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A Possible Cure for Ebola Virus Infection Discovered: BCX4430

A Possible Cure for Ebola Virus Infection Discovered: BCX4430 | Amazing Science |

Ebola is one of the scariest viruses on Earth. Along with Marburg and a few other lesser known viruses, it is a member of the Filoviridae family, a nasty group of microbes that causes hemorrhagic fever. Like most viral diseases, patients with hemorrhagic fever will first present with flu-like symptoms. As the disease progresses, patients often bleed from their body orifices, such as their eyes and ears. Death, however, does not result from blood loss, but from shock or organ failure.

Hemorrhagic fevers are not easy to catch. Transmission generally requires prolonged contact with the patient or with his bodily fluids. Mortality rates depend on the particular viral strain. For Ebola, thedeadliest strain is Zaire, which can kill up to 90% of those infected. The worst ever outbreak occurred in Congo in 1976. That year, 318 people were infected and 280 died, a mortality rate of 88%. Currently, an outbreak of Ebola has killed at least 135 people in west Africa. The virus resembles Zaire, but researchers have determined that it is a brand new strain.

Obviously, finding a treatment or cure for such a frightening disease is desirable. With our highly interconnected world, it is only a matter of time before a hemorrhagic fever shows up on our doorstep. (Actually,that's already happened.) Unfortunately, at the present time, there is little that can be done for a victim of Ebola or any other hemorrhagic fever. Mostly, patients are kept hydrated and symptoms are treated as they arise. Other than that, doctors cross their fingers and hope the patient doesn't die.

That may be about to change. In the journal Nature, scientists -- who conducted much of their work in the secretive, high-containment biological laboratory maintained by USAMRIID at Fort Detrick, Maryland -- have reported the discovery of a small molecule that rescues rodents and monkeys from various hemorrhagic fevers. Even more, the drug exhibited activity against a wide range of viruses.

The molecule, named BCX4430, resembles the "A" found in DNA: adenosine. The RNA-based filoviruses also use "A" in their genomes. BCX4430, because it resembles "A", can be accidentally used by the virus when it is trying to grow inside of our cells. For the virus, this is a fatal mistake. BCX4430 blocks further growth and reproduction.

Shouldn't this drug be expected to hurt not only the virus, but humans as well? That would be a reasonable expectation, but for some reason, BCX4430 appears to only hurt the virus. Human cells appear not to be fooled by BCX4430 and do just fine in its presence. The most compelling experiment the research team ran involved the infection of cynomolgus macaque monkeys with deadly Marburg virus. Macaques were given twice daily doses of BCX4430 for 14 days beginning 1 hour, 24 hours, or 48 hours post-infection.

Amazingly, in vitro experiments showed that BCX4430 could potentially work against a wide range of viruses, including SARS, MERS, influenza, dengue, and measles.

Source: TK Warren et al. "Protection against filovirus diseases by a novel broad-spectrum nucleoside analogue BCX4430." Nature 508: 402-405 (2014). doi:10.1038/nature13027

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Spotting the spin of the Majorana fermion under the microscope

Spotting the spin of the Majorana fermion under the microscope | Amazing Science |
Using a new twist on a technique for imaging atomic structures, researchers have detected a unique quantum property of the Majorana fermion, an elusive particle with the potential for use in quantum information systems.


Researchers at Princeton University have detected a unique quantum property of an elusive particle notable for behaving simultaneously like matter and antimatter. The particle, known as the Majorana fermion, is prized by researchers for its potential to open the doors to new quantum computing possibilities.


In this study published this week in the journal Science, the research team described how they enhanced an existing imaging technique, called scanning tunneling microscopy, to capture signals from the Majorana particle at both ends of an atomically thin iron wire stretched on the surface of a crystal of lead. Their method involved detecting a distinctive quantum property known as spin, which has been proposed for transmitting quantum information in circuits that contain the Majorana particle.


"The spin property of Majoranas distinguishes them from other types of quasi-particles that emerge in materials," said Ali Yazdani, Princeton's Class of 1909 Professor of Physics. "The experimental detection of this property provides a unique signature of this exotic particle."


The finding builds on the team's 2014 discovery, also published in Science, of the Majorana fermion in a single atom-wide chain of iron atoms atop a lead substrate. In that study, the scanning tunneling microscope was used to visualize Majoranas for the first time, but provided no other measurements of their properties.

"Our aim has been to probe some of the specific quantum properties of Majoranas. Such experiments provide not only further confirmation of their existence in our chains, but open up possible ways of using them." Yazdani said.


First theorized in the late 1930s by the Italian physicist Ettore Majorana, the particle is fascinating because it acts as its own antiparticle. In the last few years, scientists have realized that they can engineer one-dimensional wires, such as the chains of atoms on the superconducting surface in the current study, to make Majorana fermions emerge in solids. In these wires, Majoranas occur as pairs at either end of the chains, provided the chains are long enough for the Majoranas to stay far enough apart that they do not annihilate each other. In a quantum computing system, information could be simultaneously stored at both ends of the wire, providing a robustness against outside disruptions to the inherently fragile quantum states.

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Navigational View of the Brain Thanks to Powerful X-Rays

Navigational View of the Brain Thanks to Powerful X-Rays | Amazing Science |
How the brain computes can arguably be best studied on the "meso" scale, and new imaging makes brain tissue visible on that level.


If brain imaging could be compared to Google Earth, neuroscientists would already have a pretty good “satellite view” of the brain, and a great “street view” of neuron details. But navigating how the brain computes is arguably where the action is, and neuroscience’s “navigational map view” has been a bit meager.


Now, a research team led by Eva Dyer, a computational neuroscientist and electrical engineer, has imaged brains at that map-like or “meso” scale using the most powerful X-ray beams in the country. The imaging scale gives an overview of the intercellular landscape of the brain at a level relevant to small neural networks, which are at the core of the brain’s ability to compute.


Dyer, who recently joined the Georgia Institute of Technology and Emory University, also studies how the brain computes via its signaling networks, and this imaging technique could someday open new windows onto how they work.


A powerful X-ray tomography scanner allowed the researchers to image particularly thick sections of the brains of mice, which afforded them views into intact neural areas much larger than are customary in microscope imaging. The scanner operated on the same basic principle as a hospital CT scanner, but this scan used high-energy X-ray photons generated in a synchrotron, a facility the size of dozens of football fields.


"Argonne National Laboratory (ANL) generates the highest-energy X-ray beams in the country at its synchrotron," said Dyer, who co-led the study with ANL's Bobby Kasthuri at the Advanced Photon Source synchrotron. "They've studied all kinds of materials with really powerful X-rays. Then they got interested in studying the brain."


The technique also revealed capillary grids interlacing brain tissues. They dominated the images, with cell bodies of brain cells evenly speckling capillaries like pebbles in a steel wool sponge.

"Our brain cells are embedded in this sea of vasculature," said Dyer, an assistant professor in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory.


