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Future of Machine Learning: Automated tools aim to make it easier to teach a computer than to program it

Future of Machine Learning: Automated tools aim to make it easier to teach a computer than to program it | Amazing Science |

Machine learning – the ability of computers to understand data, manage results, and infer insights from uncertain information – is the force behind many recent revolutions in computing. Email spam filters, smartphone personal assistants and self-driving vehicles are all based on research advances in machine learning. Unfortunately, even as the demand for these capabilities is accelerating, every new application requires a Herculean effort.  Even a team of specially-trained machine learning experts makes only painfully slow progress due to the lack of tools to build these systems.


The Probabilistic Programming for Advanced Machine Learning (PPAML) program was launched to address this challenge. Probabilistic programming is a new programming paradigm for managing uncertain information. By incorporating it into machine learning, PPAML seeks to greatly increase the number of people who can successfully build machine learning applications and make machine learning experts radically more effective. Moreover, the program seeks to create more economical, robust and powerful applications that need less data to produce more accurate results – features inconceivable with today’s technology.


“We want to do for machine learning what the advent of high-level program languages 50 years ago did for the software development community as a whole,” said Kathleen Fisher, DARPA program manager.


“Our goal is that future machine learning projects won’t require people to know everything about both the domain of interest and machine learning to build useful machine learning applications. Through new probabilistic programming languages specifically tailored to probabilistic inference, we hope to decisively reduce the current barriers to machine learning and foster a boom in innovation, productivity and effectiveness.”


To familiarize potential participants with the technical objectives of PPAML, DARPA will host a Proposers' Day on Wednesday, April 10, 2013. For details, visit: Registration closes on Friday, April 5, 2013 at 5 p.m. ET.  




The DARPA Special Notice document describing the specific capabilities sought is available at


Associated images posted on may be reused according to the terms of the DARPA User Agreement, available here:

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Video shows how HIV spreads in real time

Video shows how HIV spreads in real time | Amazing Science |






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How to make 3-D objects totally disappear

How to make 3-D objects totally disappear | Amazing Science |

An ultra-thin invisibility “skin” cloak that can conform to the shape of an object and conceal it from detection with visible light has been developed by scientists at Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkeley.

Working with blocks of gold nanoantennas, the Berkeley researchers created a “skin cloak” just 80 nanometers in thickness that was wrapped around a three-dimensional object about the size of a few biological cells and shaped with multiple bumps and dents. The surface of the skin cloak was meta-engineered to reflect light waves, making the object invisible to optical detection when the cloak is activated.

“This is the first time a 3D object of arbitrary shape has been cloaked from visible light,” said Xiang Zhang, director of Berkeley Lab’s Materials Sciences Division. “Our ultra-thin cloak now looks like a coat. It is easy to design and implement, and is potentially scalable for hiding macroscopic objects.”


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Earth-like planets around small stars likely have protective magnetic fields, aiding chance for life

Earth-like planets around small stars likely have protective magnetic fields, aiding chance for life | Amazing Science |


Low-mass stars are among the most common in the universe. Planets orbiting near such stars are easier for astronomers to target for study because when they transit, or pass in front of, their host star, they block a larger fraction of the light than if they transited a more massive star. But because such a star is small and dim, its habitable zone—where an orbiting planet gets the heat necessary to maintain life-friendly liquid water on the surface—also lies relatively close in.



Their simulations ranged from one stellar mass—stars the size of our sun—down to about one-tenth of that size. By merging their models, they were able, Barnes said, "to produce a more realistic picture of what is happening inside these planets." Barnes said there has been a general feeling in the astronomical community that tidally locked planets are unlikely to have protective magnetic fields "and therefore are completely at the mercy of their star." This research suggests that assumption false.

Far from being harmful to a planet's magnetic field, tidal heating can actually help it along—and in doing so also help the chance for habitability. This is because of the somewhat counterintuitive fact that the more tidal heating a planetary mantle experiences, the better it is at dissipating its heat, thereby cooling the core, which in turn helps create the magnetic field.

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Printable holograms could make holograms more widespread

Printable holograms could make holograms more widespread | Amazing Science |

Holograms have a wide variety of applications, from 3D displays to data storage, but the potential applications are currently limited by the complexity and cost of hologram fabrication. In an attempt to simplify the hologram fabrication process, scientists have developed a way to print holograms using a relatively simple and inexpensive laser-printing technique. They hope that the new method will make hologram fabrication more accessible for small-scale and personal use, opening up new types of applications such as integration with smart phones. The researchers, led by Dr. Haider Butt at the University of Birmingham, have published a paper on the printable holograms in a recent issue of Applied Physics Letters.

