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Scooped by Dr. Stefan Gruenwald
August 20, 2016 1:01 PM
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Rainbow galaxies reveal why cosmos is full of spirals

Rainbow galaxies reveal why cosmos is full of spirals | Amazing Science | Scoop.it

Psychedelic pictures of 30 galactic collisions show for the first time that merging galaxies often spawn disc-shaped offspring like our Milky Way.

 

These images show the carbon monoxide gas detected in neighboring galaxies – 40 to 600 million light years from Earth – in their final stages of merging. The colors show how this gas was moving: blue represents gas that is moving towards us, while red indicates gas that is moving away.

 

Out of 37 galaxies observed, these 30 all show gas rotating around the centre of the galaxy, meaning they are disc galaxies in the making.

 

“For the first time there is observational evidence for merging galaxies that could result in disc galaxies. This is a large and unexpected step towards understanding the mystery of the birth of disc galaxies,” says Junko Ueda from the Japan Society for the Promotion of Science. Ueda and her team made the observations using data from the ALMA radio telescope.

 

Computer simulations suggested that when galaxies merge, they usually form a single blob-shaped galaxy classed as “elliptical”. However, most of the galaxies in the universe are pancake-shaped “disc” galaxies, such as lenticular galaxies and our own spiral Milky Way. As this rogues’ gallery of galactic mergers shows, a disc-shaped offspring is a common result of a collision.

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Scooped by Dr. Stefan Gruenwald
August 19, 2016 6:30 PM
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Biologists are close to reinventing the genetic code of life

Biologists are close to reinventing the genetic code of life | Amazing Science | Scoop.it

The term "life hacking" usually refers to clever tweaks that make your life more productive. But this week in Science, a team of scientists comes a step closer to the literal meaning: hacking the machinery of life itself. They have designed—though not completely assembled—a synthetic Escherichia coli genome that could use a protein-coding scheme different from the one employed by all known life. Requiring a staggering 62,000 DNA changes, the finished genome would be the most complicated genetic engineering feat so far. E. coli running this rewritten genome could become a new workhorse for laboratory experiments and a factory for new industrial chemicals, its creators predict.

 

Such a large-scale genomic hack once seemed impossible, but no longer, says Peter Carr, a bioengineer at the Massachusetts Institute of Technology Lincoln Laboratory in Lexington who is not involved with the project. "It's not easy, but we can engineer life at profound scales, even something as fundamental as the genetic code."

 

The genome hacking is underway in the lab of George Church at Harvard University, the DNA-sequencing pioneer who has become the most high-profile, and at times controversial, name in synthetic biology. The work takes advantage of the redundancy of life's genetic code, the language that DNA uses to instruct the cell's protein-synthesizing machinery. To produce proteins, cells "read" DNA's four-letter alphabet in clusters of three called codons. The 64 possible triplets are more than enough to encode the 20 amino acids that exist in nature, as well as the "stop" codons that mark the ends of genes. As a result, the genetic code has multiple codons for the same amino acid: the codons CCC and CCG both encode the amino acid proline, for example.

 

Church and others hypothesized that redundant codons could be eliminated—by swapping out every CCC for a CCG in every gene, for instance—without harming the cell. The gene that enables CCC to be translated into proline could then be deleted entirely. "There are a number of 'killer apps'" of such a "recoded" cell, says Farren Isaacs, a bioengineer at Yale University, who, with Church and colleagues, showed a stop codon can be swapped out entirely from E. coli.

 

The cells could be immune to viruses that impair bioreactors, for example, if crucial viral genes include now untranslatable codons. The changes could also allow synthetic biologists to repurpose the freed redundant codons for an entirely different function, such as coding for a new, synthetic amino acid.

 

For this study, Church's team decided to eliminate seven of the microbe's 64 codons. That target seemed like "a good balance" between the number of changes that appeared technically achievable and the number that might be too many for a cell to survive, says Matthieu Landon, one of Church's Ph.D. students. And the seven spare codons could eventually be repurposed to code up to four different unnatural amino acids.

 

But making so many changes, even with the latest DNA editing techniques such as CRISPR, still appeared impossible. Luckily, the cost of synthesizing DNA has plummeted over the past decade. So instead of editing the genome one site at a time, Church's team used machines to synthesize long stretches of the recoded genome from scratch, each chunk containing multiple changes.

 

The team has now turned to the laborious job of inserting these chunks into E. coli one by one and making sure that none of the genomic changes is lethal to the cells. The researchers have only tested 63% of the recoded genes so far, but remarkably few of the changes have caused trouble, they say.

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Scooped by Dr. Stefan Gruenwald
August 19, 2016 6:20 PM
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Physicists reach lowest temperature ever recorded in solids using laser cooling

Physicists reach lowest temperature ever recorded in solids using laser cooling | Amazing Science | Scoop.it

Dr. Mansoor Sheik-Bahae, professor of physics and astronomy, along with his research group, are advancing a technique called optical refrigeration to reach cryogenic temperature. Essentially, the group is using laser light to chill a special type of crystal, which can then be attached to a device that requires constant and reliable cooling, like infrared detectors on satellites. What sets their technique apart is the temperatures it can cool to without having any moving parts.

 

“Right now, anything that cools other parts of a system has moving parts. Most of the time, there’s liquid running through it that adds vibrations which can impact the precision or resolution of the device,” explained Aram Gragossian, a research assistant in Sheik-Bahae’s lab. “But, when you have optical refrigeration, you can go to low temperatures without any vibrations and without any moving parts, making it convenient for a lot of applications.

