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Signs of Aging, Even in the Embryo

Signs of Aging, Even in the Embryo | Amazing Science |
New research indicates that senescent cells, those that stop dividing, play an important role at both the dawn and dusk of life.


In 1961, two biologists named Leonard Hayflick and Paul Moorehead discovered that old age is built into our cells. At the time, many scientists believed that if healthy human cells were put in a flask with a steady supply of nutrients, they would multiply forever. But when Dr. Hayflick and Dr. Moorehead reared fetal human cells, that’s not what they found. Time and again, their cells would divide about 50 times and then simply stop.

In fact, it turned out, senescent cells are involved in many of the ravages of old age. Wrinkled skin, cataracts and arthritic joints are rife with senescent cells. When researchers rid mice of senescent cells, the animals become rejuvenated.


Given all this research, the last place you would expect to find senescent cells would be at the very start of life. But now three teams of scientists are reporting doing just that. For the first time, they have found senescent cells in embryos, and they have offered evidence that senescence is crucial to proper development.


The discoveries raise the prospect that the dawn and dusk of life are intimately connected. For life to get off to the right start, in other words, youth needs a splash of old age.


Scott Lowe, an expert on senescence at Memorial Sloan-Kettering Cancer Center who was not involved in the research, praised the studies for pointing to an unexpected role for senescence. He predicted they would provoke a spirited debate among developmental biologists who study how embryos form. “They’re going to really love it or really hate it,” Dr. Lowe said.


While senescence may be a powerful defense against cancer, however, it comes at a steep cost. Even as we escape cancer, we accumulate a growing supply of senescent cells. The chronic inflammation they trigger can damage surrounding tissue and harm our health.


In the mid-2000s, William Keyes, a biologist then at Cold Spring Harbor Laboratory on Long Island, was studying how senescence leads to aging with experiments on mice. By shutting down a gene called P63, he could accelerate the rate at which the mice accumulated senescent cells — and accelerate their aging.


To observe the senescent cells, Dr. Keyes added a special stain to the bodies of these mice. To see the difference between these mice and normal ones, Dr. Keyes added the same stain to normal mouse embryos.

Naturally, he expected that none of the cells in the normal mouse embryos would turn dark. After all, senescent cells had been found only in old or damaged tissues. Much to his surprise, however, Dr. Keyes found patches of senescent cells in the normal mouse embryos. Dr. Keyes decided to look again at those peculiar senescent cells in normal embryos. He and his colleaguesconfirmed that cells became senescent in many parts of an embryo, such as along the developing tips of the legs.


The researchers, however, found no evidence that the senescent cells in embryos have damaged DNA. That discovery raises the question of how the cells were triggered to become senescent. Dr. Keyes hypothesizes they did so in response to a signal from neighboring cells.


Once an embryonic cell becomes senescent, it does the two things that all senescent cells do: it stops dividing and it releases a special cocktail. 

The new experiments suggest that this cocktail plays a different role in the embryo than in the adult body. It may act as a signal to other cells to become different tissues. It may also tell those tissues to grow at different rates into different shapes.


Dr. Keyes suspects that the sculpting that senescent cells carry out may be crucial to the proper development of an embryo. Consequently, any disruption to senescent cells may have dire consequences. “Where we see senescence in the embryo is where we see a lot of different birth defects,” he said.

For an embryo to develop properly, signals have to be sent to the right places at the right times. The peculiar behavior of senescent cells may help in both regards. If a cell stops growing, it won’t spread too far from a particular spot in an embryo. And by summoning immune cells to kill it, a senescent cell may ensure that its signals don’t last too long.


It’s possible, Dr. Keyes speculates, that senescence actually evolved first as a way to shape embryos; only later in evolution did it take on a new role, as a weapon against cancer. “I like the idea that it was a simple process that was then modified,” Dr. Keyes said.

Madison Punch's comment, March 24, 2014 7:14 PM
I found this article to be among the coolest I've read from I figured that aging came with the weakening, or rather aging, of the body. Who knew it was basically "installed" into our cells? The end of cell division basically stops the flourishing of the peak of life and begins to fall into aging. Very cool.
Madison Carson's comment, September 1, 2015 8:44 PM
I found this article to be rather cool. I've never heard of some of the cells that they were talking about. I thought that the older you got, the effects of old age would just come with it. But, seeing that old age is in you from the time you were born is very interesting.
andrea luan villa's comment, February 2, 6:58 PM
I didn't know that old age is built into our cells; that very cool. I also didn't know that embryos had senses. this interesting I learned a lot from it.
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Disposable laser: Ultra-low-cost, easy to fabricate 'lasing capsules' made with inkjet printer

Disposable laser: Ultra-low-cost, easy to fabricate 'lasing capsules' made with inkjet printer | Amazing Science |

"Since lasers were invented more than 50 years ago, they have transformed a diverse swath of technology—from CD players to surgical instruments."

"Now researchers from France and Hungary have invented a way to print lasers that's so cheap, easy and efficient they believe the core of the laser could be disposed of after each use. The team reports its findings in the Journal of Applied Physics.

"The low-cost and easiness of laser chip fabrication are the most significant aspects of our results," said Sébastien Sanaur, an associate professor in the Center of Microelectronics in Provence at the Ecole Nationale Supérieure des Mines de Saint-Étienne in France.