As the researchers explain in their paper, traditional holography fabrication requires specialized knowledge, expensive equipment, and time-consuming recording techniques. Recently, scientists have developed an alternative technique that uses a laser pulse that is split into two beams to create an interference pattern on a surface, producing the characteristic 3D holographic pattern. However, this approach has its own challenges, as it requires precise alignment of the two laser beams and suffers from low light intensity after beam splitting.

In the new paper, the researchers have overcome these challenges by developing a single-pulse laser technique that can rapidly print 2D and 3D holograms in seconds on flat or curved surfaces and on a variety of materials. The nanosecond laser can print 1 cm2 of hologram area in just 5 nanoseconds. The researchers explain that the overall speed is not limited by the laser pulse, but by the need to reposition the surface in between lasing, which could potentially be done much faster using robotics.

"The technique is slightly different from the conventional methods, which divide a single pulsed beam using beam splitters and then recombine them to produce holograms and nanopatterns," Butt told "Here we use only a single beam, which is reflected normally from a mirror. The incident and reflected beams interfere, and this interference pattern is used for writing/printing holograms. The technique requires far fewer optical components, it is very simple, reliable, and can be used for ablating a myriad of materials and substrates."

The scientists demonstrated the new technique by printing a holographic 2D signature and a holographic 3D coin. They expect that the method could be especially useful for printing holograms on sensors and "smart" materials that change in response to various stimuli. Printable holograms could also be integrated into smart phones, where, as the researchers explain, they can be used to interpret colorimetric data in pictures.

"The holograms printed with this method can be printed using dynamic materials, which are able to respond to any stimuli in their environments," Butt said. "And they will change their color in response to any environmental changes. Using smart phone cameras and applications, such colorimetric changes can be read, interpreted, and communicated remotely."

Additional applications may include 3D artwork, smart windows, and bio-sensing, among others. "This work can lead to further applications, such as holographic data storage, optical sensors, and printable optical devices," Butt said. "We and our collaborators are currently pursuing all these research paths and achieving good results."

More information: Qiancheng Zhao, et al. "Printable ink holograms." Applied Physics Letters. DOI: 10.1063/1.4928046

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A new single-molecule tool to observe enzymes at work

A new single-molecule tool to observe enzymes at work | Amazing Science |

A team of scientists at the University of Washington and the biotechnology company Illumina have created an innovative tool to directly detect the delicate, single-molecule interactions between DNA and enzymatic proteins. Their approach provides a new platform to view and record these nanoscale interactions in real time. As they report Sept. 28 in Nature Biotechnology, this tool should provide fast and reliable characterization of the different mechanisms cellular proteins use to bind to DNA strands—information that could shed new light on the atomic-scale interactions within our cells and help design new drug therapies against pathogens by targeting enzymes that interact with DNA.

"There are other single-molecule tools around, but our new tool is far more sensitive," said senior author and UW physics professor Jens Gundlach. "We can really pick up atomic-scale movements that a protein imparts onto DNA." As can happen in the scientific process, they developed this tool—the single-molecule picometer-resolution nanopore tweezers, or SPRNT—while working on a related project.

The UW team has been exploring nanopore technology to read DNA sequences quickly. Our genes are long stretches of DNA molecules, which are made up of combinations of four chemical DNA "letters." In their approach, Gundlach and his team measure an electrical current through a biological pore called MspA, which is embedded within a modified cell membrane. As DNA passes through a tiny opening in the pore—an opening that is just 0.00000012 centimeters wide, or 1/10,000th the width of a human hair—the current shifts based on the sequence of DNA letters. They use these changes in current to infer DNA sequences.

Gundlach and his team, in the process of investigating nanopore sequencing, tried out a variety of molecular motors to move DNA through the pore. They discovered that their experimental setup was sensitive enough to observe motions much smaller than the distance between adjacent letters on the DNA. As they report in their paper, SPRNT is more than seven times more sensitive than existing techniques to measure interactions between DNA and proteins.

"Generally, most existing techniques to look at single-molecule movements—such as optical tweezers—have a resolution, at best, of about 300 picometers," said Gundlach. "With SPRNT, we can have 40 picometer resolution." For reference, 40 picometers are 0.000000004 centimeters, or about 0.0000000016 inches.

"We realized we can detect minute differences in the position of the DNA in the pore," said UW physics postdoctoral researcher Andrew Laszlo, a co-author on the paper. "We could pick up differences in how the proteins were binding to DNA and moving it through the pore."

