Scientists at the University of Washington have developed a new approach to study microbes in the wild, which will allow researchers to sequence the genomes of individual species from highly complex mixtures. It marks a big advance for understanding the enormous diversity of microbial communities —including the human microbiome. This new method can cluster sequence fragments from a mixed sample of yeasts into species. In the shown graph, each of the 12 species with a substantial presence in the mix are represented by a cluster. Each fragment is shown as a dot, with size indicating length, colored by species. Line widths represent the densities of links between the fragment shown.
The work is described in an article published May 22 in Early Online form in the journal G3: Genes|Genomes|Genetics, published by the Genetics Society of America.
"This new method will allow us to discover many currently unknown microbial species that can't be grown in the lab, while simultaneously assembling their genome sequences," says co-author Maitreya Dunham, a biologist at the University of Washington's Department of Genome Sciences.
Microbial communities, whether sampled from the ocean floor or a human mouth, are made up of many different species living together. Standard methods for sequencing these communities combine the information from all the different types of microbes in the sample. The result is a hodgepodge of genes that is challenging to analyze, and unknown species in the sample are difficult to discover.
"Our approach tells us which sequence fragments in a mixed sample came from the same genome, allowing us to construct whole genome sequences for individual species in the mix," says co-author Jay Shendure, also of the University of Washington's Department of Genome Sciences.
The key advance was to combine standard approaches with a method that maps out which fragments of sequence were once near each other inside a cell. The cells in the sample are first treated with a chemical that links together DNA strands that are in close proximity. Only strands that are inside the same cell will be close enough to link. The DNA is then chopped into bits, and the linked portions are isolated and sequenced.
Species-Level Deconvolution of Metagenome Assemblies with Hi-C-Based Contact Probability Maps Joshua N. Burton, Ivan Liachko, Maitreya J. Dunham, and Jay Shendure. G3: Genes|Genomes|Genetics g3.114.011825; Early Online May 22, 2014, DOI: 10.1534/g3.114.011825 ; PMID 24855317
A Mexican software company has managed to transmit audio, video and Internet across the spectrum of light emitted by LED lamps – at a data transfer rate of 10 gigabytes per second.
The technology can illuminate a large work space, such as an office, while providing full mobile Internet to every device that comes into the range of the light spectrum. The technology, called Li-Fi or light fidelity, is presented as an alternative to Wi-Fi because it will maximise the original provided speed of the internet to offer safer data transfer and a transfer rate of up to 10 gigabytes per second. The Li-Fi device circulates data via LEDs that emit an intermittent flicker at a speed imperceptible to the human eye.
“As Wi-Fi uses cables to spread our connections, wireless transmission Li-Fi uses LED lamps that emit high brightness light,” said Arturo Campos Fentanes, CEO of Sisoft in Mexico.
Another advantage in comparison to Wi-Fi is that there is no way to hack the signal since the internet is transmitted by light, there is no way to “steal it.” Furthermore, it can be installed in hospitals areas that use radiation apparatus and generally block or distort internet signal, Fentanes said.
With this new technology expansion through the market is sought, with lower costs and a service increased by five thousand per cent internet speed.
Currently in Mexico the highest transfer rate is 200 megabytes per second. Just to get an idea, with Li-Fi you could quickly download an entire HD movie in just 45 seconds.
Also known as visible light communications (VLC), this technology began with an internet speed of two Gigabits per second, but Sisoft along with researchers from the Autonomous Technological Institute of Mexico (ITAM) adapted the system to be multiplied five times.
Fentanes explained that the first experiments were conducted with audio, in which a cable is connected via 3.5 mm audio Jack from a smartphone to a protoboard table to transform the auditory signal in optical waves.
That way a special emitter transmits data across the spectrum of light generated by an LED lamp and is captured by a receptor located in a speaker that reproduces sound.
For wireless internet transmission, the mechanics is similar. The station developed by Sisoft stands above the router device that distributes the internet signal and a lamp-LED is incorporated to maximise the speed of data transfer. Light will emulate an antenna, but only the electronic apparatus that has the receptor for the “optical audio” signal and is inside the range of the halo of light will have a connection.
Surgeons are taught from textbooks which conveniently color-code the types of tissues, but that's not what it looks like in real life -- until now. At TEDMED Quyen Nguyen demonstrates how a molecular marker can make tumors light up in neon green, showing surgeons exactly where to cut.