 

Earlier this year, Sheik-Bahae, along with collaborators at UNM, and Los Alamos National Labs, reached the lowest temperatures ever recorded using an all-solid-state cryocooler – 91 kelvin or -296o Fahrenheit – temperatures that were previously only able to be reached using liquid nitrogen or helium. The research, Solid-state optical refrigeration to sub-100 Kelvin regime, was published in the journal of (Nature) Scientific Reports 6.

 

“Here at UNM, we are the only group in the world that’s been able to cool to cryogenic temperatures with an all-solid-state optical cryocooler,” said Alexander Albrecht, one of the paper’s co-authors and research assistant professor at UNM.

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Scooped by Dr. Stefan Gruenwald
August 19, 2016 12:39 PM
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Exoplanet GJ 1132b Might Have a Thin Oxygen Atmosphere

Exoplanet GJ 1132b Might Have a Thin Oxygen Atmosphere | Amazing Science | Scoop.it

New research from the Harvard-Smithsonian Center for Astrophysics reveals that the Venus-like Exoplanet GJ 1132b might possess a thin, oxygen atmosphere – but no life due to its extreme heat.

 

The distant planet GJ 1132b intrigued astronomers when it was discovered last year. Located just 39 light-years from Earth, it might have an atmosphere despite being baked to a temperature of around 450 degrees Fahrenheit. But would that atmosphere be thick and soupy or thin and wispy? New research suggests the latter is much more likely.

 

Harvard astronomer Laura Schaefer (Harvard-Smithsonian Center for Astrophysics, or CfA) and her colleagues examined the question of what would happen to GJ 1132b over time if it began with a steamy, water-rich atmosphere.

 

Orbiting so close to its star, at a distance of just 1.4 million miles, the planet is flooded with ultraviolet or UV light. UV light breaks apart water molecules into hydrogen and oxygen, both of which then can be lost into space. However, since hydrogen is lighter it escapes more readily, while oxygen lingers behind.

 

“On cooler planets, oxygen could be a sign of alien life and habitability. But on a hot planet like GJ 1132b, it’s a sign of the exact opposite – a planet that’s being baked and sterilized,” said Schaefer.

 

Since water vapor is a greenhouse gas, the planet would have a strong greenhouse effect, amplifying the star’s already intense heat. As a result, its surface could stay molten for millions of years.

 

A “magma ocean” would interact with the atmosphere, absorbing some of the oxygen, but how much? Only about one-tenth, according to the model created by Schaefer and her colleagues. Most of the remaining 90 percent of leftover oxygen streams off into space, however some might linger.

 

“This planet might be the first time we detect oxygen on a rocky planet outside the solar system,” said co-author Robin Wordsworth (Harvard Paulson School of Engineering and Applied Sciences). If any oxygen does still cling to GJ 1132b, next-generation telescopes like the Giant Magellan Telescope and James Webb Space Telescope may be able to detect and analyze it.

 

The magma ocean-atmosphere model could help scientists solve the puzzle of how Venus evolved over time. Venus probably began with Earthlike amounts of water, which would have been broken apart by sunlight. Yet it shows few signs of lingering oxygen. The missing oxygen problem continues to baffle astronomers.

 

Schaefer predicts that their model also will provide insights into other, similar exoplanets. For example, the system TRAPPIST-1 contains three planets that may lie in the habitable zone. Since they are cooler than GJ 1132b, they have a better chance of retaining an atmosphere.

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Scooped by Dr. Stefan Gruenwald
August 19, 2016 12:28 PM
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Astronomers captured a 'classical nova' explosion on camera

Astronomers captured a 'classical nova' explosion on camera | Amazing Science | Scoop.it
Polish astronomers, based in Chile, were performing a sky survey that intended the detection of dark matter. But they obtained much more, discovering the process of a classical nova explosion. Results are published in the science journal Nature as researchers collected images for the “Optical Gravitational Lensing Experiment“,  discovering they had a timeline that captured the rare event.
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Scooped by Dr. Stefan Gruenwald
August 19, 2016 12:22 PM
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Scientists uncover origin of high-temperature superconductivity in copper-oxide compound

Scientists uncover origin of high-temperature superconductivity in copper-oxide compound | Amazing Science | Scoop.it

 Since the 1986 discovery of high-temperature superconductivity in copper-oxide compounds called cuprates, scientists have been trying to understand how these materials can conduct electricity without resistance at temperatures hundreds of degrees above the ultra-chilled temperatures required by conventional superconductors. Finding the mechanism behind this exotic behavior may pave the way for engineering materials that become superconducting at room temperature. Such a capability could enable lossless power grids, more affordable magnetically levitated transit systems, and powerful supercomputers, and change the way energy is produced, transmitted, and used globally.

 

Now, physicists at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory have an explanation for why the temperature at which cuprates become superconducting is so high. After growing and analyzing thousands of samples of a cuprate known as LSCO for the four elements it contains (lanthanum, strontium, copper, and oxygen), they determined that this "critical" temperature is controlled by the density of electron pairs—the number of electron pairs per unit area. This finding, described in a Nature paper published August 17, challenges the standard theory of superconductivity, which proposes that the critical temperature depends instead on the strength of the electron pairing interaction.

 

"Solving the enigma of high-temperature superconductivity has been the focus of condensed matter physics for more than 30 years," said Ivan Bozovic, a senior physicist in Brookhaven Lab's Condensed Matter Physics and Materials Science Department who led the study. "Our experimental finding provides a basis for explaining the origin of high-temperature superconductivity in the cuprates—a basis that calls for an entirely new theoretical framework."

 

According to Bozovic, one of the reasons cuprates have been so difficult to study is because of the precise engineering required to generate perfect crystallographic samples that contain only the high-temperature superconducting phase.

