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CRISPR: the next generation of genome editing tools

CRISPR: the next generation of genome editing tools | Science Garden |

An arms race has been waged between bacteria and bacteriophage that would bring a satisfactory tear to Sun Tzu’s eye. Scientists have recently recognized that countermeasures developed by bacteria (and archaea) in response to phage infections can be retooled for use within molecular biology. In 2013, large strides have been made to co-opt this system (specifically and most commonly from Streptococcus pyogenes) for use in mammalian cells. This countermeasure, CRISPR (clustered regularly interspaced short palindromic repeats), has brought about another successive wave of genome engineering initiated by recombineering and followed more recently by zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs).


ZFNs and TALENs perform a similar function yet the learning curve appears to be more difficult for development due to the use of protein-DNA contacts rather than the simplicity of designing RNA-DNA homology contacts. Although the potential for CRISPR in regards to genome editing within mammalian cells will be of greatest interest to the reader, the CRISPR backstory is equally compelling. Just as we have evolved immune responses to pathogens, so too have bacteria. CRISPR is an adapted immune response evolved by bacteria to create an immunological memory to ward off future phage infections. When a phage infects and injects its DNA within a bacterium, the DNA commandeers bacterial proteins and enzymes for use towards lytic or lysogenic phases. However, exposure of phage DNA allows the bacterium to copy and insert snippets (called spacers) of phage DNA into its genomic DNA between direct repeats (DR). These snippets can later be expressed as an operon (pre-CRISPR RNA, pre-crRNA) alongside a trans-activating CRISPR RNA (tracrRNA) and an effector CRISPR associated nuclease (Cas). Together these components surveil for foreign crRNA cognate sequence and cleave the targeted sequence.


Although hallmarks of CRISPR have been known since the late 80’s (CRISPR timeline) and was acronymed in 2002, Jinek et al. in August 2012 were the first to suggest the suitability of CRISPR towards genome editing. In February of 2013, Feng Zhang’s and George Church’s labs simultaneously published the first papers describing the use long oligos/constructs for editing via CRISPR in mammalian cells and made their plasmids readily available on Addgene. Zhang’s lab went one step further and has supplemented their papers with a helpful website and user forum. They have even gone so far as to publish a methods paper to streamline the use of their plasmids towards a plug-and-play, modular cloning approach with your target sequence of interest.


CRISPR works fairly well out of the box yet still has some imperfections that are being addressed. For example, CRISPR relies upon a protospacer adjacent motif (PAM; S. pyogenes sequence: NGG) 3’ to the targeting sequence to permit digestion. Although the ubiquity of NGG within the genome may seem advantageous, it may be limiting in some regions. Other species make use of different PAM sites that can be considered when choosing a cut sites of interest. Since double-stranded cuts could potentially create DNA lesions (a byproduct of the cell using non-homologous end joining [NHEJ] instead of homologous recombination) some labs are choosing to use modified Cas enzymes that nick DNA, instead of creating a double-strand break. This potential weakness of CRISPR to create DNA lesions via NHEJ, however, has been exploited by Eric Lander’s and Zhang’s lab this month (Jan. 2014). They have capitalized on the cell’s use of NHEJ to manufacture DNA lesions (frameshift mutations) at cut sites within genes on a large scale as a means to perform large genetic screens. Using this technique knocks out a gene and has the obvious advantage of fully ablating a gene’s expression compared to RNAi where some residual expression can be expected.


The advantages of CRISPR lends itself to future therapies. High efficiency, low-to-no background mutagenesis and easy construction put CRISPR front and center as the tool de jour for gene therapy. In combination with induced pluripotent stem cells (iPSCs), one can imagine the creation of patient-specific iPSCs created with non-integrative iPSC vectors and modified by CRISPR, devoid of any residual DNA footprint left behind by the iPSC vector or CRISPR correction. In conjunction with whole genome sequencing, genetically clean cell lines can be selected that are suitable for differentiation towards the germ layer of interest for subsequent autologous transplantation. Proof of principle experiments have already been published in models of cystic fibrosis and cataracts.


For better or worse, CRISPR is catching on like wildfire with young investigators, as noted recently by Michael Eisen. What may be looming in the future and not as openly discussed at this time is the potential for CRISPR to open up the genome to large scale editing. We tend to think of any particular genome as fairly static with slight variations between any two individuals and increased variation down the evolutionary line. However, CRISPR has proven to be a fantastic multitasker, capable of modifying multiple loci in one fell swoop as demonstrated by the Jaenisch lab (five loci). With the creation of Caribou Biosciences and a surprising round of venture capital raised by a powerhouse team at Editas Medicine in November ($43 million), CRISPR appears to also have sparked an interest in the private sector. With large sums of money at their disposal, these companies can now begin to look at the genome, not as a static entity, but more akin to operating system, a code that now has a facile editing tool. George Church, an Editas co-founder, has speculated in the past about the potential use of the human genome as the backbone for recreating the Neanderthal genome in his recent book and interview with "Der Spiegel". In an era where the J. Craig Venter Institute can create an organism’s genome de novo and a collaboration between Synthetic Genomics and Integrated DNA Technologies has proposed to synthesize DNA upwards of 2Mbp, the combination of CRISPR, synthetic DNA and some elbow grease will make the genome more accessible and Church’s speculations a potential reality.

Via Dr. Stefan Gruenwald
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John Deere & Co. (DE) to Sell Crop Insurance Unit to Farmers Mutual Hail Insurance Company of Iowa (FMH)

John Deere & Co. (DE) to Sell Crop Insurance Unit to Farmers Mutual Hail Insurance Company of Iowa (FMH) | Science Garden |

December 18, 2014 12:00 PM EST 

Deere & Co. (NYSE: DE) has reached a definitive agreement to sell its crop insurance business, subject to regulatory approval, to Farmers Mutual Hail Insurance Company of Iowa (FMH), headquartered in West Des Moines, Iowa.


The action is a result of Deere's previously announced review of strategic options for the crop insurance business. The agreement will result in Deere selling both John Deere Insurance Company and John Deere Risk Protection, Inc., which together made up the crop insurance business unit of John Deere Financial.


"We are confident that customers of John Deere crop insurance will be well served with this action," said Don Preusser, president, John Deere Insurance Company and John Deere Risk Protection, Inc. "Farmers Mutual Hail has provided tailored crop insurance packages to farmers for more than 120 years. We believe the success and long tenure of FMH speaks volumes about their dedication to customer service."


FMH was founded in 1893 and is a provider of comprehensive risk management solutions for America's heartland, including private and federal crop insurance, reinsurance products and services, as well as farm and ranch insurance that includes auto, property, and liability coverage.


Deere has been involved in the crop insurance business for 9 years, during which John Deere Insurance Company became a top-10 provider of crop insurance with national distribution.


Closing is expected in the first quarter of the 2015 calendar year. Citi served as exclusive financial advisor to Deere & Company for this initiative.

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The First Ecological Land Units Map of the World | Esri Insider

The First Ecological Land Units Map of the World | Esri Insider | Science Garden |

The US Geological Survey (USGS) and Esri are pleased to announce the publication of the most detailed global ecological land units map in the world. This exciting new global data set provides a science platform for better understanding and accounting of the world’s resources.  Scientists, land managers, conservationists, developers, and the public will use this map to improve regional, national, and global resource management, planning, and decision making.

