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"Big Bang or the Big Bounce?" -- New Science Points to a Continuum

"Big Bang or the Big Bounce?" -- New Science Points to a Continuum | Amazing Science | Scoop.it

The big bang may not have been the beginning of the universe, but merely the beginning of one of an infinite series of universes. Two fundamental concepts in physics, both of which explain the nature of the Universe in many ways, have been difficult to reconcile with each other. European researchers have developed a mathematical approach to do so that has the potential to explain what came before the Big Bang. The big bang singularity --the single point from which the entire universe is supposed to have sprung-- is the major sticking point in the big bang theory; the calculations just can't account for such a singularity. Without evidence associated with the earliest instant of the expansion, the Big Bang theory does not provide any explanation for such an initial condition.

 

According to Einstein’s (classical) theory of general relativity, space is a continuum. Regions of space can be subdivided into smaller and smaller volumes without end. The fundamental idea of quantum mechanics is that physical quantities exist in discrete packets (quanta) rather than in a continuum. Further, these quanta and the physical phenomena related to them exist on an extremely small scale (Planck scale). So far, the theories of quantum mechanics have failed to ‘quantise’ gravity. Loop quantum gravity (LQG) is an attempt to do so. It represents space as a net of quantised intersecting loops of excited gravitational fields called spin networks. This network viewed over time is called spin foam.

 

Not only does LQG provide a precise mathematical picture of space and time, it enables mathematical solutions to long-standing problems related to black holes and the Big Bang. Amazingly, LQG predicts that the Big Bang was actually a ‘Big Bounce’, not a singularity but a continuum, where the collapse of a previous universe spawned the creation of ours.

 

European researchers initiated the ‘Effective field theory for loop quantum gravity’ (EFTFORLQG) project to further develop this exciting candidate theory reconciling classical and quantum descriptions of the Universe.

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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 | Scoop.it
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 | Scoop.it

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 | Scoop.it
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 | Scoop.it

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 | Scoop.it
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 | Scoop.it

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 | Scoop.it
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 | Scoop.it
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 | Scoop.it

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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The Genomic Revolution Reaches Crime LabS

The Genomic Revolution Reaches Crime LabS | Amazing Science | Scoop.it
How will law enforcement handle the deluge of new information available from DNA?

 

Lisa Ziegert disappeared from the gift shop where she worked on April 15, 1992, and her body was found four days later. From then until this past Monday, her murder remained unsolved.

Then on Monday, the local district attorney’s office in

 

Massachusetts announced the arrest of a 48-year-old man for Ziegert’s death. Among the clues that led police to him was a computer-generated “mug shot” based on DNA found at the crime scene 25 years ago. Back then, the idea of predicting a face based on DNA would have seemed like science fiction. It is still rare today, but law-enforcement officials can quite easily order up such a test from the Virginia-based company Parabon NanoLabs.

 

Ziegert’s case is already being touted as an example of the power of new DNA technologies to solve crimes. In many ways, it’s the perfect example to take to the media: a young female victim, an infamous murder, a 25-year-old case. It’s unclear exactly how pivotal the DNA evidence was—the district attorney said “a number of factors” contributed to narrowing down the suspects—but there will almost certainly be more cases like this involving DNA.

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Designer biosensors can detect antibiotic molecules

Designer biosensors can detect antibiotic molecules | Amazing Science | Scoop.it

Researchers from North Carolina State University have engineered designer biosensors that can detect antibiotic molecules of interest. The biosensors are a first step toward creating antibiotic-producing “factories” within microbes such as E. coli.

Macrolides are a group of naturally occurring small molecules that can have antibiotic, antifungal or anticancer effects. The antibiotic erythromycin is one example – it is a macrolide produced by soil-dwelling bacteria. Researchers are interested in using these natural antibiotics and the microbes that produce them in order to develop new antibiotics; however, microbes that produce antibiotic macrolides only make small amounts of a limited variety of antibiotics.

 

“Our ultimate goal is to engineer microbes to make new versions of these antibiotics for our use, which will drastically reduce the amount of time and money necessary for new drug testing and development,” says Gavin Williams, associate professor of bio-organic chemistry at NC State and corresponding author of a paper describing the research. “In order to do that, we first need to be able to detect the antibiotic molecules of interest produced by the microbes.”