The study on the new images appeared in the journal eNeuro on Tuesday, October 17, 2017. The team included researchers from Johns Hopkins University, the University of Chicago, Northwestern University, the Argonne National Laboratory, and the University of Pennsylvania. The work was funded by the U.S. Department of Energy, the National Institutes of Health, the Intelligence Advanced Research Projects Activity, and the Defense Advanced Research Projects Agency.

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Scientists Can Now Repaint Butterfly Wings

Scientists Can Now Repaint Butterfly Wings | Amazing Science |
Thanks to CRISPR, scientists are studying animal evolution in ways that were previously thought to be impossible.


When the butterfly emerged from its pupa, Robert Reed was stunned. It was a Gulf fritillary—a bright-orange species with a few tigerlike stripes. But this butterfly had no trace of orange anywhere. It was entirely black and silver. “It was the most heavy-metal butterfly I’ve ever seen,” Reed says. “It was amazing to see that thing crawl out of the pupa.”


Reed’s team at Cornell University had created the metal butterfly by deleting just one of its genes, using the revolutionary gene-editing technique known as CRISPR. And by performing the same feat across several butterfly species, the team showed that this one gene, known as optix, controls all kinds of butterfly patterns. Red becomes black. Matte becomes shiny. Another gene, known asWntA, produces even wilder variations when it’s deleted. Eyespots disappear. Boundaries shift. Stripes blur.


These experiments prove what earlier studies had suggested—that optix andWntA are “paintbrush genes,” says Anyi Mazo-Vargas, one of Reed’s students. “Wherever you put them, you’ll have a pattern.”

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Major advance in nanopore detection of peptides and proteins

Major advance in nanopore detection of peptides and proteins | Amazing Science |

Nanopore technology, which is used to sequence DNA, is cheap, hand-held and works in the jungle and in space. The use of this technology to identify peptides or proteins is now a step closer. University of Groningen scientists have used a patented nanopore to identify the fingerprints of proteins and peptides, and it can even detect polypeptides differing by one amino acid. The results were published on 16 October in the journal Nature Communications.


Scientists have now been able to identify a number of peptides and proteins passing through a funnel-shaped nanopore. They have solved two main problems that have hampered attempts to analyze and sequence proteins with nanopores: getting polypeptides into the pore and identifying differences in proteins by recordings of current. 'Nanopores usually carry a charge, and the amino acids that make up polypeptides are also charged. Getting the polypeptide inside the pore and to pass through nanopores is therefore a challenge', explains associate professor of Chemical Biology Giovanni Maglia.


Maglia and his team used an electro-osmotic flow to pull the polypeptides into the pores. Under an applied potential across the nanopore, a flow of ions and water passes through the pore.' If the direction of the ion current can be controlled, a fluid flow strong enough to transport polypeptides can be generated. 'We did this by tuning the charges inside the pore wall. By changing the pH of the medium, it was possible to fine-tune the balance between the electro-osmotic flow and the force of the electric field which was applied across the pore.'


Maglia tested five different polypeptides ranging from 1 to 25 kilodalton. 'We used biomarker peptides linked to disease, with different charges and shapes', he says. The polypeptides entered the pore and the current across the pore produced a 'fingerprint' for each. He thus managed to distinguish two versions of the 21 amino acid peptide endothelin, which differ by just one amino acid (tryptophan or methionine).


Getting a good reading from a nanopore is complicated. Maglia used a new kind of pore that he characterized and patented. 'Pores used in the past are barrel-shaped, which means the shape and size of the pore has fundamental limitations. But our pore has an alpha helical funnel shape, and the size of the narrow end, which is where we do our measurements, means it should contain just one amino acid, so it is more easily tuned.'


Currently, the polypeptides pass through the pore too rapidly to identify the separate amino acids. This is needed for protein sequencing at the single-molecule scale. It would be a valuable tool for research, explains Maglia: 'Proteins can be chemically modified in many unique ways, and we have very little information on the exact composition of proteins in our body.' This can only be seen at the single-molecule level.


Reference: Gang Huang, Kherim Willems, Misha Soskine, Carsten Wloka & Giovanni Maglia: Electro-Osmotic Capture and Ionic Discrimination of Peptide and Protein Biomarkers with FraC Nanopores. Nature Communications, 16 October 2016

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Whales and dolphins have rich 'human-like' cultures and societies

Whales and dolphins have rich 'human-like' cultures and societies | Amazing Science |
Whales and dolphins (Cetaceans) live in tightly-knit social groups, have complex relationships, talk to each other and even have regional dialects - much like human societies.


A major new study, published today in Nature Ecology & Evolution, has linked the complexity of Cetacean culture and behaviour to the size of their brains. The research was a collaboration between scientists at The University of Manchester, The University of British Columbia, Canada, The London School of Economics and Political Science (LSE) and Stanford University, United States.


The study is first of its kind to create a large dataset of cetacean brain size and social behaviors. The team compiled information on 90 different species of dolphins, whales, and porpoises. It found overwhelming evidence that Cetaceans have sophisticated social and cooperative behavior traits, similar to many found in human culture.


The study demonstrates that these societal and cultural characteristics are linked with brain size and brain expansion—also known as encephalisation. The long list of behavioral similarities includes many traits shared with humans and other primates such as:

  • complex alliance relationships - working together for mutual benefit
  • social transfer of hunting techniques - teaching how to hunt and using tools
  • cooperative hunting
  • complex vocalizations, including regional group dialects - 'talking' to each other
  • vocal mimicry and 'signature whistles' unique to individuals - using 'name' recognition
  • interspecific cooperation with humans and other species - working with different species
  • alloparenting - looking after youngsters that aren't their own
  • social play


Dr Susanne Shultz, an evolutionary biologist in Manchester's School of Earth and Environmental Sciences, said: "As humans, our ability to socially interact and cultivate relationships has allowed us to colonize almost every ecosystem and environment on the planet. We know whales and dolphins also have exceptionally large and anatomically sophisticated brains and, therefore, have created a similar marine based culture. "That means the apparent co-evolution of brains, social structure, and behavioral richness of marine mammals provides a unique and striking parallel to the large brains and hyper-sociality of humans and other primates on land. Unfortunately, they won't ever mimic our great metropolises and technologies because they didn't evolve opposable thumbs."


The team used the dataset to test the social brain hypothesis (SBH) and cultural brain hypothesis (CBH). The SBH and CBH are evolutionary theories originally developed to explain large brains in primates and land mammals. They argue that large brains are an evolutionary response to complex and information-rich social environments. However, this is the first time these hypotheses have been applied to 'intelligent' marine mammals on such a large scale.


Dr Michael Muthukrishna, Assistant Professor of Economic Psychology at LSE, added: "This research isn't just about looking at the intelligence of whales and dolphins, it also has important anthropological ramifications as well. In order to move toward a more general theory of human behavior, we need to understand what makes humans so different from other animals. And to do this, we need a control group. Compared to primates, cetaceans are a more "alien" control group."