Ecological Tapestry of the World online explorer application: Explore the ecological data behind the land unit map and begin planning how it can be used in your work.


This map as well as the data layers used to create it can be explored in a new story map that introduces ecological land units. The data is available in the form of services and can enrich any GIS effort.

The collaborative partnership between Esri and USGS resulted in a dynamic online map representing the world’s ecological diversity at unprecedented detail and authority. This work leveraged quantitative methods, geographic science, and big data produced by government agencies and the scientific community.  To create this map the data were processed in Esri’s ArcGIS cloud computing environment. This map provides new knowledge and understanding of geographic patterns and relationships by distinguishing the geography of the planets’ ecosystems.


To better understand the significance of the new Global Ecological Land Units (ELUs) map and the data behind it, I recently met with project leads, Roger Sayre, Ph.D., Senior Scientist for Ecosystems, USGS, and Randy Vaughan, Manager of Content Engineering, Esri.

What is Global Ecological Land Units map?

Roger Sayre, USGS: The Global ELUs map portrays a systematic division and classification of the biosphere using ecological and physiographic land surface features.

Tapestry of World Ecosystems: This story map introduces ecological land units and explores more than 100 places where diversity is highest.

How was this map created?

Randy Vaughan, Esri: The globe was divided in cells (Ecological Facets) at a base resolution of 250 meters. The Facets were then characterized (attributed) with four input layers that drive ecological processes: bioclimate, landform, lithology, and land cover parameters.  The layers chosen were the best available in terms of accuracy, currency, and global coverage.  The result was a global raster data layer with 47,650 unique combinations of the four input layers. The Facets were then aggregated into 3,923 ecological land units (ELUs).

Why was it created?

Roger Sayre: The Global ELU project goals are twofold.  The first goal is to provide, for the first time, a web-based, GIS-ready, global ecophysiographic data product for land managers, scientists, conservationists, developers, and the public to use for global, regional, and landscape analysis and accounting.

Second, the Global ELU map advances an objective, repeatable big data approach to the synthesis and classification of ecologically important data layers into distinctive and meaningful geo-referenced land units.

Can you give me some examples of what people might do with this data?

Randy Vaughan: The ELUs and other potential ecological facet aggregations provide an accounting framework to assess ecosystem services, such as carbon storage and soil formation, as well as risks such as environmental degradation.

The ELUs also lend themselves to the study of ecological diversity, rarity, and evolutionary isolation.  For example we can identify whether the most diverse landscapes in terms of proximity to the most unique ELUs are protected. Understanding diversity can point the way to conservation and preservation planning.


Roger Sayre: While ELUs do not definitively characterize ecosystems at multiple scales, they do provide information and pointers to the ecological patterns of the globe.  They will be useful for constructing research agendas and for understanding global processes such as climate change. For example, the data will be important to the study of environmental change.  The automated approach to the objective classification of ELUs means that the mapping can be updated as better or more current input layers become available.

Agro-ecological zoning is based on the synthesis of land feature information, climate, and crop characteristics.  The Global ELUs data will support the analysis and formulation of agro-ecological zoning by providing a standard foundation or starting point for zonation.

Are there future plans for the Global Ecological Land Units map?

Roger Sayre: There are known and expected deficiencies in the current input layers given the difficulty of mapping any phenomenon at the global level.  The objective of the USGS and Esri is that the underlying data layers will be improved and updated.  Users of the ELU data may help by documenting deficiencies in the current layers and suggesting improvements to the data structures to facilitate synthesis and analysis.  The Global ELU team will seek collaborators to improve the data and will continue its own program of data improvement. For example the release of the new SRTM 30 meter elevation terrain data provides an opportunity create a higher resolution landforms map.


Randy Vaughan: The approach used to aggregate and classify data may also be used for other endeavors such as human geography.  We are in the early stages of investigating what combinations of human and cultural data might be usefully combined. We note that the data production is more than just a land unit classification; all of the underlying data is available on ArcGIS Online for GIS analysis.

How can people get access to the Global ELUs map?

Introductory Story Map to the ecological land units: the online application: more about ecological land units: started using this content in ArcGIS: ArcGIS Online Landscape Layers Group

  About Matt ArtzMatt Artz joined Esri in 1989. In his current role as GIS and Science Manager, he helps communicate the value of GIS as a tool for scientific research and understanding. He writes extensively about geospatial technologies, manages the GIS and Science blog, and is the editor of Prior to joining Esri he worked as an Environmental Scientist at a large science and engineering consulting company, on such diverse projects as highway noise modeling, archaeological impact assessment, and chemical weapons disposal. His educational background includes an M.S. degree in Environmental Policy and Planning and a B.S. degree in Anthropology and Geography.View all posts by Matt Artz →

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What Do Tree Rings Sound Like When Played Like A Record? | IFLScience

What Do Tree Rings Sound Like When Played Like A Record? | IFLScience | Science Garden |
We all know that the Lorax speaks for the trees, but what do they sound like when they speak for themselves? Rings on a tree can give information about the age of the tree, as well as indicate environmental conditions such as rain levels, disease, and even forest fire. Light colored rings indicate quick growth, while darker rings indicate times when the tree did not grow as quickly. Slices of trees are not uniform, and they all tell a story about the tree’s history.
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NASA estimates that it will take 11 trillion gallons of water to recover from California's drought

NASA estimates that it will take 11 trillion gallons of water to recover from California's drought | Science Garden |
It will take about 11 trillion gallons of water (42 cubic kilometers) -- around 1.5 times the maximum volume of the largest U.S. reservoir -- to recover from California's continuing drought, according to a new analysis of NASA satellite data.


The finding was part of a sobering update on the state's drought made possible by space and airborne measurements and presented by NASA scientists Dec. 16 at the American Geophysical Union meeting in San Francisco. Such data are giving scientists an unprecedented ability to identify key features of droughts, and can be used to inform water management decisions.

A team of scientists led by Jay Famiglietti of NASA's Jet Propulsion Laboratory in Pasadena, California, used data from NASA's Gravity Recovery and Climate Experiment (GRACE) satellites to develop the first-ever calculation of this kind -- the volume of water required to end an episode of drought.

Earlier this year, at the peak of California's current three-year drought, the team found that water storage in the state's Sacramento and San Joaquin river basins was 11 trillion gallons below normal seasonal levels. Data collected since the launch of GRACE in 2002 show this deficit has increased steadily.

"Spaceborne and airborne measurements of Earth's changing shape, surface height and gravity field now allow us to measure and analyze key features of droughts better than ever before, including determining precisely when they begin and end and what their magnitude is at any moment in time," Famiglietti said. "That's an incredible advance and something that would be impossible using only ground-based observations."

GRACE data reveal that, since 2011, the Sacramento and San Joaquin river basins decreased in volume by four trillion gallons of water each year (15 cubic kilometers). That's more water than California's 38 million residents use each year for domestic and municipal purposes. About two-thirds of the loss is due to depletion of groundwater beneath California's Central Valley.

In related results, early 2014 data from NASA's Airborne Snow Observatory indicate that snowpack in California's Sierra Nevada range was only half of previous estimates. The observatory is providing the first-ever high-resolution observations of the water volume of snow in the Tuolumne River, Merced, Kings and Lakes basins of the Sierra Nevada and the Uncompahgre watershed in the Upper Colorado River Basin.