New research demonstrates that drug paraphernalia triggers the reward areas of the brain differently in dependent and non-dependent marijuana users. By letting users handle a marijuana pipe while in an fMRI, researchers found that areas of brain activation in the dependent users suggests a more emotional connection than in non-dependent users. Non-dependent users had greater activations in areas associated with memory and attention.
The potential cancer risk in non-smokers -- particularly young children -- of tobacco smoke gases and particles deposited to surfaces and dust in the home has been demonstrated by researchers. Until now, the risks of this exposure known as ‘third hand tobacco smoke’ have been highly uncertain and not considered in public policy. However, a new study has estimated for the first time the potential cancer risk by age group through non-dietary ingestion and dermal exposure to third hand smoke. The results indicate potentially severe long-term consequences, particularly to children.
Raising state-mandated math and science course graduation requirements (CGRs) may increase high school dropout rates without a meaningful effect on college enrollment or degree attainment, according to new research. To examine the effects of state-mandated CGRs on educational attainment, researchers looked at student outcomes in 44 states where CGRs were mandated in the 1980s and 1990s.
This image might have you thinking twice before knocking.
A new map called “The Patina of Feces” shows that the outer door frames of American homes wear a thin veneer of microbes that are normally found in animals’ guts. Given that the microbes had to leave those guts to travel door to door, they probably came from someone’s, or something’s, poop.
“No reason to freak out,” says project coleader Noah Fierer of the University of Colorado Boulder. We already knew that fecal bacteria are floating around in the air, and we know that we’re breathing them in all the time. They probably aren’t causing any health effects, for the most part.
One does wonder, though, about those hot spots, shown appropriately in brown. Fierer and his colleagues are still trying to figure out why doors in some places, notably north Texas, Arkansas and Missouri, have so much fecal matter. “Our current hypothesis is that these patterns are driven by proximity to livestock and, in part, by climate parameters,” Fierer says. Dry, windy places may have more fecal-laden dust moving around.
About 1,000 houses were sampled for the map, and almost all of them had some level of fecal bacteria. But the team still has a lot of work to do to figure out where the bacteria came from and whether the hot spots are real. The Texas panhandle, for example, may or may not be particularly poopy based on the two houses sampled. (No comment.)
As for the source, “some is surely human, much of it though might come from pigs, cows, chickens, squirrels or who knows what else,” Rob Dunn of North Carolina State University, who led the project with Fierer, writes in a blog post announcing the results. Urban areas also tend to have a lot of airborne dog poop, Fierer reported in 2011.
Fierer and Dunn study the microbes on and around us in our daily lives. It’s all part of a project called Your Wild Life that’s examining the biodiversity of everything from armpits and belly buttons to the insects living in our homes.
Some may say they’re happier not knowing these things. I think, though, that this provides a useful perspective on the world. It’s good to know that Stanford microbiologist Stanley Falkow was right when he reportedly said, “The world is covered in a fine patina of feces.”
Bridging the worlds of neuroscience and high-tech virtual realty, the Glass Brain, a project of the new Neuroscape Lab at the University of California San Francisco may open up new insights into the complicated mechanisms of the brain.
Researchers have developed a new way to explore the human brain through virtual reality. The system, called Glass Brain, initiated by Philip Rosedale, creator of the famous game Second Life, and Adam Gazzaley, a neuroscientist at the University of California San Francisco, combines brain scanning, brain recording and virtual reality to allow a user to journey through a person’s brain in real-time.
For a recent demonstration at the South by Southwest (SXSW) Interactive festival in Austin, Texas, Rosedale made his wife a cap studded with electroencephalogram (EEG) electrodes that measure differences in electric potential in order to record brain activity, while he wore a virtual reality headset to explore her brain in 3D, as flashes of light displayed her brain activity from the EEG.
The Glass Brain didn’t actually show what Rosedale’s wife was thinking, but Gazzaley’s team ultimately hopes to get closer to decoding brain signals and displaying them using the virtual reality system.
This is an anatomically-realistic 3D brain visualization depicting real-time source-localized activity (power and "effective" connectivity) from EEG (electroencephalographic) signals. Each color represents source power and connectivity in a different frequency band (theta, alpha, beta, gamma) and the golden lines are white matter anatomical fiber tracts. Estimated information transfer between brain regions is visualized as pulses of light flowing along the fiber tracts connecting the regions.
