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Rescooped by Dr. Stefan Gruenwald from Synthetic Biology!

Autodesk Builds Its Own Real Virus, Based on Systems Biology

Autodesk Builds Its Own Real Virus, Based on Systems Biology | Amazing Science |


Autodesk, a company which develops design software, produced a synthetic Phi-X174 bacteriophage, a virus that infects E. coli bacteria but is totally benign for humans. 

The effort was a sort of scientific homage to the work of the J. Craig Venter Institute, which first produced the self-replicating synthetic virus back in 2003, following a more than five-year research effort. In Autodesk’s case, it took a little more than two weeks and about $1,000.

That achievement says a lot about how far the science of synthetic biology has come — and a lot about where Autodesk is going.

Via Marko Dolinar
Samuel Viana's curator insight, May 23, 2014 12:56 PM
A AutoDesk, criadora do software de modelação AutoCAD, criou o seu primeiro vírus. Mas não é um vírus informático, como à primeira vista possa parecer, mas sim biológico, já que a Autodesk também se lançou neste campo de pesquisa já lá vão dez anos. Este vírus é capaz de infectar a "clássica" bactéria-modelo E. coli.
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A single female-specific piRNA is the primary determiner of sex in the silkworm

A single female-specific piRNA is the primary determiner of sex in the silkworm | Amazing Science |

The silkworm Bombyx mori uses a WZ sex determination system that is analogous to the one found in birds and some reptiles. In this system, males have two Z sex chromosomes, whereas females have Z and W sex chromosomes. The silkworm W chromosome has a dominant role in female determination12, suggesting the existence of a dominant feminizing gene in this chromosome. However, the W chromosome is almost fully occupied by transposable element sequences345, and no functional protein-coding gene has been identified so far. Female-enriched PIWI-interacting RNAs (piRNAs) are the only known transcripts that are produced from the sex-determining region of the W chromosome6, but the function(s) of these piRNAs are unknown. A team of scientists now show that a W-chromosome-derived, female-specific piRNA is the feminizing factor of B. mori. This piRNA is produced from a piRNA precursor which was named FemInhibition of Fem-derived piRNA-mediated signalling in female embryos led to the production of the male-specific splice variants of B. mori doublesex (Bmdsx), a gene which acts at the downstream end of the sex differentiation cascade78. A target gene of Fem-derived piRNA was identified on the Z chromosome of B. mori. This gene, named Masc, encodes a CCCH-type zinc finger protein. The research team was able to show that the silencing of Masc messenger RNA by Fem piRNA is required for the production of female-specific isoforms of Bmdsx in female embryos, and that Masc protein controls both dosage compensation and masculinization in male embryos. This study demonstrates that a single small RNA that is responsible for primary sex determination in the WZ sex determination system.

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Magnetar pulsars have a magnetic field 100 trillion fold stronger than Earth

Magnetar pulsars have a magnetic field 100 trillion fold stronger than Earth | Amazing Science |

New findings reveal the makings of magnetars. Astronomers have figured out how to make the universe’s most powerful magnet. All you need is two massive stars orbiting close to each other so that one swipes gas from the other, causing the thief to spin so quickly that its magnetic field dwarfs that of Earth by 100 trillion-fold. The finding offers fresh insight into how some of the galaxy's smallest but most extraordinary stars arise.

Magnetars are a special breed of pulsars, which are fast-spinning neutron stars that form when a massive star explodes as a supernova: The star's outer layers shoot off into space, while its core collapses to become the pulsar. Magnetars are as rare as they are extraordinary. Known pulsars number in the thousands; known magnetars, only a couple of dozen.

Astronomer Simon Clark of the Open University in Milton Keynes, U.K., and his colleagues observed a young star cluster named Westerlund 1, which sports one of the few known magnetars. The cluster is only 5 million years old and lies 16,000 light-years from Earth in Ara, a constellation just south of Scorpius.

The astronomers identified a peculiar blue supergiant—a star much hotter and more luminous than the sun—that they believe once orbited the star that later became the magnetar. Named Westerlund 1-5, the blue supergiant dumped large amounts of gas onto its partner, speeding up its spin the way falling water makes a water wheel twirl. As Clark's team reports online this week in Astronomy & Astrophysicsthis spin-up amplified the star's magnetic field so that when it exploded and collapsed, it became a magnetar rather than an ordinary pulsar.

Furthermore, the blue supergiant saved its partner from a bleak fate. The premagnetar star was so massive that it should have collapsed into a black hole. But before it exploded, it began to expand, as aging stars do, and its partner grabbed enough gas back that the premagnetar star slimmed down, becoming a magnetar rather than a black hole. This removal of material also kept the premagnetar star spinning fast; normally, expanding stars spin more slowly, just as spinning ice skaters do when they extend their arms.

The evidence? First, the blue supergiant is racing away from the cluster, suggesting that another star recently kicked it away when it exploded. Second, the blue supergiant has odd abundances of carbon, nitrogen, and oxygen.

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Should Smallpox’s Last Two Samples Be Destroyed Or Preserved To Best Safeguard Humanity?

Should Smallpox’s Last Two Samples Be Destroyed Or Preserved To Best Safeguard Humanity? | Amazing Science |

Although the world hasn’t seen a case of smallpox in over 30 years, it isn’t quite gone yet. Two vials of the deadly virus remain: one in the United States and the other over 5,000 miles away in Russia. Experts around the world agree that these vials need to be destroyed at some point, but some believe that, for now, humanity is safer with the vials intact. Others insist their destruction is well overdue. The fate of the vials will be decided at an upcoming World Health Assembly meeting later this month.

Smallpox was arguably one of the most deadly diseases to ever exist. It is estimated to have killed up to 500 million people in the 20th century. Throughout time, it has probably killed more people than all other infectious diseases combined. By 1980, smallpox was eradicated, and today it remains the only disease to have been eliminated by the World Health Organization (WHO).

