Tropical tree microbiome discovered in Panama

Human skin and gut microbes influence processes from digestion to disease resistance. Despite the fact that tropical forests are the most biodiverse terrestrial ecosystems on the planet, more is known about belly-button bacteria than bacteria on trees in the tropics. Smithsonian scientists and colleagues working on Panama's Barro Colorado Island discovered that small leaf samples from a single tree were home to more than 400 different kinds of bacteria. The combined sample from 57 tree species contained more than 7,000 different kinds.

Bacteria in tropical forests may also play a vital role, protecting leaves against pathogens and even affecting the ability of forests to respond to climate change.

"Just as people are realizing that microbes carried by humans can have an influence on a person's health -- positive or negative -- we hope to discover what bacteria on tree leaves can tell us about the health of a forest," said S. Joseph Wright, a Smithsonian scientist and co-author of the new study published in Proceedings of the National Academy of Sciences.

In contrast to a previous study of bacteria on leaves in a temperate forest where different leaves had different bacteria, there was a core group of species of common bacteria present on leaves of nearly all of the species sampled in Panama. Just as on human skin, many of the bacteria on tropical tree leaves were Actinobacteria and Proteobacteria.

The researchers, from the Smithsonian Tropical Research Institute, University of Quebec, University of Arizona, University of Oregon, University of California -- Los Angeles and Santa Fe Institute, also looked for relationships between the composition of bacterial communities on leaves and other plant characteristics.

Many bacteria were associated with certain functional traits such as leaf thickness, wood density or leaf nitrogen content, characteristics that directly impact tree growth, survival and reproduction.

The relationships between many of the bacteria and tree species they sampled were ancient, going back to the ancestors of both the bacteria and the trees as they evolved in tandem.

"Our ability to use molecular techniques like 16S ribosomal RNA gene sequencing to characterize nearly all of the bacteria on a leaf is going to make it possible to see how very different members of forest communities interact," said Wright. The Smithsonian forest ecologist and his colleagues hope to collaborate with researchers at the 60 Forest Global Earth Observatory sites coordinated by the Smithsonian's Center for Tropical Forest Science to compare interactions at different sites and under different environmental conditions.

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The above story is based on materials provided by Smithsonian Tropical Research Institute . Note: Materials may be edited for content and length.

Survey Says: America’s Rudest Drivers Are in Idaho

calamity_sal/Flickr

Idaho. The funny-shaped northwestern state is usually associated only with potatoes and… well, potatoes, I guess, but now we have a new stereotype: ungentlemanly drivers.

A survey by Insure.com asked two thousand motorists which states they felt had the rudest drivers. To be sure, their answers were influenced by geography: New Hampshire drivers hate Massholes and New Yorkers aren’t fond of New Jerseyans, for example. Looking at common causes for complaints—drivers talking on the phone, tailgating, not signaling, weaving through lanes, and speeding—it’s clear “rude” is a polite synonym for “crappy,” or at least “obnoxious.”

Blue states on the East Coast are heavily represented in the rudest driver rankings, with Washington D.C., New York, Massachusetts, Delaware, Vermont, and New Jersey all in the top 10. North Dakota, Maine, and New Hampshire are listed as the nicest states for drivers. Maybe there’s something in that chilly, rural air that makes people kinder behind the wheel.

As for the Idahoans? One driver quoted in the survey said the state’s drivers “feel just fine taking their time, driving 5 to 10 miles an hour under the limit,” which would surely enrage the leadfoots in Arizona, where the Idahoans are most hated.

Feel free to take to the comments to discuss the survey’s results.

Homepage image: Stuart Dee/Getty

With Minecraft Acquisition, Microsoft Reveals Its Desperation

Jim Merithew/WIRED

Microsoft just acquired Minecraft in a deal valued at $2.5 billion, and at first blush, that seems like money well spent. The popular game, a way of building your own virtual worlds, can not only feed the company’s Xbox game console, but also turn Microsoft into a real player in the world of mobile games, across both smartphones and tablets.

And yet, judging from the reports about the strategy behind the deal, it also reveals a certain amount of desperation from the tech giant.