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Filling the early universe with knots can explain why the world is three-dimensional

Filling the early universe with knots can explain why the world is three-dimensional | Amazing Science |
The next time you come across a knotted jumble of rope or wire or yarn, ponder this: The natural tendency for things to tangle may help explain the three-dimensional nature of the universe and how it formed.


An international team of physicists has developed an out-of-the-box theory that shortly after it popped into existence 13.8 billion years ago the universe was filled with knots formed from flexible strands of energy called flux tubes that link elementary particles together. The idea provides a neat explanation for why we inhabit a three-dimensional world and is described in a paper titled "Knotty inflation and the dimensionality of space time" accepted for publication in the European Physical Journal C and available on the arXiv preprint server.


"Although the question of why our universe has exactly three large spatial dimensions is one of the most profound puzzles in cosmology … it is actually only occasionally addressed in the scientific literature," the article begins. For a new solution to this puzzle, the five co-authors – physics professors Arjun Berera at the University of Edinburgh, Roman Buniy at Chapman University, Heinrich Päs (author of "The Perfect Wave: With Neutrinos at the Boundary of Space and Time") at the University of Dortmund, João Rosa at the University of Aveiro and Thomas Kephart at Vanderbilt University – took a common element from the standard model of particle physics and mixed it with a little basic knot theory to produce a novel scenario that not only can explain the predominance of three dimensions but also provides a natural power source for the inflationary growth spurt that most cosmologists believe the universe went through microseconds after it burst into existence.


The common element that the physicists borrowed is the "flux tube" comprised of quarks, the elementary particles that make up protons and neutrons, held together by another type of elementary particle called a gluon that "glues" quarks together. Gluons link positive quarks to matching negative antiquarks with flexible strands of energy called flux tubes. As the linked particles are pulled apart, the flux tube gets longer until it reaches a point where it breaks. When it does, it releases enough energy to form a second quark-antiquark pair that splits up and binds with the original particles, producing two pairs of bound particles.

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A self-propelled catheter with earthworm-like peristaltic motion

A self-propelled catheter with earthworm-like peristaltic motion | Amazing Science |
A research team has developed a mechanism of a self-propelled catheter capable of generating peristaltic motion just like an earthworm by applying pneumatic pressure inside only one tube. The goal is to develop an AutoGuide robot that propels itself inside bronchi, automatically reaching the target lesion within the lungs, and can take a lesion sample and provide treatment.


Biopsies of pulmonary lesions are essential for increasing the accuracy of diagnosis and treatment for respiratory illnesses such as lung cancer. Currently, manual biopsies are performed via bronchoscopy. However, the bronchi tends to branch thinner and more complicatedly as it goes to the periphery, which makes it a challenge to reliably choose one and fine-tune the propelling movement. Given the skill disparities in operating doctors as well, it is difficult to reliably reach the lesion with the biopsy forceps, resulting in inadequate diagnosis accuracy.


The development of instruments and mechanisms that can reliably reach the target in the lungs is required for adequately testing with an endoscope, but the looming challenge was finding a mechanism to reliably advance the biopsy forceps to the target even inside the ultrafine and widely branching bronchi.


Now, Prof. Yuichiro Takai of Department of Respiratory Medicine, Omori Medical Center at Toho University and Prof. Hideyuki Tsukagoshi, of Department of System and Control Engineering at Tokyo Tech collaborate in developing the new self-propelled catheter designed to generate traveling waves in multiple chambers just by adding and reducing pressure inside one tube. This allowed for moving forward with peristaltic motion within an ultrafine structure such as a bronchus. This catheter also has an actively curving function for choosing the direction of propulsion, and a flexing drive function for adjusting to changes in line diameter. Their effectiveness was verified using a bronchus model.


The goal is to increase the accuracy of branches which can be propelled, include a camera to collect information on the inside of the bronchi, develop functions applicable to biopsies and treatment, and put instruments to practical use.

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Grafting human cancer cells into mice alters tumor evolution

Grafting human cancer cells into mice alters tumor evolution | Amazing Science |

An analysis of more than 1,000 mouse models of cancer has challenged their ability to predict patients’ response to therapy.

The study, published today in Nature Genetics1, catalogues the genetic changes that occur in human tumors after they have been grafted into mouse hosts. Such models, called patient-derived xenografts (PDXs), are used in basic research and as ‘avatars’ for individual patients. Researchers use these avatar mice to test a bevy of chemotherapies against a person's tumor, in the hope of tailoring a treatment plan for the patient's specific cancer.

But fresh data from geneticists at the Broad Institute of MIT and Harvard in Cambridge, Massachusetts, suggest that transplanting human cancer cells into a mouse alters the cells' evolution, reshaping the tumor's genome in ways that could affect responses to chemotherapy.


“The assumption is that what grows out in the PDX is reflective of the bulk of the tumor in the patient,” says cancer geneticist Todd Golub, a lead author on the study. “But there’s quite dramatic resculpting of the tumor genome.” No animal model is perfect, and researchers have long acknowledged that PDXs have their limitations. To avoid an immune assault on the foreign tumor, for example, PDXs are typically grafted into mice that lack a functioning immune system. This compromises scientists' ability to study how immune cells interact with the tumor — an area of increasing interest given the success of cancer therapies that unleash the immune system. PDXs can also take months to generate, making them too slow to serve as avatars for those patients who need to make immediate decisions about their therapy.


But previous research had suggested that the PDXs were reasonably faithful reproductions of the human tumors they are meant to model, offering researchers a chance to explore the tumor’s interaction with its environment in ways that are not possible using cells grown in a Petri dish. The US National Cancer Institute has developed a library of more than 100 PDXs for distribution to researchers, and European scientists have launched EurOPDX, a consortium that boasts more than 1,500 models for more than 30 tumor types. One company, Champions Oncology of Hackensack, New Jersey, creates and tests mouse avatars for individual patients and for pharmaceutical companies to use in research.

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Astronomers Detect Gravitational Waves From Two Colliding Neutron Stars For The First Time

Astronomers Detect Gravitational Waves From Two Colliding Neutron Stars For The First Time | Amazing Science |
In an astonishing discovery, astronomers used gravitational waves to locate two neutron stars smashing together. The collision created 200 Earth masses of pure gold, along with other elements.


For the first time, scientists have caught two neutron stars in the act of colliding, revealing that these strange smashups are the source of heavy elements such as gold and platinum. The discovery, announced Monday at a news conference and in scientific reports written by some 3,500 researchers, solves a long-standing mystery about the origin of these heavy elements — which are found in everything from wedding rings to cellphones to nuclear weapons.


It's also a dramatic demonstration of how astrophysics is being transformed by humanity's newfound ability to detect gravitational waves, ripples in the fabric of space-time that are created when massive objects spin around each other and finally collide. "It's so beautiful. It's so beautiful it makes me want to cry. It's the fulfillment of dozens, hundreds, thousands of people's efforts, but it's also the fulfillment of an idea suddenly becoming real," says Peter Saulson of Syracuse University, who has spent more than three decades working on the detection of gravitational waves.


