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Scooped by Dr. Stefan Gruenwald!

Origin of birds as modified dinosaurs

Origin of birds as modified dinosaurs | Amazing Science |

Geneticist Arkhat Abzhanov on Archosaurs, paedomorphosis, and the evolution of birds

One of the biggest challenges in evolutionary biology is trying to understand the origin of true novelties. Some of these novelties, innovations in evolution, are also called key innovations because they allow a group of organisms to take over a whole ecological niche and expand well beyond their ancestors.

Birds are one of the most successful groups of animals on our planet. There are over ten thousand species, dozens of families and orders of birds, and they can be found almost anywhere on this planet.

To understand the evolution of birds, we need to look at the history of the entire lineage of Archosauria which began back in the Triassic era. About 250 million years ago, reptiles separated into two major groups. One group (called Squamata) stayed small eating mainly small prey such as insects. These are the ancestors of modern day lizards and snakes . The other group was large and consumed large prey. This group is called Archosauria and they tended to dominate the ecological systems in which they lived and occupied for hundreds of millions of years. Their close relatives today are crocodiles and birds. The Archosaurs also gave rise to Pterosaurs, the flying reptiles, which were highly successful during their time but died out.

Paedomorphosis is a phenomenon of evolution where a change in timing of developments can cause interesting morphological changes. Paedomorphosis can be seen when descendant adults resemble the juveniles of their own ancestors. There are actually two different ways to become paedomorphic. One of them is called neoteny. One famous example is salamanders like the axolotl. Even though the axolotl looks like a larva, it is actually a sexual mature adult salamander. That’s neoteny when your somatic development is retarded relative to your sexual development. You develop very slowly and at the time you are mature you still look like a larva.

The other way to become paedomorphic is called progenesis and that’s basically what all the birds are doing today. In progenesis your body is developing normally but you become sexual mature much-much faster. In modern-day songbirds it takes just a few weeks for them to become sexual mature. It takes only about two weeks for a robin to look like an adult, so, by the time it is ready to fly just off the nest it looks very similar to its adult parents.

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Novel Genetic Patterns May Make Us Rethink Biology and Individuality - The Almagest

Novel Genetic Patterns May Make Us Rethink Biology and Individuality - The Almagest | Amazing Science |

Professor of Genetics Scott Williams, PhD, of the Institute for Quantitative Biomedical Sciences (iQBS) at Dartmouth’s Geisel School of Medicine, has made two novel discoveries: first, a person can have several DNA mutations in parts of their body, with their original DNA in the rest—resulting in several different genotypes in one individual—and second, some of the same genetic mutations occur in unrelated people. We think of each person’s DNA as unique, so if an individual can have more than one genotype, this may alter our very concept of what it means to be a human, and impact how we think about using forensic or criminal DNA analysis, paternity testing, prenatal testing, or genetic screening for breast cancer risk, for example. Williams’ surprising results indicate that genetic mutations do not always happen purely at random, as scientists have previously thought. His work, done in collaboration with Professor of Genetics Jason Moore, PhD, and colleagues at Vanderbilt University, was published in PLOS Genetics journal.[1]

Genetic mutations can occur in the cells that are passed on from parent to child and may cause birth defects. Other genetic mutations occur after an egg is fertilized, throughout childhood or adult life, after people are exposed to sunlight, radiation, carcinogenic chemicals, viruses, or other items that can damage DNA. These later or “somatic” mutations do not affect sperm or egg cells, so they are not inherited from parents or passed down to children. Somatic mutations can cause cancer or other diseases, but do not always do so. However, if the mutated cell continues to divide, the person can develop tissue, or a part thereof, with a different DNA sequence from the rest of his or her body.

“We are in reality diverse beings in that a single person is genetically not a single entity—to be philosophical in ways I do not yet understand—what does it mean to be a person if we are variable within?” says Williams, the study’s senior author, and founding Director of the Center for Integrative Biomedical Sciences in iQBS. “What makes you a person? Is it your memory? Your genes?” He continues, “We have always thought, ‘your genome is your genome.’ The data suggest that it is not completely true.”

In the past, it was always thought that each person contains only one DNA sequence (genetic constitution). Only recently, with the computational power of advanced genetic analysis tools that examine all the genes in one individual, have scientists been able to systematically look for this somatic variation. “This study is an example of the type of biomedical research project that is made possible by bringing together interdisciplinary teams of scientists with expertise in the biological, computational and statistical sciences.” says Jason Moore, Director of the iQBS, who is also Associate Director for Bioinformatics at the Cancer Center, Third Century Professor, and Professor of Community and Family Medicine at Geisel.

Having multiple genotypes from mutations within one’s own body is somewhat analogous to chimerism, a condition in which one person has cells inside his or her body that originated from another person (i.e., following an organ or blood donation; or sometimes a mother and child—or twins—exchange DNA during pregnancy. Also, occasionally a person finds out that, prior to birth, he or she had a twin who did not survive, whose genetic material is still contained within their own body).[2] Chimerism has resulted in some famous DNA cases: one in which a mother had genetic testing that “proved” that she was unrelated to two of her three biological sons.[3]

As suggested by Maria Schnee (

1 Williams, Scott, et al., Recurrent tissue-specific mtDNA mutations are common in humans.

2 Strain L, Dean JC, Hamilton MP, Bonthron D. A true hermaphrodite chimera resulting from embryo amalgamation after in vitro fertilization. N Engl J Med 1998;(338):166-9/

3 Norton AT and Zehner O. Project MUSE: Today’s Research, Tomorrow’s Inspiration.

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Interactive Scientific Visualizations On The Web — D3

Interactive Scientific Visualizations On The Web — D3 | Amazing Science |

When D3 came out in 2011, it became clear pretty quickly that it was going to be a powerful tool for creating data visualizations. But it’s certainly not the first — or only — tool. Why did it succeed when so many other libraries have failed?