Via Dr. Stefan Gruenwald
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Here's when you should be drinking your coffee, according to science

Here's when you should be drinking your coffee, according to science | Science Garden |

It probably doesn’t surprise you when I say that caffeine is the most widely consumed psycho-active substance on the planet. One of the most popular vehicles for caffeine consumption - coffee - is so popular, worldwide production is now over 7 million metric tonnes. If averaged out, that equates to 1.3 kg of coffee per person per year. So it’s safe to say we like the stuff. 

Why? It’s not just because it tastes good and suppresses our appetites. It’s also because at a time when, as a society, we have way more things to get done than we have hours in the day, it wakes us up and keeps us going. 


But not all coffee breaks are created equal. Research into the dips and peaks of hormone production in our bodies suggests that we need to be strategic about when we consume caffeine, in order to maximise that buzz and keep productive.

 According to Steven Miller at the NeuroscienceDC blog, this is because a) caffeine is a drug, and b) drugs have an affect on our internal chemistry. Which means to use a drug strategically, you need to know the rhythms of your body chemistry and sync your consumption up with that. There’s an entire scientific discipline that examines how drugs interact with our biological rhythms, he says, called chronopharmacology.

One of the most important biological rhythms for a good deal of species on the planet is our internal circadian clock. It’s controlled by a tiny region in the brain’s hypothalamus called the suprachiasmatic nucleus (SCN), and serves a number of different functions. "The SCN controls your sleep-wake cycle, feeding and energy consumption, sugar homeostasis, and in addition to a few other things it controls your hormones. And, with respect to your alertness, the SCN’s control of cortisol (often referred to as the "stress" hormone) production is extremely important,” says Miller.


This means if you’re producing too much cortisol, you’re not doing too good, but having moderate levels of the hormone helps keep you alert. And, says Miller, healthy levels of cortisone naturally peak between the hours of 8 am and 9 am. So that’s a good time to drink caffeine right? That would be super-convenient because that’s what I’ve been doing for the past, I don’t know, decade.


Turns out that consuming caffeine at the same time as your cortisol levels are naturally peaking is pretty much a waste of time. As Miller explains at NeuroscienceDC:


“One of the key principles of pharmacology is [to] use a drug when it is needed (although I’m sure some scientists might argue that caffeine is always needed). Otherwise, we can develop tolerance to a drug administered at the same dose. In other words, the same cup of morning coffee will become less effective and this is probably why I need a shot of espresso in mine now. 

Although your cortisol levels peak between 8 and 9 am, there are a few other times where - on average - blood levels peak again and are between noon to 1 pm, and between 5:30 to 6:30 pm. In the morning then, your coffee will probably be the most effective if you enjoy it between 9:30 am and 11:30 am, when your cortisol levels are dropping before the next spike.”

Sources: Neuroscience DC, Fast Company

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Why the #$%! Do We Swear? For Pain Relief

Why the #$%! Do We Swear? For Pain Relief | Science Garden |
July 12, 2009* |By Frederik Joelving 



Bad language could be good for you, a new study shows. For the first time, psychologists have found that swearing may serve an important function in relieving pain.

The study, published today* in the journalNeuroReport, measured how long college students could keep their hands immersed in cold water. During the chilly exercise, they could repeat an expletive of their choice or chant a neutral word. When swearing, the 67 student volunteers reported less pain and on average endured about 40 seconds longer.

Although cursing is notoriously decried in the public debate, researchers are now beginning to question the idea that the phenomenon is all bad. "Swearing is such a common response to pain that there has to be an underlying reason why we do it," says psychologist Richard Stephens of Keele University in England, who led the study. And indeed, the findings point to one possible benefit: "I would advise people, if they hurt themselves, to swear," he adds.

How swearing achieves its physical effects is unclear, but the researchers speculate that brain circuitry linked to emotion is involved. Earlier studies have shown that unlike normal language, which relies on the outer few millimeters in the left hemisphere of the brain, expletives hinge on evolutionarily ancient structures buried deep inside the right half.

One such structure is the amygdala, an almond-shaped group of neurons that can trigger a fight-or-flight response in which our heart rate climbs and we become less sensitive to pain. Indeed, the students' heart rates rose when they swore, a fact the researchers say suggests that the amygdala was activated.

That explanation is backed by other experts in the field. Psychologist Steven Pinker of Harvard University, whose book The Stuff of Thought (Viking Adult, 2007) includes a detailed analysis of swearing, compared the situation with what happens in the brain of a cat that somebody accidentally sits on. "I suspect that swearing taps into a defensive reflex in which an animal that is suddenly injured or confined erupts in a furious struggle, accompanied by an angry vocalization, to startle and intimidate an attacker," he says.

But cursing is more than just aggression, explains Timothy Jay, a psychologist at the Massachusetts College of Liberal Arts who has studied our use of profanities for the past 35 years. "It allows us to vent or express anger, joy, surprise, happiness," he remarks. "It's like the horn on your car, you can do a lot of things with that, it's built into you."

In extreme cases, the hotline to the brain's emotional system can make swearing harmful, as when road rage escalates into physical violence. But when the hammer slips, some well-chosen swearwords might help dull the pain.

There is a catch, though: The more we swear, the less emotionally potent the words become, Stephens cautions. And without emotion, all that is left of a swearword is the word itself, unlikely to soothe anyone's pain.

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Genes for speciation: testicular weight, size & gene activity role in hybrid infertility

Genes for speciation: testicular weight, size & gene activity role in hybrid infertility | Science Garden |

December 09, 2014

 Three from one: Half a million years ago, the house mouse, Mus musculus, split into three subspecies, two of which are native to Europe. Within a transition zone, the two European forms interbreed to produce hybrids that are less fertile than their purebred kin. Two scientists at the Max Planck Institute for Evolutionary Biology in Plön have now identified sections in the genomes of such hybrid mice that reduce the animals’ fertility. The genes control testicular gene activity and testicular weight. The researchers’ analysis uncovered a complex web of interactions between various gene regions that can suppress reproduction between the hybrids in the course of evolution. Consequently, the mouse forms continue to diverge until the two subspecies give rise to entirely distinct species.Zoom Image

The distribution of the house mouse subspecies cuts across Central Europe:Mus musculus musculus lives to the east, Mus ... [more]

© MPI for Evolutionary Biology/ B. Harr 

Biological science has proposed a number of different species concepts. One thing is certain though: evolution is an ongoing process, and we only observe a brief snapshot of it. A species that exists today can soon split into two subtypes. The process of speciation is particularly easy to study in emerging species: Before the flow of genes is completely interrupted, hybrids are often produced that are viable but are largely or fully infertile.


Male fertility is often related to testicular weight and size. Changes in gene regulation in the testicles can also lead to infertility. Bettina Harr and Leslie Turner of the Max Planck Institute for Evolutionary Biology therefore looked for regions in the genotype of mice that affect testicular weight and testicular gene activity. To this end, they studied normal and partially sterile hybrid mice in a genome-wide association analysis. “The study shows that many different gene regions play a role in the fertility of hybrid males, some of which have never previously been associated with fertility,” explains Turner.


Once the researchers had identified specific areas in the genome, they looked for interactions between them. Many theories suggest that impaired fertility in hybrids is due to interactions between the genes originating from the different subspecies forms. “With one exception, all the loci we identified interact with at least one other region. Most have multiple interaction partners,” says Bettina Harr.