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Perplexing new 'snakeskin' image of Pluto terrain from New Horizons

Perplexing new 'snakeskin' image of Pluto terrain from New Horizons | Amazing Science |
The newest high-resolution images of Pluto from NASA's New Horizons are both dazzling and mystifying, revealing a multitude of previously unseen topographic and compositional details. The image below—showing an area near the line that separates day from night—captures a vast rippling landscape of strange, aligned linear ridges that has astonished New Horizons team members.

It's a unique and perplexing landscape stretching over hundreds of miles," said William McKinnon, New Horizons Geology, Geophysics and Imaging (GGI) team deputy lead from Washington University in St. Louis. "It looks more like tree bark or dragon scales than geology. This'll really take time to figure out; maybe it's some combination of internal tectonic forces and ice sublimation driven by Pluto's faint sunlight."

The "snakeskin" image of Pluto's surface is just one tantalizing piece of data New Horizons sent back in recent days. The spacecraft also captured the highest-resolution color view yet of Pluto, as well as detailed spectral maps and other high-resolution images.

The new "extended color" view of Pluto – taken by New Horizons' wide-angle Ralph/Multispectral Visual Imaging Camera (MVIC) on July 14 and downlinked to Earth on Sept. 19 – shows the extraordinarily rich color palette of Pluto.

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NASA Confirms Evidence That Liquid Water Flows on Today’s Mars

NASA Confirms Evidence That Liquid Water Flows on Today’s Mars | Amazing Science |





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Macaque Experiment Shows Vaccination Not Linked to Autism

Macaque Experiment Shows Vaccination Not Linked to Autism | Amazing Science |


During the most recent Republican presidential debate, frontrunner Donald Trump once again dragged out the still widespread myth that vaccines cause autism. This dangerous fiction was debunked as early as 2002 by the New England Journal of Medicine and has been consistently contradicted by research ever since. As a result, anti-vaxxers changed strategy: Instead of blaming thimerosal for causing autism, they now focus on the vaccine schedule itself, essentially claiming that too many shots in too short of a timespan overwhelms a child's immune system.

That is nonsense. The number of antigens (i.e., molecules that trigger an antibody response) contained within vaccines has decreased dramatically over the past several decades. In the Genetic Expert News Service, Emory University infectious disease professor Dr. Walter Orenstein says that the total number of antigens in all vaccines combined is about 150, which is practically nothing compared to the roughly2,000-6,000 antigens children face every single day. By crawling around on the floor and sticking their hands in their mouths, children are "vaccinating" themselves all day long.

Despite the lack of scientific logic to the anti-vaxxers' argument, a team of researchers decided to address the issue of vaccine schedules head-on. Their results are reported in the journal PNASThe team divided 79 rhesus macaque monkeys into six experimental groups, each containing 12-16 animals. They then administered various combinations of vaccines to the animals in those groups. [Note that some vaccines contain EtHg, a metabolic derivative of thimerosal, while others do not. Also note that the vaccines used are the same as or similar to those used to vaccinate children (PDF).]

After all shots were administered, the macaques' behavior was assessed and their brains were examined for signs of autism. What did they find? Nothing. Absolutely nothing. There were neither significant differences in brain structure nor significant differences in the negative behaviors associated with autism. In other words, all the monkeys developed normally.

Critics will argue that this experiment was performed in macaques, not humans, and is therefore unreliable. Of course, it is unethical to give children placebos in place of vaccines (not to mention cutting their brains open), so this experiment cannot be performed in humans.

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Accelerating Drug Discovery with Machine Learning on Big Medical Data

Accelerating Drug Discovery with Machine Learning on Big Medical Data | Amazing Science |

Pharmaceutical companies spend billions testing prospective drugs by conducting “wet lab” experiments that can take years to complete. But what if the same results could be obtained in a matter of minutes by running computer model simulations instead? A Silicon Valley startup says it has created a novel machine learning algorithm that does just that.

TwoXar (pronounced “two-czar”) was founded last year by two men both named Andrew Radin (more on that later). The Radins were interested in using advances in data science and large-scale computing to speed up the pace of drug discovery, which would give pharmaceutical companies better candidates for clinical studies.

“The traditional method of drug discovery is you examine a disease, you devise that there’s a protein of interest to you, and if you can regulate an activity with a drug, then perhaps it will help out,” TwoXar CEO Andrew A. Radin tells Datanami. “That’s a multi-year process to do all that work.”