Sanaur and his colleagues made organic lasers, which amplify light with carbon-containing materials. Organic lasers are not as common as inorganic lasers, like those found in laser pointers, DVD players, and optical mice, but they offer benefits such as high-yield photonic conversion, easy fabrication, low-cost and a wide range of wavelengths."

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Scientists make 3D holograms of atoms inside molecular structures

Scientists make 3D holograms of atoms inside molecular structures | Amazing Science |

"Researchers have developed the first imaging technique that can clearly see inside molecular structures, and have used it to create 3D holograms of the atomic arrangements inside these structures.

Before now, reliable imaging techniques (for example, scanning tunneling microscopy) could only scan the surfaces of molecules. The ability to peer deep inside a molecular structure and see all of the individual atoms will be essential for developing new materials and understanding their unique physical and chemical properties.

The researchers, Tobias Lühr et al., have published a paper on the new imaging technique in a recent issue of Nano Letters.

The new holographic imaging method significantly improves upon the previous methods: It almost completely eliminates image artifacts, has the ability to image thousands of atoms, and can also distinguish between different types of atoms.

The researchers demonstrated the technique by creating 3D holograms of pyrite (FeS2).

The holography method works by scattering electron waves off a molecule's atoms. Interference between the emitted and scattered electron waves creates diffraction patterns. This information is then used to reconstruct 3D holographic images showing the atoms' true locations."

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Scientists Create a 5-atom Quantum Computer That Could Make Today's Encryption Obsolete

Scientists Create a 5-atom Quantum Computer That Could Make Today's Encryption Obsolete | Amazing Science |

MIT scientists have developed a 5-atom quantum computer, one that is able to render traditional encryption obsolete. The creation of this five atom quantum computer comes in response to a challenge posed in 1994 by Professor Peter Shor of MIT. Professor Shor developed a quantum algorithm that’s able to calculate a large number’s prime factors more efficiently than traditional computers, with 15 being the smallest figure to meaningfully demonstrate the algorithm.


The new system was able to return the correct factors and with a confidence upwards of 99 percent. Professor Isaac Chuan of MIT said: “We show that Shor’s algorithm, the most complex quantum algorithm known to date, is realizable in a way where, yes, all you have to do is go in the lab, apply more technology, and you should be able to make a bigger quantum computer.”


Of course, this may be a little easier said than done. “It might still cost an enormous amount of money to build—you won’t be building a quantum computer and putting it on your desktop anytime soon—but now it’s much more an engineering effort, and not a basic physics question,” Chuang added.


Yet, Chuang has his team are hopeful for the future of quantum computing, saying that they “foresee it being straightforwardly scalable, once the apparatus can trap more atoms and more laser beams can control the pulses…We see no physical reason why that is not going to be in the cards.”


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How Craig Venter is fighting ageing with genome sequencing

How Craig Venter is fighting ageing with genome sequencing | Amazing Science |

Nine years ago, Craig Venter sequenced the first complete individual human genome - his own. Now, he's finally starting to decode what it means for his future. 

Via Integrated DNA Technologies
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Just 40 light years from Earth, three planets might host life forms adapted to infrared worlds

Just 40 light years from Earth, three planets might host life forms adapted to infrared worlds | Amazing Science |
Is there life beyond our solar system? If there is, our best bet for finding it may lie in three nearby, Earth-like exoplanets.


For the first time, an international team of astronomers from MIT, the University of Liège in Belgium, and elsewhere have detected three planets orbiting an ultracool dwarf star, just 40 light years from Earth. The sizes and temperatures of these worlds are comparable to those of Earth and Venus, and are the best targets found so far for the search for life outside the solar system. The results are published today in the journal Nature.


The scientists discovered the planets using TRAPPIST (TRAnsiting Planets and PlanetesImals Small Telescope), a 60-centimeter telescope operated by the University of Liège, based in Chile. TRAPPIST is designed to focus on 60 nearby dwarf stars—very small, cool stars that are so faint they are invisible to optical telescopes. Belgian scientists designed TRAPPIST to monitor dwarf stars at infrared wavelengths and search for planets around them.


The team focused the telescope on the ultracool dwarf star, 2MASS J23062928-0502285, now known as TRAPPIST-1, a Jupiter-sized star that is one-eighth the size of our sun and significantly cooler. Over several months starting in September 2015, the scientists observed the star's infrared signal fade slightly at regular intervals, suggesting that several objects were passing in front of the star.


With further observations, the team confirmed the objects were indeed planets, with similar sizes to Earth and Venus. The two innermost planets orbit the star in 1.5 and 2.4 days, though they receive only four and two times the amount of radiation, respectively, as the Earth receives from the sun. The third planet may orbit the star in anywhere from four to 73 days, and may receive even less radiation than Earth. Given their size and proximity to their ultracool star, all three planets may have regions with temperatures well below 400 kelvins, within a range that is suitable for sustaining liquid water and life.


Because the system is just 40 light years from Earth, co-author Julien de Wit, a postdoc in the Department of Earth, Atmospheric, and Planetary Sciences, says scientists will soon be able to study the planets' atmospheric compositions, as well as assess their habitability and whether life actually exists within this planetary system.