Hence, an intricate web of interactions exists that reduces the reproductive capacity of hybrid mice within the hybrid zone. It is not yet clear precisely which genes lead to altered gene activity or testicular size, but the Max Planck scientists have already made progress in narrowing down the search. Some of the genome sections identified contain fewer than ten genes and therefore present some promising candidates.

Via idtdna
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This vending machine can use facial recognition to deny you junk food

This vending machine can use facial recognition to deny you junk food | Science Garden |
The vending machine of the future is here, and it's going to food-shame you. The Luce X2 Touch TV vending machine , recently released in England, can use facial recognition to deny certain customers junk food.
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Sparks literally fly when an egg meets sperm, world-first images reveal

Sparks literally fly when an egg meets sperm, world-first images reveal | Science Garden |
Researchers in the US have captured the first images of the exact moment when a mammal's egg is fertilised to show that, in response, it releases billions of zinc atoms that create tiny ‘zinc sparks’ at the point of conception. The team, from...
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Chinese Walnut Trading Website Lists Single Pair For $31,000

Chinese Walnut Trading Website Lists Single Pair For $31,000 | Science Garden |
Reuters  | By Jason Subler and Jane Lanhee LeePosted: 08/28/2012 4:00 pm EDT Updated: 08/28/2012 4:11 pm EDT

BEIJING, Aug 28 (Reuters) - China is trying hard to revive interest in its ailing stock market, but some investors are instead shelling out big money on an asset they can hold in the palms of their hands - walnuts.


With more traditional investments like stocks and property offering only small, or sometimes negative, returns over the last few years, a market in so-called "cultural playthings" has sprouted up, sending prices for large walnuts, for instance, into the tens of thousands of dollars.


Once the toys of China's imperial court, the walnuts -- which when rotated in one's palm are thought to stimulate blood circulation -- are making a comeback among the wealthy, some of whom see them as not only a place to put their cash, but as a distinctly Chinese status symbol.


The bigger, older and more symmetrical, the better, says collector Kou Baojun in Beijing, who owns over 30 pairs of walnuts, most of which are over a century old and have taken on a reddish shine from years of polishing in the palm.


"Look how well these have aged. Playing with these kinds of walnuts isn't for ordinary people," Kou said.


Interest from collectors like Kou has made walnuts big business for merchants like Hu Zhenyuan, who buys entire trees from farmers ahead of the harvest to supply his shop in Beijing.


"Walnut investments go up every year. A pair of walnuts at 350 yuan ($55) 10 years ago can sell for 3,500 yuan or even 20,000 or 30,000 yuan," Hu said.



The walnut craze peaked in 2010, as Beijing's steps to put the brakes on property market speculation left few places for the wealthy to park their money.


But with the stock market now down by nearly 40 percent over the past three years and few options for investing overseas, the market for walnuts and other trinkets, such as gourds to house crickets, continues to thrive. One pair for sale on a popular walnut trading website is listed at over $31,000.


And walnuts are not alone.


In 2006, a frenzy of speculation drove up the price of pu'er tea, a fermented variety from southwestern Yunnan province, to astronomical levels. In 2009, garlic prices soared as punters moved on to more pungent ground.


More recently, there has been a surge of interest in traditional mahogany furniture.


"There are a lot of people in China with disposable savings who at the moment have very poor investment options," said Mark Williams, an economist with Capital Economics in London.


"They look at the property market where there are concerns about prices. The equity market has gone nowhere for years. Bank deposits don't do anything for you. That fuels this speculative activity."


China's securities regulator is trying to change that, seeking to entice investors back to the stock market by cracking down on insider trading and other wrongdoing, cutting trading transaction fees and pushing companies to pay out higher dividends so that investors can expect more regular returns.


Many analysts say that winning them over will take time, as many lost large sums of money in past market slumps and remain skeptical about whether the stock market is stacked against individual investors -- and even whether the fund managers they entrust their money to act in their best interests.


Chi Rui, who set up a walnut information website nearly 10 years ago, suspects that Beijing actually doesn't mind money going into products like walnuts because that way it at least does not drive up food prices, as the recent garlic bubble did.


"The government has been hoping for more money to flow into traditional collectables because their price rise doesn't affect politics or normal people's lives," Chi said.

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Colliding Galaxies Are Producing A Spectacular Light Show

Colliding Galaxies Are Producing A Spectacular Light Show | Science Garden |

Some 130 million light years away, within the constellation Canis Major, two twinkling spiral galaxies are in the process of colliding, treating our eyes to a dazzling show. The pair—NGC 2207 and IC 2163—has hosted the explosive deaths of three stars as supernovas in the last 15 years, and is also spawning stars at an intense rate. But scientists have become particularly interested in these merging galaxies for another reason: They are home to one of the largest known collections of super bright X-ray objects. These so-called “ultraluminous X-ray sources” have been spotted using NASA’s Chandra X-ray Observatory, which is partly responsible for the lustrous composite image shown above.

Just like the Milky Way, these galaxies are teeming with bright sources of X-rays called X-ray binaries. These are systems in which a normal star is closely orbiting a collapsed star, such as a neutron star or black hole. Strong gravitational forces from the compact star draw material from the normal star, a process known as accretion. And when the material hits the companion star, it is heated to millions of degrees, a process that generates a huge amount of X-rays. While intense, the emission from these systems pales in comparison to that from ultraluminous X-ray sources (ULXs).

As the name suggests, ULXs are exceedingly bright; they emit more radiation in the X-rays than a million suns would at all wavelengths. Although they are not well understood, many believe they could be black holes of approximately 10 solar masses that are collecting, or accreting, material onto a disk, emitting X-rays in an intense beam. ULXs are also extremely rare; our galaxy doesn’t have one, most galaxies don’t, but those that do usually only have one. Between NGC 2207 and IC 2163, however, there are 28.

Via Dr. Stefan Gruenwald
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A Worm's Mind In A Lego Body: Scientists Map Brain Connectome of C.elegans and Upload it to a Lego Robot

A Worm's Mind In A Lego Body: Scientists Map Brain Connectome of C.elegans and Upload it to a Lego Robot | Science Garden |

Take the connectome of a worm and transplant it as software in a Lego Mindstorms EV3 robot - what happens next? It is a deep and long standing philosophical question. Are we just the sum of our neural networks. Of course, if you work in AI you take the answer mostly for granted, but until someone builds a human brain and switches it on we really don't have a concrete example of the principle in action.

The nematode worm Caenorhabditis elegans (C. elegans) is tiny and only has 302 neurons. These have been completely mapped and the OpenWorm project is working to build a complete simulation of the worm in software. One of the founders of the OpenWorm project, Timothy Busbice, has taken the connectome and implemented an object oriented neuron program.

The model is accurate in its connections and makes use of UDP packets to fire neurons. If two neurons have three synaptic connections then when the first neuron fires a UDP packet is sent to the second neuron with the payload "3". The neurons are addressed by IP and port number. The system uses an integrate and fire algorithm. Each neuron sums the weights and fires if it exceeds a threshold. The accumulator is zeroed if no message arrives in a 200ms window or if the neuron fires. This is similar to what happens in the real neural network, but not exact.

The software works with sensors and effectors provided by a simple LEGO robot. The sensors are sampled every 100ms. For example, the sonar sensor on the robot is wired as the worm's nose. If anything comes within 20cm of the "nose" then UDP packets are sent to the sensory neurons in the network.