An opinion piece on the fate of the last two remaining strains of smallpox was released on PLoS Pathogens Thursday. In it, experts explain how research with the live smallpox virus is “not yet finished.” If the virus were to reappear, some researchers believe humanity is not prepared to fight it off. Although there is a vaccine against smallpox, it is in limited supply. This vaccine is also known to have a high rate of adverse and sometimes severe side effects. It can infect the brain and cause permanent damage. The International Business Times reports that the WHO's original goals for a newer and safer vaccine, fully licensed antiviral drugs, and better diagnostics are still underway. The researchers believe that further screening and using new approaches such as genomics or proteomics can help enhance man’s preparedness against a possible smallpox resurgence.

So far, there have been two new antivirals that seem promising in treating smallpox. Neither has been licensed for use yet, and researchers feel they need live samples of the virus to continue their research. “Variola is unusual in that it is known to be a sole human pathogen, the viral and host factors responsible for this human-specific tropism remain essentially unknown to this day,” the researcher explained, IBT reported. Live samples of smallpox are also used to help understand other viruses and develop treatments for them.

Advances in synthetic biology mean that one day it may be possible to create smallpox from scratch. “The synthetic biology adds a new wrinkle to it. We now aren’t as sure that our countermeasures are going to be as effective as we’d though even five years ago,” Jimmy Kolker, Health and Human Services assistant secretary for global affairs told The Associated Press. Even if all traces of smallpox are essentially eliminated, there is still no saying that the virus won’t reappear again in the future. The researchers believe further observation of the living virus can help “to better respond to any future emergency situation resulting from a smallpox appearance.”

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Diamond planets may be more common than astronomers thought

Diamond planets may be more common than astronomers thought | Amazing Science |

Carbon-rich planets may be more common than previously thought, according to new research by Yale University astronomers.

Some of these planets, all located far beyond Earth’s solar system, could contain vast deposits of graphite or diamonds, and their apparent abundance prompts new questions about the implications of carbon-intense environments for climate, plate tectonics, and other geological processes, as well as for life.

“Despite the relatively small amount of carbon on Earth, carbon has been critical for the emergence of life and the regulation of our climate through the carbon-silicate cycle,” said Yale doctoral candidate John Moriarty, who led the research, recently published in Astrophysical Journal. “It’s an open question as to how carbon-rich chemistry will affect the habitability of exoplanets. We hope our findings will spark interest in research to help answer these questions.”

Moriarty collaborated with Yale astronomy professor Debra Fischer and Nikku Madhusudhan, a former Yale postdoctoral researcher now at Cambridge University.

Exoplanets are planets outside Earth’s solar system. In October 2012 Madhusudhan published a paper arguing that 55 Cancri e, a rocky exoplanet twice Earth’s size, is likely covered in graphite and diamond.

Astronomers generally believe that rocky exoplanets are composed — as Earth is — largely of iron, oxygen, magnesium, and silicon, with only a small fraction of carbon. In contrast, carbon-rich planets could have between a small percentage and three-quarters of their mass in carbon. (Earth has 0.005%.)

Moriarty, Madhusudhan, and Fischer developed an advanced model for estimating exoplanet composition. Previous models were based on static snapshots of the gaseous pools (or disks) in which planets form. Their new model tracks changes in the composition of the disk as it ages.

The researchers found that, in disks with carbon-oxygen ratios greater than 0.8, carbon-rich planets can form farther from the center of the disk than previously understood. They also found that carbon-rich planets can form in disks with a carbon-oxygen ratio as low as 0.65 if those planets form close to their host star.

Previous models predicted carbon-rich planets could only form in disks with carbon-oxygen ratios higher than 0.8. This is important, the researchers said, because there are many more stars with carbon-oxygen ratios greater than 0.65 than there are with carbon-oxygen ratios greater than 0.8.

Said Madhusudhan, "Our study shows that extraterrestrial worlds can be extremely diverse in their chemical compositions, including many that are drastically different from our earthly experience.

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Transistors that wrap around tissues and morph with them

Transistors that wrap around tissues and morph with them | Amazing Science |

Electronic devices that become soft when implanted inside the body and can deploy to grip 3-D objects, such as large tissues, nerves and blood vessels have been created by researchers from The University of Texas at Dallas and the University of Tokyo.

These biologically adaptive, flexible transistors might one day help doctors learn more about what is happening inside the body, and also could be used to stimulate the body for treatments.

The research, published in Advanced Materials, is one of the first demonstrations of transistors that can change shape and maintain their electronic properties after they are implanted in the body, said Jonathan Reeder, a graduate student in materials science and engineering and lead author of the work.

“Scientists and physicians have been trying to put electronics in the body for a while now, but one of the problems is that the stiffness of common electronics is not compatible with biological tissue,” he said.

“You need the device to be stiff at room temperature so the surgeon can implant the device, but soft and flexible enough to wrap around 3-D objects so the body can behave exactly as it would without the device. By putting electronics on shape-changing and softening polymers, we can do just that.”

Shape memory polymers (plastics) developed by Dr. Walter Voit, assistant professor of materials science and engineering and mechanical engineering and an author of the paper, are key to enabling the technology.

The polymers respond to the body’s environment and become less rigid when they’re implanted. In addition to the polymers, the electronic devices are built with layers that include thin, flexible electronic foils first characterized by a group including Reeder in work published last year in Nature.

The Voit and Reeder team from the Advanced Polymer Research Lab in the Erik Jonsson School of Engineering and Computer Science fabricated the devices with an organic semiconductor but used adapted techniques normally applied to create silicon electronics that could reduce the cost of the devices.

“We used a new technique in our field to essentially laminate and cure the shape memory polymers on top of the transistors,” said Voit, who is also a member of the Texas Biomedical Device Center. “In our device design, we are getting closer to the size and stiffness of precision biologic structures, but have a long way to go to match nature’s amazing complexity, function and organization.”

Keith Wayne Brown's curator insight, May 15, 2014 9:39 AM

A necessary step for posthumanity.

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IEA: Decarbonising the economy will save $71 trillion by 2050

IEA: Decarbonising the economy will save $71 trillion by 2050 | Amazing Science |

Economic growth can be decoupled from emissions, while natural gas could lose 'low carbon' status by 2025 as renewables boom. Replacing fossil fuels with renewables as the world’s primary source of energy will not only save the planet from dangerous levels of warming – it will also save the global economy US$ 71trillion by 2050.