 

"It is a materials science problem. Cuprates can have up to 50 atoms per unit cell and the elements can form hundreds of different compounds, likely resulting in a mixture of different phases," said Bozovic.

 

That's why Bozovic and his research team grew their more than 2,500 LSCO samples by using a custom-designed molecular beam epitaxy system that places single atoms onto a substrate, layer by layer. This system is equipped with advanced surface-science tools, such as those for absorption spectroscopy and electron diffraction, that provide real-time information about the surface morphology, thickness, chemical composition, and crystal structure of the resulting thin films.

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Scooped by Dr. Stefan Gruenwald
August 19, 2016 12:19 PM
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From MACHOs to WIMPs—top five candidates for 'dark matter'

From MACHOs to WIMPs—top five candidates for 'dark matter' | Amazing Science | Scoop.it

There are four fundamental forces that a dark matter particle could interact with. There is the strong force that binds together the atomic nucleus; the weak force which governs the decay of particles such as radioactivity; an electromagnetic force that mediates the force between charged particles; and the gravitational force which governs gravitational interaction. To observe matter in space we need it to interact via the electromagnetic force, as this involves the release of light or other electromagnetic radiation that a telescope can register.

 

Here are the five candidates for particles that I think have the best chance:

 

1. The WIMP

The weakly interacting massive particle, or WIMP, is a hypothetical particle that looks promising. It would be completely different from the type of matter we know and would interact via the electromagnetic force, which would explain why they are largely invisible in space. Roughly 100,000 of these would pass through every square centimeter of the Earth each second, interacting only via the weak force and gravity with surrounding matter. WIMPs have been the subject of a lot of extensive research, especially beyond the Standard Model of physics, which independently predicted that such a particle must exist – a coincidence dubbed the "WIMP miracle".

 

2. The Axion

Axions are low-mass, slow-moving particles that don't have a charge and only interact weakly with other matter which makes them difficult – but but not impossible – to detect. Only axions of a specific mass would be able to explain the invisible nature of dark matter – if they are any lighter or heavier we would be able to see them. And if axions do exist they would be able to decay into a pair of light particle (photons), which means we could detect them by looking for such pairs. Experiments including the Axion Dark Matter Experiment is currently looking for axions in this way.

 

3. The MACHO

MACHO stands for "massive astrophysical compact halo object" and was one of the first proposed candidates for dark matter. These objects, including neutron stars, and brown and white dwarfs, are composed of ordinary matter. So how could they be invisible? The reason is that they emit very little to no light.

One way to observe them is by monitoring the brightness of distant stars. As light rays bend when they pass close to a massive object, light from a distant source may be focused by a closer object to produce a sudden brightening of the distant object. This effect, known as gravitational lensing, depends on how much matter, both normal and dark, is in a galaxy – we can use it to calculate the amount of matter lurking around. However, we now know it is unlikely that enough of these dark bodies could accumulate to make up the vast amount of dark matter that exists.

 

4. The Kaluza-Klein particle

The Kaluza-Klein theory is built around the existence of an invisible "fifth dimension" curled up in space, in addition to the three spatial dimensions we know (height, width, depth), and time. This theory, a precursor to string theory, predicts the existence of a particle that could be a dark matter particle, which would have the same mass as 550 to 650 protons (these make up the atomic nucleus together with neutrons).

This kind of particle could interact both via electromagnetism and gravity. However, as it is curled up in a dimension we can't see, we wouldn't observe it by just by looking at the sky. Luckily, the particle should be is easy to look for in experiments as it should decay into particles we can measure – into neutrinos and photons. However, powerful particle accelerators like the Large Hadron Collider are yet to detect it.

 

5. The Gravitino

Theories combining general relativity and "supersymmetry" predict the existence of a particle called the gravitino. Supersymmetry, which is a successful theory explaining a lot of observations in physics, states that all "boson" particles – such as the photon (light particle)– have a "superpartner", the photino, with a property called "spin" (a type of angular momentum) that differs by a half-integer. The gravitino would be the superpartner of the hypothetical "graviton", thought to mediate the force of gravitation. And in some models of supergravity where the gravitino is very light, it could account for dark matter.

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Scooped by Dr. Stefan Gruenwald
August 17, 2016 2:49 PM
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Catalog of genetic information from 60,000 people reveals unexpected surprises

Catalog of genetic information from 60,000 people reveals unexpected surprises | Amazing Science | Scoop.it

More than one million people have now had their genome sequenced, or its protein-coding regions (the exome). The hope is that this information can be shared and linked to phenotype — specifically, disease — and improve medical care. An obstacle is that only a small fraction of these data are publicly available:

 

 

In an important step, we report this week the first publication from the Exome Aggregation Consortium (ExAC), which has generated the largest catalogue so far of variation in human protein-coding regions. It aggregates sequence data from some 60,000 people. Most importantly, it puts the information in a publicly accessible database that is already a crucial resource (http://exac.broadinstitute.org).

 

There are challenges in sharing such data sets — the project scientists deserve credit for making this one open access. Its scale offers insight into rare genetic variation across populations. It identifies more than 7.4 million (mostly new) variants at high confidence, and documents rare mutations that independently emerged, providing the first estimate of the frequency of their recurrence. And it finds 3,230 genes that show nearly no cases of loss of function. More than two-thirds have not been linked to disease, which points to how much we have yet to understand.