 

Williams and his team used a naturally occurring molecular switch – a protein called MphR – as their biosensor. In E. coli, MphR can detect the presence of macrolide antibiotics being secreted by microbes that are attacking E. coli. When MphR senses the antibiotic, it turns on a resistance mechanism to negate the antibiotic’s effects.

 

The researchers created a large library of MphR protein variants and screened them for the ability to switch on production of a fluorescent green protein when they were in the presence of a desired macrolide. They tested the variants against erythromycin, which MphR already recognizes, and found that some of the MphR variants improved their detection ability tenfold. They also successfully tested the variants against macrolides that were not closely related to erythromycin, such as tylosin.

 

“Essentially we have co-opted and evolved the MphR sensor system, increasing its sensitivity in recognizing the molecules that we’re interested in,” says Williams. “We know that we can tailor this biosensor and that it will detect the molecules we’re interested in, which will enable us to screen millions of different strains quickly. This is the first step toward high-throughput engineering of antibiotics, where we create vast libraries of genetically modified strains and variants of microbes in order to find the few strains and variants that produce the desired molecule in the desired yield.”

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Predatory bacteria: The quest for a new class of antibiotics

Predatory bacteria: The quest for a new class of antibiotics | Amazing Science | Scoop.it
OIST researchers take one step forward toward understanding and genetically manipulating B. bacteriovorus, a type of bacteria with promising potential use as a living antibiotic.

 

In 2016 the World Health Organization named antibiotic resistance as "one of the biggest threats to global health, food security, and development today." The announcement cited a growing list of infections, such as tuberculosis and gonorrhea, that are becoming more difficult to treat each year as resistance to current antibiotic treatments increases. Yet antibiotics are essential--without them, the human race would be plagued by persistent infections. So what is the solution to ensuring continual treatment while also addressing the alarming rise in resistance?

 

One potential solution lies within a unique type of predatory bacteria that feeds on other bacteria, such as those that cause diseases. Dubbed "living antibiotics," this group of carnivorous fauna have caught researchers' attention, including those at the Okinawa Institute of Science and Technology Graduate University (OIST). In a recently published paper in ACS Synthetic Biology, OIST researchers have taken the first steps toward genetic manipulation of one such tiny cannibal, B. bacteriovorus. They have identified tools that may allow for the manipulation of genes that influence this bacteria's predatory behavior.

 

"In the future, we want to control the predation of the bacteria--the timing and extent of predation," explains Dr. Mohammed Dwidar from the Nucleic Acid Chemistry and Engineering Unit and first author on the paper. "[At the moment] we lack the basic engineering tools in order to do this."

 

B. bacteriovorus is harmless to humans yet lethal to its prey--Gram-negative bacteria--which includes baddies such as E. coli, Salmonella, Legionella, and others. As such, being able to control it could potentially treat many different types of infections. However, due to its unusual predatory nature and other unique features, genetic manipulation of B. bacteriovorus has been limited.

The OIST researchers used riboswitches, which are gene expression-controlling tools known to function well in other bacteria, to tackle the challenge of understanding and manipulating B. bacteriovorus's predation. The way in which a gene is expressed follows a specific pathway--DNA is converted into RNA via transcription, RNA is converted into proteins via translation, and then the proteins carry out different functions. The riboswitch comes in at the translation phase. By putting a riboswitch at the beginning of a strand of RNA, and then "activating" it with a chemical, the riboswitch can start or stop the RNA from being translated into a protein.

 

For their study, the OIST researchers inserted a riboswitch into one of the genes believed to be important to B. bacteriovorus's predatory behavior: flagellar sigma factor fliA. They then activated it with the chemical theophylline. After placing the modified bacteria in petri dishes together with some delicious E. coli prey, the modified B. bacteriovorus seemed to multiply more quickly in presence of theophylline than in its absence. This quicker multiplication implies that B. bacteriovorus was consuming its prey faster, and thus multiplying faster. This in turn shows that the predatory lifecycle can be controlled by theophylline.

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Major advance in nanopore detection of peptides and proteins

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

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 | Scoop.it
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 | Scoop.it
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 | Scoop.it
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 | Scoop.it

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 | Scoop.it
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 ligo.org/partners.php

 

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 | Scoop.it

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 | Scoop.it
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 | Scoop.it
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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Green algae could be key to engineering faster-growing crops

Green algae could be key to engineering faster-growing crops | Amazing Science | Scoop.it
How do green algae grow so quickly? Two new collaborations offer insight into how these organisms siphon carbon dioxide from the air for use in photosynthesis, a key factor in their ability to rapidly take over a swimming pool or pond. Understanding this process may someday help researchers improve the growth rate of agricultural crops such as wheat and rice.