The same idea is applied to the 95 motor neurons but these are mapped from the two rows of muscles on the left and right to the left and right motors on the robot. The motor signals are accumulated and applied to control the speed of each motor.  The motor neurons can be excitatory or inhibitory and positive and negative weights are used. 


And the result? It is claimed that the robot behaved in ways that are similar to observed C. elegans. Stimulation of the nose stopped forward motion. Touching the anterior and posterior touch sensors made the robot move forward and back accordingly. Stimulating the food sensor made the robot move forward.

More Information: The Robotic Worm (Biocoder pdf - free on registration)

Via Dr. Stefan Gruenwald
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'Non-echolocating' fruit bats actually do echolocate, with wing clicks

'Non-echolocating' fruit bats actually do echolocate, with wing clicks | Science Garden |
In a discovery that overturns conventional wisdom about bats, researchers reporting in the Cell Press journal Current Biology on December 4 have found that Old World fruit bats—long classified as 'non-echolocating'—actually do use a rudimentary form of echolocation. Perhaps most surprisingly, the ...

Via Debra Dawson
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Can electrons split? New evidence of exotic behaviors in quasi 2D magnetic materials

Can electrons split? New evidence of exotic behaviors in quasi 2D magnetic materials | Science Garden |
Electrons may be seen as small magnets that also carry a negative electrical charge. On a fundamental level, these two properties are indivisible. However, in certain materials where the electrons are constrained in a quasi one-dimensional world, they appear to split into a magnet and an electrical charge, which can move freely and independently of each other. A longstanding question has been whether or not similar phenomenon can happen in more than one dimension. A team lead by EPFL scientists now has uncovered new evidence showing that this can happen in quasi two-dimensional magnetic materials. Their work is published in Nature Physics.


A strange phenomenon occurs with electrons in materials that are so thin that they can be thought of as being one-dimensional, e.g. nanowires. Under certain conditions, the electrons in these materials can actually split into an electrical charge and a magnet, which are referred to as "fractional particles". An important but still unresolved question in fundamental particle physics is whether this phenomenon could arise and be observed in more dimensions, like two- or three-dimensional systems.

Under temperatures close to absolute zero, electrons bind together to form an exotic liquid that can flow with exactly no friction. While this was previously observed at near-absolute zero temperatures in other materials, this electron liquid can form in cuprates at much higher temperatures that can be reached using liquid nitrogen alone. Consequently, there is currently an effort to find new materials displaying high-temperature superconductivity at room temperature. But understanding how it arises on a fundamental level has proven challenging, which limits the development of materials that can be used in applications. The advances brought by the EPFL scientists now bring support for the theory of superconductivity as postulated by Anderson.

"This work marks a new level of understanding in one of the most fundamental models in physics," says Henrik M. Rønnow. "It also lends new support for Anderson's theory of high-temperature superconductivity, which, despite twenty-five years of intense research, remains one of the greatest mysteries in the discovery of modern materials."

Via Dr. Stefan Gruenwald
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The soil microbial community predicts the importance of plant traits in plant–soil feedback

The soil microbial community predicts the importance of plant traits in plant–soil feedback | Science Garden |
Reciprocal interaction between plant and soil (plant–soil feedback, PSF) can determine plant community structure. Understanding which traits control interspecific variation of PSF strength is crucial for plant ecology. Studies have highlighted either plant-mediated nutrient cycling (litter-mediated PSF) or plant–microbe interaction (microbial-mediated PSF) as important PSF mechanisms, each attributing PSF variation to different traits. However, this separation neglects the complex indirect interactions between the two mechanisms.
We developed a model coupling litter- and microbial-mediated PSFs to identify the relative importance of traits in controlling PSF strength, and its dependency on the composition of root-associated microbes (i.e. pathogens and/or mycorrhizal fungi).
Results showed that although plant carbon: nitrogen (C : N) ratio and microbial nutrient acquisition traits were consistently important, the importance of litter decomposability varied. Litter decomposability was not a major PSF determinant when pathogens are present. However, its importance increased with the relative abundance of mycorrhizal fungi as nutrient released from the mycorrhizal-enhanced litter production to the nutrient-depleted soils result in synergistic increase of soil nutrient and mycorrhizal abundance. Data compiled from empirical studies also supported our predictions.
We propose that the importance of litter decomposability depends on the composition of root-associated microbes. Our results provide new perspectives in plant invasion and trait-based ecology.

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Changing Our DNA through Mind Control?

Changing Our DNA through Mind Control? | Science Garden |
December 16, 2014 |By Bret Stetka 

Mindfulness can help Credit: Thinkstock

“I think, therefore I am” is perhaps the most familiar one-liner in western philosophy. Even if the stoners, philosophers and quantum mechanically-inclined skeptics who believe we’re living an illusion are right, few existential quips hit with such profound, approachable simplicity.  The only catch is that in Descartes’ opinion, “we” – our thoughts, our personalities, our “minds” – are mostly divorced from our bodies.


The polymathic Frenchman and other dualist philosophers proposed that while the mind exerts control over our physical interaction with the world, there is a clear delineation between body and mind; that our material forms are simply temporary housing for our immaterial souls. But centuries of science argue against a corporeal crash pad. The body and mind appear inextricably linked. And findings from a new study published in Cancer by a Canadian group suggest that our mental state has measurable physical influence on us – more specifically on our DNA.


Lead investigator Dr. Linda E. Carlson and her colleagues found that in breast cancer patients, support group involvement and mindfulness meditation – an adapted form of Buddhist meditation in which practitioners focus on present thoughts and actions in a non-judgmental way, ignoring past grudges and future concerns -- are associated with preserved telomere length. Telomeres are stretches of DNA that cap our chromosomes and help prevent chromosomal deterioration -- biology professors often liken them to the plastic tips on shoelaces. Shortened telomeres aren't known to cause a specific disease per se, but they do whither with age and are shorter in people with cancer, diabetes, heart disease and high stress levels. We want our telomeres intact.


In Carlson’s study distressed breast cancer survivors were divided into three groups. The first group was randomly assigned to an 8-week cancer recovery program consisting of mindfulness meditation and yoga; the second to 12-weeks of group therapy in which they shared difficult emotions and fostered social support; and the third was a control group, receiving just a 6-hour stress management course. A total of 88 women completed the study and had their blood analyzed for telomere length before and after the interventions. Telomeres were maintained in both treatment groups but shortened in controls.


Previous work hinted at this association. A study led by diet and lifestyle guru Dr. Dean Ornish from 2008 reported that the combination of a vegan diet, stress management, aerobic exercise and participation in a support group for 3 months resulted in increased telomerase activity in men with prostate cancer, telomerase being the enzyme that maintains telomeres by adding DNA to the ends of our chromosomes. More recent work looking at meditation reported similar findings. And though small and un-randomized, a 2013 follow up study by Ornish, again looking at prostate cancer patients, found that lifestyle interventions are associated with longer telomeres.


The biologic benefits of meditation in particular extend well beyond telomere preservation. Earlier work by Carlson found that in cancer patients, mindfulness is associated with healthier levels of the stress hormone cortisol and a decrease in compounds that promote inflammation. Moreover, as she points out, “generally healthy people in a work-based mindfulness stress reduction program have been shown to produce higher antibody titers to the flu vaccine than controls, and there has been promising work looking at the effects of mindfulness in HIV and diabetes.” Past findings also show that high stress increases the risk of viral infections – including the common cold – as well as depression and cardiovascular disease.