 

The study also raises concern about how genetic variants have been linked to rare disease. The average ExAC participant has some 54 variants previously classified as causal for a rare disorder; many show up at an implausibly high frequency, suggesting that they were incorrectly classified. The authors review evidence for 192 variants reported earlier to cause rare Mendelian disorders and found at a high frequency by ExAC, and uncover support for pathogenicity for only 9. The implications are broad: these variant data already guide diagnoses and treatment (see, E. V. Minikel et al. Sci. Transl. Med. 8, 322ra9; 2016 and R. Walsh et al. Genet. Med. http://dx.doi.org/10.1038/gim.2016.90; 2016).

 

These findings show that researchers and clinicians must carefully evaluate published results on rare genetic disorders. And it demonstrates the need to filter variants seen in sequence data, using the ExAC data set and other reference tools — a practice widely adopted in genomics.

 

The ExAC project plans to grow over the next year to include 120,000 exome and 20,000 whole-genome sequences. It relies on the willingness of large research consortia to cooperate, and highlights the huge value of sharing, aggregation and harmonization of genomic data. This is also true for patient variants — there is a need for databases that provide greater confidence in variant interpretation, such as the US National Center for Biotechnology Information’s ClinVar database.

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Scooped by Dr. Stefan Gruenwald
August 17, 2016 2:09 PM
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Scientists Watch Bacterial Sensor Respond to Light in Real Time

Scientists Watch Bacterial Sensor Respond to Light in Real Time | Amazing Science | Scoop.it
High-speed X-ray camera reveals ultrafast atomic motions at the root of organisms’ ability to turn light into biological function.

 

Now, researchers have made a giant leap forward in taking snapshots of these ultrafast reactions in a bacterial light sensor. Using the world’s most powerful X-ray laser at the Department of Energy’s SLAC National Accelerator Laboratory, they were able to see atomic motions as fast as 100 quadrillionths of a second – 1,000 times faster than ever before.

 

Further, “We’re the first to succeed in taking real-time snapshots of an ultrafast structure transition in a protein, in which a molecule excited by light relaxes by rearranging its structure in what is known as trans-to-cis isomerization,” says the study’s principal investigator, Marius Schmidt from the University of Wisconsin, Milwaukee.

 

The technique could widely benefit studies of light-driven, ultrafast atomic motions. For example, it could reveal:

 

  • How visual pigments in the human eye respond to light, and how absorbing too much of it damages them.
  • How photosynthetic organisms turn light into chemical energy – a process that could serve as a model for the development of new energy technologies.
  • How atomic structures respond to light pulses of different shape and duration – an important first step toward controlling chemical reactions with light.

 

“The new data show for the first time how the bacterial sensor reacts immediately after it absorbs light,” says Andy Aquila, a researcher at SLAC’s Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility. “The initial response, which is almost instantaneous, is absolutely crucial because it creates a ripple effect in the protein, setting the stage for its biological function. Only LCLS’s X-ray pulses are bright enough and short enough to capture biological processes on this ultrafast timescale.” The results were published today in Science.

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Scooped by Dr. Stefan Gruenwald
August 17, 2016 1:26 PM
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Developing Novel Techniques to Visualize Uncultured Microbial Cell Activity

Developing Novel Techniques to Visualize Uncultured Microbial Cell Activity | Amazing Science | Scoop.it

Short for BioOrthogonal Non-CanonicalAmino acid Tagging, BONCAT is a technique developed at Caltech for bioengineering studies, but was adapted by Hatzenpichler and Orphan for use in microbial ecology investigations. BONCAT uses synthetic amino acids to label protein-making cells. These amino acids can then be stained with a fluorescent tag, lighting up active cells in their habitat. For this study, Hatzenpichler and his colleagues used sediment samples collected from deep-sea methane seep sediments off the coasts of Oregon and California for a series of incubation experiments, tracking the slow growth of methane-metabolizing bacterial and archaeal populations.

 

The microbial communities in these sediments include aggregates of methane-oxidizing archaea called ANME (for ANaerobic MEthanotrophs) and sulfate-reducing bacteria (SRB) that live together symbiotically and help to remove some 80 percent of the methane released from ocean sediments.

The Caltech researchers combined BONCAT with fluorescent in situ hybridization (FISH) to analyze active microbes within these simulated environments and identify under which conditions they were active. “Typically, every methane seep site hosts several different groups of archaeal methane-oxidizers,” Hatzenpichler said. “A long-standing hypotheses has been that different members from these groups are differently active at different times. By exploiting the capability to do BONCAT analyses in comparatively high-throughput mode, we found members of all groups of methane-oxidizing archaea were anabolically active during the incubation. Now we can start asking why.”

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Scooped by Dr. Stefan Gruenwald
August 17, 2016 1:20 PM
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Quantum effects of Hawking radiation seen in the lab for the first time

Quantum effects of Hawking radiation seen in the lab for the first time | Amazing Science | Scoop.it

Jeff Steinhauer, a physicist at the Israel Institute of Technology, has published a paper in the journal Nature Physics describing experiments in which he attempted to create a virtual black hole in the lab in order to prove that Stephen Hawking's theory of radiation emanating from black holes is correct —though his experiments are based on sound, rather than light. In his paper, he claims to have observed the quantum effects of Hawking radiation in his lab as part of a virtual black hole—which, if proven to be true, will be the first time it has ever been achieved.

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Scooped by Dr. Stefan Gruenwald
August 17, 2016 1:13 PM
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Blocking a human branched DNA enzyme offers new ways of targeting cancer

Blocking a human branched DNA enzyme offers new ways of targeting cancer | Amazing Science | Scoop.it

Branched or flapped DNAs with single stranded ends are formed during healthy human DNA replication and DNA repair.

These single-stranded flaps can be removed by enzymes such as flap endonuclease 1 (FEN1) to restore the integrity of the DNA to its double-stranded state.