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Fermi Links Neutrino Blast To Known Extragalactic Blazar - Universe Today

Fermi Links Neutrino Blast To Known Extragalactic Blazar - Universe Today | Amazing Science |

A unique observatory buried deep in the clear ice of the South Pole region, an orbiting observatory that monitors gamma rays, a powerful outburst from a black hole 10 billion light years away, and a super-energetic neutrino named Big Bird. These are the cast of characters that populate a paper published in Nature Physics, on Monday April 18th.


The observatory that resides deep in the cold dark of the Antarctic ice has one job: to detect neutrinos. Neutrinos are strange, standoffish particles, sometimes called ‘ghost particles’ because they’re so difficult to detect. They’re like the noble gases of the particle world. Though neutrinos vastly outnumber all other atoms in our Universe, they rarely interact with other particles, and they have no electrical charge. This allows them to pass through normal matter almost unimpeded. To even detect them, you need a dark, undisturbed place, isolated from cosmic rays and background radiation.


This explains why they built an observatory in solid ice. This observatory, called the IceCube Neutrino Observatory, is the ideal place to detect neutrinos. On the rare occasion when a neutrino does interact with the ice surrounding the observatory, a charged particle is created. This particle can be either an electron, muon, or tau. If these charged particles are of sufficiently high energy, then the strings of detectors that make up IceCube can detect it. Once this data is analyzed, the source of the neutrinos can be known.


The next actor in this scenario is NASA’s Fermi Gamma-Ray Space Telescope. Fermi was launched in 2008, with a specific job in mind. Its job is to look at some of the exceptional phenomena in our Universe that generate extraordinarily large amounts of energy, like super-massive black holes, exploding stars, jets of hot gas moving at relativistic speeds, and merging neutron stars. These things generate enormous amounts of gamma-ray energy, the part of the electromagnetic spectrum that Fermi looks at exclusively.


Next comes PKS B1424-418, a distant galaxy with a black hole at its center. About 10 billion years ago, this black hole produced a powerful outburst of energy, called a blazar because it’s pointed at Earth. The light from this outburst started arriving at Earth in 2012. For a year, the blazar in PKS B1424-418 shone 15-30 times brighter in the gamma spectrum than it did before the burst.


Detecting neutrinos is a rare occurrence. So far, IceCube has detected about a hundred of them. For some reason, the most energetic of these neutrinos are named after characters on the popular children’s show called Sesame Street. In December 2012, IceCube detected an exceptionally energetic neutrino, and named it Big Bird. Big Bird had an energy level greater than 2 quadrillion electron volts. That’s an enormous amount of energy shoved into a particle that is thought to have less than one millionth the mass of an electron.

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Model brains shows where we store thousands of words

Model brains shows where we store thousands of words | Amazing Science |
The latest study focused on the brain's system for decoding language, called the semantic system.

Scientists at the University of California, Berkeley played seven volunteers two hours of narrative stories and recorded their brain activity using functional MRI scanners.

These scans recorded changes in the flow of oxygenated blood to different regions of the brain - measured as tiny cubes called voxels - which coincided with words being spoken.

In the first round of experiments, volunteers were played the audio while being scanned, and the audio was then transcribed to synchronise the words and fMRI responses. But as a second test, to see if they could predict the fMRI activity, the team made the volunteers listen to a new story.

Analysis from the first test showed increased activity in the voxels correlated with the meanings and context - so the fMRI observations served as an indirect measurement of brain activity for more than 10,470 words in total.

The team used this information to build computer models to predict brain activity for the new story, and found that their models could predict the brain responses relatively well, building up the detailed views of the semantic system.

The UCB team explained: 'These semantic maps give us, for the first time, a detailed map of how meaning is represented across the human cortex. Rather than being limited to a few brain areas, we find that language engages very broad regions of the brain.'
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Novel model illustrates the finer details of nuclear fission

Novel model illustrates the finer details of nuclear fission | Amazing Science |

For nearly 80 years, nuclear fission has awaited a description within a microscopic framework. In the first study of its kind, scientists collaborating from the University of Washington, Warsaw University of Technology (Poland), Pacific Northwest National Laboratory, and Los Alamos National Laboratory, developed a novel model to take a more intricate look at what happens during the last stages of the fission process. Using the model, they determined that fission fragments remain connected far longer than expected before the daughter nuclei split apart. Moreover, they noted the predicted kinetic energy agreed with results from experimental observations. This discovery indicates that complex calculations of real-time fission dynamics without physical restrictions are feasible and opens a pathway to a theoretical microscopic framework with abundant predictive power.

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Autonomous quantum error correction method greatly increases qubit coherence times

Autonomous quantum error correction method greatly increases qubit coherence times | Amazing Science |

It might be said that the most difficult part of building a quantum computer is not figuring out how to make it compute, but rather finding a way to deal with all of the errors that it inevitably makes. In order to flip the qubits back to their correct states, physicists have been developing an assortment of quantum error correction techniques. Most of them work by repeatedly making measurements on the system to detect errors and then correct the errors before they can proliferate. These approaches typically have a very large overhead, where a large portion of the computing power goes to correcting errors.


In a new paper published in Physical Review Letters, Eliot Kapit, an assistant professor of physics at Tulane University in New Orleans, has proposed a different approach to quantum error correction. His method takes advantage of a recently discovered unexpected benefit of quantum noise: when carefully tuned, quantum noise can actually protect qubits against unwanted noise. Rather than actively measuring the system, the new method passively and autonomously suppresses and corrects errors, using relatively simple devices and relatively little computing power.