The therapeutic potential of the mind-body intersect is well-known. Biofeedback – in which sensor-clad patients learn awareness of and control over various physiologic functions – has been around for decades and is used to treat pain, headache, high blood pressure and sleep problems, among numerous other conditions. And of course there’s the placebo effect, the complicated yet very real psychobiological benefit achieved from a patient’s expectations of a treatment rather than the treatment itself.


Though optimistic that meditative and social approaches are mental means toward better physical, and not just psychologic well-being, Carlson rightly hedges. “The meaning of the maintenance of telomere length in this study is unknown. However, I think that processing difficult emotions is important for both emotional and physical health, and this can be done both through group support with emotional expression, and through mindfulness meditation practice,” she says.


Carlson wonders if mentally-rooted telomeric changes are long-lasting, if the same patterns would hold true in other cancers and conditions, and what the effects of mental intervention would be if offered at the time of diagnosis and treatment – all questions she hopes to pursue.


According to a report published by Harvard Medical School in 2011, 6.3 million Americans were using mind-body therapies at the advice of conventional doctors – a surprisingly high number that has surely since grown. Still, prescription meditation – especially in the interest of physical health -- is far from the norm in Western medicine. And it remains unclear whether or not preserved telomeres actually prolong survival in cancer patients; or in anyone for that matter. But stress reduction in the interest of chromosomal preservation, and other possible health benefits, seems like a pursuit even a 17th Century dualist philosopher could get behind.


Bret Stetka is an Editorial Director at Medscape (a subsidiary of WebMD) and a freelance health, science and food writer. He received his MD in 2005 from the University of Virginia and writes regularly for Wired Magazine about brains, genomics and sometimes both. Follow Bret on Twitter @BretStetka

Are you a scientist who specializes in neuroscience, cognitive science, or psychology? And have you read a recent peer-reviewed paper that you would like to write about? Please send suggestions to Mind Matters editor Gareth Cook. Gareth, a Pulitzer prize-winning journalist, is the series editor of Best American Infographics and can be reached at garethideas AT or Twitter @garethideas.

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Three short walks can reverse the damage of three hours of sitting

Three short walks can reverse the damage of three hours of sitting | Science Garden |

Image: Sebastian Kaulitzki/Shutterstock


We all know by now that sitting for long periods of time can be deadly - recent research has linked prolonged sitting to high cholesterol, obesity and cardiovascular problems. This is partly because sitting makes the muscles in our bodies become lazy and stop contracting, causing blood to pool in our legs instead of being pumped back to the heart. This causes instant damage to the endothelial function of the arteries, which means that the inner lining of the blood vessels (the endothelium) begin to fail at dilating and contracting.


But new research by scientists from Indiana University in the US suggests we’re not all doomed. By taking three slow, five-minute walks, we can actually reverse the damage to our arteries caused by three hours of sitting down, the study shows.


The researchers investigated this by dividing up 12 non-obese men into two groups - one that sat at a desk for three hours without  moving their legs or feet (like most of us do each day), and another that sat at the desk for three hours but got up and took slow, five-minute walks on a treadmill three times during the period. This second group only walked at 3.2 kilometres an hour (2 miles per hour) at 30 minutes, 1.5 hours and 2.5 hours into the sitting.


After the three hours, the researchers used ultrasound to see what state the inner lining of the femoral arteries of the test subjects were in - the femoral artery is the large artery in the thigh which supplies blood to the leg. 


The arteries of the first group of men, who sat for three hours straight, had decreased dilation by an astonishing 50% compared to the start of the experiment. Their rate of blood flow had also dropped.


On the other hand, the group who took three short walks during the study didn’t experience any decrease in artery dilation. Although this experiment involved a small sample size, the results were so striking that they were statistically significant. The results are published in Medicine & Science in Sports & Exercise.


"There is plenty of epidemiological evidence linking sitting time to various chronic diseases and linking breaking sitting time to beneficial cardiovascular effects, but there is very little experimental evidence," said lead author Saurabh Thosar, who is now a researcher with Oregon Health & Science University, in a press release. "We have shown that prolonged sitting impairs endothelial function, which is an early marker of cardiovascular disease, and that breaking sitting time prevents the decline in that function."

While these results will now need to be replicated on a larger scale, the study gives us all hope that by simply setting a reminder to get up and walk for five minutes every hour or so, we might actually be able to reverse some of the damage our modern lifestyle does.

“American adults sit for approximately eight hours a day," said Thosar. "The impairment in endothelial function is significant after just one hour of sitting. It is interesting to see that light physical activity can help in preventing this impairment."


Source: Neomatica, Indiana University
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Are Real #Christmas trees better for your health?

Are Real #Christmas trees better for your health? | Science Garden |
Dr Birgitta Gatersleben, an environmental psychologist at the University of Surrey, said there was “plenty of evidence” that real Christmas trees helped people recover from stress


By Bill Gardner

9:50AM GMT 16 Dec 2014

It is possibly the messiest Christmas tradition of all - dragging a chopped-down tree into the house to shed needles all over the living room floor.

But one academic has suggested ditching a real tree for a plastic replacement could be bad for your health.


Dr Birgitta Gatersleben, an environmental psychologist at the University of Surrey, said there was “plenty of evidence” that households enjoying a real festive fir tree benefit from “exposure to natural environments”.

She said: “People who live near nature report higher wellbeing and satisfaction with life. There is a lot of evidence to suggest that people recover more quickly from stress and mental fatigue when exposed to natural, as opposed to built-up and ‘fake’ environments.


“Indeed, plants in offices have been shown to have a positive effect on the wellbeing and creativity of workers.”


For centuries, people have been decorating their homes in winter with real evergreen plants such as holly, ivy, bay and laurel.


Ancient Egyptians used evergreen wreaths to symbolise eternal life. During solstice, Norse pagans would bring in evergreen plants and even entire trees to ward off the sprits and bless the inhabitants.

Early Christians displayed green in their homes as signs of everlasting life, and the eternal spiritual life of man was represented by coniferous trees.


“Evergreen plants seem alive when everything else appears dead. Indeed, it is the depth of colour of real trees and the smell that really appeals to people, as well as the notion that something alive is coming indoors,” Dr Gatersleben said.

Via David Cant CMIOSH, Royal Green Tree Service
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An Evolving View of Animals

An Evolving View of Animals | Science Garden |
Tim Flach wants us to look at animals the way we look at people. Not so much to humanize them, but to get humans to consider how they relate to animals.
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Mysterious martian gouges carved by dry ice

Mysterious martian gouges carved by dry ice | Science Garden |
By Kerry Klein 15 December 2014 3:45 pm 

SAN FRANCISCO, CALIFORNIA—After the Mars Reconnaissance Orbiter began beaming back close-up images of the Red Planet, researchers spotted peculiar features along the slopes of dunes: long, sharply defined grooves (pictured) that seem to appear and disappear seasonally. They look like trails left behind by tumbling boulders, but rocks never appear in the sunken pits at the trail ends. Researchers initially took these gullies as signs of flowing liquid water, but a new model suggests they’re the result of sand-surfing dry ice. During the martian winter, carbon dioxide ice freezes over parts of the planet’s surface and sublimates back into a gas during the spring thaw. But according to the model presented here today at a meeting of the American Geophysical Union, chunks of warming dry ice may also break off from the crests of dunes and skid down slopes. This is no ordinary tumble—according to the model, the bases of the chunks are continually sublimating, resulting in a hovercraftlike motion that gouges the dune while propelling the ice down slopes. Solid ice that survives to the bottom settles into a pit before dissipating back into the atmosphere. Experiments dropping dry ice and water ice onto dunes in Utah show that dry ice is up to the task, at least on Earth. While researchers continue to hone their model, they hope to eventually spot sand-surfing ice in action on Mars.