This is the finding of a report, Energy Technology Perspectives 2014, released today by the International Energy Agency, which looks at the direction of the energy sector over the next 40 years.

The changes needed to keep the world within 2C of warming— a widely agreed target in efforts to tackle climate change – will benefit the global economy, confirms the report, although a “coordinated policy approach” will be required to unlock these savings.

“The USD 44 trillion additional investment needed to decarbonise the energy system in line with the 2DS [2C scenario] by 2050 is more than offset by over USD 115 trillion in fuel savings – resulting in net savings of USD 71 trillion,” its says.

The findings support those who say that it is possible to decouple economic growth from emissions—something the EU has strongly advocated as it has increased its wealth while at the same time remaining on track to reduce its emissions by 20% by 2020. In China, meanwhile, emissions have rocketed in order to sustain economic growth of around 10% a year.

Eli Levine's curator insight, May 13, 2014 12:50 PM

Ah, but unfortunately, we discount the damages.


We'd rather save a penny now and get hit for 2 dollars later than save the dollar now and get hit by a penny later as a result of the difference.


So what?  It means we're in trouble and are going to get ourselves into deeper trouble.


Silly uncorrected species.  Silly uncorrected brains.


Think about it.

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Are material constants alterable after all?Heat conduction in graphene varies with size

Are material constants alterable after all?Heat conduction in graphene varies with size | Amazing Science |
Based on recent experiments and computer simulations, scientists at the Max Planck Institute for Polymer Research and the National Univ. of Singapore have attested that the thermal conductivity of graphene diverges with the size of the samples. This discovery challenges the fundamental laws of heat conduction for extended materials.

Scientists at the Max Planck Institute for Polymer Research (MPI-P) in Mainz and the National Univ. of Singapore have attested that the thermal conductivity of graphene diverges with the size of the samples. This discovery challenges the fundamental laws of heat conduction for extended materials.

Davide Donadio, head of a Max Planck Research Group at the MPI-P, and his partner from Singapore were able to predict this phenomenon with computer simulations and to verify it in experiments. Their research and their results have now been presented in the scientific journalNature Communications.

"We recognized mechanisms of heat transfer that actually contradict Fourier’s law in the micrometer scale. Now all the previous experimental measurements of the thermal conductivity of graphene need to be reinterpreted. The very concept of thermal conductivity as an intrinsic property does not hold for graphene, at least for patches as large as several micrometers", says Davide Donadio.

The French physicist Joseph Fourier had postulated the laws of heat propagation in solids. Accordingly, thermal conductivity is an intrinsic material property that is normally independent of size or shape. In graphene, a two-dimensional layer of carbon atoms, it is not the case, as our scientists now found out. With experiments and computer simulations, they found that the thermal conductivity logarithmically increases as a function of the size of the graphene samples: i.e., the longer the graphene patches, the more heat can be transferred per length unit. This is another unique property of this highly praised wonder material that is graphene: it is chemically very stable, flexible, a hundred times more tear-resistant than steel and at the same time very light. Graphene was already known to be an excellent heat conductor: The novelty here is that its thermal conductivity, which was so far regarded as a material constant, varies as the length of graphene increases. After analyzing the simulations, Davide Donadio found that this feature stems from the combination of reduced dimensionality and stiff chemical bonding, which make thermal vibration propagate with minimal dissipation at non-equilibrium conditions.

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The World's Oldest Underground Fire Has Been Burning For 6,000 Years

The World's Oldest Underground Fire Has Been Burning For 6,000 Years | Amazing Science |

If you've heard of underground coal fires, then you've probably heard of the one raging under the abandoned town of Centralia, Pennsylvania, since 1962. Fifty-two years is a long time—and a lot of coal—but that's barely a blink compared to Burning Mountain in Australia, which has been ablaze for 6,000 years.

Coal seam fires are incredibly common, as it happens, and thousands of them are now burning underground across the world. A coal seam some 700 miles south of Australia's Burning Mountain caught fire a month ago, spewing poisonous gases and prompting intense firefighting efforts. Once an subterranean coal seam fire gets out of hand—as in Centralia, as in Burning Mountain—it's nearly impossible to put out.

At Burning Mountain, also known as Mount Wingen, sulfur-tinged smoke is the only hint of a massive coal seam burning 70 feet under the ground. Heat and toxic gases from the fire have left it rocky and jagged in parts, and the land has caved in.

How the mountain was first set ablaze is a mystery. It could have been a lightning strike, forest fire, spontaneous combustion, or even aboriginal burning practices could even have been the initial spark.

It's with human intervention that coal seam fires have really caught on, so to speak, in the past century. Mining exposes coal to oxygen, and coal, as we know, burns very, very easily. With plenty of fuel and oxygen, a small spark can ignite a blaze that grows to cover miles and miles.

China, with its thousands of small-scale mines, and India, with its crumbling old and large mines, have the most serious underground fire problems. The burning coal releases potentially toxic elements like arsenic, fluorine, and selenium into the air.

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‘Heart disease-on-a-chip’: Merged stem cell and "organ-on-a-chip" technologies

‘Heart disease-on-a-chip’: Merged stem cell and "organ-on-a-chip" technologies | Amazing Science |
Harvard scientists have merged stem cell and “organ-on-a-chip” technologies to grow, for the first time, functioning human heart tissue carrying an inherited cardiovascular disease. The research appears to be a big step forward for personalized medicine, because it is working proof that a chunk of tissue containing a patient’s specific genetic disorder can be replicated in the laboratory.

The work, published in the journal Nature Medicine, is the result of a collaborative effort bringing together scientists from the Harvard Stem Cell Institute (HSCI), the Wyss Institute for Biologically Inspired Engineering,Boston Children’s Hospital, the Harvard School of Engineering and Applied Sciences (SEAS), and Harvard Medical School (HMS). It combines the “organs-on-chips” expertise of Kevin Kit Parker and stem cell and clinical insights byWilliam Pu.

Using their interdisciplinary approach, the investigators modeled the cardiovascular disease Barth syndrome, a rare X-linked cardiac disorder caused by mutation of a single gene called Tafazzin, or TAZ. The disorder, which is currently untreatable, primarily appears in boys, and is associated with a number of symptoms affecting heart and skeletal muscle function.