First of all, it works on the web. Data visualizations are only good if people see them, and there’s no better place to see them than on the internet, in your browser. Protovis was the first library to make any real headway in this direction, despite other libraries and services that tried. Manyeyes is cool, but it lacks graphic flexibility and the resulting visualizations can’t just live anywhere seamlessly.

Prefuse and Flare (both predecessors to D3) are nice, but neither one runs in a browser without a plugin. Quadrigram (previously Impure) has the same plugin problem.

Another reason it has worked so well is because of its flexibility. Since it works seamlessly with existing web technologies, and can manipulate any part of the document object model, it is as flexible as the client side web technology stack (HTML, CSS, SVG).

This gives it huge advantages over other tools because it can look like anything you want, and it isn’t limited to small regions of a webpage like Processing.jsPaper.jsRaphael.js, or other canvas or SVG-only based libraries. It also takes advantage of built in functionality that the browser has, simplifying the developer’s job, especially for mouse interaction.

All of these features have been timed perfectly to coincide with the rise of new browsers and a push towards documents created using open standards rather than relatively walled-in plugins. The death of Internet Explorer as the top browser plays no small role in this, and the rendering and javascript engines in other browsers have made huge strides with their newfound attention. Some of this momentum has carried over to D3 as a way to take advantage of the new features and technology buzz.

But snazzy new technologies that work seamlessly aren’t the only reason that D3 has become successful.

Great documentationexamplescommunity, and the accessibility of Mike Bostock have all played major roles in its rise to prominence. Without these components, D3 would likely have taken much longer to catch on.

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Micro Electron Diffraction Could Revolutionize Structural Biology Studies

Micro Electron Diffraction Could Revolutionize Structural Biology Studies | Amazing Science |

For structural biologists, the first step in determining a protein's precise molecular structure is often the hardest: coaxing the protein to grow into the orderly, three-dimensional crystals that are the starting material for most structural studies. For particularly difficult cases, it can take years to generate usable crystals – and sometimes the protein never crystallizes despite intense effort. Howard Hughes Medical Institute (HHMI) scientists have developed a new method that generates a high-resolution protein structure from crystals one-million times smaller than those needed for X-ray crystallography, the most common method for determining protein structure.

The new technique, called MicroED (micro electron diffraction), has the potential to accelerate structural biologists' efforts and to expand the repertoire of proteins whose high-resolution structures can be solved. “Biochemically, it is always easier to generate smaller crystals,” says structural biologist Tamir Gonen, who developed the technique with colleagues in his lab at HHMI's Janelia Farm Research Campus. “There are many proteins where you either don't get crystals or you get crystals that are very, very small. They might be good enough for microED.”

Gonen and colleagues describe MicroED in a report published November 19, 2013, in the open access journal eLife. Using Gonen’s new technique, scientists can use electrons from an electron microscope to determine the structure of protein microcrystals. This approach, known as electron crystallography, had previously been limited to studies of proteins that could be grown into very thin, two-dimensional crystals. “People have put 3D crystals in electron microscopes before, but no one was able to solve their structures,” Gonen says.

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Is time travel allowed by the laws of physics?

Is time travel allowed by the laws of physics? | Amazing Science |

Albert Einstein's relativistic laws of physics tell us that passing of time is "relative". If you and I move differently or are at different locations in a gravitational field, then the rate of flow of time that you experience (the rate that governs the ticking of any very good clock you carry with you and that governs the aging of your body) is different from the rate of time flow that I experience.

This personal character of time allows one person to travel forward in time much faster than another, a phenomenon embodied in the so-called twins paradox. One twin (call him Methuselah) stays at home on Earth, the other (Florence) travels out into the Universe at high speed and then returns. When they meet at the end of the trip, Florence will have aged far less than Methuselah; for example, Florence may have aged 30 years and Methuselah 4,500 years. The twin that ages least is the one who undergoes huge accelerations, to get up to high speed, slow down, reverse direction, then accelerate back and slow to a halt on Earth. The twin who leads the sedate life ages the most.

A massive black hole is another vehicle for rapid forward time travel: If Methuselah remains in orbit high above the event horizon of a massive black hole (say, one whose gravitational pull is that of a billion suns) and Florence travels down to near the event horizon and hovers just above it for, say, 30 years and then returns, Methuselah can have aged thousands or millions of years. This is because time flows much more slowly near a black hole's event horizon (where the acceleration of gravity is huge) than far above it (where one can live sedately). These time travel phenomena have been tested in the laboratory. Muons — short-lived elementary particles — travelling around and around in a storage ring at 0.9994 of the speed of light, at the Brookhaven National Laboratory on Long Island, New York, have been seen to age 29 times more slowly than muons at rest in the laboratory. And atomic clocks on the surface of the Earth have been seen to run more slowly than atomic clocks high above the Earth's surface — more slowly by about 4 parts in 10 billion.

Physicists have been working hard since the late 1980s to understand whether the laws of physics allow backward time travel. We do not have a definitive answer yet, but the likely answer has been summarised by Stephen Hawking, in his Chronology Protection Conjecture (see [1]): The laws of physics always conspire to prevent anything from travelling backward in time, thereby keeping the Universe safe for historians.