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Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests

Carbon sequestration is related to mycorrhizal fungal community shifts during long-term succession in boreal forests | Science Garden |
Boreal forest soils store a major proportion of the global terrestrial carbon (C) and below-ground inputs contribute as much as above-ground plant litter to the total C stored in the soil. A better understanding of the dynamics and drivers of root-associated fungal communities is essential to predict long-term soil C storage and climate feedbacks in northern ecosystems.
We used 454-pyrosequencing to identify fungal communities across fine-scaled soil profiles in a 5000 yr fire-driven boreal forest chronosequence, with the aim of pinpointing shifts in fungal community composition that may underlie variation in below-ground C sequestration.
In early successional-stage forests, higher abundance of cord-forming ectomycorrhizal fungi (such as Cortinarius and Suillus species) was linked to rapid turnover of mycelial biomass and necromass, efficient nitrogen (N) mobilization and low C sequestration. In late successional-stage forests, cord formers declined, while ericoid mycorrhizal ascomycetes continued to dominate, potentially facilitating long-term humus build-up through production of melanized hyphae that resist decomposition.
Our results suggest that cord-forming ectomycorrhizal fungi and ericoid mycorrhizal fungi play opposing roles in below-ground C storage. We postulate that, by affecting turnover and decomposition of fungal tissues, mycorrhizal fungal identity and growth form are critical determinants of C and N sequestration in boreal forests.

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Molecular link discovered between prostate and breast cancer, suggesting new treatment approach for men's tumor

Molecular link discovered between prostate and breast cancer, suggesting new treatment approach for men's tumor | Science Garden |
Prostate cancer can be driven by the same estrogen receptor responsible for the most common form of breast cancer, Weill Cornell Medical College researchers report.Dr. Dimple Chakravarty
Photo credit: Weill Cornell Art & Photography

Their findings suggest why the most aggressive forms of prostate cancer do not respond to traditional therapy. The study also opens up potential for new prognostic biomarkers and treatments, researchers say.


Prostate cancer is thought to be exclusively fueled by male hormones known as androgen (which includes testosterone), which bind on to and turn on androgen receptors to promote growth. For that reason, a common prostate cancer treatment is androgen-deprivation therapy, which cuts the fuel supply of the hormone. But the strategy fails when prostate cancer stops depending on androgen, yet still continues to grow — a phenomenon that has not been understood.

In the study, published Nov. 21 in Nature Communications, the research team discovered that estrogen receptors hijack the androgen-signaling pathway to promote prostate cancer growth.


"The signal to grow comes from the estrogen receptor," says the study's lead investigator, Dr. Dimple Chakravarty, an assistant professor of pathology and laboratory medicine at Weill Cornell.


"The estrogen receptor mimics the androgen receptor pathway, regulating almost all of the genes that are downstream from the androgen receptor," she says. Dr. Chakravarty and her team made the discovery by using next-generation sequencing technology on a Weill Cornell cohort of 74 prostate cancer samples and confirmed the prognostic value of their discovery by analyzing 594 prostate cancer samples shared by the Mayo Clinic. The group was specifically looking for estrogen receptor activity, which had not been examined in such a way before in prostate cancer.


"Men use both hormones — androgen and estrogen — and their levels are physiologically balanced in early and mid-life," Dr. Chakravarty says. "But as men age, the levels of androgen go down and estrogen rises, for reasons that are not understood. We wanted to see what role the estrogen receptor might be playing in prostate cancer."


They looked deeply into RNA molecules that produce proteins, as well as so-called long non-coding RNAs that don’t provide a template for proteins but which control gene expression in ways that are only now beginning to be appreciated, says co-author Dr. Andrea Sboner, a Weill Cornell assistant professor of pathology and laboratory medicine. "These long non-coding RNAs are working in the cell's nucleus, doing more than coding RNAs can do," he says.


Researchers found the estrogen receptor in a significant percentage of samples was activating NEAT1, a known long non-coding RNA. NEAT1, they discovered, drives cancer growth independently of androgen receptor growth. NEAT1 had not been linked to any form of cancer before the study.


The data revealed that estrogen receptor-regulated NEAT1 is the most significantly over-expressed long non-coding RNA in prostate cancer. It is found in both early stage prostate cancer, and in the most aggressive, androgen-resistant cancer, Dr. Chakravarty says, adding that it may be that androgen-deprivation therapy pushes cancer to switch to the estrogen receptor and NEAT1 activation to continue growing.


Because long non-coding RNAs like NEAT1 can be detected in urine, it may be possible to use NEAT1 as a biomarker for the existence of prostate cancer as well as potential prognostic marker, Dr. Sboner says. "The fact that NEAT1 is present in urine may help distinguish men who might need more aggressive treatment from men who have an indolent, slow-growing cancer," he says.

It may be possible to shut down NEAT1 activation with a small molecule inhibitor, Dr. Chakravarty adds. She and her collaborators, which include senior author Dr. Mark Rubin, director of Weill Cornell’s Institute for Precision Medicine, are working on such an agent, and they are continuing to confirm NEAT1’s link to aggressive, androgen-independent prostate cancer.


"This is a new and very exciting way to think about prostate cancer," she says. "Now we have two hormonal culprits to target, instead of one."

Posted December 15, 2014 10:40 AM | Permalink to this post

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Plastic Pollution: More than 5 Trillion Plastic Pieces Weighing over 250,000 Tons Afloat at Sea

Plastic Pollution: More than 5 Trillion Plastic Pieces Weighing over 250,000 Tons Afloat at Sea | Science Garden |

Nearly 269,000 tons of plastic pollution may be floating in the world's oceans, according to a new study. Microplastic pollution is found in varying concentrations throughout the oceans, but estimates of the global abundance and weight of floating plastics, both micro and macroplastic, lack sufficient data to support them. To better estimate the total number of plastic particles and their weight floating in the world's oceans, scientists from six countries contributed data from 24 expeditions collected over a six-year period from 2007-2013 across all five sub-tropical gyres, coastal Australia, Bay of Bengal, and the Mediterranean Sea.

Microplastic pollution is found in varying concentrations throughout the oceans, but estimates of the global abundance and weight of floating plastics, both micro and macroplastic, lack sufficient data to support them. To better estimate the total number of plastic particles and their weight floating in the world's oceans, scientists from six countries contributed data from 24 expeditions collected over a six-year period from 2007-2013 across all five sub-tropical gyres, coastal Australia, Bay of Bengal, and the Mediterranean Sea. The data included information about microplastics collected using nets and large plastic debris from visual surveys, which were then used to calibrate an ocean model of plastic distribution.

Based on the data and model, the authors of the study estimate a minimum of 5.25 trillion plastic particles weighing nearly 269,000 tons in the world's oceans. Large plastics appear to be abundant near coastlines, degrading into microplastics in the 5 subtropical gyres, and that the smallest microplastics were present in more remote regions, such as the subpolar gyres, which the authors did not expect. The distribution of the smallest microplastics in remote regions of the ocean may suggest that gyres act as 'shredders' of large plastic items into microplastics, after which they eject them across the ocean.