Albert Einstein predicted the existence of these ripples more than a century ago, but scientists didn't manage to detect them until 2015. Until now, they'd made only four such detections, and each time the distortions in space-time were caused by the collision of two black holes.


That bizarre phenomenon, however, can't normally be seen by telescopes that look for light. Neutron stars, by contrast, spew out visible cosmic fireworks when they come together. These incredibly dense stars are as small as cities like New York and yet have more mass than our sun.


In this case, what scientists managed to spot was a pair of neutron stars that likely spent more than 11 billion years circling each other more and more closely before finally slamming together about 130 million years ago.


LIGO is funded by the NSF, and operated by Caltech and MIT, which conceived of LIGO and led the Initial and Advanced LIGO projects. Financial support for the Advanced LIGO project was led by the NSF with Germany (Max Planck Society), the U.K. (Science and Technology Facilities Council) and Australia (Australian Research Council) making significant commitments and contributions to the project.


More than 1,200 scientists and some 100 institutions from around the world participate in the effort through the LIGO Scientific Collaboration, which includes the GEO Collaboration and the Australian collaboration OzGrav. Additional partners are listed at


The Virgo collaboration consists of more than 280 physicists and engineers belonging to 20 different European research groups: six from Centre National de la Recherche Scientifique (CNRS) in France; eight from the Istituto Nazionale di Fisica Nucleare (INFN) in Italy; two in the Netherlands with Nikhef; the MTA Wigner RCP in Hungary; the POLGRAW group in Poland; the University of Valencia in Spain; and the European Gravitational Observatory, EGO, the laboratory hosting the Virgo detector near Pisa in Italy, funded by CNRS, INFN, and Nikhef.

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CRISPR gene therapy could turn your skin into a glucose sensor

CRISPR gene therapy could turn your skin into a glucose sensor | Amazing Science |

Diabetics might ultimately have glucose sensors built into their bodies.


For diabetics, the constant finger pricks to obtain a blood drop and measure its glucose level is an annoyance. But it’s essential, too. Out-of-whack blood sugar can be fatal. That’s why engineers have tried for decades to create a noninvasive glucose sensor,  but developing one has proved difficult. It’s just not feasible to accurately measure sugar levels through the skin.


So why not, instead, redesign a person’s body to do the measuring instead? That’s the bright idea that Xiaoyang Wu and colleagues at the University of Chicago’s Ben May Department for Cancer Research had. 


In a fascinating mashup of technologies, the Chicago team says it has genetically edited skin cells from a mouse and turned them into a glucose detector that, once grafted onto the animals, works all the time and doesn’t need a battery.


It’s the first time living skin has been turned into a sensor, says Wu, adding that “a skin-based technology would have a lot of advantages” over finger pricks or even the continuous monitors some diabetics use.


Skin is one of the largest organs in the body, Wu and his colleagues point out in their report, which appeared last week on the publishing website bioRxiv. Skin is easy to get ahold of and—they say—easy to remove later if things go wrong. To make their biological invention, Wu and team first collected from mice some of the stem cells whose job it is to make new skin. Next, they used the gene-editing technique CRISPR to create their built-in glucose detector. That involved adding a gene from E. coli bacteria whose product is a protein that sticks to sugar molecules. 

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Scientists create genetically modified mosquitoes and bacteria in mosquitoes' guts to combat deadly malaria

Scientists create genetically modified mosquitoes and bacteria in mosquitoes' guts to combat deadly malaria | Amazing Science |
Scientists explore genetically modifying mosquitoes and bacteria in mosquitoes' guts to combat deadly malaria.


The first study focused on whether mosquitoes that have been genetically modified to be more resistant to the malaria-causing parasite would become weaker and less able to mate and breed.

If modified mosquitoes are going to be used against malaria, the transformed mosquitoes must be as fit as wild ones and able to pass on their genetic modification in large scale to future generations.


The study, led by mosquito vector biologist George Dimopoulos, found that one type of genetically modified mosquito not only bred well, but became more attractive to normal mosquitoes.


Dimopoulos took a group of genetically modified mosquitoes and a group of wild normal mosquitoes and locked them up together. To his surprise, the normal male mosquitoes preferred the genetically modified females, while the genetically modified males went wild over the normal females. Those mating preferences meant that within one generation, the mosquito population was becoming 90 percent genetically modified.


“We found the modification was changing the microbiome and bacteria of the genetically modified mosquitoes,” Dimopoulos said. “It made them smell different, better to their mates.”

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Haplobank: A biobank of reversible mutant embryonic stem cells

Haplobank: A biobank of reversible mutant embryonic stem cells | Amazing Science |
Scientist have developed a biobank of revertible, mutant embryonic stem cells – called Haplobank - which contains over 100,000 mutated, conditional mouse embryonic stem cell lines, targeting about 70% of the protein-coding genome.


Genetic screens have revolutionized our understanding of biological processes and disease mechanisms. Recent technical advances have broadened the available approaches for disrupting gene function in a cell population prior to screening, from chemical and insertional mutagenesis to RNA interference, and, most recently, CRISPR-mediated genome editing. However, RNA interference and CRISPR-mediated gene targeting often suffer from poor efficiency and off-target effects. In addition, most mutagenesis approaches are not reversible -- making it difficult to rigorously control for the frequent genetic and epigenetic differences between ostensibly identical cells. These issues can confound the reproducibility, interpretation and overall success of genetic screens.


Major concerns about scientific reproducibility and rigor have emerged in recent years. Amgen and Bayer, as well as The Reproducibility Initiative, have been unable to replicate many high-profile cancer studies. Indeed, it is not uncommon to obtain different results from experiments with the same cell line in two different laboratories. These inconsistencies can arise for various reasons. Regardless, irreproducible results waste money, damage the credibility of science and scientists, and delay or undo progress, including the development of effective therapies.


To overcome these problems, the Penninger lab at the IMBA developed a biobank of revertible, mutant embryonic stem cells, published in the current issue of Nature. This cell bank -- called Haplobank -- contains over 100,000 mutated, conditional mouse embryonic stem cell lines, targeting about 70% of the protein-coding genome (almost 17,000 genes). "Haplobank is available to all scientists, and represents the largest ever library of hemizyogous mutant embryonic stem cell lines to date. The resource overcomes issues arising from clonal variability, because mutations can be repaired in single cells and at whole genome scale," explains Ulrich Elling, first and corresponding author of the current publication in Nature.

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200 Earth masses of gold and 500 Earth masses of platinum from a neutron star merger

200 Earth masses of gold and 500 Earth masses of platinum from a neutron star merger | Amazing Science |
What many thought would be a long way off, the detection of gravitational waves from the merger of binary neutron stars, actually happened on Aug. 17. The observation of a blue and then red glow from the radioactive debris cloud left behind matched simulations of what the merger should look like, proving that such mergers are the source of most of the very heavy elements in the universe, including gold.