 

Higher levels of FEN1 have been seen in cancer cells with clinically worse prognosis3 and these cells are more reliant on this repair enzyme especially in the absence of other supporting DNA damage response proteins. These latter cells are sensitive to and die when FEN1 is blocked – a term called synthetic lethality. Preventing the action of enzymes like FEN1 maybe a way of selectively killing such cancer cells.

 

The collaborative, interdisciplinary team of scientists from the University of Sheffield, Pelago Bioscience and AstraZeneca took detailed images of the way previously confirmed inhibitors4 bind and block FEN1 to provide clues as to how the functionality of the protein is prevented.

 

“It’s been an exciting privilege for us to work with AstraZeneca and apply this knowledge to potentially intervene in a serious human disease.”

 

At AstraZeneca, the collaboration was led by Dr Steve Durant, Dr Cliff Jones and Dr Willem Nissink from AstraZeneca’s Innovative Medicine & Early Development Biotech Unit.

 

Dr Durant said: “This has been a fantastic collaboration between us, the University of Sheffield and the Biotech company Pelago.

“It has really boosted our understanding of how a specific set of compounds we previously confirmed as FEN1 inhibitors work. This insight helps us develop ways of blocking nucleases, a crucial family of enzymes in the cellular DNA Damage Response and one of AstraZeneca’s key strategic areas of focus in Oncology drug development”.

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August 16, 2016 5:19 PM
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After 100 Years, Ramanujan Gap Filled

After 100 Years, Ramanujan Gap Filled | Amazing Science | Scoop.it

Who was Ramanujan?

 

A century ago, Srinivasa Ramanujan and G. H. Hardy started a famous correspondence about mathematics so amazing that Hardy described it as “scarcely possible to believe.” On May 1, 1913, Ramanujan was given a permanent position at the University of Cambridge. Five years and a day later, he became a Fellow of the Royal Society, then the most prestigious scientific group in the world. In 1919 Ramanujan was deathly ill while on a long ride back to India, from February 27 to March 13 on the steamship Nagoya. All he had was a pen and pad of paper (no Mathematica at that time), and he wanted to write down his equations before he died. He claimed to have solutions for a particular function, but only had time to write down a few before moving on to other areas of mathematics. He wrote the following incomplete equation with 14 others, only 3 of them solved.

 

Within months, he passed away, probably from hepatic amoebiasis. His final notebook was sent by the University of Madras to G. H. Hardy, who in turn gave it to mathematician G. N. Watson. When Watson died in 1965, the college chancellor found the notebook in his office while looking through papers scheduled to be incinerated. George Andrews rediscovered the notebook in 1976, and it was finally published in 1987. Bruce Berndt and Andrews wrote about Ramanujan’s Lost Notebook in a series of books (Part 1, Part 2, and Part 3). Berndt said, “The discovery of this ‘Lost Notebook’ caused roughly as much stir in the mathematical world as the discovery of Beethoven’s tenth symphony would cause in the musical world.”

 

In his book analyzing Ramanujan’s results, Berndt investigates the existence of a solution for many of Ramanujan's equations. Now we know, sometimes a solution exists as elegant as other values found by Ramanujan himself.

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August 19, 2016 6:33 PM
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Microbe-ID: an open source toolbox for microbial genotyping and species identification

Microbe-ID: an open source toolbox for microbial genotyping and species identification | Amazing Science | Scoop.it

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available.

 

To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database.

 

Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database.

 

Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org).

 

In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.


Via Jean-Michel Ané, Eric Vincill
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August 19, 2016 6:22 PM
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Newly discovered material property may lead to high temp superconductivity

Newly discovered material property may lead to high temp superconductivity | Amazing Science | Scoop.it

Researchers at the U.S. Department of Energy's (DOE) Ames Laboratory have discovered an unusual property of purple bronze that may point to new ways to achieve high temperature superconductivity. While studying purple bronze, a molybdenum oxide, researchers discovered an unconventional charge density wave on its surface.

 

A charge density wave (CDW) is a state of matter where electrons bunch together in a repeating pattern, like a standing wave of surface of water. Superconductivity and charge density waves share a common origin, often co-exist, and can compete for dominance in certain materials.

 

Conventional CDWs and superconductivity both arise from electron-phonon interactions, the interaction of electrons with the vibrations of the crystal lattice. Electron-electron interactions are the likely origin of unconventional, high-temperature superconductivity such as found in copper- and iron-based compounds.

 

Unconventional, electron-electron driven CDW are extremely rare and its discovery here is important, because the material showed an 'extraordinary' increase of CDW transition temperature from 130K (-143C) to 220K (-53C) and a huge increase of energy gap at the surface.

 

Both are properties essential for CDW and high-temperature superconductivity, explained Adam Kaminski, Ames Laboratory scientist and professor in the Department of Physics and Astronomy at Iowa State University.

 

"This was an accidental but very exciting discovery," said Kaminski. "We were studying this material because its one-dimensional structure makes it quite interesting. We saw strange things happening to the electronic band structure, but when we looked at the surface we were stunned by extraordinary enhancement of transition temperature and energy gap."

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August 19, 2016 6:10 PM
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New Chinese Plant Wants to Clone 1 Million Cows Annually

New Chinese Plant Wants to Clone 1 Million Cows Annually | Amazing Science | Scoop.it
The world’s largest cloning plant is expected to clone 1 million cattle annually and is currently under construction in China.

 

Imagine one million identical cows marching shoulder to shoulder and rib to rib down a path to the slaughterhouse. Imagine one million identical cows getting the same idea simultaneously to turn around and storm the cloning plant that created them. Somewhere in between is what probably will happen when the world’s largest cloning plant, currently under construction in China, goes into full operation in early 2016.