Two mechanisms might protect chronology: (1) Exotic material that is required for manufacturing of any time machine might be forbidden to exist — by the laws of physics. (2) Time machines might always self-destruct, explosively, when one tries to activate them. These mechanisms (1) and (2) are descriptive translations of mathematical results that we physicists have derived using the laws of physics expressed in their own natural language: mathematics. The sentences (1) and (2) capture the essence of our calculations, but crucial details are lost in translation. For anyone who wishes to struggle to understand those details, good places to start are a recent beautiful but highly technical review article by John Friedman (see [2]), and a much less technical but older and slightly outdated article by Matt Visser (see [3]).

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Human-Specific Genes: How a Gene Duplication Helped our Brains Become ‘Human’

Human-Specific Genes: How a Gene Duplication Helped our Brains Become ‘Human’ | Amazing Science |

What genetic changes account for the vast behavioral differences between humans and other primates? Researchers so far have catalogued only a few, but now it seems that they can add a big one to the list. A team led by scientists at The Scripps Research Institute has shown that an extra copy of a brain-development gene, which appeared in our ancestors’ genomes about 2.4 million years ago, allowed maturing neurons to migrate farther and develop more connections.

Surprisingly, the added copy doesn’t augment the function of the original gene, SRGAP2, which makes neurons sprout connections to neighboring cells. Instead it interferes with that original function, effectively giving neurons more time to wire themselves into a bigger brain.

“This appears to be a major example of a genomic innovation that contributed to human evolution,” said Franck Polleux, a professor at The Scripps Research Institute. “The finding that a duplicated gene can interact with the original copy also suggests a new way to think about how evolution occurs and might give us clues to human-specific developmental disorders such as autism and schizophrenia.”

Polleux is the senior author of the new report, which was published online ahead of print on May 3, 2012 by the journal Cell. The same issue features a related paper on SRGAP2’s recent evolution by the laboratory of Evan E. Eichler at the University of Washington, Seattle.

Polleux specializes in the study of human brain development, and, several years ago, his lab began researching the function of the newly-discovered SRGAP2. He and his colleagues found that in mice, the gene’s protein product plays a key role during brain development: It deforms the membranes of young neurons outward, forcing the growth of root-like appendages called filopodia. As young neurons sprout these filopodia, they migrate more slowly through the expanding brain; eventually they reach their final position where they form connections. Most excitatory connections  made on pyramidal neurons in the cortex are formed on spines, which are microscopic protrusions from the dendrite playing a critical role in integrating synaptic signals from other neurons.

Shortly after beginning the project, Polleux learned from other labs’ work that SRGAP2 was among the few genes (approximately 30) that had been duplicated in the human genome less than six million years ago after separation from other apes. “These evolutionarily recent gene duplications are so nearly identical to the original genes that they aren’t detectable by traditional genome sequencing methods,” said Polleux. “Only in the last five years have scientists developed methods to reliably map these hominid-specific duplications.”

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Giant floods on Mars eons ago likely carved the U-shaped canyons

Giant floods on Mars eons ago likely carved the U-shaped canyons | Amazing Science |

South-central Idaho and the surface of Mars have an interesting geological feature in common: amphitheater-headed canyons.

These U-shaped canyons with tall vertical headwalls are found near the Snake River in Idaho, as well as on the surface of Mars, according to photographs taken by satellites.

Various explanations for how these canyons formed have been offered—some for Mars, some for Idaho, some for both—researchers now offer the plausible account that enormous floods created all these canyons.

“A very popular interpretation for the amphitheater-headed canyons on Mars is that groundwater seeps out of cracks at the base of the canyon headwalls and that no water ever went over the top,” Lamb says. Judging from the evidence in Idaho, however, it seems more likely that on Mars, as on Earth, amphitheater-headed canyons were created by enormous flood events, suggesting that Mars was once a very watery planet.

Via YEC Geo
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Why hospitals will soon sequence the genes of every single patient

Why hospitals will soon sequence the genes of every single patient | Amazing Science |

We are now on the verge of a health data breakthrough, in which computers will be able to do similar diagnostic tasks, by analyzing massive amounts of data, including genome sequences, risk factors, medical histories, drug interactions, and more.

Looking at this trend last year, venture capitalist Vinod Khosla made the bold claim that technology will replace 80 percent of companies eventually. The reality is probably more nuanced: Far from threatening to put doctors out of jobs, the falling prices of data analysis and genome sequencing are enabling them with tools they could only dream of even a few years ago.

At the Mount Sinai Hospital in New York, Joel Dudley, Ph.D. uses Ayasdi’s products to discover how patients with certain genes are more likely to develop some diseases (diabetes, cardiovascular conditions…) as well as how genes influence the performance of a treatment, or may reveal risks of later relapses that can be prepared for.

Already 11,000 patients at Mount Sinai have had their genome sequenced, a pool large enough for meaningful analysis, although Ayasdi tells us “those are still early days for the industry. There are no plans to act on that data directly with individual patients just yet.”

Right now the Mount Sinai community is working at organizing itself to make the useful information available to the frontline staff. And another 30,000 patients may soon sign the consent form and opt in to participate in this new way to explore which care is best for them.

The exploration of big data by the enterprise is becoming less of a competitive edge and turning into more of a must-have. Similarly, hospitals may have to adopt genetic analysis as a rule of thumb sooner rather than later.  Mount Sinai is unusual today in pioneering regular genetic screenings, but it soon may become commonplace.

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Intercepting asteroids to avoid Armageddon

Intercepting asteroids to avoid Armageddon | Amazing Science |
It sounds like the script for a Hollywood film: a giant meteorite from outer space heading straight for the Earth and threatening the destruction of mankind.