TwoXar’s DUMA Drug Discovery platform can replace years’ worth of biological lab work with a digital equivalent that leans heavily on data science and leverages the incredible amount of medical, biological, and drug data that already exists in the public sphere.

“Our core IP [intellectual property], if you will, is this ability to take extremely diverse data sets and draw relationships between those data sets,” Radin says. “We’re combining clinical data in combination with gene expression assays, protein interaction networks, drug protein binding databases, and physical attributes about the molecules themselves.”

The hardest part is actually obtaining the relevant data. Most of the data is in the public sphere, thanks to the billions in spent by the NIH, the FDA, the European Union, and the Canadian government to back primary medical, chemical, and biological research. Once the right data is loaded into the system, it’s as simple as pressing the “go” button and waiting for the system to spit out its answer.

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Research advances potential for test and vaccine for genital and oral herpes

Research advances potential for test and vaccine for genital and oral herpes | Amazing Science |
Findings from a pair of new studies could speed up the development of a universally accurate diagnostic test for human herpes simplex viruses (HSV), according to researchers at Johns Hopkins and Harvard universities and the National Institutes of Health (NIH). The work may also lead to the development of a vaccine that protects against the virus.

Depending on the strain and other factors, HSV can cause cold sores -- classically associated with HSV1 -- or genital herpes -- classically HSV2 -- with the latter being the more serious of the two diseases, particularly because studies show that HSV2 makes carriers more susceptible to contracting HIV. Currently, individuals are screened for HSV using a test that distinguishes between a glycoprotein -- or a molecule containing a carbohydrate and a protein -- present in HSV1, which is common throughout the population, and the considerably rarer HSV2. Whereas the test discriminates between the two variants with high accuracy in the United States and Europe, it largely fails in Africa, where rates of HIV and HSV are highest.

HSV was first genetically sequenced using only European patient strains, and the resulting diagnostic test was developed to identify sequences common to those strains. Scientists have long suspected that the glycoproteins present in African patients who are HSV-positive might differ from patients in the U.S. and Europe.

"Because HSV2 enhances HIV transmission, we have been testing people across East Africa for genital herpes, but everybody was coming up positive. The test was just not as specific as it should be," says Thomas Quinn, M.D., professor of medicine at the Johns Hopkins University School of Medicine and associate director of international research and senior investigator in the Division of Intramural Research at NIH's National Institute of Allergy and Infectious Diseases.

Quinn, who has been conducting research in East Africa for 30 years, was a senior author on both studies, which will appear in print in the August issue of the Journal of Virology.
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Fish Got Each Others Back Covered

Fish Got Each Others Back Covered | Amazing Science |

Reciprocal cooperation is assumed to require complex cognitive and social skills, skills that we thought fishes don’t have.

New research from the ARC Centre of Excellence for Coral Reef Studies at James Cook University discovered that a particular kind of fish (rabbitfish) are especially guard-like, thus while one is feeding the other will help, support and cooperate with the other.

While we already have studies confirming that mammals and highly social birds have such reciprocal skills, until now we believed these weren’t probable for fishes.

Dr. Simon Brandl from the ARC Centre of Excellence for Coral Reef Studies said: “We found that rabbitfish pairs coordinate their vigilance activity quite strictly, thereby providing safety for their foraging partner, in other words, one partner stays ‘on guard’ while the other feeds – these fishes literally watch each others’ back this behaviour is so far unique among fishes and appears to be based on reciprocal cooperation between pair members.”

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New flat transistor defies theoretical limit

New flat transistor defies theoretical limit | Amazing Science |




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Ultrafast Lasers Offer 3-D Micropatterning of Biocompatible Silk Hydrogels







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Self-assembling material that grows and changes shape could lead to artificial arteries | Amazing Science |
Researchers at QMUL have developed a way of assembling organic molecules into complex tubular tissue-like structures without the use of moulds or techniques like 3D printing.

The study, which will appear on Monday 28 September in the journal Nature Chemistry, describes how peptides and proteins can be used to create materials that exhibit dynamic behaviors found in biological tissues like growth, morphogenesis, and healing.

The method uses solutions of peptide and protein molecules that, upon touching each other, self-assemble to form a dynamic tissue at the point at which they meet. As the material assembles itself it can be easily guided to grow into complex shapes.

This discovery could lead to the engineering of tissues like veins, arteries, or even the blood-brain barrier, which would allow scientists to study diseases such as Alzheimer’s with a high level of similarity to the real tissue, which is currently impossible. The technique could also contribute to the creation of better implants, complex tissues, or more effective drug screening methods.