Plant where 1 million cows will be cloned annually

The $31 million plant is being built in Tianjin (160 km (100 miles) from Beijing) by BoyaLife, a three-year-old biotech firm specializing in stem cell and regenerative medicine, biological products, drug innovation and hereditary diseases research. The plan for the 14,000 square meter (150,000 sq. ft.) plant is to produce 100,000 cloned cattle embryos the first year and ramp quickly up to a million annually to satisfy China’s rapidly-growing demand for beef.

 

In addition to cattle, the company will clone pet dogs, police dogs, racehorses and “non-human primates,” with the somewhat altruistic goal of being the first to someday clone endangered pandas.

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Scooped by Dr. Stefan Gruenwald
August 19, 2016 12:30 PM
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Natural scale caterpillar soft robot is powered and controlled with light

Natural scale caterpillar soft robot is powered and controlled with light | Amazing Science | Scoop.it
Researchers at the Faculty of Physics at the University of Warsaw, using the liquid crystal elastomer technology, originally developed in the LENS Institute in Florence, demonstrated a bioinspired micro-robot capable of mimicking caterpillar gaits in natural scale. The 15-millimeter long soft robot harvests energy from green light and is controlled by spatially modulated laser beam. Apart from travelling on flat surfaces, it can also climb slopes, squeeze through narrow slits and transport loads.

For decades scientists and engineers have been trying to build robots mimicking different modes of locomotion found in nature. Most of these designs have rigid skeletons and joints driven by electric or pneumatic actuators. In nature, however, a vast number of creatures navigate their habitats using soft bodies - earthworms, snails and larval insects can effectively move in complex environments using different strategies. Up to date, attempts to create soft robots were limited to larger scale (typically tens of centimeters), mainly due to difficulties in power management and remote control.

Liquid Crystalline Elastomers (LCEs) are smart materials that can exhibit large shape change under illumination with visible light. With the recently developed techniques, it is possible to pattern these soft materials into arbitrary three dimensional forms with a pre-defined actuation performance. The light-induced deformation allows a monolithic LCE structure to perform complex actions without numerous discrete actuators.

Researchers from the University of Warsaw with colleagues from LESN (Italy) and Cambridge (UK) have now developed a natural-scale soft caterpillar robot with an opto-mechanical liquid crystalline elastomer monolithic design. The robot body is made of a light sensitive elastomer stripe with patterned molecular alignment. By controlling the travelling deformation pattern the robot mimics different gaits of its natural relatives. It can also walk up a slope, squeeze through a slit and push objects as heavy as ten times its own mass, demonstrating its ability to perform in challenging environments and pointing at potential future applications.
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Scooped by Dr. Stefan Gruenwald
August 19, 2016 12:25 PM
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Sea ice strongly linked to climate change in past 90 000 years

Sea ice strongly linked to climate change in past 90 000 years | Amazing Science | Scoop.it

“The Arctic sea ice responded very rapidly to past climate changes. During the coldest periods of the past 90,000 years the sea ice edge spread relatively quickly to the Greenland-Scotland Ridge, and probably far into the Atlantic Ocean.” says Ulrike Hoff, a researcher at Centre for Arctic Gas Hydrate, Environment and Climate (CAGE).

 

Sea ice amplifies the climate changes that are occurring at any given time. Its growth and melting has profound effects on climate, the marine environment and ocean circulation.

 

Hoff and colleagues studied the past distribution of sea ice, in the so far longest existing sea ice record in a marine sediment core. The core was retrieved from 1200m water depth from the ocean floor of the Nordic Seas, just off the Faroe Islands. The core represents 90,000 years of sediment layers, and it is by studying those layers that scientist can reveal the changes in sea ice and past climate.

 

It was the tiniest of evidence in these layers that brought this strong confirmation of sea ice behavior to light. They are a type of phytoplankton, called diatoms, and they are everywhere around you. Diatoms are single celled algae with a cell wall made up of silica.

 

“They are the golden brown coating in the glass of a street lamp, and shiny stuff in your make-up. They are even used in tooth paste as a cleaning agent.,” says Hoff. “Diatoms are truly amazing, and can be preserved in marine and lake sediments for millions of years. I have personally examined diatom fossils that are 65 million of years old, and they look much the same as the diatoms that we find living today.”

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August 19, 2016 12:21 PM
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Neuromorphic computing mimics important brain features

Neuromorphic computing mimics important brain features | Amazing Science | Scoop.it

In the future, level-tuned neurons may help enable neuromorphic computing systems to perform tasks that traditional computers cannot, such as learning from their environment, pattern recognition, and knowledge extraction from big data sources.

The researchers, Angeliki Pantazi et al., at IBM Research-Zurich and École Polytechnique Fédérale de Lausanne, both in Switzerland, have published a paper on the new neuromorphic architecture in a recent issue of Nanotechnology.

 

Like all neuromorphic computing architectures, the proposed system is based on neurons and their synapses, which are the junctions where neurons send signals to each other. In this study, the researchers physically implemented artificial neurons using phase-change materials. These materials have two stable states: a crystalline, low-resistivity state and an amorphous, high-resistivity state. Just as in traditional computing, the states can be switched by the application of a voltage. When the neuron's conductance reaches a certain threshold, the neuron fires.

 

"We have demonstrated that phase-change-based memristive devices can be used to create artificial neurons and synapses to store and process data," coauthor Evangelos Eleftheriou at IBM Research-Zurich explains. "A phase-change neuron uses the phase configuration of the phase-change material to represent its internal state, the membrane potential. For the phase-change synapse, the synaptic weight—which is responsible for the plasticity—is encoded by the conductance of the nanodevice."