Researchers say we can expect an asteroid to collide with Earth every few hundred years. The European research project NEOShield was set up to protect our planet from just such a catastrophe, with teams of researchers working to develop concepts designed to help avert these sorts of impacts and to alter asteroids’ orbits as they race toward Earth. Research scientists from Fraunhofer EMI in Freiburg are among those contributing to the work on the asteroid impact avoidance system.

»One solution would be to launch a relatively solid space probe designed to hit the asteroid at high speed,« says Professor Alan Harris from the German Aerospace Center’s Institute of Planetary Research as he explains the basic concept. »Asteroids are typically made of porous materials, so the first step is to build up a basic understanding of what happens when materials like that are hit by a foreign object,« says Dr. Frank Schäfer, head of the spacecraft technology group at Fraunhofer EMI.

To do this, he and his team use a light gas gun – one of the fastest accelerator facilities in the world. Within the gun’s approximately one-and-a-half-meter barrel, millimeter-sized pellets are accelerated to speeds of almost 10km per second. That equates to a speed of around 36,000 kilometers per hour.

The Fraunhofer scientists use what is known as a target chamber to bombard stone blocks used to approximate asteroids with a high-velocity mini projectile. The aim is to analyze with as much precision as possible how the material reacts. High-speed cameras document the experiment by taking up to 30,000 pictures per second. As in the crash testing of vehicles, the Fraunhofer researchers are interested in quantifying the force of the collision. Data are adjusted to account for actual scale and are imported continuously into computer simulations.

In the long term, NEOShield project leader Professor Harris would like to see the defense techniques that are the subject of this research tested in international space missions: »This kind of test mission is bound to throw up a few surprises, and will teach us a great deal.«

Incidentally, Harris reckons that averting an oncoming asteroid from its collision course by means of a huge explosion – just like in a Hollywood film – could in fact be an option in an emergency. Time would have to be pressing though, or the object concerned at least a kilometer in diameter.

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Forbes: Machine Learning (CS 229) is Stanford's Most Popular Course

Forbes: Machine Learning (CS 229) is Stanford's Most Popular Course | Amazing Science |

Why Is Machine Learning (CS 229) The Most Popular Course At Stanford?  It turns out that artificial intelligence (AI) and the robotics that is tied to it, consists of two primary systems, control and perception.

Via Ben van Lier
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Midair levitation of objects using sound waves

The essence of levitation technology is the countervailing of gravity. It is known that an ultrasound standing wave is capable of suspending small particles at its sound pressure nodes and, so far, this method has been used to levitate lightweight particles, small creatures, and water droplets.
The acoustic axis of the ultrasound beam in these previous studies was parallel to the gravitational force, and the levitated objects were manipulated along the fixed axis (i.e. one-dimensionally) by controlling the phases or frequencies of bolted Langevin-type transducers. In the present study, we considered extended acoustic manipulation whereby millimetre-sized particles were levitated and moved three-dimensionally by localised ultrasonic standing waves, which were generated by ultrasonic phased arrays. Our manipulation system has two original features. One is the direction of the ultrasound beam, which is arbitrary because the force acting toward its centre is also utilised. The other is the manipulation principle by which a localised standing wave is generated at an arbitrary position and moved three-dimensionally by opposed and ultrasonic phased arrays. We experimentally confirmed that various materials could be manipulated by our proposed method.

Yoichi Ochiai, Takayuki Hoshi, Jun Rekimoto: Three-dimensional Mid-air Acoustic Manipulation by Ultrasonic Phased Arrays arXiv:1312.4006

Yoichi Ochiai (The University of Tokyo)
Takayuki Hoshi (Nagoya Institute of Technology)
Jun Rekimoto (The University of Tokyo / Sony CSL) 

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Western Australian sharks send tweets to swimmers when they approach

Western Australian sharks send tweets to swimmers when they approach | Amazing Science |

More shark attacks occur in Western Australia than almost anyplace else on Earth. In order to help protect swimmers and surfers, the state government relies largely on helicopter-based spotters, plus members of the public who report their own sightings. Now, however, the Department of Fisheries has introduced a new system, in which the toothy fishes announce their own presence via Twitter.

Known as the Shark Monitoring Network, the system utilizes acoustic tags that are attached to the fins of individual sharks, along with buoyed monitoring devices that pick up the signals transmitted by those tags. When a tagged shark swims within range of one of the monitors, its species, size and location is automatically recorded.

That information is transmitted via satellite to a computer, which immediately posts it on Twitter. A tweet made just today reads, "Fisheries advise: tagged Bronze whaler shark detected at Garden Island (north end) receiver at 08:46:00 PM on 31-Dec-2013." By contrast, a fair amount of time can elapse between a sighting being made by a person, and that information being manually written up and shared via more traditional media.

So far the system utilizes 19 satellite-linked monitors, that keep track of 338 tagged sharks – species include great whites, tigers and bulls. Needless to say, there are still plenty of untagged sharks swimming near the beaches of Western Australia, plus the monitors don't cover every square kilometer of coastline. For that reason, the network is intended to augment existing spotting systems, not replace them.

The Surf Life Saving WA (SLSWA) Twitter feed at is the best way to keep up-to-date with any detection of tagged sharks, by the State Government’s Shark Monitoring Network, as well as any sightings reported by members of the community to Water Police.

This information is also available on the SLSWA website at and via a link on the Department of Fisheries’ website shark pages at

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Nuclear power and nuclear weapons: what's the difference?