Last week, both the New York Times and Reuters reported that the real reason Microsoft wants Minecraft is to bring the hit game onto its Windows Phone operating systems and into its mobile app store, the Windows Store. That too may seem like a good move. But it shows just how far behind Microsoft has fallen in the race for the hearts and minds of mobile users, and it raises many questions about whether it can climb back into this race. Ultimately, the company is so far behind, this $2.5 billion deal may not bear as much fruit as Microsoft would like.

One of the main problems with Microsoft’s Windows Phone operating system—an OS quite far behind in terms of market share—is that it’s plagued by a dearth of applications compared to Android and iOS. Many popular mobile apps, such as Instagram, arrived on Windows Phone much later than other platforms. Others, such as Dropbox, Flipboard and Snapchat, still aren’t officially available for Windows Phone. It’s something of a chicken-and-egg problem for the company. Customers don’t want to buy Windows handhelds unless the apps they want are available. But developers don’t want to spend time developing for the platform if the users aren’t there. That has left Microsoft to pick up much of the slack on its own. Earlier this year, for instance, it built its own YouTube client for the OS.

If Microsoft gets Minecraft on Windows Phone, it could help attract users to its phones and tablets, especially younger people for whom the lack of the game would be a deal breaker. The trouble is that it’s only a small step in closing the “app gap,” and the fact that it had to acquire Mojang to bring the game to its mobile operating system doesn’t bode well. While it’s true that Apple and Google sometimes acquire companies for the exclusive use of their technologies, they needn’t buy a company just to force its developers to build a version for their platforms.

Because Microsoft is now so far behind in mobile—where so much of the gaming industry is moving—it must walk a rather fine line if this acquisition is to ultimately pay off. In a way, it would behoove the company to turn Minecraft into something that is only available on Microsoft platforms, shamelessly trying to drive people to its own hardware. But then it risks alienating its existing fan base, who are already skeptical about the acquisition.

Buying a game studio and making its products exclusive to a single platform is par for the course for both Microsoft and the larger game industry. Microsoft acquired Bungie, the company behind the Xbox’s flagship title Halo, in 2000 and turned it into an exclusive property. Sony does much the same, snapping game studios to bring new titles to the PlayStation exclusively. Microsoft could simply draw from this old playbook. It could leave the existing game in tact, but then publish sequels and spin-offs exclusive to Microsoft platforms.

But this is about more than just game consoles. The trouble is that, whereas the Xbox One is a very much a viable alternative to competing devices, Windows Phone is not—at least not today. In the end, limiting mobile use of a new Minecraft to Microsoft phones may do more harm than good. If the company wants Minecraft to thrive on Xbox, it might have no choice but to offer it on iPhones and Android devices. With so much game play moving onto phones, the balance of power has shifted. And not in Microsoft’s favor.

Strategic self-sabotage? MRSA inhibits its own growth

Scientists at the University of Western Ontario have uncovered a bacterial mystery. Against all logic, the most predominant strain of methicillin-resistant Staphylococcus aureus (MRSA) in North American produces an enzyme that degrades skin secretions into compounds that are toxic to itself. The research is published online ahead of print in the Journal of Bacteriology.

S. aureus is a normal commensal bacterium that benignly inhabits around 30 percent of the human population, in the nasal passages and on the skin. Yet it can become opportunistic. As such, it represents a major, growing public health threat now comparable to HIV, tuberculosis, and viral hepatitis. A particularly hypervirulent strain of MRSA, USA300, has become the predominant strain in both the community and in hospitals across North America.

Recent studies have indicated that USA300's emergence and rapid spread were due at least in part, to enhanced ability to abide on human skin, a skill which has been traced to a gene that confers resistance to toxic polyamines on the skin. That gene is absent from all other S. aureus strains.

That aside, the skin is not exactly a hospitable environment. To S. aureus, sebum, a waxy or oily substance secreted by the sebaceous glands in the skin, is a witch's brew of free fatty acids and other bacterial poisons. Sebum also contains triglycerides, to keep the skin from drying out.

The mystery involves the production by all strains of S. aureus of a lipase enzyme, SAL2, that snips these innocuous triglycerides into more of the antimicrobial free fatty acids.

"In previous work, SAL2… was identified as one of just seven secreted proteins that was universally produced by 63 diverse strains of S. aureus and, as such, it is unlikely that S. aureus would have evolved to maintain abundant production of SAL2 if it did not confer a substantial benefit to the bacterium," the investigators write, adding that this is especially true for the USA300 strain of community-acquired methicillin resistant S. aureus (CA-MRSA).