In this architecture, each neuron is tuned to a specific range, or level. Neurons receive signals from many other neurons, and a level is defined as the cumulative contribution of the sum of these incoming signals.

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August 18, 2016 3:30 PM
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Theory of everything? How spacetime is built by quantum entanglement

Theory of everything? How spacetime is built by quantum entanglement | Amazing Science | Scoop.it

A collaboration of physicists and a mathematician has made a significant step toward unifying general relativity and quantum mechanics by explaining how spacetime emerges from quantum entanglement in a more fundamental theory. 

 

Physicists and mathematicians have long sought a Theory of Everything (ToE) that unifies general relativity and quantum mechanics. General relativity explains gravity and large-scale phenomena such as the dynamics of stars and galaxies in the universe, while quantum mechanics explains microscopic phenomena from the subatomic to molecular scales.

 

The holographic principle is widely regarded as an essential feature of a successful Theory of Everything. The holographic principle states that gravity in a three-dimensional volume can be described by quantum mechanics on a two-dimensional surface surrounding the volume. In particular, the three dimensions of the volume should emerge from the two dimensions of the surface. However, understanding the precise mechanics for the emergence of the volume from the surface has been elusive.

 

The paper announcing the discovery by Hirosi Ooguri, a Principal Investigator at the University of Tokyo's Kavli IPMU, with Caltech mathematician Matilde Marcolli and graduate students Jennifer Lin and Bogdan Stoica, will be published in Physical Review Letters as an Editors' Suggestion "for the potential interest in the results presented and on the success of the paper in communicating its message, in particular to readers from other fields."

 

Now, Ooguri and his collaborators have found that quantum entanglement is the key to solving this question. Using a quantum theory (that does not include gravity), they showed how to compute energy density, which is a source of gravitational interactions in three dimensions, using quantum entanglement data on the surface. This is analogous to diagnosing conditions inside of your body by looking at X-ray images on two-dimensional sheets. This allowed them to interpret universal properties of quantum entanglement as conditions on the energy density that should be satisfied by any consistent quantum theory of gravity, without actually explicitly including gravity in the theory. The importance of quantum entanglement has been suggested before, but its precise role in emergence of spacetime was not clear until the new paper by Ooguri and collaborators.

 

Quantum entanglement is a phenomenon whereby quantum states such as spin or polarization of particles at different locations cannot be described independently. Measuring (and hence acting on) one particle must also act on the other, something that Einstein called "spooky action at distance." The work of Ooguri and collaborators shows that this quantum entanglement generates the extra dimensions of the gravitational theory.

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August 17, 2016 2:32 PM
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Bacteria Have ‘Biological Wheels’ That We Can Finally See In 3D For First Time

Bacteria Have ‘Biological Wheels’ That We Can Finally See In 3D For First Time | Amazing Science | Scoop.it

Among bacteria’s many attributes, perhaps one of its most overlooked yet important ones is its ability to propel itself via flagellum, a unique appendage hanging off its end. This mechanism is a perfect example of a naturally occurring, biological wheel.

 

Now, for the first time, scientists were able to take a high resolution, 3D look at these wheels at work, using an electron microscope. Their work was published online yesterday in the journal, PNAS.

 

A flagella is like a tiny tail at the end of the bacteria, allowing it to move through various mediums. It generates torque (that's twisting force) from stators, a ring of structures around the motor part of the organ. These act as the wheel providing the power.

 

The amount of torque varies depending on the number of stators, which result in varying degrees of power. Different bacteria have different numbers of stators. For example, as New Scientist points out, the motor of Campylobacter has enough force to drive itself through your intestines, resulting in a bad case of food poisoning.

 

At the same time, another bacteria that the scientists looked at, which is closely related to Vibrio cholerae (the bacteria that produce cholera), have a motor that only has a moderate degree of power.

 

This variety, as well as the fact that flagellum has evolved independently multiple times, adds evidence to the fact that it evolved gradually via natural selection, rather than intelligent design. To capture these images, a team of researchers, headed by Morgan Beeby at Imperial College London, used a technique called electron cryotomography. That's where you first freeze the bacteria, then use an electron microscope to capture images of it from various angles, finally stitching the resulting images together into one 3D composite.

 

Aside from the beautiful novelty of these images, researchers could study them to develop better motors for nano-robots, or to design better antibiotics that target the flagellum specific to a certain bacteria.

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August 17, 2016 1:47 PM
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Self-Destructing Battery Can Dissolve Itself in 30 Minutes

Self-Destructing Battery Can Dissolve Itself in 30 Minutes | Amazing Science | Scoop.it

A new self-destructing battery can power a simple electronic device for up to 15 minutes and then dissolve in water. It could pave the way for so-called transient power sources for scientific instruments or tools of espionage, according to a new study.

 

Engineers have developed a novel variety of battery capable of powering a simple electronic device, such as a four-function calculator, and then dissolving in water in half an hour. The new transient battery represents a marked improvement in voltage and disintegration time over its predecessors, the researchers said.

 

The lithium-ion battery, the first transient battery of its kind, is "very similar to a conventional battery," study co-author Reza Montazami, who heads the Advanced Materials Lab at Iowa State University, explained.

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August 17, 2016 1:23 PM
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The 226-Million-Year Milky-Way Orbit of our Solar System

The 226-Million-Year Milky-Way Orbit of our Solar System | Amazing Science | Scoop.it

In 1999 astronomers focusing on a star at the center of the Milky Way, measured precisely how long it takes the sun to complete one orbit (a galactic year) of our home galaxy: 226 million years. The last time the sun was at that exact spot of its galactic orbit, dinosaurs ruled the Earth. The Solar System is thought to have completed about 20–25 orbits during its lifetime or 0.0008 orbit since the origin of humans. When the last red embers of our Sun die out billions of years from now, we will have completed approximately 60 orbits of our home galaxy.