Alvaro Mata, Director of the Institute of Bioengineering at QMUL and lead author of the paper, said: “What is most exciting about this discovery is the possibility for us to use peptides and proteins as building-blocks of materials with the capacity to controllably grow or change shape, solely by self-assembly.

Karla Inostroza-Brito, PhD student and first author of the paper said: “The system is dynamic so it can be triggered on demand to enable self-assembly with a high degree of control, which allows the creation of complex shapes with a structure that resembles elements of native tissue.“

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NASA is developing the capabilities needed to send humans to an asteroid by 2025 and Mars in the 2030s | Amazing Science |

NASA is developing the capabilities needed to send humans to an asteroid by 2025 and Mars in the 2030s – goals outlined in the bipartisan NASA Authorization Act of 2010 and in the U.S. National Space Policy, also issued in 2010.

Mars is a rich destination for scientific discovery and robotic and human exploration as mankind expands its presence into the solar system. Its formation and evolution are comparable to Earth, helping us to learn more about our own planet’s history and future. Mars had conditions suitable for life in its past. Future exploration could uncover evidence of life, answering one of the fundamental mysteries of the cosmos: Does life exist beyond Earth?


Our next step is deep space, where NASA will send a robotic mission to capture and redirect an asteroid to orbit the moon. Astronauts aboard the Orion spacecraft will explore the asteroid in the 2020s, returning to Earth with samples. This experience in human spaceflight beyond low-Earth orbit will help NASA test new systems and capabilities, such as Solar Electric Propulsion, which we’ll need to send cargo as part of human missions to Mars. Beginning in FY 2018, NASA’s powerful Space Launch System rocket will enable these “proving ground” missions to test new capabilities. Human missions to Mars will rely on Orion and an evolved version of SLS that will be the most powerful launch vehicle ever flown.



• NASA's Orion Flight Test and the Journey to Mars

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CDK8/CDK19 inibitor isolated from sea sponges may be an effective treatment against AML

CDK8/CDK19 inibitor isolated from sea sponges may be an effective treatment against AML | Amazing Science |
A team of Harvard researchers and other collaborators led by Professor of Chemistry and Chemical Biology Matthew Shair has demonstrated that a molecule isolated from sea sponges and later synthesized in Shair's lab, can halt the growth of cancerous cells and could open the door to a new treatment for leukemia. The study is described in a September 28th paper in Nature.

"Once we learned this molecule named cortistatin A was very potent and selective in terms of inhibiting the growth of AML cells, we tested it in mouse models of AML and found that it was as efficacious as any other molecule we had seen, without having deleterious effects," Shair said. "This suggests we have identified a promising new therapeutic approach."

It's one that could be available to test in patients relatively soon. "We synthesized cortistatin A and we are working to develop novel therapeutics based on it by optimizing its drug-like properties," Shair said. "Given the dearth of effective treatments for AML, we recognize the importance of advancing it toward clinical trials as quickly as possible."

The drug development process takes years, but Shair's lab is very close to having what is known as a development candidate that could be taken into late-stage preclinical development and then into clinical trials. An industrial partner will be needed to progress the technology along that path and toward eventual regulatory approval. Harvard's Office of Technology Development (OTD) is engaged in advanced discussions toward that end.

The molecule works, Shair explained, by inhibiting a pair of nearly identical kinases, called CDK8 and CDK19, that his work indicates play a key role in the growth of AML cells. 

Shair's lab became interested in the molecule several years ago, shortly after it was first isolated and described by other researchers. The early studies suggested it appeared to inhibit just a handful of kinases. "We tested approximately 400 kinases, and found that it inhibits only CDK8 and CDK19 in cells, which makes it among the most selective kinase inhibitors identified to date," Shair said. "Having compounds that precisely hit a specific target, like cortistatin A can help reduce side-effects and increase efficacy. In a way, it shatters a dogma because we thought it wasn't possible for a molecule to be this selective and bind in a site common to all ~500 human kinases, but this molecule does it, and it does it because of its three-dimensional structure. What's interesting is that most kinase inhibitor drugs do not have this type of three-dimensional structure. Nature is telling us that one way to achieve this level of specificity, is to make molecules more like cortistatin A."

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World's smallest snail discovered in China that can fit 10 times in the eye of a needle

World's smallest snail discovered in China that can fit 10 times in the eye of a needle | Amazing Science |

Snails small enough to fit almost 10 times into the eye of a needle have been discovered in Guangxi province, Southern ChinaWith their shells measuring 0.86mm in height, the researchers believe they are the smallest land snails ever found.