"The most interesting thing about my work is that it shows just how simple and small a fully error corrected quantum circuit can be, which is why I call the device the 'Very Small Logical Qubit,'" Kapit told "Also, the error correction is fully passive—unwanted error states are quickly repaired by engineered dissipation, without the need for an external computer to watch the circuit and make decisions. While this paper is a theoretical blueprint, it can be built with current technology and doesn't require any new insights to make it a reality."


The new passive error correction circuit consists of just two primary qubits, in contrast to the 10 or more qubits required in most active approaches. The two qubits are coupled to each other, and each one is also coupled to a "lossy" object, such as a resonator, that experiences photon loss.


"In the absence of any errors, there are a pair of oscillating photon configurations that are the 'good' logical states of the device, and they oscillate at a fixed frequency based on the circuit parameters," Kapit explained. "However, like all qubits, the qubits in the circuit are not perfect and will slowly leak photons into the environment. When a photon randomly escapes from the circuit, the oscillation is broken, at which point a second, passive error correction circuit kicks in and quickly inserts two photons, one which restores the lost photon and reconstructs the oscillating logical state, and the other is dumped to a lossy circuit element and quickly leaks back out of the system. The combination of careful tuning of the resonant frequencies of the circuit and adding photons two at a time to correct losses ensures that the passive error correction circuit can operate continuously but won't do anything to the two good qubits unless their oscillation has been broken by a photon loss."

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Modular proteins can be used to track or manipulate RNA inside living cells

Modular proteins can be used to track or manipulate RNA inside living cells | Amazing Science |

MIT researchers have devised a new set of proteins that can be customized to bind arbitrary RNA sequences, making it possible to image RNA inside living cells, monitor what a particular RNA strand is doing, and even control RNA activity. The new strategy is based on human RNA-binding proteins that normally help guide embryonic development. The research team adapted the proteins so that they can be easily targeted to desired RNA sequences. “You could use these proteins to do measurements of RNA generation, for example, or of the translation of RNA to proteins,” says Edward Boyden, an associate professor of biological engineering and brain and cognitive sciences at the MIT Media Lab. “This could have broad utility throughout biology and bioengineering.”


Unlike previous efforts to control RNA with proteins, the new MIT system consists of modular components, which the researchers believe will make it easier to perform a wide variety of RNA manipulations. “Modularity is one of the core design principles of engineering. If you can make things out of repeatable parts, you don’t have to agonize over the design. You simply build things out of predictable, linkable units,” says Boyden, who is also a member of MIT’s McGovern Institute for Brain Research.


Boyden is the senior author of a paper describing the new system in the Proceedings of the National Academy of Sciences. The paper’s lead authors are postdoc Katarzyna Adamala and grad student Daniel Martin-Alarcon.


Living cells contain many types of RNA that perform different roles. One of the best known varieties is messenger RNA (mRNA), which is copied from DNA and carries protein-coding information to cell structures called ribosomes, where mRNA directs protein assembly in a process called translation. Monitoring mRNA could tell scientists a great deal about which genes are being expressed in a cell, and tweaking the translation of mRNA would allow them to alter gene expression without having to modify the cell’s DNA.


To achieve this, the MIT team set out to adapt naturally occurring proteins called Pumilio homology domains. These RNA-binding proteins include sequences of amino acids that bind to one of the ribonucleotide bases that make up RNA. In recent years, scientists have been working on developing these proteins for experimental use, but until now it was more of a trial-and-error process to create proteins that would bind to a particular RNA sequence.


“It was not a truly modular code,” Boyden says, referring to the protein’s amino acid sequences. “You still had to tweak it on a case-by-case basis. Whereas now, given an RNA sequence, you can specify on paper a protein to target it.”


To create their code, the researchers tested out many amino acid combinations and found a particular set of amino acids that will bind each of the four bases at any position in the target sequence. Using this system, which they call Pumby (for Pumilio-based assembly), the researchers effectively targeted RNA sequences varying in length from six to 18 bases.


“I think it’s a breakthrough technology that they’ve developed here,” says Robert Singer, a professor of anatomy and structural biology, cell biology, and neuroscience at Albert Einstein College of Medicine, who was not involved in the research. “Everything that’s been done to target RNA so far requires modifying the RNA you want to target by attaching a sequence that binds to a specific protein. With this technique you just design the protein alone, so there’s no need to modify the RNA, which means you could target any RNA in any cell.”

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The next step in DNA computing: GPS mapping?

The next step in DNA computing: GPS mapping? | Amazing Science |

Conventional silicon-based computing, which has advanced by leaps and bounds in recent decades, is pushing against its practical limits. DNA computing could help take the digital era to the next level. Scientists are now reporting progress toward that goal with the development of a novel DNA-based GPS. They describe their advance in ACS' The Journal of Physical Chemistry B.


Jian-Jun Shu and colleagues note that Moore's law, which marked its 50thanniversary in April, posited that the number of transistors on a computer chip would double every year. This doubling has enabled smartphone and tablet technology that has revolutionized computing, but continuing the pattern will come with high costs. In search of a more affordable way forward, scientists are exploring the use of DNA for its programmability, fast processing speeds and tiny size. So far, they have been able to store and process information with the genetic material and perform basic computing tasks. Shu's team set out to take the next step.