The researchers took skin cells from two Barth syndrome patients, and manipulated the cells to become stem cells that carried the patients’ TAZ mutations. Instead of using the stem cells to generate single heart cells in a dish, the cells were grown on chips lined with human extracellular matrix proteins that mimicked their natural environment, tricking the cells into joining together as they would if they were forming a diseased human heart. The engineered diseased tissue contracted very weakly, as would the heart muscle of a Barth syndrome patient.

The investigators then used genome editing, a technique pioneered by Harvard collaborator George Church, to mutate TAZ in normal cells, confirming that this mutation is sufficient to cause weak contraction in the engineered tissue. On the other hand, delivering the TAZ gene product to diseased tissue in the laboratory corrected the contractile defect, creating the first tissue-based model of correction of a genetic heart disease.

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Automated 'killer robots' to be debated at UN in Geneva

Automated 'killer robots' to be debated at UN in Geneva | Amazing Science |

A killer robot is a fully autonomous weapon that can select and engage targets without any human intervention. They do not currently exist but advances in technology are bringing them closer to reality. Those in favor of killer robots believe the current laws of war may be sufficient to address any problems that might emerge if they are ever deployed, arguing that a moratorium, not an outright ban, should be called if this is not the case.

However, those who oppose their use believe they are a threat to humanity and any autonomous "kill functions" should be banned.

"Autonomous weapons systems cannot be guaranteed to predictably comply with international law," Prof Sharkey told the BBC. "Nations aren't talking to each other about this, which poses a big risk to humanity."

Prof Sharkey is a member and co-founder of the Campaign Against Killer Robots and chairman of the International Committee for Robot Arms Control. Side events at the CCW will be hosted by the Campaign to Stop Killer Robots.

Prof Arkin from the Georgia Institute of Technology told the BBC he hoped killer robots would be able to significantly reduce non-combatant casualties but feared they would be rushed into battle before this was accomplished.

"I support a moratorium until that end is achieved, but I do not support a ban at this time," said Prof Arkin. He went on to state that killer robots may be better able to determine when not to engage a target than humans, "and could potentially exercise greater care in so doing".

Prof Sharkey is less optimistic. "I'm concerned about the full automation of warfare," he says.

The discussion of drones is not on the agenda as they are yet to operate completely autonomously, although there are signs this may change in the near future.

The UK successfully tested the Taranis, an unmanned intercontinental aircraft in Australia this year and America's Defense Advanced Research Projects Agency (Darpa) has made advances with the Crusher, an unmanned ground combat vehicle, since 2006.

The MoD has claimed in the past that it currently has no intention of developing systems that operate without human intervention.

On 21 November 2012 the United States Defense Department issued a directive that, "requires a human being to be 'in-the-loop' when decisions are made about using lethal force," according to Human Rights Watch.

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New brain cells erase old memories

New brain cells erase old memories | Amazing Science |
Neurogenesis interferes with past learning in infant and adult mice.

For anyone fighting to save old memories, a fresh crop of brain cells may be the last thing they need. Research published today in Sciencesuggests that newly formed neurons in the hippocampus — an area of the brain involved in memory formation — could dislodge previously learned information1. The work may provide clues as to why childhood memories are so difficult to recall.

“The finding was very surprising to us initially. Most people think new neurons mean better memory,” says Sheena Josselyn, a neuroscientist who led the study together with her husband Paul Frankland at the Hospital for Sick Children in Toronto, Canada.

Humans, mice and several other mammals grow new neurons in the hippocampus throughout their lives — rapidly at first, but more and more slowly with age. Researchers have previously shown that boosting neural proliferation before learning can enhance memory formation in adult mice23. But the latest study shows that after information is learned, neuron growth can degrade those memories.

Although seemingly counterintuitive, the disruptive role of these neurons makes some sense, says Josselyn. She notes that some theoretical models have predicted such an effect4. “More neurons increase the capacity to learn new memories in the future,” she says. “But memory is based on a circuit, so if you add to this circuit, it makes sense that it would disrupt it.” Newly added neurons could have a useful role in clearing old memories and making way for new ones, says Josselyn.

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Enhanced Anticancer Efficacy by ATP-Mediated Liposomal Drug Delivery

Enhanced Anticancer Efficacy by ATP-Mediated Liposomal Drug Delivery | Amazing Science |

A liposome-based co-delivery system composed of a fusogenic liposome encapsulating ATP-responsive elements with chemotherapeutics and a liposome containing ATP was developed for ATP-mediated drug release triggered by liposomal fusion. The fusogenic liposome had a protein–DNA complex core containing an ATP-responsive DNA scaffold with doxorubicin (DOX) and could release DOX through a conformational change from the duplex to the aptamer/ATP complex in the presence of ATP. A cell-penetrating peptide-modified fusogenic liposomal membrane was coated on the core, which had an acid-triggered fusogenic potential with the ATP-loaded liposomes or endosomes/lysosomes. Directly delivering extrinsic liposomal ATP promoted the drug release from the fusogenic liposome in the acidic intracellular compartments upon a pH-sensitive membrane fusion and anticancer efficacy was enhanced both in vitro and in vivo.

In a mouse model, the researchers found that the new technique significantly decreased the size of breast cancer tumors compared to treatment that used Dox without the nanoscale liposomes.

“This work is somewhat similar to previous research we’ve done with polymer-based nanogels – but there is a key difference,” says Dr. Zhen Gu, senior author of the paper and an assistant professor in the joint biomedical engineering program. “The difference is that this liposome-based technique allows us to introduce additional ATP into the cancer cell, releasing the drug more quickly.

“Being able to adjust ATP levels is important because some cancer cells are ATP deficient,” Gu adds. “But this technique would work even in those environments.”

The paper, “Enhanced Anticancer Efficacy by ATP-Mediated Liposomal Drug Delivery,” is published online in Angewandte Chemie.