 

In fact, our Sun's orbit has only happened 20.4 times since the Sun itself formed 4.6 billion years ago. It’s estimated that the Sun will continue fusing hydrogen for another 7 billion years. In other words, it only has another 31 orbits it can make before it runs out of fuel.

 

Is there a genocidal countdown built into the motion of our solar system? Research at Cardiff University suggests that our system's orbit through the Milky Way encounters regular speedbumps - and by "speedbumps," we mean "potentially extinction-causing asteroids."

 

Our orbit through the Milky Way is not a perfect circle or an ellipse, since the galaxy itself is a landscape of undulating concentrations of mass and complex gravitational fields. As Caleb Scharf observes in The Copernicus Complex, "none of the components of the galaxy are stationary; they, too, are orbiting and drifting in a three-dimensional ballet. The result is that our solar system, like billions of others, must inevitably encounter patches of interstellar space containing the thicker molecular gases and microscopic dust grains of nebulae. It takes tens of thousands to hundreds of thousands of years to pass through one of these regions.

 

"This may happen only once every few hundred million years," Scharf adds, "but if modern human civilization had kicked off during such an episode, we would have barely seen more than the nearest stars— certainly not the rest of our galaxy or the cosmos beyond. But could our planetary circumstances have been that different and still produced us? Would more changeable orbits in a planetary system, or bad weather, or passage through interstellar clouds, also thwart the emergence of life in some way?

 

"Phenomena such as these could be bad news, causing hostile surface environments on a planet. So it’s a possibility that the planetary requirements for forming sentient life like us will necessarily always present the senses and minds of such creatures with a specific cosmic tableau, a common window onto the universe."

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August 17, 2016 1:16 PM
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Without oxygen from ancient moss you wouldn’t be alive today

Without oxygen from ancient moss you wouldn’t be alive today | Amazing Science | Scoop.it

Earth’s air is only breathable today because of moss-like plants that colonised the land 470 million years ago. The moss enriched the atmosphere with oxygen and triggered a cycle that maintained its levels, paving the way to complex life.

 

Oxygen in its current form first appeared on Earth 2.4 billion years ago in what has become known as the Great Oxidation Event. But it was not until around 400 million years ago that oxygen in the atmosphere approached present day levels. Scientists have long debated what caused this shift, without which humans could not have evolved.

 

A team from the University of Exeter, in the UK, used computer simulations to show how the first land plants contributed to the Earth’s oxygen. The earliest terrestrial plants were simple bryophytes, such as moss, which lack vein-like systems to transport water and minerals.

 

Factoring the properties of modern bryophytes into the simulations indicated that thanks to the ancient mosses, modern levels of atmospheric oxygen would have been achieved by 420 to 400 million years ago.

 

The emergence of the plants eventually led to a stable and self-sustaining cycle of oxygen flowing between sedimentary rocks, living things and the atmosphere. Today, the air we breathe consists of of 78 per cent nitrogen and 21 per cent oxygen, with smaller amounts of argon, carbon dioxide, water vapour and trace gases.

 

As well as making the air breathable, oxygen generates the ozone layer that protects life on Earth from the harmful effects of ultraviolet radiation from the sun. “It’s exciting to think that without the evolution of the humble moss, none of us would be here today,” said lead scientist Tim Lenton, from the University of Exeter. “Our research suggests that the earliest land plants were surprisingly productive and caused a major rise in the oxygen content of the Earth’s atmosphere.”

 

Journal reference: PNAS, DOI: 10.1073/pnas.1604787113


Via Dr. Catherine Russell
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August 16, 2016 5:50 PM
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Blue Supergiant Stars in our Universe

Blue Supergiant Stars in our Universe | Amazing Science | Scoop.it

Blue supergiant stars are amongst the largest and brightest stars in the world. They are characterized by high temperatures ranging from 20,000 - 50,000 kelvin (35,540.3 - 89,540.3 °F). These bright and hot stars are roughly the size of 20 solar masses. However, their size can vary a lot. A blue supergiant star can be as big as 1,000 solar masses.

 

Here are some interesting facts about blue supergiant stars:

  • Blue supergiants are highly luminous stars formed as a result of stellar evolution. The process of stellar evolution continues for millions of years. The lifespan of a blue supergiant star can be up to 10 million years.
  • Blue supergiant stars are known for the fast stellar winds which blow on their surfaces. However, these winds, although fast, occur sparsely.
  • These stars have short lifespans in comparison to most stars; which is why they are found in cosmic structures such as spiral galaxies and open clusters. These structures are younger in comparison to other cosmic structures.
  • Blue supergiant stars are of rare occurrence in comparison to other kinds of stars. However, the luminosity of these stars makes them easily visible.

 

Stars that rotate at a fast pace are known to contain high proportions of helium. These stars also exhibit a mixture of different kinds of elements.

 

Blue supergiant stars have heavy elements in their spectra. The quantities of heavy elements vary with the age of the star. Another factor which determines the quantity of heavy elements is the efficiency with which nucleosynthesis products are convected from the core of a star to its surface.

 

The process of their evolution is a bit complicated to understand. Even after years of research, the process is not completely understood, till date.

 

Recently, a blue supergiant star was discovered by astronomers Dr. Youichi Ohyama (Institute of Astronomy and Astrophysics, Academia Sinica or ASIAA, Taiwan) and Dr. Ananda Hota (UM-DAE Center for Excellence in the Basic Sciences or CBS, India). This star emerged 55 million years ago.

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