The researchers built a programmable DNA-based processor that performs two computing tasks at the same time. On a map of six locations and multiple possible paths, it calculated the shortest routes between two different starting points and two destinations. The researchers say that in addition to cost- and time-savings over other DNA-based computers, their system could help scientists understand how the brain's "internal GPS" works.

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Atoms placed precisely in silicon can act as quantum simulator

Atoms placed precisely in silicon can act as quantum simulator | Amazing Science |

In a proof-of-principle experiment, researchers at UNSW Australia have demonstrated that a small group of individual atoms placed very precisely in silicon can act as a quantum simulator, mimicking nature -- in this case, the weird quantum interactions of electrons in materials.


"Previously this kind of exact quantum simulation could not be performed without interference from the environment, which typically destroys the quantum state," says senior author Professor Sven Rogge, Head of the UNSW School of Physics and program manager with the ARC Centre of Excellence for Quantum Computation and Communication Technology (CQC2T).


"Our success provides a route to developing new ways to test fundamental aspects of quantum physics and to design new, exotic materials -- problems that would be impossible to solve even using today's fastest supercomputers."


The study is published in the journal Nature Communications. The lead author was UNSW's Dr Joe Salfi and the team included CQC2T director Professor Michelle Simmons, other CQC2T researchers from UNSW and the University of Melbourne, as well as researchers from Purdue University in the US.


Two dopant atoms of boron only a few nanometres from each other in a silicon crystal were studied. They behaved like valence bonds, the "glue" that holds matter together when atoms with unpaired electrons in their outer orbitals overlap and bond.

The team's major advance was in being able to directly measure the electron "clouds" around the atoms and the energy of the interactions of the spin, or tiny magnetic orientation, of these electrons.


They were also able to correlate the interference patterns from the electrons, due to their wave-like nature, with their entanglement, or mutual dependence on each other for their properties. "The behavior of the electrons in the silicon chip matched the behaviour of electrons described in one of the most important theoretical models of materials that scientists rely on, called the Hubbard model," says Dr Salfi.


"This model describes the unusual interactions of electrons due to their wave-like properties and spins. And on of its main applications is to understand how electrons in a grid flow without resistance, even though they repel each other," he says. The team also made a counterintuitive find -- that the entanglement of the electrons in the silicon chip increased the further they were apart. "This demonstrates a weird behaviour that is typical of quantum systems," says Professor Rogge.

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Black Hole Merger Confirmed

Black Hole Merger Confirmed | Amazing Science |

Two black holes, with masses 29 and 35 times the mass of the Sun, merged to form an even bigger black hole.  The merger resulted in three entire suns worth of matter converted to pure energy in the form of gravitational waves. The waves travelled a billion light years before a tiny meat-filled species on a pale blue dot in space figured how to see them.  Thanks to the smartest one that species had seen in a century, they knew that black holes might merge, and that they would produce these waves if they ever collided.  They put so much trust in his proven theory, that they searched for many years to find the waves he predicted.  Exactly 100 years after his famous theory was released, their hard work paid off, and they celebrated one of the most significant discoveries in meat-filled history.

Via CineversityTV
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Immune cells glue broken blood vessels back together

Immune cells glue broken blood vessels back together | Amazing Science |

"As we age, tiny blood vessels in the brain stiffen and sometimes rupture, causing "microbleeds." This damage has been associated with neurodegenerative diseases and cognitive decline, but whether the brain can naturally repair itself beyond growing new blood-vessel tissue has been unknown.  


A zebrafish study published on May 3 in Immunity describes for the first time how white blood cells called macrophages can grab the broken ends of a blood vessel and stick them back together. "

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Asthma linked to DNA damage caused by dust mites

Asthma linked to DNA damage caused by dust mites | Amazing Science |

A study from MIT and the National University of Singapore links allergies caused by house dust mites to DNA damage. The findings could help predict asthma patients’ risk for lung tissue damage.


House dust mites, which are a major source of allergens in house dust, can cause asthma in adults and children. Researchers from MIT and the National University of Singapore have now found that these mites have a greater impact than previously known — they induce DNA damage that can be fatal to lung cells if the damaged DNA is not adequately repaired. 


The findings suggest that DNA repair capacity, which varies widely among healthy individuals, could be a susceptibility factor that places an asthmatic patient at increased risk of developing asthma-associated pathologies, the researchers say.


“DNA damage is a component in asthma development, potentially contributing to the worsening of asthma. In addition to activation of immune responses, patients’ DNA repair capacity may affect disease progression,” says Bevin Engelward, a professor of biological engineering at MIT and a senior author of the study. “Ultimately, screening for DNA repair capacity might be used to predict the development of severe asthma.”


Fred Wong Wai-Shiu, head of the Department of Pharmacology at the National University of Singapore, is also a senior author of the study, which appears in the May 1 issue of theJournal of Allergy and Clinical Immunology. The paper’s lead author is Tze Khee Chan, a graduate student in the Singapore-MIT Alliance for Research and Technology (SMART).

Via Integrated DNA Technologies
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Breast cancer: towards personalized treatment 

Breast cancer: towards personalized treatment  | Amazing Science |

Largest-ever study of breast cancer genomes, led by Wellcome Genome Campus researchers, reveals new genes and mutations involved in the disease.