While hydrogen and helium were formed in the Big Bang 13.8 billion years ago, heavier elements like carbon and oxygen were formed later in the cores of stars through nuclear fusion of hydrogen and helium. But this process can only build elements up to iron. Making the heaviest elements requires a special environment in which atoms are repeatedly bombarded by free neutrons. As neutrons stick to the atomic nuclei, elements higher up the periodic table are built.


Where and how this process of heavy element production occurs has been one of the longest-standing questions in astrophysics. Recent attention has turned to neutron star mergers, where the collision of the two stars flings out clouds of neutron-rich matter into space, where they could assemble into heavy elements.


Speculation that astronomers might see light from such heavy elements traces back to the 1990s, but the idea had mostly been gathering dust until 2010, when Brian Metzger, then a freshly minted graduate student at UC Berkeley, now a professor of astrophysics at Columbia University, co-authored a paper with Quataert and Kasen in which they calculated the radioactivity of the neutron star debris and estimated its brightness for the first time.


"As the debris cloud expands into space," Metzger said, "the decay of radioactive elements keeps it hot, causing it to glow."

Metzger, Quataert, Kasen and collaborators showed that this light from neutron star mergers was roughly one thousand times brighter than normal nova explosions in our galaxy, motivating them to name these exotic flashes "kilonovae." Still, basic questions remained as to what a kilonova would actually look like.


"Neutron star merger debris is weird stuff -- a mixture of precious metals and radioactive waste," Kasen said. Astronomers know of no comparable phenomena, so Kasen and collaborators had to turn to fundamental physics and solve mathematical equations describing how the quantum structure of heavy atoms determines how they emit and absorb light.


Jennifer Barnes, an Einstein postdoctoral fellow at Columbia, worked as a Berkeley graduate student with Kasen to make some of the first detailed predictions of what a kilonova should look like. "When we calculated the opacities of the elements formed in a neutron star merger, we found a lot of variation. The lighter elements were optically similar to elements found in supernovae, but the heavier atoms were more than a hundred times more opaque than what we're used to seeing in astrophysical explosions," said Barnes. "If heavy elements are present in the debris from the merger, their high opacity should give kilonovae a reddish hue."


"I think we bummed out the entire astrophysics community when we first announced that," Kasen said. "We were predicting that a kilonova should be relatively faint and redder than red, meaning it would be an incredibly difficult thing to find. On the plus side, we had defined a smoking-gun -- you can tell that you are seeing freshly produced heavy elements by their distinctive red color." That is just what astronomers observed.


The August LIGO/Virgo discovery of a neutron star merger meant that "judgment day for the theorists would come sooner than expected," Kasen said. "For years the idea of a kilonova had existed only in our theoretical imagination and our computer models," he said. "Given the complex physics involved, and the fact that we had essentially zero observational input to guide us, it was an insanely treacherous prediction -- the theorists were really sticking their necks out." But as the data trickled in, one night after the next, the images began to assemble into a surprisingly familiar picture.

On the first couple nights of observations, the color of the merger event was relatively blue with a brightness that matched the predictions of kilonova models strikingly well if the outer layers of the merger debris are made of light precious elements such as silver. However, over the ensuing days the emission became increasingly red, a signature that the inner layers of the debris cloud also contain the heaviest elements, such as platinum, gold and uranium.


"Perhaps the biggest surprise was how well-behaved the visual signal acted compared to our theoretical expectations," Metzger noted. "No one had ever seen a neutron star merger up close before. Putting together the complete picture of such an event involves a wide range of physics -- general relativity, hydrodynamics, nuclear physics, atomic physics. To combine all that and come up with a prediction that matches the reality of nature is a real triumph for theoretical astrophysics."


Kasen, who was also a member of observational teams that discovered and conducted follow-up observations of the source, recalled the excitement of the moment: "I was staying up past 3 a.m. night after night, comparing our models to the latest data, and thinking, 'I can't believe this is happening; I'm looking at something never before seen on Earth, and I think I actually understand what I am seeing.'"


Kasen and his colleagues have presented updated kilonova models and theoretical interpretations of the observations in a paper released Oct. 16 in advance of publication in Nature. Their models are also being used to analyze a wide-ranging set of data presented in seven additional papers appearing in Nature,Science and the Astrophysical Journal.


Not only did the observations confirm the theoretical predictions, but the modeling allowed Kasen and his colleagues to calculate the amount and chemical makeup of the material produced. The scientists inferred that around 6 percent of a solar mass of heavy elements were made. The yield of gold alone was around 200 Earth masses, and that of platinum nearly 500 Earth masses.

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As 'Flesh-Eating' Leishmania Come Closer, a Vaccine Against Them Does, Too

As 'Flesh-Eating' Leishmania Come Closer, a Vaccine Against Them Does, Too | Amazing Science |
A potentially deadly parasite that can ulcerate skin, nose, mouth and organs could someday meet its match in an experimental vaccine that has now worked in lab tests on humanized mice.


Parasites that ulcerate the skin, can disfigure the face, and can fatally mutilate internal organs are creeping closer to the southern edges of the United States. No vaccine is available against Leishmania yet, but researchers have now come closer to changing that. A new experimental vaccine, made with a proprietary biological particle developed at the Georgia Institute of Technology, has immunized laboratory mice that were genetically altered to mimic the human immune system.


The vaccine exploits a weakness in Leishmania’s tricky chemical camouflage, which normally hides it from the victim’s disease-fighting cells, to trigger a forceful immune response against the parasite, according to a new study.

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Newfoundland populated multiple times by distinct groups, DNA evidence shows

Newfoundland populated multiple times by distinct groups, DNA evidence shows | Amazing Science |

Indigenous people have been on the far northeastern edge of Canada for most of the last 10,000 years, moving in shortly after the ice retreated from the Last Glacial Maximum. Archaeological evidence suggests that people with distinct cultural traditions inhabited the region at least three different times with a possible hiatus for a period between 2,000 and 3,000 years ago.


Now, researchers who've examined genetic evidence from mitochondrial DNA provide evidence that two of those groups, known as the Maritime Archaic and Beothuk, brought different matrilines to the island, adding further support to the notion that those groups had distinct population histories. The findings are published in Current Biology on October 12.


"Our paper suggests, based purely on mitochondrial DNA, that the Maritime Archaic were not the direct ancestors of the Beothuk and that the two groups did not share a very recent common ancestor," says Ana Duggan of McMaster University. "This in turn implies that the island of Newfoundland was populated multiple times by distinct groups."


The relationship between the older Maritime Archaic population and Beothuk hadn't been clear from the archaeological record. With permission from the current-day indigenous community, Duggan and her colleagues, led by Hendrik Poinar, examined the mitochondrial genome diversity of 74 ancient remains from the island together with the archaeological record and dietary isotope profiles. All samples were collected from tiny amounts of bone or teeth.