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The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts

The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts | Amazing Science |

Experimental efforts to characterize the human microbiota often use bacterial strains that were chosen for historical rather than biological reasons. A team of scientists report now an analysis of 380 whole-genome shotgun samples from 100 subjects from the NIH Human Microbiome Project. By mapping their reads to 1,751 reference genome sequences and analyzing the resulting relative strain abundance in each sample they present metrics and visualizations that can help identify strains of interest for experimentalists. They also show that approximately 14 strains of 10 species account for 80% of the mapped reads from a typical stool sample, indicating that the function of a community may not be irreducibly complex. Some of these strains account for >20% of the sequence reads in a subset of samples but are absent in others, a dichotomy that could underlie biological differences among subjects. These data should serve as an important strain selection resource for the community of researchers who take experimental approaches to studying the human microbiota.

Via Mel Melendrez-Vallard
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Gemini Planet Imager captures best photo ever of an exoplanet

Gemini Planet Imager captures best photo ever of an exoplanet | Amazing Science |

A team of researchers at the Gemini South telescope in Chile, which has recently been retrofitted with the Gemini Planet Imager (GPI) is reporting in Proceedings of the National Academy of Sciences, that they have captured the best photo ever of an exoplanet orbiting its star. The planet, Beta Pictoris b, orbits its sun approximately 63.5 light years from us, and the GPI has allowed for calculating its orbit at 20.5 years.

Taking pictures of exoplanets is difficult, not only because they are so far away, but also because of Earth's atmosphere and of course because they are near to a star that is much brighter, which tends to overcome the light reflected off its planets. The engineers who designed the GPI used multiple techniques (a field spectrograph that has both low spectral resolution and high spatial resolution and a coronagraph that suppresses diffraction) to mask direct starlight, while simultaneously enhancing the light that is bounced off of nearby planets. The result, the team reports is an instrument capable of producing images of exoplanets that are an order of magnitude higher than any other previous imaging systems.

Beta Pictoris b is a gas giant similar in size to Jupiter, though its star is much younger than ours—just 12 million years old. The picture of it was created with an exposure of just one minute, which is a record for an image of an exoplanet—the planet orbits its star just a little closer than does Saturn in our solar system. It was first discovered in 2006 by researchers working with data from the Hubble Space Telescope and verified three years later by researchers at Europe's VLT. Pictures taken at the time suggested that Beta Pictoris b had to regularly plow through space debris of some sort, causing it to appear murky at times.

Beta Pictoris b was chosen as a first test run due to its designation as an easy target. The research team at Gemini South plan to move on to imaging other exoplanets, eventually taking pictures of at least 600 that appear promising. Doing so will help with better understanding orbit times and perhaps help with refining their ages and masses.

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New blood test accurately detects presence of breast cancer and monitors response to treatment

New blood test accurately detects presence of breast cancer and monitors response to treatment | Amazing Science |
Johns Hopkins Kimmel Cancer Center investigators report they have designed a blood test that accurately detects the presence of advanced breast cancer and also holds promise for precisely monitoring response to cancer treatment.

The test, called the cMethDNA assay, accurately detected the presence of cancer DNA in the blood of patients with metastatic breast cancers up to 95 percent of the time in laboratory studies. The findings were described in the April 15 issue of the journal Cancer Research.

Currently, there is no useful laboratory test to monitor patients with early stage breast cancer who are doing well, but could have an asymptomatic recurrence, says Saraswati Sukumar, Ph.D., who is the Barbara B. Rubenstein Professor of Oncology and co-director of the Breast Cancer Program at the Johns Hopkins Kimmel Cancer Center.

Generally, radiologic scans and standard blood tests are indicated only if a woman complains of symptoms, such as bone aches, shortness of breath, pain, or worrisome clinical exam findings. Otherwise, routine blood tests or scans in asymptomatic patients often produce false positives, leading to additional unnecessary tests and biopsies, and have not been shown to improve survival outcomes in patients with early stage breast cancer who develop a recurrence.

Sukumar, also a professor of pathology at Johns Hopkins, says that the current approach to monitoring for recurrence is not ideal, and that "the goal is to develop a test that could be administered routinely to alert the physician and patient as soon as possible of a return of the original cancer in a distant spot. With the development of cMethDNA, we've taken a first big step toward achieving this goal."

To design the test, Sukumar and her team scanned the genomes of primary breast cancer patients, as well as DNA from the blood of metastatic cancer patients. They selected 10 genes specifically altered in breast cancers, including newly identified genetic markers AKR1B1, COL6A2, GPX7, HIST1H3C, HOX B4, RASGRF2, as well as TM6SF1, RASSF1, ARHGEF7, and TMEFF2, which Sukumar's team had previously linked to primary breast cancer.

The test, developed by Sukumar, collaborator Mary Jo Fackler, Ph.D., and other scientists, detects so-called hypermethyation, a type of chemical tag in one or more of the breast cancer-specific genes present in tumor DNA and detectable in cancer patients' blood samples. Hypermethylation often silences genes that keep runaway cell growth in check, and its appearance in the DNA of breast cancer-related genes shed into the blood indicates that cancer has returned or spread.

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Deadly MERS Virus Circulates Among Arabian Camels

Deadly MERS Virus Circulates Among Arabian Camels | Amazing Science |
A new virus in the Middle East has sickened more than 180 people and killed an alarming 43 percent of them. But scientists haven't been sure where the virus originates or how people catch it.

Scientists have gotten close to pinning down the origin of Middle East Respiratory Syndrome, a dangerous respiratory disease that emerged in Saudi Arabia 17 months ago. It turns out the MERS virus has been circulating in Arabian camels for more than two decades, scientists report in a study published Tuesday.

So far MERS has sickened more than 180 people, killing at least 77 of them — an alarming 43 percent. But scientists haven't been sure where the virus came from or how people catch it.

A report in the journal mBIO suggests the virus is ubiquitous among Saudi Arabiandromedary camels, the one-humped variety. The animals get the virus when they're young, and it often doesn't make them sick.

"We now know the answers to several questions," says the report's senior author, Ian Lipkinof Columbia University. "First, this virus infection is very common in camels. It probably occurs early in these camels. So this is a reservoir that is constantly replenishing itself. It can go directly from camels to humans, with no need for adaptation in another animal. And there's a lot of virus."

"This really confirms that this is a camel virus," says virologist Marion Koopmans of Erasmus University, who wasn't involved in the study. 