In the study, the investigators engineered strains of CA-MRSA that could not make SAL2 lipase, and compared, in vitro, how the mutant and the wildtype responded to triglycerides. The mutants grew well in the presence of triglycerides.

"But in the case of the wildtype, the activity of SAL2 lipase produced high concentrations of fatty acids that inhibited bacterial growth," says corresponding author David E. Heinrichs, of the University of Western Ontario, London.

That seemingly illogical result is driving further research, says Heinrichs. "Our continued efforts are directed toward finding out why these bacteria have evolved a growth-inhibiting system of releasing large amounts of fatty acids from skin secretions."

Somehow, the investigators suggest in their conclusion, the evolutionary conservation of ample production of SAL2 lipase's activity must be helping the bacterium to colonize and persist on human skin. But they hint at the difficulty of determining how it works when they write that a number of different models will be needed to examine persistence and virulence not only on the skin, but in abscesses beneath the skin, and in bacteremia. Some of those studies are already underway.

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The above story is based on materials provided by American Society for Microbiology . Note: Materials may be edited for content and length.

Technological leap in treating pcb contamination in the environment: Three new bacteria could break down pcb

A team of researchers from the National University of Singapore (NUS) Faculty of Engineering have developed a novel approach that could greatly enhance the effectiveness of destroying polychlorinated biphenyls (PCBs) in the environment. They discovered three powerful bacteria from a genus called Dehalococcoides which can degrade PCBs. In addition, the researchers also developed an effective method of culturing these PCB dechlorinators in large quantities to enhance their degradation efficiency.

Working with A*STAR's Genome Institute of Singapore (GIS), the team was able to identify the functional genes responsible for breaking down PCBs. With these research findings, it is now possible to design and engineer methods which can rid our environment of harmful PCBs more effectively. Their findings were recently published in the journal, Proceedings of the National Academy of Sciences (PNAS).

PCB contamination and challenges posed to environment

PCBs are synthetic organic chemical compounds of chlorine and biphenyl. They have been widely used as coolant fluids in many electrical products. However, they are toxic and exposure to PCBs has been known to show symptoms almost immediately. Though PCBs are no longer used (they have been banned since the 1970s), they are virtually indestructible and can possibly remain in the environment forever. Hence they continue to contaminate rivers, lakes and harbours worldwide, posing a threat to human and ecosystem health.

There have only been seven known enzymes associated with Dehalococcoides found to have confirmed function on chlorinated compounds. The NUS-GIS research team is proud to add the three new bacteria to the list -- each with distinct specificities.

An in-situ microbial detoxification strategy, which involves applying microbes directly to break down (dechlorinate) PCBs on-site, would be very effective for PCB bioremediation. However, these microbes are extremely hard to culture, hence limiting efforts to characterise them for such applications.

Currently, the only treatment is capping or dredging and landfilling the PCBs. An example is the ongoing SuperFund project to dredge the upper Hudson River to remove PCBs which has already cost nearly US$1 billion. In this regard, the novel technique developed by the research team to culture PCB dechlorinators could pave the way for alternative, and possibly more effective, methods of degrading PCBs on-site.

Novel substrate for culturing PCB dechlorinators

Associate Professor He Jianzhong, who is from the NUS Department of Civil & Environmental Engineering, explained, "While the scientific community has found out that certain bacteria can dechlorinate PCBs and make them more susceptible to oxidation, it was not until three decades ago that some were identified. However, challenges still remain in growing these organisms in quantities that will make an impact. Their low biomass has also prevented us from studying closely the process, especially in identifying the enzymes responsible. Furthermore, as PCBs are extremely insoluble, they are unsuitable as substrates for culturing the helpful bacteria."

To overcome this problem, the NUS team came out with an alternative substrate called Terrachloroethene (PCE) which can be used to boost the cell numbers of PCB dechlorinators.

"This discovery is a quantum leap forward in our understanding of microbial PCB dechlorination and hence open up new possibilities of developing more effective ways of destroying PCBs in our environment," said Assoc Prof He.