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‘Ridiculously healthy’ elderly have the same gut microbiome as healthy 30 year-olds

‘Ridiculously healthy’ elderly have the same gut microbiome as healthy 30 year-olds | Amazing Science |

In one of the largest microbiota studies conducted in humans, researchers atWestern University, Lawson Health Research Institute and Tianyi Health Science Institute in Zhenjiang, Jiangsu, China have shown a potential link between healthy aging and a healthy gut.


With the establishment of the China-Canada Institute, the researchers studied the gut bacteria in a cohort of more than 1,000 Chinese individuals in a variety of age-ranges from 3 to over 100 years-old who were self-selected to be extremely healthy with no known health issues and no family history of disease. The results showed a direct correlation between health and the microbes in the intestine.


“The aim is to bring novel microbiome diagnostic systems to populations, then use food and probiotics to try and improve biomarkers of health,” said Gregor Reid, PhD, professor at Western’s Schulich School of Medicine & Dentistry and Scientist at Lawson Health Research Institute. “It begs the question – if you can stay active and eat well, will you age better, or is healthy aging predicated by the bacteria in your gut?”


The study, published this month in the journal mSphere, showed that the overall microbiota composition of the healthy elderly group was similar to that of people decades younger, and that the gut microbiota differed little between individuals from the ages of 30 to over 100.


“The main conclusion is that if you are ridiculously healthy and 90 years old, your gut microbiota is not that different from a healthy 30 year old in the same population,” said Greg Gloor, PhD, the principal investigator on the study and also a professor at Western’s Schulich School of Medicine & Dentistry and Scientist at Lawson Health Research Institute. Whether this is cause or effect is unknown, but the study authors point out that it is the diversity of the gut microbiota that remained the same through their study group.


“This demonstrates that maintaining diversity of your gut as you age is a biomarker of healthy aging, just like low-cholesterol is a biomarker of a healthy circulatory system,” Gloor said. The researchers suggest that resetting an elderly microbiota to that of a 30-year-old might help promote health.

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Collapse of Aztec society linked to catastrophic salmonella outbreak based on DNA evidence

Collapse of Aztec society linked to catastrophic salmonella outbreak based on DNA evidence | Amazing Science |
DNA of 500-year-old bacteria is first direct evidence of an epidemic — one of humanity's deadliest — that occurred after Spanish conquest.


One of the worst epidemics in human history, a sixteenth-century pestilence that devastated Mexico’s native population, may have been caused by a deadly form of salmonella from Europe, a pair of studies suggest.


In one study, researchers say they have recovered DNA of the stomach bacterium from burials in Mexico linked to a 1540s epidemic that killed up to 80% of the country's native inhabitants. The team reports its findings in a preprint posted on the bioRxiv server on 8 February1.


This is potentially the first genetic evidence of the pathogen that caused the massive decline in native populations after European colonization, says Hannes Schroeder, an ancient-DNA researcher at the Natural History Museum of Denmark in Copenhagen who was not involved in the work. “It’s a super-cool study.”


In 1519, when forces led by Spanish conquistador Hernando Cortés arrived in Mexico, the native population was estimated at about 25 million. A century later, after a Spanish victory and a series of epidemics, numbers had plunged to around 1 million.


The largest of these disease outbreaks were known as cocoliztli (from the word for ‘pestilence’ in Nahuatl, the Aztec language). Two major cocoliztli, beginning in 1545 and 1576, killed an estimated 7 million to 18 million people living in Mexico’s highland regions. “In the cities and large towns, big ditches were dug, and from morning to sunset the priests did nothing else but carry the dead bodies and throw them into the ditches,” noted a Franciscan historian who witnessed the 1576 outbreak.


There has been little consensus on the cause of cocoliztli — although measles, smallpox and typhus have all been mooted. In 2002, researchers at the National Autonomous University of Mexico (UNAM) in Mexico City proposed that a viral haemorrhagic fever, exacerbated by a catastrophic drought, was behind the carnage2. They compared the magnitude of the 1545 outbreak to that of the Black Death in fourteenth-century Europe. 

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New imaging approach maps whole-brain changes from Alzheimer's disease in mice

New imaging approach maps whole-brain changes from Alzheimer's disease in mice | Amazing Science |

An estimated 5.5 million Americans live with Alzheimer's disease, a type of dementia that causes problems with memory, thinking and behavior. 


Optical visualization of pathological changes in Alzheimer’s disease (AD) can facilitate exploration of disease mechanisms and treatments. However, existing optical imaging methods have limitations on mapping pathological evolution in the whole mouse brain. Previous research indicated endogenous fluorescence contrast of senile plaques. Therefore, it is important to develop cryo-micro-optical sectioning tomography (cryo-MOST) to capture intrinsic fluorescence distribution of senile plaques at a micrometer-level resolution in the whole brain. Validation using immunofluorescence demonstrates the capacity of cryo-MOST to visualize and distinguish senile plaques with competent sensitivity and spatial resolution. Compared with imaging in room temperature, cryo-MOST provides better signal intensity and signal-to-noise ratio. Using cryo-MOST, the inventors obtained whole-brain coronal distribution of senile plaques in a transgenic mouse without exogenous dye. Capable of label-free brainwide visualization of Alzheimer’s pathology, cryo-MOST may be potentially useful for understanding neurodegenerative disease mechanisms and evaluating drug efficacy.

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Baltic clams and worms release as much greenhouse gas as 20,000 dairy cows

Baltic clams and worms release as much greenhouse gas as 20,000 dairy cows | Amazing Science |
Scientists have shown that ocean clams and worms are releasing a significant amount of potentially harmful greenhouse gas into the atmosphere.


The team, from Cardiff University and Stockholm University, have shown that the ocean critters are producing large amounts of the strongest greenhouse gases - methane and nitrous oxides - from the bacteria in their guts. Methane gas is making its way into the water and then finally out into the atmosphere, contributing to global warming - methane has 28 times greater warming potential than carbon dioxide. A detailed analysis showed that around 10 per cent of total methane emissions from the Baltic Sea may be due to clams and worms.


The researchers estimate that this is equivalent to as much methane given off as 20,000 dairy cows. This is as much as 10 per cent of the entire Welsh dairy cow population and 1 per cent of the entire UK dairy cow population.


The findings, which have been published in the journal Scientific Reports, point to a so far neglected source of greenhouse gases in the sea and could have a profound impact on decision makers. It has been suggested that farming oysters, mussels and clams could be an effective solution against human pressures on the environment, such as eutrophication caused by the run-off of fertilizers into our waters. The authors warn that stakeholders should consider these potential impacts before deciding whether to promote shellfish farming to large areas of the ocean.

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Shaping animal, vegetable and mineral | Harvard John A. Paulson School of Engineering and Applied Sciences

Shaping animal, vegetable and mineral | Harvard John A. Paulson School of Engineering and Applied Sciences | Amazing Science |

Researchers develop mathematical techniques for designing shape-shifting shells.