The study has uncovered five new genes associated with the disease and 13 new mutational signatures that influence tumor development. Published in Nature and Nature Communications, two studies from the Wellcome Genome Campus pinpoint where genetic variations in breast cancers occur. The findings provide insights into the causes of breast tumours and demonstrate that breast-cancer genomes are highly individual.


Each patient’s cancer genome provides a complete historical account of the genetic changes that person has acquired throughout life. As they develop from a fertilised egg into full adulthood, a person’s DNA gathers genetic changes along the way. Human DNA is constantly being damaged, either by things in the environment or simply from regular wear and tear in the cell. These mutations form patterns–mutational signatures–that can be detected, and give us clues about the causes of cancer.


Via Integrated DNA Technologies
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Sonogenetics: Controlling Memories with Ultrasound

Sonogenetics: Controlling Memories with Ultrasound | Amazing Science |

Ultrasound is also called sonography and is essentially a type of ‘medical sonar’. It has revolutionized medicine since the 1940s, giving us the ability to look into the body in a completely safe way without leaving icky radiation behind, like xrays.


Beyond predicting whether your baby shower will be blue or pink, lesser known applications of ultrasound include the ability to essentially burn and destroy cells inside your body. As such, it has been successfully used to do surgery without making any cuts into the human body. This is a technique that has been used to remove cancerous cells while not affecting any of the surrounding tissue, and without any of the side-effects associated with other kinds of cancer treatment. This is referred to by scientist Yoav Medan as focused ultrasound. If you are unfamiliar with this, you need to watch this TED talk. Non-invasive procedures like this are the future of surgery.


Non-invasive procedures are also the future of neuroscience. It is at this point that we find ourselves at the application of this astonishing science to memory research. As of very recently, scientists have been able to use ultrasound toselectively and non-invasively control brain cells. In other words, we can remote-control individual cells in the brain. We can send a pulse of sound into a brain and change what that creature thinks and does. Crazy, right?


The underlying technology is called sonogenetics, and it was first announced as a technique that can modify brain cells in a paper published by scientist Stuart Ibsen and colleagues in 2015.


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The Shrinking Mitochondrion Phenomenom

The Shrinking Mitochondrion Phenomenom | Amazing Science |
Scanning the mitochondrial genomes of thousands of species is beginning to shed light on why some genes were lost while others were retained.


Billions of years ago, one cell—the ancestral cell of modern eukaryotes—engulfed another, a microbe that gave rise to today’s mitochondria. Over evolutionary history, the relationship between our cells and these squatters has become a close one; mitochondria provide us with energy and enjoy protection from the outside environment in return. As a result of this interdependence, our mitochondria, which once possessed their own complete genome, have lost most of their genes: while the microbe that was engulfed so many years ago is estimated to have contained thousands of genes, humans have just 13 remaining genes in their mitochondrial DNA (mtDNA).


Some mitochondrial genes have disappeared completely; others have been transferred to our cells’ nuclei for safekeeping, away from the chemically harsh environment of the mitochondrion. This is akin to storing books in a nice, dry, central library, instead of a leaky shed where they could get damaged. In humans, damage to mitochondrial genes can result in devastating genetic diseases, so why keep any books at all in the leaky shed?


Researchers have proposed diverse hypotheses to explain mitochondrial gene retention. Perhaps the products of some genes are hard to introduce into the mitochondrion once they’ve been made elsewhere. (Mitochondria have their own ribosomes and are capable of translating their retained genes in-house.) Or perhaps keeping some mitochondrial genes allows the cell to control each organelle individually. Historically, it has been hard to gather quantitative support for any of these ideas, but in the world of big (and growing) biological data we now have the power to shed light on this question. The mtDNA sequences of thousands of organisms as diverse as plants, worms, yeasts, protists, and humans have now been sequenced, yielding information on the patterns of gene loss and on the gene properties that may have governed this loss.

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How NASA's Next Big Telescope Could Take Pictures of Another Earth

How NASA's Next Big Telescope Could Take Pictures of Another Earth | Amazing Science |

Can NASA’s next big space telescope take a picture of an alien Earth-like planet orbiting another star? Astronomers have long dreamed of such pictures, which would allow them to study worlds beyond our solar system for signs of habitability and life.


But for as long as astronomers have dreamed, the technology to make those dreams a reality has seemed decades away. Now, however, a growing number of experts believe NASA’s Wide-Field Infrared Survey Telescope (WFIRST) could take snapshots of “other Earths”—and soon. The agency formally started work on WFIRST in February of this year and plans to launch the observatory in 2025.


WFIRST was conceived in 2010 as the top-ranked priority of the National Academy of Sciences’ Decadal Survey, a report from U.S. astronomers that proposes a wish list of future missions for NASA and other federal science agencies. The telescope’s heart is a 2.4-meter mirror that, although the same size and quality as the Hubble Space Telescope’s, promises panoramic views of the heavens a hundred times larger than anything Hubble could manage. Using a camera called the Wide Field Instrument, WFIRST’s primary objective will be to study dark energy, the mysterious force driving the universe’s accelerating expansion. But another hot topic—the existential quest to know whether we are alone in the universe—is already influencing the mission.


Researchers have discovered more than a thousand exoplanets—planets around other stars—since the Decadal Survey’s crucial recommendation of WFIRST as NASA’s top-priority next-generation astrophysics mission. They expect to find tens of thousands more within the next 10 years. Many will be discovered by WFIRST itself when it surveys the Milky Way’s galactic bulge for stars that briefly brighten as planets cross in front of them, acting as gravitational lenses to magnify their light.