"Our findings show that the garbage patches in the middle of the five subtropical gyres are not the final resting places for the world's floating plastic trash. The endgame for micro-plastic is interactions with entire ocean ecosystems," says Marcus Eriksen, PhD, Director of Research for the 5 Gyres Institute.

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‘Radiogenetics’ seeks to remotely control cells and genes

‘Radiogenetics’ seeks to remotely control cells and genes | Science Garden |

It’s the most basic of ways to find out what something does, whether it’s an unmarked circuit breaker or an unidentified gene — flip its switch and see what happens. New remote-control technology may offer biologists a powerful way to do this with cells and genes. A team at Rockefeller University and Rensselaer Polytechnic Institute is developing a system that would make it possible to remotely control biological targets in living animals — rapidly, without wires, implants or drugs.


Tied together: Researchers experimented with different configurations for their remote control system, and they found the best relies on an iron nanoparticle (blue), which is tethered by a protein (green) to an ion channel (red). Above, all three appear within cell membranes.


Today (December 15) in the journal Nature Medicine, the team describes successfully using electromagnetic waves to turn on insulin production to lower blood sugar in diabetic mice. Their system couples a natural iron storage particle, ferritin, to activate an ion channel called TRPV1 such that when the metal particle is exposed to a radio wave or magnetic field it opens the channel, leading to the activation of an insulin producing gene. Together, the two proteins act as a nano-machine that can be used to trigger gene expression in cells.


“The method allows one to wirelessly control the expression of genes in a living animal and could potentially be used for conditions like hemophilia to control the production of a missing protein. Two key attributes are that the system is genetically encoded and can activate cells remotely and quickly,” saysJeffrey Friedman, Marilyn M. Simpson Professor head of theLaboratory of Molecular Genetics at Rockefeller. “We are now exploring whether the method can also be used to control neural activity as a means for noninvasively modulating the activity of neural circuits.” Friedman and his Rensselaer colleague Jonathan S. Dordick were co-senior researchers on the project.


Other techniques exist for remotely controlling the activity of cells or the expression of genes in living animals. But these have limitations. Systems that use light as an on/off signal require permanent implants or are only effective close to the skin, and those that rely on drugs can be slow to switch on and off.


The new system, dubbed radiogenetics, uses a signal, in this case low-frequency radio waves or a magnetic field, to heat or move ferritin particles. They, in turn, prompt the opening of TRPV1, which is situated in the membrane surrounding the cell. Calcium ions then travel through the channel, switching on a synthetic piece of DNA the scientists developed to turn on the production of a downstream gene, which in this study was the insulin gene.


In an earlier study, the researchers used only radio waves as the ‘on’ signal, but in the current study, they also tested out a related signal – a magnetic field –to activate insulin production. They found it had a similar effect as the radio waves.


“The use of a radiofrequency-driven magnetic field is a big advance in remote gene expression because it is non-invasive and easily adaptable,” says Dordick, who is Howard P. Isermann Professor of Chemical and Biological Engineering and vice president of research at Rensselaer. “You don’t have to insert anything — no wires, no light systems — the genes are introduced through gene therapy. You could have a wearable device that provides a magnetic field to certain parts of the body and it might be used therapeutically for many diseases, including neurodegenerative diseases. It’s limitless at this point.”


The choice to look at insulin production was driven by the equipment they used to generate the radio waves and magnetic fields. Because the coil that generates these signals is currently small i.e; only three centimeters in diameter, it was necessary to anesthetize the mice to keep them still. Since anesthesia can repress the production of insulin, the hormone that reduces blood sugar, Stanley and her colleagues designed the genetically encoded system to replace the insulin that is normally reduced by anesthesia in mice.


“Ferritin, a protein-coated iron storage molecule, is normally found throughout the mouse and human body, but in our experiments, we modified it, placing the ferritin particles in different positions to see if we could improve our results,” says co-first author Sarah Stanley, a senior research associate in Friedman’s lab. “We found tethering the ferritin to the channel to be most effective.”


The team’s positive results suggest other applications for the system. In late September, Stanley received a first-round BRAIN grant from the ambitious federal initiative seeking to create a dynamic map of the brain in action. Stanley and colleagues plan to adapt this system to switch neurons on and off, and so examine their roles within the brain.

“In this current study, we’ve shown that by opening the TRPV1 channel to allow calcium ions to enter the cell, we can turn on a gene. Since neurons can be depolarized by calcium and other positively charged ions, such as those the TRPV1 channel controls, we hope that this system may be effective at regulating neural activity.”


Nature Medicine online: December 15, 2014
Remote regulation of glucose homeostasis in mice using genetically encoded nanoparticles
Sarah A Stanley, Jeremy Sauer, Ravi S Kane, Jonathan S Dordick and Jeffrey M Friedman

Share on facebookShare on twitterShare on google_plusone_share Tags: BRAIN Initiative, ferritin, Jeffrey Friedman, Laboratory of Molecular Genetics, magnetic field, radio waves, radiogenetics, remote control, Sarah Stanleynewswire@rockefeller.eduContact: Zach Veilleux | 212-327-8982

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An anti-anxiety drug has "woken up" a minimally-conscious patient

An anti-anxiety drug has "woken up" a minimally-conscious patient | Science Garden |
FIONA MACDONALD   15 DEC 20142.3k10  

A minimally-conscious patient in Pisa, Italy, who was given a common anti-anxiety medication has unexpectedly “woke up” and started chatting with the anaesthesiologist.


He also called his aunt over the phone and congratulated his brother on his recent graduation. Then, just as suddenly, he returned to a near-vegetative state when the drug wore off, as Michael Byrne reports for Motherboard.


The patient, who suffered brain injury as a result of a motorcycle accident, was given the drug called midazolam in order to lightly sedate him for a CT scan, but instead it appeared to restore him to a normal state with no memory of his accident or current situation.


The team has since given him the drug again, and it repeatedly woke him up out of his state, and allowed him to converse and interact “appropriately”.


Described by a group of neuroscientists in the current issue of Restorative Neurology and Neuroscience, the case is the first recorded example of midazolam awakening a patient from a minimally-conscious state. 


While giving the drug to the patient, neuroscientists used an EEG device to record the activity in the task-positive network and the linguistic network. 


The authors write in the article:

"Our attention has focused on these two particular networks because we believe that their functional improvement has substantially contributed to determine the awakening reaction presented by our patient.

The task-positive network, in fact, has to deal with the ability to cope with and solve cognitive tasks that require explicit behavioural responses, while the linguistic one deals with language comprehension and production.”

As you can see in the images below, the drug caused a change in the pattern of these regions. The regions shaded grey represent the time during with the patient woke up.

Maria Chiara Carboncinia et al.

These types of awakenings have occurred before with other depressants, as well as some stimulants. But this is the first time midazolam has been used in this way.


The researchers believe it could be helping to increase the frequency of brain waves in the patient.


Byrne writes for Motherboard: "The "power spectrum" of these frequencies is biased in different ways in minimally-conscious or catatonic patients; the peak frequency for this particular patient is around 7 Hz. Midazolam appears to smooth the power spectrum out, limiting the harmful bias.”


While this treatment may not work for everyone, it offers a new therapy option that other doctors and researchers can try.


Source: Motherboard, Restorative Neurology and Neuroscience

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