Nature has a way of making complex shapes from a set of simple growth rules. The curve of a petal, the swoop of a branch, even the contours of our face are shaped by these processes. What if we could unlock those rules and reverse engineer nature's ability to grow an infinitely diverse array of shapes?


Scientists from the Harvard John A. Paulson School of Engineering and Applied Sciences(SEAS) have done just that. In a paper published in the Proceedings of the National Academy of Sciences, a team of researchers from SEAS and the Wyss Institute for Biologically Inspired Engineering demonstrate a technique to grow any target shape from any starting shape.


In previous research, the Mahadevan group used experiments and theory to explain how naturally morphing structures -- such as Venus flytraps, pine cones and flowers -- changed their shape in the hopes of one day being able to control and mimic these natural processes. And indeed, experimentalists have begun to harness the power of simple, bioinspired growth patterns. For example, in 2016, in a collaboration with the group of Jennifer Lewis, the Hansjorg Wyss Professor of Biologically Inspired Engineering at SEAS and Core Faculty Member of the Wyss Institute, the team printed a range of structures that changed its shape over time in response to environmental stimuli.


"The challenge was how to do the inverse problem," said Wim van Rees, a postdoctoral fellow at SEAS and first author of the paper. "There's a lot of research on the experimental side but there's not enough on the theoretical side to explain what's actually happening. The question is, if I want to end with a specific shape, how do I design my initial structure?"


Inspired by the growth of leaves, the researchers developed a theory for how to pattern the growth orientations and magnitudes of a bilayer, two different layers of elastic materials glued together that respond differently to the same stimuli. By programming one layer to swell more and/or in a different direction than the other, the overall shape and curvature of the bilayer can be fully controlled. In principle, the bilayer can be made of any material, in any shape, and respond to any stimuli from heat to light, swelling, or even biological growth.

The team unraveled the mathematical connection between the behavior of the bilayer and that of a single layer.


"We found a very elegant relationship in a material that consists of these two layers," said van Rees. "You can take the growth of a bilayer and write its energy directly in terms of a curved monolayer."

That means that if you know the curvatures of any shape you can reverse engineer the energy and growth patterns needed to grow that shape using a bilayer.


"This kind of reverse engineering problem is notoriously difficult to solve, even using days of computation on a supercomputer," said Etienne Vouga, former postdoctoral fellow in the group, now an Assistant Professor of Computer Science at the University of Texas at Austin. "By elucidating how the physics and geometry of bilayers are intimately coupled, we were able to construct an algorithm that solves for the needed growth pattern in seconds, even on a laptop, no matter how complicated the target shape."


The researchers demonstrated the system by modeling the growth of a snapdragon flower petal from a cylinder, a topographical map of the Colorado river basin from a flat sheet and, most strikingly, the face of Max Planck, one of the founders of quantum physics, from a disk.

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How the United States plans to trap its biggest stash of nuclear-weapons waste in glass

How the United States plans to trap its biggest stash of nuclear-weapons waste in glass | Amazing Science |
After decades of delays, a challenging clean-up project is gaining ground.


There's a building boom at the Hanford Site, a once-secret complex on the windswept plains of southeastern Washington state. Construction crews are working to finish a 27-meter-tall concrete structure there by June. If all goes well, the facility will finally enable the US Department of Energy (DOE) to begin treating the toxic, radioactive waste that accumulated at the site for more than 40 years, starting during the Second World War.


Decades after the site stopped producing plutonium for nuclear weapons, the legacy of Hanford's activities is still causing trouble. Just this year, a tunnel holding railway carriages full of radioactive material collapsed. Separately, at least a dozen employees who were tearing down a contaminated building reportedly tested positive for plutonium inhalation. But the site's biggest challenge lies underground, in 177 carbon-steel tanks. Together, these buried containers hold more than 200 million liters of highly hazardous liquids and peanut-buttery sludge — enough to fill 80 Olympic-size swimming pools. More than one-third of the tanks have leaked, contaminating groundwater with radioactive and chemical waste.


In a 1989 legal agreement with the state of Washington and the US Environmental Protection Agency, the DOE committed to immobilizing the most dangerous waste in sturdy glass logs through a process called vitrification. Several years later, the agency agreed to vitrify other tank waste as well. All told, the process is expected to generate tens of thousands of logs, each weighing multiple tons. Those containing high-level waste would be shipped to a permanent storage facility; the rest could be stored on site. But the effort has been plagued by cost overruns, delays and safety concerns. Although the DOE has spent roughly US$20 billion on the tank problem since 1997, no waste has been vitrified.


Four years ago, the agency hit reset. Rather than making a single vitrification plant, it split the project in two. One plant — the building now under construction — would begin vitrifying the less-hazardous, 'low-activity' liquid in the tanks. A bigger, more-complex plant to process the high-level sludge would follow once researchers resolved some thorny safety questions.


On both fronts, there have been signs of progress. This year, the DOE reported that it had resolved crucial questions related to treating the high-level waste. And a laboratory needed for real-time analysis of the low-level waste is nearing completion. If work continues as planned, the site could crank out its first glass logs as early as 2022.

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What are Fractals and why do we care?

What are Fractals and why do we care? | Amazing Science |

Fractal geometry is a field of maths born in the 1970’s and mainly developed by Benoit Mandelbrot. The geometry that is taught in school is about how to make shapes; fractal geometry is no different. While the shapes in classical geometry are ‘smooth’, such as a circle or a triangle, the shapes that come out of fractal geometry are ‘rough’ and infinitely complex. However fractal geometry is still about making shapes, measuring shapes and defining shapes, just like classical geomety.


There are two reasons why people should care about fractal geometry:


  1. The process by which shapes are made in fractal geometry is amazingly simple yet completely different to classical geometry. While classical geometry uses formulas to define a shape, fractal geometry uses iteration. It therefore breaks away from giants such as Pythagoras, Plato and Euclid and heads in another direction. Classical geometry has enjoyed over 2,000 years of scrutinization. Fractal geometry has enjoyed only 40.
  2. The shapes that come out of fractal geometry look like nature derived. This is an amazing fact that is hard to ignore. As we all know, there are no perfect circles in nature and no perfect squares. Not only that, but when you look at trees or mountains or river systems, they don’t resemble any shapes one is used to in math. However with simple formulas iterated multiple times, fractal geometry can model these natural phenomena with alarming accuracy. If you can use simple mathematics to make things look like the world around us, you know you’re onto a winner. Fractal geometry does this with ease.


This article shall give a quick overview of how to make fractal shapes and show how these shapes can resemble nature. It shall then go on to talk about dimensionality, which is a good way to measure fractals. It ends by discussing how fractal geometry is also beneficial because randomness can be introduced into the structure of a fractal shape.

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GMO Apples That Don’t Brown to Reach U.S. Shelves This Fall

GMO Apples That Don’t Brown to Reach U.S. Shelves This Fall | Amazing Science |
Can genetic modification appeal to consumers? A new apple will test the market.