Genomic technologies to the fore

Dr Niranjan Nagarajan, who leads the research at GIS, said, "Through synergy generated from traditional culture techniques combined with state of the art genomic technologies, we could successfully cultivate and characterise three PCB dechlorinating microbial strains. From these efforts, we were able to be the first to identify the functional genes responsible for breaking down PCBs. These genes could be very useful as biomarkers for monitoring PCB bioremediation."

Assoc Prof He added, "Finding useful bacteria can be tough. Our work shows how advanced genomic technologies can be combined with culturing to sift through bacteria in the environment and find the gems. This is a big step forward in the development of in-situ microbial detoxification technologies for PCB bioremediation."

These discoveries promise to move the bioremediation technology for PCBs into the realm of reality because for the first time, bioaugmentation is feasible. The impact of this outstanding research is tremendous, which makes in-situ bioremediation possible by saving significant amount of time and labor. Future research will be focused on application of genomic technologies for in-situ degradation of PCBs and other halogenated compounds.

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

Video: The Next Frontier for Big Data

DropCam can keep tabs on loved ones, storing many hours of video. DropCam

Years of video are recorded and uploaded to the cloud each day to sites like YouTube, Vine, and Facebook from devices like mobile phones, personal drones, or home surveillance cameras. With the new capabilities of computer vision technology, we have the ability to mine this visual data to get valuable insights about what’s happening in the world. However, video content has largely been ignored in the conversation about big data.

Video as a data source has the power to give us information about how people interact with the world around them unlike any other data source. Video provides real-time data about behavior happening in the present, not just the past — whether it’s traffic patterns for the commute in and out of San Francisco or what time most kids get home from school in Palo Alto, California.

Video data stored in the cloud is exploding. Nest, Google’s internet of things investment, just bought Dropcam, a home security camera company. Silicon Valley companies are building fleets of satellites that will orbit the earth and be able to take thousands of high resolution photos or record video for up to 90 seconds of any spot, and revisit that spot several times per day. Inexpensive consumer drones like the DJI Phantom are selling in the thousands per week. Much of that data captured by these technologies is being uploaded to public sites such as YouTube where anyone can access them.

How can we extract value from all this video, in the way that we do from other “big data” sources?

To move forward, we have to get past our current fixation on the devices — drones being the largest example — and focus on the software that will extract the useful data they collect, and the answers that can come from that data. To find these answers we need to have a way to mine video content for data.

Until now, extracting intelligence from video content has mostly “manual,” through human observation — literally, a human watching the video and writing down what is happening. Think about a documentary filmmaker “logging” their footage, marking down interesting occurrences in the video, what they are, and when they occur. This was the process for police and FBI who mined hours of surveillance video collected after the Boston Marathon Bombings to find moments where the bombers passed the cameras.

To make video data into useful big data, we need to leap beyond this. We need true video analytics, powered by computer vision. Current search technology looks at the metadata stored with videos — like tags you include when you upload a YouTube video (“science”, “kids,” “cat dancing” or other keywords). Or, some sites use still image techniques (like classification) to find objects, cars, or company logos in videos. True video analytics involves using computer vision algorithms to analyze video pixels automatically, and over time — not only identifying objects in the scene, but also tracking their movements and behavior. With true video analytics you can track patterns of movement of hundreds of objects in the scene, as well as their size, shape, speed, and direction of movement.

To see the influence that data gathered from video would have, let’s take a mundane government question like, “Is it worth it to invest in new infrastructure to address traffic issues in the Bay Area?” Here in Burlingame, local citizens wanted a new crosswalk built across a busy intersection. The town had to employ a full-time person to stand and manually count every adult and child that crossed that intersection over a week — in order to measure how many citizens would benefit from that investment. This could have been accomplished with a single surveillance camera and video analytics, measuring people (adults, kids), and vehicles, turning the data into something that is actionable (and provides good ROI).

We could assess things like how many, and what type of vehicles are using a new highway overpass? Were the tax breaks given to the company who asked for it worth it? Is the local sewage facility operating within regulations? Are there sewage outflows after heavy rains? How big are they?

Over the longer term, as video analytics of aerial or space data become more widely accessible, it will change the way we understand the world. It will give everyone access to the data that, until recently, only militaries and intelligence agencies had at their disposal. It will let everyone see for themselves what is really happening around the world and disrupt the current notion of the big data revolution. This is true freedom of information and it is on the horizon.

Dr. Sean Varah is founder and CEO of MotionDSP.

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.