Nuclear power and nuclear weapons: what's the difference? | Amazing Science |
It is the received wisdom that nuclear weapons and nuclear power are inseparable. Consequently, any country that builds a civilian nuclear power station is able to build an atomic bomb within a couple of years.

Clearly there are overlaps in knowledge and technology between the civil and military nuclear industries. There are five declared and four other nuclear-armed countries (assuming Israel's warheads detonate). There are 31 nations with nuclear power stations and 58 with research reactors. Only seven of the nine nuclear-armed countries have civilian power programs.

All of the technical factors can be circumvented with sufficient time and money. Uneconomic fuel cycles can be run and warheads built with high levels of radioactivity. However, no country has developed indigenous nuclear weapons after deploying civilian nuclear power stations. Historically, if a country wants to produce a nuclear bomb, they build reactors especially for the job of making plutonium, and ignore civilian power stations.

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Triple star system might reveal secrets of gravity

Triple star system might reveal secrets of gravity | Amazing Science |

Astronomers have discovered a unique triple star system which could reveal the true nature of gravity. They found a pulsar with two white dwarfs all packed in a space smaller than Earth's orbit of the Sun.

The trio's unusually close orbits allow precise measurements of gravity and could resolve difficulties with Einstein's theories. The results appear in Nature journal and will be presented at the 223rd American Astronomical Society meeting.

"This triple system gives us a natural cosmic laboratory far better than anything found before for learning exactly how such three-body systems work and potentially for detecting problems with general relativity that physicists expect to see under extreme conditions," said Scott Ransom of the US National Radio Astronomy Observatory (NRAO) in Charlottesville, VA.

"This is a fascinating system in many ways, including what must have been a completely crazy formation history, and we have much work to do to fully understand it."

Pulsars emit lighthouse-like beams of radio waves that rapidly sweep through space as the stars spin on their axes. They are formed after a supernova collapses a burnt-out star to a dense, highly magnetised ball of neutrons. Using the Green Bank Telescope, the astronomers discovered a pulsar 4,200 light-years from Earth, spinning nearly 366 times per second.

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New therapeutic target (BRD4) for an incurable, rare type of soft-tissue cancer identified

New therapeutic target (BRD4) for an incurable, rare type of soft-tissue cancer identified | Amazing Science |

A deadly, rare type of soft-tissue cancer may be completely eradicated simply by inhibiting a key protein involved in its growth, researchers report: Inhibiting the action of a protein called BRD4 caused cancer cells to die in a mouse model of malignant peripheral nerve sheath tumors (MPNSTs). MPNSTs are highly aggressive sarcomas that form around nerves.

“This recent study identifies a potential new therapeutic target to combat MPNST, an incurable type of cancer that is typically fatal,” said Dr. Lu Le, Assistant Professor of Dermatology at UT Southwestern and senior author of the study. “The findings also provide important insight into what causes these tumors to develop.”

These tumors can develop sporadically, but about half of cases are in patients with genea tic disorder called neurofibromatosis type 1 (NF1) that affects 1 in 3,500 people. About 10 percent of NF1 patients will develop MPNST, which usually evolves from a benign but often large and disfiguring tumor called a plexiform neurofibroma.

Up to now, the preferred treatment for MPNST has been surgical removal, but that oftentimes is difficult or impossible due to the tumor’s location around nerves. Radiation and chemotherapy are other options, but their effectiveness is limited. The five-year survival rate for MPNST patients is about 50 percent.

“These treatments suppressed tumor growth and caused the cancer cells to undergo apoptosis, or cell death. This is why BRD4 inhibition is exquisitely effective against MPNSTs and may represent a paradigm shift in therapy for these patients,” Dr. Le said.

The same class of drug used in the experiments is currently being evaluated in phase 1 and 2 trials for treatment of leukemia and a subtype of lung cancer. Meanwhile, UT Southwestern is working with a pharmaceutical company to develop a similar BRD4-inhibiting drug to launch a clinical trial for MPNST patients.

New drugs are desperately needed to treat MPNST and provide hope to NF1 patients at highest risk for this cancer, said Dr. Le, who also serves as Co-director of UT Southwestern’s Comprehensive Neurofibromatosis Clinic. The clinic offers neurofibromatosis patients access to the latest clinical trials and treatments. Co-directed by Dr. Laura Klesse, Assistant Professor of Pediatrics, the clinic is part of the Harold C. Simmons Comprehensive Cancer Center and serves patients with all three types of hereditary neurofibromatosis, including the dominant NF1 type and rarer NF2 and Schwannomatosis forms.

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Ford Demonstrates First Solar-Powered Hybrid Car With Sun-Tracking Technology

Ford Demonstrates First Solar-Powered Hybrid Car With Sun-Tracking Technology | Amazing Science |

Ford's new concept for solar-powered hybrid car can run for 21 electric-only miles on a day's worth of sunlight. That possibility comes courtesy of sun-tracking software that works in combination with a concentrator lens to focus the sunlight falling on the car's rooftop solar panels.

The C-MAX Solar Energi Concept car—a modified C-MAX plug-in hybrid—won't achieve the dream of driving forever on sunshine just yet. But Ford's clever use of a concentrating lens does provide an inkling of new hope for solar power to someday become viable in hybrid or all-electric vehicles. Until now, solar power's energy density problem has limited its use in commercial vehicles to not much beyond a symbolic rooftop solar panel that runs a cooling fan for Toyota's Prius hybrid car.