The so-called Arctic apples are genetically altered to suppress browning and may be offered for sale as bagged slices in up to 400 stores in the Midwest and Southern California, according to the company. The launch is the first significant test of a GMO whose modification is meant to appeal to consumers, rather than help farmers increase production, since a slow-ripening tomato called the Flavr Savr flopped in the 1990s.


The modified Golden Delicious apples were developed by Okanagan Specialty Fruits, a privately owned company acquired for $41 million in 2015 by the Maryland biotech Intrexon. Other divisions of that company are already marketing genetically modified salmon, cloned cattle, and self-destructing mosquitoes.


The company plans to sell the apples as bags of pre-sliced fruit but say they will not be labeled as “produced with genetic engineering” and will not come with any other packaging identifying them as GMOs. Instead, as allowed under a 2016 labeling law, there will be a QR code that links to a Web page with detailed information on how the apples were made.

“We didn’t want put ‘GMO’ and a skull and crossbones on the package,” Neal Carter, Okanagan’s founder, said this week, during a presentation in San Francisco.


A package of golden delicious apple slices. The fruit has been genetically modified so they don't turn brown. The GM apple is notable partly because Carter, an apple grower and farming innovator, independently developed it and won regulatory approval to sell it. Most GMOs have been developed and marketed as seeds by large corporations like Monsanto or DuPont and involve large-acre crops like soybeans and corn. Using a technique called gene silencing, Carter and his research team engineered the apple’s DNA to produce less polyphenol oxidase, or PPO, the enzyme that causes the flesh to turn brown. Carter says slices of the engineered apples can stay free of browning as long as three weeks.To some, genetic slowing of the browning process could seem like a solution in search of a problem.


Commercial apple slices are already preserved with a mixture of calcium and vitamin C, which keeps them from browning long enough to be ordered via Amazon. At home, many cooks know a squirt of lemon juice does the trick, at least for a few hours.Groups opposing GMOs have protested the introduction of Okanagan’s apples and pressured food companies including Burger King not to sell them. Friends of the Earth told the Independent that the Arctic apple is “understudied, unlabeled, and unnecessary.” Because of widespread opposition, genetically modified foods are subject to an array of labeling rules and even outright bans around the world.  

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Tech Showcase: Ribocomputing

Tech Showcase: Ribocomputing | Amazing Science |
A novel method of programming cells to operate like computers, called Ribocomputing, will be aided by Twist Bioscience's streamlined DNA manufacturing process.


One goal of synthetic biology is to engineer life to recognize desired inputs and in turn respond with desired outputs. Biocomputing is the management of this input/output system, designing genetic parts that allow life to perform logic based decisions in a manner not dissimilar to the computer you're using to read this article. 
Researchers at the Wyss Institute for Biologically Inspired Engineering and Arizona State University, in a recent article in Nature, demonstrated a novel method of programming cells to operate like computers. They call their method ribocomputing because their engineered cells carry out complex logic-based computations exclusively using ribonucleic acids, more commonly known as RNA.
Unlike the digital computers ubiquitous in the modern world, which use electricity to accomplish all higher-order functions, these ribocomputers perform logical operations on biological materials, such as proteins, toxins, and immune system molecules. Adding programmability to cells opens up exciting new possibilities for ways to control cells and their interactions with organisms and their environment. The ribocumputing researchers propose that using this new technique, cells and microorganisms can be programmed to accomplish tasks ranging from disease diagnostics and therapeutic drug delivery to green energy production and environmental cleanup.
In their ribocomputing demonstration, the research team engineered the bacteria E. coli to sense the presence of 12 different molecules, and then use a computational circuit encoded in RNA to calculate the correct level of green fluorescent protein (GFP) to express. GFP is commonly used as a marker in biological experiments, as its green glow makes it simple for researchers to assess the behavior of genes or pathways in question. 
In the ribocomputing experiment, the researchers first designed an RNA circuit to map different combinations and levels of input molecules to specific GFP intensities, as controlled by expression levels. Next, the researchers introduced controlled levels of the input molecules into the engineered E. coli’s cellular environments, and then checked whether GFP was lighting up at the specified levels. By confirming that GFP was behaving in a manner that they expected, the researchers demonstrated the viability of their RNA circuits to carry out computations.
In general, the principles in this experiment can be applied to other kinds of bio-computation. Using the same methodology, cells can be engineered to respond with specified behavior to any number of the diverse chemical arrangements they encounter in their complicated environments.
The demonstration of successful RNA-based computing represents a significant advancement for cellular computing technology. Although such computing had been described in publications almost two decades ago, the conventional methods required resources and included drawbacks that made the techniques unattractive to pursue for commercial, industrial, and clinical applications. In previous experiments, researchers used combinations of DNA, RNA, proteins, and other molecules to design biological circuits. Incorporating these disparate computing elements into a circuit design is more error-prone: successful operation of the circuit would hinge on the precise coordination of these multifarious components. Each component adds a source of noise to the logical circuit, degrading the results. As the computational load increases, it can limit the effectiveness and applicability of the method. By using RNA only, various sources of noise can be muted.
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Quasars release more energy then 100 galaxies combined

Quasars release more energy then 100 galaxies combined | Amazing Science |

In 2013, researchers discovered a quasar known as SDSS J1106+1939 with the most energetic outflow ever, a finding that may answer questions about how the mass of a galaxy is linked to its central black hole mass and why there are so few large galaxies in the universe. The rate that energy is carried away by the huge mass of material ejected is equivalent to two trillion times the power output of the sun. The black hole at the heart of quasar SDSS J1106-1939 is massive, estimated to be a thousand times heavier than the black hole in the Milky Way.


"This is about 100 times higher than the total power output of the Milky Way galaxy — it's a real monster outflow," said Nahum Arav, an associate professor of physics in College of Science atVirginia Tech and leader of the research team, which includes Benoit Borguet, now a postdoctoral researcher now at the University of Liege, Belgium; Doug Edmonds and Carter Chamberlain, both graduate research assistants at Virginia Tech, and Chris Benn, a collaborator who works with the Isaac Newton Group of Telescopes in Spain.


Researchers studied the quasar in great detail using the European Southern Observatory's Very Large Telescope in Paranal, Chile – the world's most advanced visible-light astronomical observatory, and found the most energetic quasar outflow ever discovered. The findings were released today (Wednesday, Nov. 28, 2012) by the European Southern Observatory.


Theorists have predicted energy flows of this magnitude, and simulations have suggested these outflows impact the galaxies around them, but it has all been speculation — until now.


"For the last 15 years many theorists have said that if there were such powerful outflows it would help answer many questions on the formation of galaxies, on the behavior of black holes, and on the enrichment of the intergalactic medium with elements other than hydrogen and helium," Arav said. "This discovery means we can better explain the formation of galaxies. There are hundreds of people doing the theoretical side of the work. They hypothesize outflows in their simulations, and now we've found an outflow in the magnitude that has only been theorized in the past. Now they can refine their already impressive models and base them on empirical data."

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