That survey could yield at least as many worlds as NASA’s wildly successful planet-hunting Kepler space telescope, which used different techniques to net about 5,000 probable planets before hardware failures ended its primary mission in 2013.


Already, rough statistics from the entirety of known planets suggest that every star in the sky is accompanied by at least one, and that perhaps one in five sunlike stars bears a rocky orb in a not-too-hot, not-too-cold “habitable zone” where liquid water can exist. The best way to learn whether any of these worlds are Earth-like is to see them—but taking a planet’s picture from light-years away is far from easy. A habitable world would be a faint dot lost in the overpowering glare of its larger, 10-billion-times-brighter star. Glimpsing it would be like seeing a firefly fluttering next to a searchlight or a wisp of bioluminescent algae on a wave crashing against a lighthouse.

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Antibodies protect monkeys for nearly 6 months from HIV-like virus

Antibodies protect monkeys for nearly 6 months from HIV-like virus | Amazing Science |

The specificity and flexibility of antibodies has made them essential and ubiquitous research tools. For those same reasons many antibody based therapies are currently in development. This week in the journal Nature researchers have described the development and application of a potential antibody based HIV vaccine alternative. The researchers report that a single dose of monoclonal antibodies can protect research animals nearly 6 months from repeated exposure to an HIV-like virus.


For reasons both ethical and practical the scientists conducted their research using a cohort of Rhesus macaques, and an HIV-like virus known as a simian/human (SIV/HIV) chimaeric virus (SHIV). HIV is only capable of infecting human beings and so the study of HIV in animals requires the use of other viruses including SHIVs which are genetically modified HIV-like viruses containing DNA from both HIV and the related Simian immunodeficiency virus.


In the newly reported work animals within experimental groups were prophylactically treated intravenously with one of four different monoclonal antibodies.  Both the antibody protected experimental animals and the unprotected control animals were then exposed weekly to low doses of an SHIV. While the experimental group of animals was exposed to the prophylactic antibodies intravenously, viral challenged occurred intrarectally. Both experimental and control animals were exposed to the SHIV by infusing the rectal cavity with a 1 mL suspension of the virus. Research animals were exposed to the virus one week after treatment with the prophylactic antibodies and every week thereafter. This aspect of the experimental procedure differed from other previously reported work.


While previous experiments have examined the utility of using antibodies to prevent infection following single high doses of virus, the newly reported work sought to better mimic real world exposure by exposing animals repeatedly to smaller viral titres.

Animals given the prophylactic antibodies were protected from the virus for up to 23 weeks, with the average duration of protection being 12 to 14 weeks. In contrast the animals within the control group, lacking the protective benefit of the antibodies, were infected within an average of 3 weeks.

This new work is promising. In an interview with The Verge Dr. David Montefiori, a specialist who took no part in the study, suggested that with improving technologies the antibody based therapeutics may be capable of offer protection for periods even longer than six months.

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Google patent filing proposes device in eye to address poor vision

Google patent filing proposes device in eye to address poor vision | Amazing Science |

What are Google's visionaries up to these days? You may be sorry you asked. Discovery reported that an electronic device injected into an eyeball is the focus of a patent filed by Google.


The Google patent application was reported in Forbes. Aaron Tilley said "the device is injected in fluid that then solidifies to couple the device with the eye's lens capsule, the transparent membrane surrounding the lens." The device is injected into the eye and it has tiny components, said Lilley: storage, sensors, radio, battery and an electronic lens. The device gets power wirelessly from an "energy harvesting antenna."


"The whole endeavor appears to be a way of correcting poor vision," saidDiscovery. Tilley at Forbes said, "According to the patent, the electronic lens would assist in the process of focusing light onto the eye's retina." The inventor in the application is listed as Andrew Jason Conrad.


The patent application said, "Elements of the human eye (e.g., the cornea, lens, aqueous and vitreous humor) operate to image the environment of the eye by focusing light from the environment onto the retina of the eye, such that images of elements of the environment are presented in-focus on the retina. The optical power of the natural lens of the eye can be controlled (e.g., by ciliary muscles of the eye) to allow objects at different distances to be in focus at different points in time (a process known as accommodation)."


A variety of reasons, however, are behind decreased focus and degradation of images presented to the retina. "Issues with poor focus can be rectified by the use of eyeglasses and/or contact lenses or by the remodeling of the cornea. Further, artificial lenses can be implanted into the eye (e.g., into the space in front of the iris, into the lens capsule following partial or full removal of the natural lens, e.g., due to the development of cataracts) to improve vision."

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Light-powered 3-D printer creates terahertz lens

Light-powered 3-D printer creates terahertz lens | Amazing Science |

From visible light to radio waves, most people are familiar with the different sections of the electromagnetic spectrum. But one wavelength is often forgotten, little understood, and, until recently, rarely studied.


"Terahertz is somewhat of a gap between microwaves and infrared," said Northwestern University's Cheng Sun. "People are trying to fill in this gap because this spectrum carries a lot of information."