Ford envisions its concept car parking beneath a tall carport with a roof made of a Fresnel lens—a lens originally developed for lighthouses that acts similar to a magnifying glass. The car company enlisted the help of Georgia Institute of Technology researchers to come up with the carport's sunlight-concentrating design.

The car's software would track the sun's path across the sky on any given day of the year and direct the car to move beneath the carport so that it continually receives the full impact of concentrated sunlight, according to Technology Review. That novel concept eliminates the need for an expensive tracking system that would change the angle of the carport's lens to keep sunlight focused on an immobile car's rooftop solar panels. The concept car also has a traditional charging port so that it can plug into the power grid if needed.

Such concentrated sunlight could reach 8 times the amount of sunshine that would typically fall on the C-MAX Solar Energi's rooftop. A day's worth of charging in the sun—about 8 kilowatts over four hours—would go into the lithium-ion battery that provides the 21 electric-only miles in the car's total range of 620 miles. Ford estimates suggest the C-MAX Solar Energi Concept would have the same total range on a full charge as compared to the conventional C-MAX Energi.

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DNA nanorobot from Wyss could potentially seek out cancer cells and cause them to self-destruct

More information:

We've seen various experimental approaches that aim to increase the efficacy of chemotherapy while also reducing its damaging side effects by specifically targeting cancer cells. The latest encouraging development comes from Harvard's Wyss Institute for Biologically Inspired Engineering where researchers have created a barrel-like robotic device made from DNA that could carry molecular instructions into specific cells and tell them to self-destruct. Because the DNA-based device could be programmed to target a variety of cells, it could be used to treat a range of diseases in addition to providing hope in the fight against cancer.

The team based their programmable nanotherapeutic approach on the body's own immune system in which white blood cells circulate in the blood ready to attack an infection where it has developed. Just like white blood cells that are able to hone in on specific cells in distress and bind to them, the researchers created a DNA barrel that can recognize and seek out combinations of cell-surface proteins, including disease markers.

By folding strands of DNA in what is known as the "DNA origami" method, the researchers create a three-dimensional open barrel shape whose two halves are connected by a hinge. The container is held shut by special DNA latches that reconfigure when they find their specific target - cancer cells, for example - causing the two halves to swing open and expose the container's payload. These payloads can be of various types, including molecules with encoded instructions that can interact with surface signaling receptors.

Shawn Douglas, Ph.D., and Ido Bachelet, Ph.D., used the DNA barrel to deliver instructions encoded in antibody fragments to two different types of cancer cells - leukemia and lymphoma. Since leukemia and lymphoma speak different languages the messages were written in different antibody combinations. But the message was the same - activate the cell's so called "suicide gene," which will cause a cell to kill itself through apoptosis.

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Mini-pancreas grown from stem cells has implications for future insulin delivery

Mini-pancreas grown from stem cells has implications for future insulin delivery | Amazing Science |

With diabetes at epidemic levels in the U.S., and worldwide rates growing ever higher, new and improved insulin delivery methods are constantly in vogue. Devices like the artificial pancreas, insulin pills, inhaled treatments--all of these have some iteration with clinical results to show. And researchers are now in the very early stages of creating a true miniature pancreas from stem cells.

Scientists at the Danish Stem Cell Centre have shown that they can "grow" mouse pancreatic cells into expanded, branched structures in a 3D culture. In the long term, this could have implications for building a human pancreas, which, although currently envisioned as a drug-testing tool, could also lead to insulin-producing mini-organs built from stem cells, according to a report from the University of Copenhagen.

In work published in the journal Development, the team studied first and foremost how these cells proliferate on their own. The scientists noted in particular the development potential of pancreas cells, demonstrating that cells in a cluster have a community effect that allows them to expand more efficiently than individual cells. Down the road, this information could lead to a more fully developed method of creating beta cells, which produce the insulin-releasing characteristic of a healthy pancreas, according to the abstract.

Via Jacob Blumenthal, Carlos Garcia Pando
Jacob Blumenthal's curator insight, October 16, 2013 2:02 AM

In a paper, published in Development journal, researchers from the  Danish Stem Cell Centre have shown that they can culture mouse pancreatic cells into expanded, branched structures in a 3D culture.

By manipulating the medium composition they  generated either hollow spheres, which are mainly composed of pancreatic progenitors, or complex organoids that spontaneously undergo pancreatic morphogenesis and differentiation.

Manipulation and improvement of  culture and expansion techniques 

 could lead to a more efficient and  developed method of creating insulin-releasing beta cells, which will eventually be used for cell therapy of diabetes.


To learn about pancreatic development:


To learn about stem cells differentiation protocols:



Carlos Garcia Pando's curator insight, October 16, 2013 2:04 PM

Another wonder result from tissue engineering!

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Gecko feet will let robots do space walks and crawl around an orbiting spacecraft

Gecko feet will let robots do space walks and crawl around an orbiting spacecraft | Amazing Science |

It may look like a circuit board stuck to the ceiling – but this is actually a climbing robot. Stranger still, it is in a vacuum, testing its ability to use dry but sticky gecko-like feet to crawl around an orbiting spacecraft.

The idea is that one day astronauts won't have to risk their lives in daring spacewalks to fix things on a craft's exterior, like they did recently on the International Space Station to repair a cooling system. Instead, they will command swarms of hull-crawling automatons to do the job.

The gecko robot, called Abigaille III, is the work of Michael Henrey and his colleagues at Simon Fraser University in Burnaby, Canada. To test Abigaille's space flight credentials, Henrey took it to the European Space Agency's labs in Noordwijk, the Netherlands, where it was put through its paces at the extreme temperatures and zero-pressure conditions of space.