 

In two studies published this week in the journal Cell, a Princeton-led team with collaborators from Carnegie and the Max Planck Institute of Biochemistry reported the first detailed inventory of the cellular compartment called the pyrenoid, which algae use to collect and concentrate carbon dioxide, making the photosynthetic process more efficient than it is in most other algae and plants.

The researchers also found that the pyrenoid, long thought to be a solid structure, actually behaves like a liquid droplet that can dissolve into the surrounding cellular medium when the algal cells divide.

 

"Understanding how algae can concentrate carbon dioxide is a key step toward the goal of improving photosynthesis in other plants," said study leader Martin Jonikas, an assistant professor of molecular biology at Princeton and former Carnegie staff associate. "If we could engineer other crops to concentrate carbon, we could address the growing world demand for food.”

Aquatic algae and a handful of other plants have developed carbon-concentrating mechanisms that boost the rate of photosynthesis, the process by which plants turn carbon dioxide and sunlight into sugars for growth. All plants use an enzyme called Rubisco to "fix" carbon dioxide into sugar that can be used or stored by the plant.

 

Algae have an advantage over many land plants because they cluster the Rubisco enzymes inside the pyrenoid, where the enzymes encounter high concentrations of carbon dioxide pumped in from the air. Having more carbon dioxide around allows the Rubisco enzymes to work faster.

 

In one study, the researchers conducted a sweeping search for proteins involved in the carbon-concentrating mechanism of an algae species known as Chlamydomonas reinhardtii. The researchers developed methods for rapidly labeling and evaluating algal proteins, which they used to identify their locations and functions, detailing the physical interactions between the proteins to create a pyrenoid "interactome."

 

The search revealed 89 new pyrenoid proteins, including ones that the researchers think usher carbon into the pyrenoid and others that are required for formation of the pyrenoid. They also identified three previously unknown layers of the pyrenoid that surround the organelle like the layers of an onion.

 

"The information represents the best assessment yet of how this essential carbon-concentrating machinery is organized and suggests new avenues for exploring how it works," said Luke Mackinder, the study's first author and a former Carnegie McClintock postdoctoral fellow who now leads a team of researchers at the University of York.

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Massively Parallel De Novo Protein Design for Targeted Therapeutics

Massively Parallel De Novo Protein Design for Targeted Therapeutics | Amazing Science | Scoop.it

Researchers say they have developed a technique to generate many small, different proteins that can be designed to bind to therapeutic targets. They add that their methodology, which reportedly produces thousands of new drug candidates, may lead to protection against infectious diseases, such as influenza, and antidotes to nerve toxins.

 

The computer-designed proteins, which did not previously exist in nature, combine the stability and bioavailability of small-molecule drugs with the specificity and potency of larger biologics, according to David Baker, Ph.D., who led the multi-institutional research project and is professor of biochemistry at the University of Washington School of Medicine and director of the UW Institute for Protein Design

 

"These mini-protein binders have the potential of becoming a new class of drugs that bridge the gap between small-molecule drugs and biologics. Like monoclonal antibodies, they can be designed to bind to targets with high selectivity, but they are more stable and easier to produce and to administer," said Dr. Baker who with colleagues published their study in Nature ("Massively Parallel De Novo Protein Design for Targeted Therapeutics").

 

The technique relies on the Rosetta computer platform, developed by Dr. Baker and colleagues at the University of Washington. They designed thousands of short proteins, about 40 amino acids in length, that the Rosetta program predicted would bind tightly to the molecular target.

 

Computer modeling identified the amino acid sequences of thousands of short proteins that would fit into and bind to the influenza and botulinum targets. The team created short pieces of DNA that coded each of these proteins, grew the proteins in yeast cells, and then looked at how tightly they bound to their targets. The targets were Influenza H1 hemagglutinin and botulinum neurotoxin B. 

 

The technique allowed them to design and test 22,660 proteins in just a few months, with more than than 2000 of them bound to their targets with high affinity, according to Dr. Baker. He pointed out that of the best candidates found the anti-influenza proteins neutralized viruses in cell culture and other designed proteins prevented the botulinum toxin from entering brain cells.

 

A nasal spray containing one of the custom-designed proteins completely protected mice from the flu if administered before or as much as 72 hours after exposure. The protection that the treatment provides equaled or surpassed that seen with antibodies, the researchers report.