Sun and his team have used metamaterials and 3-D printing to develop a novel lens that works with terahertz frequencies. Not only does it have better imaging capabilities than common lenses, but it opens the door for more advances in the mysterious realm of the terahertz. Supported by the National Science Foundation, the work was published online on April 22 in the journal Advanced Optical Materials.


"Typical lenses—even fancy ones—have many, many components to counter their intrinsic imperfections," said Sun, associate professor of mechanical engineering at Northwestern's McCormick School of Engineering. "Sometimes modern imaging systems stack several lenses to deliver optimal imaging performance, but this is very expensive and complex."


The focal length of a lens is determined by its curvature and refractive index, which shapes the light as it enters. Without components to counter imperfections, resulting images can be fuzzy or blurred. Sun's lens, on the other hand, employs a gradient index, which is a refractive index that changes over space to create flawless images without requiring additional corrective components.

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Demonstration of DNA switch could lead to new bioelectronics

Demonstration of DNA switch could lead to new bioelectronics | Amazing Science |

A team of researchers from the University of California, Davis and the University of Washington have demonstrated that the conductance of DNA can be modulated by controlling its structure, thus opening up the possibility of DNA’s future use as an electromechanical switch for nanoscale computing. Although DNA is commonly known for its biological role as the molecule of life, it has recently garnered significant interest for use as a nanoscale material for a wide-variety of applications.


In their paper published in Nature Communications, the team demonstrated that changing the structure of the DNA double helix by modifying its environment allows the conductance (the ease with which an electric current passes) to be reversibly controlled. This ability to structurally modulate the charge transport properties may enable the design of unique nanodevices based on DNA. These devices would operate using a completely different paradigm than today’s conventional electronics.


“As electronics get smaller they are becoming more difficult and expensive to manufacture, but DNA-based devices could be designed from the bottom-up using directed self-assembly techniques such as ‘DNA origami’,” said Josh Hihath, assistant professor of electrical and computer engineering at UC Davis and senior author on the paper. DNA origami is the folding of DNA to create two- and three-dimensional shapes at the nanoscale level.


“Considerable progress has been made in understanding DNA’s mechanical, structural, and self-assembly properties and the use of these properties to design structures at the nanoscale. The electrical properties, however, have generally been difficult to control,” said Hihath.


In addition to potential advantages in fabrication at the nanoscale level, such DNA-based devices may also improve the energy efficiency of electronic circuits.  The size of devices has been significantly reduced over the last 40 years, but as the size has decreased, the power density on-chip has increased. Scientists and engineers have been exploring novel solutions to improve the efficiency.


“There’s no reason that computation must be done with traditional transistors. Early computers were fully mechanical and later worked on relays and vacuum tubes,” said Hihath. “Moving to an electromechanical platform may eventually allow us to improve the energy efficiency of electronic devices at the nanoscale.”


This work demonstrates that DNA is capable of operating as an electromechanical switch and could lead to new paradigms for computing. To develop DNA into a reversible switch, the scientists focused on switching between two stable conformations of DNA, known as the A-form and the B-form. In DNA, the B-form is the conventional DNA duplex that is commonly associated with these molecules. The A-form is a more compact version with different spacing and tilting between the base pairs. Exposure to ethanol forces the DNA into the A-form conformation resulting in an increased conductance.


Similarly, by removing the ethanol, the DNA can switch back to the B-form and return to its original reduced conductance value.

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Virus trading cards

Virus trading cards | Amazing Science |

Viruses are surprisingly symmetrical, and each trading card shows the structure of the viral capsid - the protein shell protecting the genetic material inside a virus. To make the 3D animations I used UCSF Chimera, a free molecular modeling program. When scientists discover a new protein structure they upload it to the worldwide Protein Data Bank. Each entry is assigned a unique ID number, which you can use to call up the structure in programs like Chimera or PyMol.

Use Tom Goddard’s tutorial to learn how to display viral capsids, and it’s actually a fairly simple process. You can even 3D print structures straight from Chimera.


Molecular Modeling: Molecular graphics and analyses were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311).

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Tracking Zika Virus' Evolution

Tracking Zika Virus' Evolution | Amazing Science |

Sequence analysis of 41 viral strains reveals more than a half-century of change.


Comparing the sequences of 30 strains of Zika virus isolated from humans, 10 from mosquitoes, and one from monkeys has revealed significant evolutionary change over the past 70 years, according to a study published today (April 15) in Cell Host & Microbe. Specifically, the sequences of the viral strains showed notable divergence between the Asian and African lineages and suggest that modern Zika virus strains derived from the Asian lineage, as they are more similar to the Malaysian/1966 strain than the Nigerian/1968 strain. Additionally, the gene for the pre-membrane precursor protein has very high variability among the Zika strains examined, which modeling work suggests may affect the protein’s structure.


“We believe these changes may, at least partially, explain why the virus has demonstrated the capacity to spread exponentially in the human population in the Americas,” study coauthor Genhong Cheng of the University of California, Los Angeles, said in a press release. “These changes could enable the virus to replicate more efficiently, invade new tissues that provide protective niches for viral propagation, or evade the immune system, leading to viral persistence.”


But it is not possible to directly test whether these mutations affect the virus’s spread in humans, virologist Vincent Racaniello noted on his blog. “It’s easy to blame mutations in the viral genome for novel patterns of transmission or pathogenesis,” he wrote. “There is no reason to assume that such changes influence virulence, disease patterns, or transmission in humans.”

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