The modeling pipeline includes MRI (Magnetic Resonance Imaging) brain scanning to generate a high-resolution 3D model of an individual's brain, skull, and scalp tissue, DTI (Diffusion Tensor Imaging) for reconstructing white matter tracts, and BCILAB (http://sccn.ucsd.edu/wiki/BCILAB) / SIFT (http://sccn.ucsd.edu/wiki/SIFT) to remove artifacts and statistically reconstruct the locations and dynamics (amplitude and multivariate Granger-causal (http://www.scholarpedia.org/article/G...) interactions) of multiple sources of activity inside the brain from signals measured at electrodes on the scalp (in this demo, a 64-channel "wet" mobile system by Cognionics/BrainVision (http://www.cognionics.com)).
The final visualization is done in Unity and allows the user to fly around and through the brain with a gamepad while seeing real-time live brain activity from someone wearing an EEG cap.
All over the world researchers are investigating solar cells which imitate plant photosynthesis, using sunlight and water to create synthetic fuels such as hydrogen. Empa researchers have developed such a photoelectrochemical cell, recreating a moth’s eye to drastically increase its light collecting efficiency. The cell is made of cheap raw materials – iron and tungsten oxide. Rust – iron oxide – could revolutionise solar cell technology. This usually unwanted substance can be used to make photoelectrodes which split water and generate hydrogen. Sunlight is thereby directly converted into valuable fuel rather than first being used to generate electricity. Unfortunately, as a raw material iron oxide has its limitations. Although it is unbelievably cheap and absorbs light in exactly the wavelength region where the sun emits the most energy, it conducts electricity very poorly and must therefore be used in the form of an extremely thin film in order for the water splitting technique to work. The disadvantage of this is that these thin-films absorb too little of the sunlight shining on the cell.
Empa researchers Florent Boudoire and Artur Braun have now succeeded in solving this problem. A special microstructure on the photoelectrode surface literally gathers in sunlight and does not let it out again. The basis for this innovative structure are tiny particles of tungsten oxide which, because of their saturated yellow colour, can also be used for photoelectrodes. The yellow microspheres are applied to an electrode and then covered with an extremely thin nanoscale layer of iron oxide. When external light falls on the particle it is internally reflected back and forth, till finally all the light is absorbed. All the entire energy in the beam is now available to use for splitting the water molecules.
In principle the newly conceived microstructure functions like the eye of a moth, explains Florent Boudoire. The eyes of these night active creatures need to collect as much light as possible to see in the dark, and also must reflect as little as possible to avoid detection and being eaten by their enemies. The microstructure of their eyes especially adapted to the appropriate wavelength of light. Empa's photocells take advantage of the same effect.
In order to recreate artificial moth eyes from metal oxide microspheres, Florent Boudoire sprays a sheet of glass with a suspension of plastic particles, each of which contains at its centre a drop of tungsten salt solution. The particles lie on the glass like a layer of marbles packed close to each other. The sheet is placed in an oven and heated, the plastic material burns away and each drop of salt solution is transformed into the required tungsten oxide microsphere. The next step is to spray the new structure with an iron salt solution and once again heat it in an oven.
Reference: Florent Boudoire, Rita Toth, Jakob Heier, Artur Braun, Edwin C. Constable, Photonic light trapping in self-organized all-oxide microspheroids impacts photoelectrochemical water splitting, Energy & Environmental Sciences, in press.
Using a newly developed, ultrafast femtosecond infrared light source, chemists at the University of Chicago have been able to directly visualize the coordinated vibrations between hydrogen-bonded molecules -- the first time this sort of chemical interaction, which is found in nature everywhere at the molecular level, has been directly visualized. They describe their experimental techniques and observations in The Journal of Chemical Physics.
Political ideology and education levels affect when people search for climate information, research indicates. Republicans search the net for information about the weather, climate change and global warming during extremely hot or cold spells. Democrats Google these terms when they experience changes in the average temperatures. These are some of the surprising findings from a study that tracked how the temperature fluctuations and rainfall that Americans experience daily in their own cities make them scour the Internet in search of information about climate change and global warming.
An international team of researchers has found new evidence that our prehistoric ancestors had a detailed understanding of plants long before the development of agriculture. By extracting chemical compounds and microfossils from dental calculus (calcified dental plaque) from ancient teeth, the researchers were able to provide an entirely new perspective on our ancestors' diets. Their research suggests that purple nut sedge (Cyperus rotundus) -- today regarded as a nuisance weed -- formed an important part of the prehistoric diet.
Scientists have shown how the main psychoactive ingredient in cannabis, THC, could reduce tumor growth in cancer patients. New research reveals the existence of previously unknown signaling platforms which are responsible for the drug's success in shrinking tumors.