain traction despite integration with televisions from LG and other manufacturers. Without software updates or new partnership announcements, it seems to have died a quiet death over the past few years.

But Android TV promises to be different. Where Google TV made your television experience more smartphone-like, bringing ill-suited apps to the big screen, Android TV wants to be an entertainment hub like Apple TV or Roku. One part of that is its focus on recommending content, and the other is its user interface. And indeed, the interface looks strikingly similar to these existing set top boxes. You can control this interface using a gaming controller, remote, or an app. You can also use an Android Wear watch as a D-pad to navigate through the interface.

The interface is based on cards you can scroll through. Cards are organized into Movies, Shows, Games and Apps sections and look reminiscent of a small movie poster. And as for apps, Android TV will support a host of custom apps made for the platform, including Netflix, Hulu, and Pandora, and Google’s own apps, like YouTube, Hangouts, and Play Movies. These will be available in a store that opens this fall with the launch of Android TV.

Like Google TV before it, you’ll be able to control Android TV with your voice. And Google Search functionality is built into the interface so it’s super easy to search for content or information (“Who played Katniss in The Hunger Games?”, for example).

Gaming is also a big focus of Android TV. You can use an Android tablet as a controller, for example, while an Android game is broadcast on your TV set.

Android TV features full Google Cast support, so you can also use it just like a Chromecast. And as Google Cast improves, so will Android TV—like the new ability to cast straight to a Chromecast or Android TV without needing to be on the same Wi-Fi network (by pressing the cast button on the YouTube Android app, for example, it will connect through the cloud over the cellular network so friends can cast to your TV with very little friction).

Google Cast will also have a new ambient option called Backdrop, which lets you add personal photos, information like the weather, or specific genre images to the screen when you’re not casting something.

All of Sony’s 4K televisions and Phillips TVs will support Android TV. Streaming boxes by Razer and Asus will also be available this fall.

The Generation Raised on Touchscreens Will Forever Alter Tech Design

Fjord

We now live in the touchscreen paradigm. These interactive glowing rectangles are infiltrating our lives: from our desks to our wrists to our living rooms.

As the father of two young boys in this touchscreen era, I’ve noticed the magnetism with which these screens attract children. This is Generation Moth: a whole new generation that is growing up with screens—screens which always hold the promise of interactivity and something more engaging than the rest of the environment that they inhabit.

Despite the live magic show, all of the kids (including my son) flocked around the smartphone, like moths to a light.

My one-year old is obsessed with my Adidas miCoach Smart Run watch, climbing on me so that he can tap and swipe at the 1-inch screen. His six-year old brother has already spent years interacting with touchscreen interfaces. Recently, at a classmate’s birthday party, one child had his own smartphone to play games on. Despite the live magic show, all of the kids (including my son) flocked around the smartphone, like moths to a light.

Olof Schybergson

Olof Schybergson is the CEO and co-founder of service design consultancy, Fjord (part of Accenture Interactive). He is passionate about elegant simplicity and its power to solve challenges, big or small.

It wasn’t that long ago that the primary digital device was a desktop computer, but now, digital technology is hiding in plain sight, in objects from thermostats and espresso machines to watches and glasses. We move between and interact with them consciously and unconsciously, feeding them inputs and information far beyond point-and-click: gestural, biometric, audio, haptic, location, etc. All of this will be commonplace for Generation Moth.

As the touchscreen itself increasingly merges with its environment, and embedded technology goes mainstream, this raises questions around design for the next generation of digital experiences and services. Designing for Generation Moth is going to require very different skillsets and ways of thinking beyond what we do now. So, how will designers and the companies that they work for maintain relevance to meet the expectations of this up-and-coming generation?

Relationships Will Be in 4-D

Technology will build thriving interpersonal relationships for Generation Moth, who will share more experiences together without ever having to physically be in the same place.