Koopmans and her team had previously found the MERS virus in camels as far afield as Africa and the Canary Islands. But the current study, she says, ends the discussion about whether camels get the virus from people. "It shows this virus is circulating in camels, period," Koopmans tells Shots.

At the same time, the new data leave other questions unanswered and even deepen some of the mystery around MERS.

The symptoms of MERS — often a life-threatening lung infection — can look similar to regular pnuemonias. So one question is whether people have been getting the virus for decades without anyone noticing or diagnosing it.

"What argues against that," Koopmans says, "is genetic sequence data from viruses picked up in people indicating that the virus emerged around mid-2012, not before that. That does not add up to infections having gone on for a long time, but that's still an open question."

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Gene Sequencing Could One Day Make Malaria Easier To Treat

Gene Sequencing Could One Day Make Malaria Easier To Treat | Amazing Science |
A malaria patient can carry different parasites that respond differently to drugs. Now there's a way to profile the parasites, which could someday lead to more tailored treatments.

Malaria has proved one of the hardest diseases on the planet to treat. The World Health Organization estimates there are nearly 200 million cases each year, and the parasitic infection is blamed for some 700,000 deaths annually.

One reason malaria may be so difficult to treat is that different types of malaria parasites can be streaming through the victim's body at the same time. Researchers at the Texas Biomedical Research Institute in Austin are now applying a form of DNA analysis called single-cell genome sequencing to better understand the various parasites in a single case.

For instance, the researchers found that people who'd come down with malaria along the Thai/Myanmar border had both Plasmodium vivax and Plasmodium falciparum parasites in their blood. This is problematic, because the standard drugs to treat each of these types are completely different. In addition, the Austin academics found that some of the parasites multiplying in the blood cells are resistant to antimalarial drugs, while others show no resistance.

Older DNA sequencing methods didn't allow researchers to analyze single parasites, according to Dr. Ian Cheeseman, who led the study.

"There were so many different strains of parasites within [a malaria infection] that we couldn't tell which was responsible for drug resistance or disease severity," Cheeseman tells Shots. "We really needed a method where we could work out the individual genome sequence of each parasite."

With single-cell genome sequencing Cheeseman and his colleagues found that some of the parasites were very closely related, but others were completely different strains. This raises the question of which strain is driving the illness inside the sick person, whether that could help tailor treatment.

According to Cheeseman's co-author, Shalini Nair, up to 70 percent of malaria cases in sub-Saharan Africa are "multiple genotype infections," meaning they're caused by multiple strains of the parasite.

"And we currently don't know how many genotypes are present and whether parasites come from a single mosquito bite or multiple mosquito bites," says Nair.

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Confirmed: An Asteroid Killed the Dinosaurs –– Date confirmed to accuracy of +/- 11,000 years

Confirmed: An Asteroid Killed the Dinosaurs –– Date confirmed to accuracy of +/- 11,000 years | Amazing Science |

Scientists have unearth credible evidence to confirm a large asteroid was responsible for the extinction of the dinosaurs over 66 million years ago, it has been announced. This particular extinction event, which paved the way for the evolution of our species, has been attributed to several different things over the years. From climate change, a nuclear winter caused by basaltic lava eruptions of massive volcanoes in western India, an influx of radiation from a nearby supernova explosion (or perhaps a gamma-ray burst) to finally, an asteroid impact, which has been a favorite of biologist and paleontologist over the course of the past few decades.

According to Paul Renne, the director at Berkeley University’s Geochronology Center in California, the asteroid impact was quite likely one of several contributing factors to the downfall of the prehistoric animals, as many of them were already on their way to extinction; however, Renne claims that this was the main catalyst that “pushed Earth past the tipping point.”

The collision was never in question, but the exact date of it is. Scientists have been trying to determine if the impact took place more than 300,000 years after the last of the dinosaurs had already died off in the Cretaceous-Tertiary extinction event, which is where Renne and his team comes in: Using high-precision radiometric dating analysis, in this case “argon-argon dating,” the team were able to determine the most precise date yet of the impact: 66,038,000 years ago – give or take 11,000, which coincides with the impact of an asteroid or a comet in the Caribbean off the Yucatan coast of Mexico. “We have shown that these events are synchronous to within a gnat’s eyebrow,” Renne continued. Potassium-argon dating is perhaps, one of the most reliable means of determine how long a sample of materials have been decaying, as it utilizes the fact that potassium, a naturally radioactive element, decays into argon with regularity.

It only takes a relatively small asteroid to cause quite a bit of destruction on our planet, as any object large enough to survive the descent through Earth’s atmosphere would acquire quite a bit of kinetic energy before it hits the surface of the planet, traveling at VERY fast speeds. Just to throw out one example of this, if an object had a diameter of about 10 kilometers and was traveling at speeds between [approximately] 15 to 20 kilometers per second, it would have a kinetic energy equal to 300 million nuclear bombs, going off simultaneously.

Almost instantly after the impact, the Earth would undergo rapid changes, including; “intense blinding light, severe radiation burns, a crushing blast wave, lethal balls of hot glass, winds with speeds of hundreds of kilometers per hour, and flash fires.” The rubble would be forced into the stratosphere, where it would block a majority of the sunlight from the plants and animals on the ground, which becomes problematic for the photosynthesis plants must undergo to derive energy to survive. With no plants converting sunlight into energy, our oxygen levels would decrease dramatically. I don’t have to explain why that is not an ideal situation to find ourselves in.

The asteroid that hit our planet at the end of the Mesozoic Era was almost 6 miles (10 km) across, generating more energy than nearly 100 trillion tons of TNT, which is more than a billion times more energetic than the bombs that destroyed Nagasaki and Hiroshima during WWII — ultimately leaving behind a crater named Chicxulub, which is more than 110 miles (180 kilometers) wide.

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West Antarctic Ice Sheet collapse is under way

West Antarctic Ice Sheet collapse is under way | Amazing Science |

University of Washington researchers used detailed topography maps and computer modeling to show that the collapse appears to have already begun. The fast-moving Thwaites Glacier will likely disappear in a matter of centuries, researchers say, raising sea level by nearly 2 feet. That glacier also acts as a linchpin on the rest of the ice sheet, which contains enough ice to cause another 10 to 13 feet (3 to 4 meters) of global sea level rise. The study is published May 16 in Science

“There’s been a lot of speculation about the stability of marine ice sheets, and many scientists suspected that this kind of behavior is under way,” said lead author Ian Joughin, a glaciologist at the UW’s Applied Physics Laboratory. “This study provides a more quantitative idea of the rates at which the collapse could take place.”