The Angustopila dominikae snail – named after the wife of one of the authors ofthe study published in the journal ZooKeys – is just visible to the naked eye but very difficult to spot. Barna Páll-Gergely, co-author and scientist from Shinshu university in Japan said he was excited to find the “really really tiny” snails. 

“These are very probably extreme endemic species. If we find them in more than one locality that is somewhat surprising,” he said. The seven species of record-breaking “microsnails” were discovered by the researchers while collecting soil samples from the base of limestone rocks in Guangxi province. They say it is likely they are indigenous to the area, with the most similar species living about 621 miles away in Thailand.

M. Philip Oliver's curator insight, September 29, 8:37 AM

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First optical rectenna—combined rectifier and antenna—converts light to DC current

First optical rectenna—combined rectifier and antenna—converts light to DC current | Amazing Science |

Based on multiwall carbon nanotubes and tiny rectifiers fabricated onto them, the optical rectennas could provide a new technology for photodetectors that would operate without the need for cooling, energy harvesters that would convert waste heat to electricity - and ultimately for a new way to efficiently capture solar energy.

In the new devices, developed by engineers at the Georgia Institute of Technology, the carbon nanotubes act as antennas to capture light from the sun or other sources. As the waves of light hit the nanotube antennas, they create an oscillating charge that moves through rectifier devices attached to them. The rectifiers switch on and off at record high petahertz speeds, creating a small direct current.

Billions of rectennas in an array can produce significant current, though the efficiency of the devices demonstrated so far remains below one percent. The researchers hope to boost that output through optimization techniques, and believe that a rectenna with commercial potential may be available within a year.

"We could ultimately make solar cells that are twice as efficient at a cost that is ten times lower, and that is to me an opportunity to change the world in a very big way" said Baratunde Cola, an associate professor in the George W. Woodruff School of Mechanical Engineering at Georgia Tech. "As a robust, high-temperature detector, these rectennas could be a completely disruptive technology if we can get to one percent efficiency. If we can get to higher efficiencies, we could apply it to energy conversion technologies and solar energy capture."

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Deep-diving whales have ultra-stable myoglobin, which could lead to improved synthetic blood

Deep-diving whales have ultra-stable myoglobin, which could lead to improved synthetic blood | Amazing Science |
The ultra-stable properties of the proteins that allow deep-diving whales to remain active while holding their breath for up to two hours could help Rice University biochemist John Olson and his colleagues finish a 20-year quest to create lifesaving synthetic blood for human trauma patients.

In a new study featured this week in the Journal of Biological Chemistry, Olson and colleagues George Phillips, Lucian Smith and Premila Samuel compared the muscle protein myoglobin from humans, whales and other deep-diving mammals. Myoglobin holds oxygen for ready use inside muscle cells, and the study found that marine mammals have ultra-stable versions of myoglobin that tend not to unfold. The researchers found that stability was the key for cells to make large amounts of myoglobin, which is explains why deep-diving mammals can load their muscle cells with far more myoglobin than humans.

“Whales and other deep-diving marine mammals can pack 10-20 times more myoglobin into their cells than humans can, and that allows them to ‘download’ oxygen directly into their skeletal muscles and stay active even when they are holding their breath,” said Olson, Rice’s Ralph and Dorothy Looney Professor of Biochemistry and Cell Biology. “The reason whale meat is so dark is that it’s filled with myoglobin that is capable of holding oxygen. But when the myoglobin is newly made, it does not yet contain heme. We found that the stability of heme-free myoglobin is the key factor that allows cells to produce high amounts of myoglobin.”

That’s important to Olson because he wants to create a strain of bacteria that can generate massive quantities of another protein that’s closely related to myoglobin. Olson has spent two decades studying hemoglobin, a larger, more complex oxygen-carrying protein in blood. Olson’s goal is to create synthetic blood for use in transfusions. Hospitals and trauma specialists currently rely on donated whole blood, which is often in short supply and has a limited storage life. A crucial part of Olson’s plan is maximizing the amount of hemoglobin that a bacterium can express.

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Smart robot accelerates cancer treatment research by finding optimal treatment combinations

Smart robot accelerates cancer treatment research by finding optimal treatment combinations | Amazing Science |

A new smart research system developed at Uppsala University accelerates research on cancer treatments by finding optimal treatment drug combinations. It was developed by a research group led by Mats Gustafsson, Professor of Medical Bioinformatics.

The “lab robot” system plans and conducts experiments with many substances, and draws its own conclusions from the results. The idea is to gradually refine combinations of substances so that they kill cancer cells without harming healthy cells.