Henrey's trick is to use foot pads based on a dry polymer adhesive covered in mushroom-like structures with a large surface area. A dry adhesive was chosen because wet ones would collect dust and release fumes that might damage spacecraft instruments.

Meanwhile, back on Earth, gravity means that climbing robots need to lift several times their own weight if they are to be any use. Abigaille's feet wouldn't get it very far if it had to carry a load, but robots with electrically heated sticky footpads are showing their mettle in these sorts of applications.

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Mixed reality — where the virtual and real world collides

Mixed reality — where the virtual and real world collides | Amazing Science |
Virtual reality is so 2013 – a new, immersive blending of physical and virtual worlds suggests we could one day live our lives in mixed reality

Via Ben van Lier
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Breaking down one of cancer’s defence mechanisms by targeting fibroblast activation protein (FAP)

Breaking down one of cancer’s defence mechanisms by targeting fibroblast activation protein (FAP) | Amazing Science |

A possible new method for treating pancreatic cancer which enables the body’s immune system to attack and kill cancer cells has been developed by researchers.

The method uses a drug which breaks down the protective barrier surrounding pancreatic cancer tumours, enabling cancer-attacking T cells to get through. The drug is used in combination with an antibody that blocks a second target, which improves the activity of these T cells.

Cancer immune evasion is well described. In some cases, this may be overcome by enhancing T-cell responses. Researchers show that despite the presence of antitumor T cells, immunotherapeutic antibodies are ineffective in a murine pancreatic cancer model recapitulating the human disease. Removing the carcinoma-associated fibroblast (CAF) expressing fibroblast activation protein (FAP) from tumors permitted immune control of tumor growth and uncovered the efficacy of these immunotherapeutic antibodies. FAP+ CAFs are the only tumoral source of chemokine (C-X-C motif) ligand 12 (CXCL12), and administering AMD3100, an inhibitor of chemokine (C-X-C motif) receptor 4, a CXCL12 receptor, also revealed the antitumor effects of an immunotherapeutic antibody and greatly diminished cancer cells.

Initial tests of the combined treatment, carried out by researchers at the University’s Cancer Research UK Cambridge Institute, resulted in almost complete elimination of cancer cells in one week. The findings, reported in the journal PNAS, mark the first time this has been achieved in any pancreatic cancer model. In addition to pancreatic cancer, the approach could potentially be used in other types of solid tumour cancers. These findings may have wide clinical relevance because FAP+ cells are found in almost all human adenocarcinomas.

Dr. Stefan Gruenwald's insight:

Comment from Twitter: by Alison G. ‏@AliRae8:
@sgruenwald Halozyme conducting studies targeting hyaluronan matrix surrounding pancreatic ca.

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NATURE: The Method of the Year for 2013 is… single-cell sequencing

NATURE: The Method of the Year for 2013 is… single-cell sequencing | Amazing Science |

Single-cell sequencing edged out other contenders as our choice of Method of the Year in 2013. These techniques really came into their own in 2013 and are fast providing new insights into the workings of single cells that ensemble methods are incapable of.

Back in 2008 we chose next-generation sequencing as our Method of the Year not only because of how the new techniques would improve performance in conventional sequencing applications, but also because they opened up whole new applications, unthinkable with traditional Sanger sequencing. Our choice of Method of the Year in 2013 bears this out, as none of these single-cell sequencing applications would be possible without next-generation sequencing. And in some applications the sequencing is used almost exclusively for identifying and counting tagged molecules.

Our choice likely comes as a surprise to all those who were certain that we would pick CRISPR/Cas9 technology for targeted genome modification. This is certainly an exciting technology, and not only for genome engineering, but also for epigenome editing as described in a Method to Watch. But genome editing with engineered nucleases was our pick for the 2011 Method of the Year and although CRISPR/Cas9 provides a huge practical improvement by largely dispensing with the need to engineer the nuclease and relying instead on a programmable guide RNA, the advance over 2011 is mostly one of ease-of-use.

Methods to investigate biology at the level of single cells have been of keen interest to Nature Methods since the journal started. Our first research article from Robert Singer described a paraffin-embedded tissue FISH (peT-FISH) method to simultaneously detect expression of several genes in situ in single cells while maintaining tissue morphology (Capodieci, P. 2005). This was followed by many other imaging-based methods for such things as measuring cell growth (Groisman, A. 2006), quantifying mRNA (Raj, A. 2008) and protein (Gordon, A. 2006) levels, profiling intracellular signaling (Krutzik, P.O. & Nolan, G.P. 2006) (Loo, L.-H. 2007) and DNA insertion-site analysis (Schmidt, M. 2008) in single cells.

The publication of M. Azim Surani’s article on mRNA-Seq whole-transcriptome analysis of a single cell (Tang, F. 2009) in 2009 helped signal the rise of sequencing-based methods for single-cell analysis. But even two years later the Reviews and Perspectives in our supplement on single-cell analysis were more focused on imaging-based than sequencing-based aproaches to single-cell analysis.

It was only in 2013 that we finally saw an explosion of original research articles using or reporting single-cell sequencing methods in Nature-family journals. Numerous studies reported new biological results that relied on sequencing of whole or partial genomes or transcriptomes from single cells.

Nature's Method of the Year special feature has three Commentaries by researchers in the field, including some of the earliest developers and users of methods for single-cell analysis. An Editorial, News Feature and Primer describe our choice and provide helpful background information. We hope you enjoy the selection of articles in our special feature.