The good news is that while the word “collapse” implies a sudden change, the fastest scenario is 200 years, and the longest is more than 1,000 years. The bad news is that such a collapse may be inevitable.

“Previously, when we saw thinning we didn’t necessarily know whether the glacier could slow down later, spontaneously or through some feedback,” Joughin said. “In our model simulations it looks like all the feedbacks tend to point toward it actually accelerating over time; there’s no real stabilizing mechanism we can see.”

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The First Comprehensive Phylogenetic Reconstruction of the Order Actiniaria Reveals a Novel Group of Hexacorals

The First Comprehensive Phylogenetic Reconstruction of the Order Actiniaria Reveals a Novel Group of Hexacorals | Amazing Science |

Sea anemones (order Actiniaria) are among the most diverse and successful members of the anthozoan subclass Hexacorallia, occupying benthic marine habitats across all depths and latitudes. Actiniaria comprises approximately 1,200 species of solitary and skeleton-less polyps and lacks any anatomical synapomorphy. Although monophyly is anticipated based on higher-level molecular phylogenies of Cnidaria, to date, monophyly has not been explicitly tested and at least some hypotheses on the diversification of Hexacorallia have suggested that actiniarians are para- or poly-phyletic. Published phylogenies have demonstrated the inadequacy of existing morphological-based classifications within Actiniaria.

Superfamilial groups and most families and genera that have been rigorously studied are not monophyletic, indicating conflict with the current hierarchical classification. Scientists now tested the monophyly of Actiniaria using two nuclear and three mitochondrial genes with multiple analytical methods. These analyses are the first to include representatives of all three currently-recognized suborders within Actiniaria. They do not recover Actiniaria as a monophyletic clade: the deep-sea anemone Boloceroides daphneae, previously included within the infraorder Boloceroidaria, is resolved outside of Actiniaria in several of the analyses. This study erects a new genus and family for B. daphneae, and rank this taxon incerti ordinis.

Based on this comprehensive phylogeny, the authors of the study propose a new formal higher-level classification for Actiniaria composed of only two suborders, Anenthemonae and Enthemonae. Suborder Anenthemonae includes actiniarians with a unique arrangement of mesenteries (members of Edwardsiidae and former suborder Endocoelantheae). Suborder Enthemonae includes actiniarians with the typical arrangement of mesenteries for actiniarians (members of former suborders Protantheae, Ptychodacteae, and Nynantheae and subgroups therein). They also erect subgroups within these two newly-erected suborders. Although some relationships among these newly-defined groups are still ambiguous, morphological and molecular results are consistent enough to proceed with a new higher-level classification and to discuss the putative functional and evolutionary significance of several morphological attributes within Actiniaria.

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Genetic cause behind hemifacial microsomia found: Transcription factor OTX2 is to blame

Genetic cause behind hemifacial microsomia found: Transcription factor OTX2 is to blame | Amazing Science |

Whitehead Institute scientists have identified a genetic cause of a facial disorder known as hemifacial microsomia (HFM). The researchers find that duplication of the geneOTX2 induces HFM, the second-most common facial anomaly after cleft lip and palate. HFM affects approximately one in 3,500 births. While some cases appear to run in families, no gene had been found to be causative. That is until Whitehead Fellow Yaniv Erlich and his lab set out to do just that. Their work is described in this week’s issue of the journal PLOS ONE.

Patients with HFM tend to have asymmetrical faces—typically with one side of the upper and lower jaws smaller than the opposite side—a smaller or malformed ear on the affected side, and, in some cases, neurological or developmental abnormalities. Thought to be brought on by circulation difficulties during embryonic development, HFM is also thought to be sporadic—meaning that it occurs spontaneously rather than through inheritance. However, one family in northern Israel has more than its share of the anomaly.

To identify the origin of this family’s disorder, Erlich and lab technician Dina Zielinski began studying the genomes of a five-year-old female member of the family, along with those of her mother, grandmother, and male cousin, who all exhibited traits of HFM. Later, the genetic information from the grandmother’s Russian cousin, who resides in the Philadelphia area, was recruited to the study.

“What’s unique here is that this is the largest family with this disorder described in the literature,” says Erlich. “Most of the time, you see one person affected, or perhaps two people—a parent and a child. Such a large family increases the power of the genetic study and clearly signals that there is a genetic component to a disease.”

Within this large piece of DNA, Zielinski identified eight candidate genes that could cause the type of HFM running in this family. She then used two algorithms to compare the molecular signatures of these eight genes to other genes known to be responsible for various facial malformations with features similar to HFM. After this analysis, the gene OTX2 that codes for a transcription factor rose above the seven other candidates.

These results are supported by what is known of OTX2’s function. Previous data indicates that the gene codes for a protein that is expressed in the heads and pharyngeal arches of mouse embryos in developmental stages corresponding to the periods when HFM abnormalities are thought to arise in humans.

Although this is a tantalizing hint as to OTX2’s activity during development, Zielinski cautions that little is known about its overall role, in part because it serves as a transcription factor that regulates other genes.

OTX2’s activity is very complicated,” says Zielinski, who is first author of the PLOS ONE paper. “Development is dependent on tight control of these transcription factors that turn other genes on and off. The feedback between OTX2 and other transcription factors is complex but we know thatOTX2 plays a critical role in craniofacial patterning.”

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Beyond Cell Divisions : Synthetic Biology - Where Is The Field Headed?

Beyond Cell Divisions : Synthetic Biology - Where Is The Field Headed? | Amazing Science |

Since its debut in 2000, synthetic biology has seen considerable growth and now constitutes a vibrant research discipline that aims to apply engineering principles in the design and construction of complex biological systems. This Nature special charts the progress of the multidisciplinary field through reports, reviews and commentaries from NatureNature Methods and Nature Reviews Microbiology. Together, these explore the field’s potential and its challenges in developing clear goals, standards of practice and pathways to commercialization. A selection of material from the archives of Nature Publishing Group is also available.