Ross, the 10-year old son of my colleague in New York, spends lots of time hanging out with his best friend, alone and with others. However, this friend actually lives in London—he visits Ross at home via Skype. Ross and his Skype buddy met once briefly in real life, during a tourist trip to London, but it was through Skype that they grew close. For Generation Moth, digitally mediated presence will feel completely natural.

Fjord

This sharing will go well beyond videos and emojis and, as the acquisition of Oculus Rift by Facebook indicates, could move into the sharing of physical and immersive experiences: Generation Moth may be able to share a warm embrace; the view, sounds, breeze, and smells of the beach; even a memory or thought. These rich, shared experiences, can all be had without ever having met someone in-person. Through wearable devices on our bodies, connected to our brains, and in our clothing, as well as immersive and connected environments, Generation Moth could have thriving relationships with people where other generations would never have had a chance to connect.

For Generation Moth, digitally mediated presence will feel completely natural.

However, the experiences that Generation Moth have in their daily lives will also have to provide the stimulation and interactivity that they experience socially. These expectations will impact a variety of industries, and there will be more appetite for experiencing virtually: online shoppers can try-on and sample products; travel planning could involve testing out a hotel bed or feeling what the weather there is like; a checkup with a physician may not require a visit.

Work Will Have to Be Fun

This expectation of stimulation and interactivity will also extend into the workplace. Generation Moth will have grown up learning through games and customized education programs personalized to them. Corporate structure, inflexible workplaces, and monotonous tasks that don’t allow them to multitask, bring an element of fun, or provide a game-like mechanic will not inspire them to perform.

Fjord

They will be fluent in experimenting their way through situations and in learning-by-doing over reading training modules or following directions. Growing up in an interactive world of instant gratification, attention spans and patience will continue to get shorter. Workplaces that do not inspire an element of creativity and keep them stimulated will be shunned or can expect poor employee performance.

In addition, being connected all the time will further blur the lines between work and life, particularly as communication through technology will be a standard to Generation Moth. The 9-to-5 mindset and even the concept of an office will fade away.

Services Will Run Their Lives

Generation Moth may be digitally literate, but their grasp of the analog world will be quite different: grocery shopping, driving a car, mapping a route, and planning an itinerary may be things they have never done before. Services such as Amazon’s anticipatory shipping and Google Now are the beginning of a future in which data and artificial intelligence are making decisions for us and completing our basic tasks. For Generation Moth, there will be implicit trust in the services they use to do the work of managing their analog lives; but one breach of this trust will prove a major inconvenience and they may instantly switch to a competing service.

Generation Moth will be fluent and fearless in a digitally mediated existence, where most of their analog needs are met with the help of digital services.

This new way of living will require several businesses to overhaul their operations to meet these heightened demands around personalization and anticipation. There will be services that plug all of their data around their schedules, location, and preferences. Their homes will be connected to know when they’re out of groceries, if a light bulb needs to be changed, when to turn off the air conditioning. Their cars will automatically route and drive them to their next appointment and the show they were watching will pick up where it left off from the TV during the ride.

Fjord

Generation Moth will be fluent and fearless in a digitally mediated existence, where most of their analog needs are met with the help of digital services. They will use their bodies and all their senses as instruments for interaction, in a way that’s infinitely more varied and sophisticated than the touch screen paradigm we’re living in right now.

As Generation Moth becomes influential across commerce and society, we will need to completely reimagine and reinvent the relationships that brands have with people. People-centered design will be a baseline, and the design of services that consider personalization, fluidity, predictiveness, and expressiveness will be key to success. This screen-addicted generation is going to massively change the way people live and attitudes towards the world, for generations to come.

Prepare Your Wallet For This Massive Auction of Vintage Cartoon Stills

'Captain Caveman and the Teen Angels' Publicity Cel (1977)

This cel of superhero Captain Caveman has been placed over a hand-painted production background. It is, however, sadly lacking in teen angels.

Estimated Value: $500+ (Expand this video widescreen for larger images)

Photos by courtesy of Heritage Auctions