Instead of just combining a couple of substances at a time, the new lab robot can handle about a dozen drugs simultaneously. The future aim is to handle many more, preferably hundreds. The method is iterative search for anti-cancer drug combinations. The procedure starts by generating an initial generation (population) of drug combinations randomly or guided by biological prior knowledge and assumptions. In each iteration the aim is to propose a new generation of drug combinations based on the results obtained so far. The procedure iterates through a number of generations until a stop criterion for a predefined fitness function is satisfied.

There are a few such laboratories in the world with this type of lab robot, but researchers “have only used the systems to look for combinations that kill the cancer cells, not taking the side effects into account,” says Gustafsson.

The next step: Make the robot system more automated and smarter. The scientists also want to build more knowledge into the guiding algorithm of the robot, such as prior knowledge about drug targets and disease pathways.

For patients with the same cancer type returning multiple times, sometimes the cancer cells develop resistance against the pharmacotherapy used. The new robot systems may also become important in the efforts to find new drug compounds that make these resistant cells sensitive again.

The research is described in an open-access article published Tuesday (Sept. 22, 2015) in Scientific Reports.

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The rise of X-ray beam chemistry

The rise of X-ray beam chemistry | Amazing Science |
By using powerful photon beams, researchers have shown that they can now control the chemical environment and provide nanoscale structural detail while simultaneously imaging the mineral calcite as it is pushed to its extremes.

For scientists to understand a system, they often push it to its limits. In geochemistry, that means putting minerals under extreme conditions and watching how they react. This can be done in a number of ways, but the approach is usually the same: develop tools necessary to observe reactions in better detail and look at how minerals react when their natural environment is destabilized.

The X-ray Reflection Interfacial Microscope, a new surface microscope at the U.S. Department of Energy's (DOE's) Argonne National Laboratory, has led to a major breakthrough. By using powerful photon beams generated by the Advanced Photon Source (APS), a DOE User Facility located at Argonne, researchers have shown that they can now control the chemical environment and provide nanoscale structural detail while simultaneously imaging the mineral calcite as it is pushed to its extremes.

"There are some very extreme natural environments on our planet," said Argonne's Paul Fenter, Interfacial Processes Group Leader and co-author of the study appearing today in the journal Science. "If you can understand how minerals react at the most extreme conditions, this gives you confidence in our understanding of reactions under less extreme conditions."

Our natural world rests in a delicate balance controlled by the movement of nutrients and toxins through waterways. Minerals like calcite grow and dissolve in response to changes in the water composition, which can be characterized by its level of acidity (i.e., the pH). A key feature of this experiment was the use of the X-rays to drive the calcite out of equilibrium while simultaneously observing how it dissolves.

"These reactions are well-known," said Nouamane Laanait, the paper's first author and current Eugene P. Wigner Fellow at Oak Ridge National Laboratory. "They are the same as those that control how calcite dissolves in oceans in response to increased CO2 levels. This work demonstrates that if one has precise control over the beam probe and appropriate modeling of the beam interactions [with the sample], then one can learn a great deal that would be inaccessible otherwise."

To see what happens to the calcite when it is destabilized, researchers used a technique called X-ray reflection interface microscopy (XRIM) at the APS. Piercing through water solution and reflecting off the calcite's surface like a mirror, focused X-rays changed the water's acidity level, starting a chain of reactions that lowered the pH and caused the calcite to dissolve. Tiny pits, similar to ones observed in previous experiments, began to form with simple round or rectangular shapes. The rate at which these pits formed and grew let researchers know that the X-ray beam was, in fact, controlling the local chemistry as predicted. What they didn't predict came next.

As the X-rays pushed the calcite to more extreme levels of instability, researchers were surprised to see that the dissolving pits became distorted and formed ink splatter-like irregularities, indicating that some parts were dissolving quicker than others. Known as reaction front instabilities, these irregularities had not previously been observed in real time.

"Calcite is well-studied," said Fenter, "and so we have a very good understanding of how it grows and dissolves over a wide range of conditions. That we were able to observe a new mode of dissolution was exciting since it suggests that there is still much to be learned."

Alayna Anthony's comment, September 29, 7:54 PM
I just couldn't stay focused on this article. I thought it would interest me but to be honest I just didn't like it. I couldn't stay sucked in. It was too scientific to be interesting. There needs to be a balance between interesting and facticious. That's really all I can say about this article.
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Alternative CRISPR system could improve genome editing, make it simpler and more exact

Alternative CRISPR system could improve genome editing, make it simpler and more exact | Amazing Science |

The CRISPR/Cas9 technique is revolutionizing genetic research: Scientists have already used it to engineer crops, livestock andeven human embryos, and it may one day yield new ways to treat disease.