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Unorthodox Study Claims Drug Prolongs Lives of Children With Premature Aging Disease

Unorthodox Study Claims Drug Prolongs Lives of Children With Premature Aging Disease | Amazing Science |

Survival numbers for progeria draw optimism from some, skepticism from others.

Despite an unpromising start for development of farnesyltransferase inhibitors (FTIs) in cancer indications, lonafarnib is now providing new hope for children with the rare and life-threatening genetic disease, progeria. Results from the first-ever clinical trial in children with progeria have recently been published, with every child showing an improvement in her symptoms (weight gain, bone structure, hearing and/or vascular stiffness).

Affecting one in eight million live births, progeria (also known as Hutchinson-Gilford Progeria Syndrome or HGPS), is a rare and fatal disease characterized by symptoms of premature aging in children.

Children with the disorder appear healthy at birth, but then fail to thrive. By the age of 18–24 months, symptoms such as limited growth, whole-body alopecia and distinctive facial features, become apparent. As the children age, signs and symptoms get progressively worse, with kidney failure, loss of eyesight and cardiovascular problems commonly reported.

Similarly to elderly people, affected children develop musculoskeletal degeneration with a loss of body fat and muscle, stiff joints, osteoporosis and often dislocation of the hips. The average lifespan of children with progeria is 13 (range 8–20) years, with death usually a consequence of heart attack or stroke caused by atherosclerosis.

Rarely inherited, progeria is caused by a sporadic, single-base mutation at position 1824 in the lamin A (LMNA) gene, resulting in substitution of thymine instead of cytosine. Lamin A is the structural scaffold that holds the cell nucleus together. Specifically, this occurs when a farnesyl functional group is attached to prelamin A, allowing temporary attachment to the nuclear rim and subsequent removal of the farnesyl group to produce lamin A.

The mutated lamin A protein that causes progeria is called progerin. Permanent farnesylation in progerin results in irreversible attachment to the nuclear membrane, causing inadequate structural support and interference with mitosis and other such processes.

In 2005, a study led by researchers at the University of California, Los Angeles, showed that a class of drugs called farnesyltransferase inhibitors (FTIs), which block the attachment of a molecule to the faulty protein that allows it to accumulate around the nucleus, restored normal shape to cells from kids with progeria. Several groups working with mice having the same mutation next established that the drug also reduced signs of premature aging in those rodents. Because FTIs had already been tested in children with cancer, with no significant side effects, PRF quickly pushed to start a trial of the FTI lonafarnib in 2007. Gordon, working with a team led by oncologist Mark Kieran of the Dana-Farber Cancer Institute in Boston, initially followed 25 children as they received the drug for at least 2 years. The trial results, published in 2012, showed that many of the patients had small weight gains and reductions in the stiffness of their blood vessels, though some scientists found the results inconclusive and hard to interpret.

In the new analysis, Gordon and her colleagues wanted to see whether children treated so far—including those in the first lonafarnib trial and those in an ongoing trial that adds two other drugs to the treatment—survived longer than untreated kids. But because there are so few children with progeria, and the disease is invariably fatal, PRF and the study designers had agreed not to create a group receiving a placebo; all who participated in the study received the drug, including Gordon’s son. For a comparison group, Gordon and her colleagues instead collected data about untreated children from historical records in the foundation’s international registry, previously published case reports, and public databases.

The finding “is very gratifying and encouraging,” says physician-geneticist Francis Collins, who is director of the National Institutes of Health in Bethesda, Maryland, and whose research team has studied the mechanisms of and potential treatments for progeria. Collins acknowledges that the lack of a direct control group enrolled in the trial is “not ideal,” but he notes “there really wasn’t much of an alternative to what was done—namely, to do an open-label trial where all of the kids were given the chance to have access to the drug.”

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First Sonic Tractor Beam Invented

First Sonic Tractor Beam Invented | Amazing Science |
Doctor Who visited Star Trek, and the crossover showed up in our reality as a macroscopic acoustic tractor beam. The newly-developed acoustic tractor beam can pull objects six orders of magnitude -- that's a million times! -- larger than any previous experiments.

The concept of manipulating matter through the careful application of fields first showed up in science fiction in Edward E. Smith's Spacehounds of IPC, a novel by the author/chemical engineer serialized in Amazing Science starting in 1931. Now, tractor beams have propagated to just about every corner of space-based science fiction. While some previous success has been achieved for tiny nanoparticles, a collaboration between researchers in Scotland and Illinois has managed to use tractor beams to manipulate relatively enormous centimeter-sized objects.

Getting the limitations out of the way, this tractor beam uses acoustic waves, and as every nit-picking scifi-fan knows, sound does not propagate in space. Even more inconveniently, shape matters: the tractor beam only works on objects that have a not-flat backside. But, for objects in the atmosphere that have junk in trunk, this beam can exert enough pressure to move it at will! long as it only takes a few millinewtons of force to haul it around. It really is as though the Doctor watched a bit too much Star Trek and tinkered with his sonic screwdriver just enough to add a handy new mini-tractor beam to his multitool.

Depending on the target object's shape, size, and interaction with the wave field, the scattering is going to be different. The end result can be anything from increasing negative radiation pressure (same as for plane waves) to decreasing positive radiation pressure: pushing things away or pulling them in.

So, what works best to haul in using an acoustic tractor beam? A hollow isosceles triangular prism. The researchers suspended the prism above the array, bombarded it with 550 kHz acoustic waves, then measured the pressure field.

Pointed at a hollow, light object with a nice, pointy backside, the tractor beam worked perfectly, producing a pressure differential in front of the object, pulling it in just like a good scif-fi tractor beam should. Had the triangle been flipped around to point into the beam and with a flat backside, the scattering would have been far less beneficial and the tractor beam rendered inoperable. Borg Cubes are safe between hiding in space, having an uncooperatively flat backside, and occupying substantially more than a few tens of cubic centimeters volume.

Why does it only work for sound, not light? The linear momentum of light is a it more complicated, with reflection, refraction, and absorption all playing a role, while sounds waves are pretty much just reflected or absorbed.

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