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San Diego Startup Uses Algae Feedstock to Make Renewable Flip-Flops

San Diego Startup Uses Algae Feedstock to Make Renewable Flip-Flops | Amazing Science | Scoop.it

Every year, petroleum-based feedstocks are used worldwide to make roughly 3 billion flip-flops, the rubbery, flat-sole sandals held on the foot by a Y-shaped strap that fits between the first and second toes.

 

It might seem like a throwaway product—and it is, according to Stephen Mayfield, a UC San Diego professor of biology and director of the California Center for Algae Biotechnology. The petrochemicals used to produce flip-flops make them impervious to the elements—and they end up as non-biodegradable rubbish in rivers and oceans, and in landfills and trash heaps. Yet flip-flops also are the No. 1 shoe in the world. “These are the shoes of a fisherman and a farmer,” Mayfield says. “This is the No. 1 shoe in India, the No. 1 shoe in China, and the No. 1 shoe in Africa.”

 

So Mayfield and colleagues at UC San Diego recently unveiled prototype flip-flopsmade from algae-derived polymeric polyols instead of petroleum-based polyurethanes. The idea is to offer consumers more environmentally friendly flip-flops, made with renewable materials and perhaps even biodegradable after a year or two.

 

Mayfield, who was a scientific co-founder of the unsuccessful algal biofuel company Sapphire Energy, worked with UC San Diego chemists Michael Burkart and Robert “Skip” Pomeroy to make a pliable foam from algae-based polyols that could replace conventional polyurethanes. To advance the commercial prospects for biodegradable flip-flops, Mayfield, Burkart, and Pomeroy founded an industrial biotech, Algenesis Materials, in early 2016.

 

“Our goal is to get to 100 percent renewable, and 100 percent biodegradable,” said Mayfield, who is an environmentally conscious surfer and coastal enthusiast. “Burkart’s convinced that we’re going to throw these [flip-flops] in a compost pile, and in six months they’ll be gone. But we’re not there yet.”

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CRISPR-Cas9 fixes Duchenne muscular dystrophy mutation in mice

CRISPR-Cas9 fixes Duchenne muscular dystrophy mutation in mice | Amazing Science | Scoop.it

Scientists at the University of California, Berkeley, have engineered a new way to deliver CRISPR-Cas9 gene-editing technology inside cells and have demonstrated in mice that the technology can repair the mutation that causes Duchenne muscular dystrophy, a severe muscle-wasting disease.

 

A new study shows that a single injection of CRISPR-Gold, as the new delivery system is called, into mice with Duchenne muscular dystrophy led to an 18-times-higher correction rate and a two-fold increase in a strength and agility test compared to control groups.

 

Since 2012, when study co-author Jennifer Doudna, a professor of molecular and cell biology and of chemistry at UC Berkeley, and colleague Emmanuelle Charpentier, of the Max Planck Institute for Infection Biology, repurposed the Cas9 protein to create a cheap, precise and easy-to-use gene editor, researchers have hoped that therapies based on CRISPR-Cas9 would one day revolutionize the treatment of genetic diseases. Yet developing treatments for genetic diseases remains a big challenge in medicine. This is because most genetic diseases can be cured only if the disease-causing gene mutation is corrected back to the normal sequence, and this is impossible to do with conventional therapeutics.

 

CRISPR/Cas9, however, can correct gene mutations by cutting the mutated DNA and triggering homology-directed DNA repair. However, strategies for safely delivering the necessary components (Cas9, guide RNA that directs Cas9 to a specific gene, and donor DNA) into cells need to be developed before the potential of CRISPR-Cas9-based therapeutics can be realized. A common technique to deliver CRISPR-Cas9 into cells employs viruses, but that technique has a number of complications. CRISPR-Gold does not need viruses.

 

In the new study, research lead by the laboratories of Berkeley bioengineering professors Niren Murthy and Irina Conboy demonstrated that their novel approach, called CRISPR-Gold because gold nanoparticles are a key component, can deliver Cas9 – the protein that binds and cuts DNA – along with guide RNA and donor DNA into the cells of a living organism to fix a gene mutation.

 

“CRISPR-Gold is the first example of a delivery vehicle that can deliver all of the CRISPR components needed to correct gene mutations, without the use of viruses,” Murthy said.

 

The study was published October 2 in the journal Nature Biomedical Engineering.

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