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Mysteries of the Unseen World 3D

Mysteries of the Unseen World will transport audiences to places on the planet they've never been before, to see things that are beyond their normal vision yet are literally right in front of their eyes:

Via David McConville
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Geeky math equation creates beautiful 3D world

Geeky math equation creates beautiful 3D world | Amazing Science |

The quest by a group of math geeks to create a three-dimensional analogue for the mesmerizing Mandelbrot fractal has ended in success. They call it the Mandelbulb. The 3-D renderings were generated by applying an iterative algorithm to a sphere. The same calculation is applied over and over to the sphere’s points in three dimensions. In spirit, that’s similar to how the original 2-D Mandelbrot set generates its infinite and self-repeating complexity. If you were ever mesmerized by the Mandelbrot screen saver, the Mandelbulb 3-D images are worth a look. Each photo is a zoom on one of these Mandelbulbs.

Daniel White, the amateur fractal image maker who coordinated the Mandelbulb effort, admits this creation isn’t exactly the Mandelbrot in 3-D. It’s mesmerizing and beautiful, but as he notes, only some versions of their original formula generate the kind of detail and complexity they are looking for. Their original equation doesn’t work very well unless you take it beyond the 2nd power. The picture above, White says, doesn’t have the level of detail that should be there.

“That means the biggest secret is still under wraps, open to anyone who has the inclination, and appreciation for how cool this thing would look,” White writes. If you take the original equation to the 8th power, it generates the most beautiful and detailed images. White and his collaborators aren’t sure why, but it’s hard to argue with the obtained stunningly beautiful images. White and his collaborators spend quite a lot of time zooming through their creation looking for interesting structures. One example is what they call the “Mandelbrot gateau,” a reference to the French cake. Even though the entire structure is generated from just the single equation, what it produces after thousands of iterations can seem like the geological features of a planet we’ve yet to discover. At times, the complexity of the structures inside the Mandelbulb astonishes even White himself. “Seriously, this universe has got to be quite messed up to be harboring math secrets capable of this kind of Baroquian beauty,” he wrote in the caption for this image of pillars and bridges.

Another area of interest is the “Cave of Lost Secrets.” They’ve even created an almost Tweetably short science-fiction story about the region. “This ancient half-mile-high cave still exists (now underwater) from a planet several billions of light years away from Earth,” he wrote. “It was built by a (now extinct) intelligent race of beings who also discovered the 3-D Mandelbulb we are witnessing in our expedition. Inside the cave however, lies — amongst other technological and mathematical secrets — the last remaining scroll which contains the much deeper secret of the even more incredible real 3-D Mandelbrot formula.”

Some of the best evidence that a better Mandelbulb could be out there is that some sections of the current version just don’t have enough detail, even at the 8th power. “Whipped cream” parts like the one above are not what a true 3-D Mandelbrot would look like.

In the meantime, White and the rest of, a hub of discussion and collaboration about the project, will content themselves with making images of sections of a 3-D structure that doesn’t actually exist, generated by a software algorithm that’s functioning remains opaque. Sociologically, it might be odd. Mathematically, it might be obscure. But the geek in all of us — the homunculus that handbuilds a model of the starship Enterprise or spends weeks taking photos of space or visits every single location in World of Warcraft— just gets it.

Original article appeared in WIRED

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One way to solve the bandwidth crisis is to switch to light transmission

One way to solve the bandwidth crisis is to switch to light transmission | Amazing Science |

FLICKERING lights are annoying but they may have an upside. Visible light communication (VLC) uses rapid pulses of light to transmit information wirelessly. Now it may be ready to compete with conventional Wi-Fi.

"At the heart of this technology is a new generation of high-brightness light-emitting diodes," says Harald Haas from the University of Edinburgh, UK. "Very simply, if the LED is on, you transmit a digital 1, if it's off you transmit a 0," Haas says. "They can be switched on and off very quickly, which gives nice opportunities for transmitting data."

It is possible to encode data in the light by varying the rate at which the LEDs flicker on and off to give different strings of 1s and 0s. The LED intensity is modulated so rapidly that human eyes cannot notice, so the output appears constant.

More sophisticated techniques could dramatically increase VLC data rates. Teams at the University of Oxford and the University of Edinburgh are focusing on parallel data transmission using arrays of LEDs, where each LED transmits a different data stream. Other groups are using mixtures of red, green and blue LEDs to alter the light's frequency, with each frequency encoding a different data channel.

Li-Fi, as it has been dubbed, has already achieved blisteringly high speeds in the lab. Researchers at the Heinrich Hertz Institute in Berlin, Germany, have reached data rates of over 500 megabytes per second using a standard white-light LED. Haas has set up a spin-off firm to sell a consumer VLC transmitter that is due for launch next year. It is capable of transmitting data at 100 MB/s - faster than most UK broadband connections.

Once established, VLC could solve some major communication problems. In 2009, the US Federal Communications Commission warned of a looming spectrum crisis: because our mobile devices are so data-hungry we will soon run out of radio-frequency bandwidth. Li-Fi could free up bandwidth, especially as much of the infrastructure is already in place.

"There are around 14 billion light bulbs worldwide, they just need to be replaced with LED ones that transmit data," says Haas. "We reckon VLC is a factor of ten cheaper than Wi-Fi." Because it uses light rather than radio-frequency signals, VLC could be used safely in aircraft, integrated into medical devices and hospitals where Wi-Fi is banned, or even underwater, where Wi-Fi doesn't work at all.

"The time is right for VLC, I strongly believe that," says Haas, who presented his work at TED Global in Edinburgh last week.

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