But now one of the technique's pioneers thinks that he has found a way to make CRISPR even simpler and more precise. In a paper published in Cell on 25 September, a team led by synthetic biologist Feng Zhang of the Broad Institute in Cambridge, Massachusetts, reports the discovery of a protein1 called Cpf1 that may overcome one of CRISPR-Cas9’s few limitations; although the system works well for disabling genes, it is often difficult to truly edit them by replacing one DNA sequence with another.

The CRISPR/Cas9 system evolved as a way for bacteria and archaea to defend themselves against invading viruses. It is found in a wide range of these organisms, and uses an enzyme called Cas9 to cut DNA at a site specified by 'guide' strands of RNA. Researchers have turned CRISPR/Cas9 into a molecular-biology powerhouse that can be used in other organisms. The cuts made by the enzyme are repaired by the cell’s natural DNA-repair processes.

CRISPR is much simpler than previous gene-editing methods, but Zhang thought there was still room for improvement. So he and his colleagues searched the bacterial kingdom to find an alternative to the Cas9 enzyme commonly used in laboratories. In April, they reported that they had discovered a smaller version of Cas9 in the bacterium Staphylococcus aureus2. The small size makes the enzyme easier to shuttle into mature cells — a crucial destination for some potential therapies. The team was also intrigued by Cpf1, a protein that looks very different from Cas9, but is present in some bacteria with CRISPR. The scientists evaluated Cpf1 enzymes from 16 different bacteria, eventually finding two that could cut human DNA.

They also uncovered some curious differences between how Cpf1 and Cas9 work. Cas9 requires two RNA molecules to cut DNA; Cpf1 needs only one. The proteins also cut DNA at different places, offering researchers more options when selecting a site to edit. “This opens up a lot of possibilities for all the things we could not target before,” says epigeneticist Luca Magnani of Imperial College London.

Cpf1 also cuts DNA in a different way. Cas9 cuts both strands in a DNA molecule at the same position, leaving behind what molecular biologists call ‘blunt’ ends. But Cpf1 leaves one strand longer than the other, creating a 'sticky' end. Blunt ends are not as easy to work with: a DNA sequence could be inserted in either end, for example, whereas a sticky end will only pair with a complementary sticky end. “The sticky ends carry information that can direct the insertion of the DNA,” says Zhang. “It makes the insertion much more controllable.”

Zhang’s team is now working to use these sticky ends to improve the frequency with which researchers can replace a natural DNA sequence. Cuts left by Cas9 tend to be repaired by sticking the two ends back together, in a relatively sloppy repair process that can leave errors. Although it is possible that the cell will instead insert a designated, new sequence at that site, that kind of repair occurs at a much lower frequency. Zhang hopes that the unique properties of how Cpf1 cuts may be harnessed to make such insertions more frequent.

For Bing Yang, a plant biologist at the Iowa State University in Ames, this is the most exciting aspect of Cpf1. “Boosting the efficiency would be a big step for plant science,” he says. “Right now, it is a major challenge.”

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Atmospheric levels of a little known by-product from diesel engines are up 70 times higher than expected

Atmospheric levels of a little known by-product from diesel engines are up 70 times higher than expected | Amazing Science |

Researchers found that long-chain hydrocarbons are significantly under-reported in car manufacturer's data. These hydrocarbons are a key component of two of the worst air pollutants, ozone and particulate matter. The authors believe these "hidden" emissions are having a large impact on air quality in cities like London. The tailpipes of diesel fueled trucks and cars produce an array of emissions that have different impacts on the air that people breathe.

The nitrogen dioxide and particles that are emitted from burning diesel have a direct impact on human health in cities. But diesel also contains more complex, long-chain hydrocarbons, whose role in air pollution has been little understood until now. They can form dangerous air pollutants, especially ozone and particulate matter, which are emitted into the air as unburned fuel or diesel vapor. Researchers from the University of York have been able to detect these complicated compounds in the London air, using sophisticated measuring technology.

The researchers found that close to 50% of the ozone production potential in London in winter was due to these diesel elements. In summertime, it was around 25%. The authors believe that these hydrocarbons are having a direct effect on health.

"I think it is having a large impact on air quality in our cities, the number of deaths associated with particle pollution are much higher than those from nitrogen dioxide, this is a route to increase particle pollution so it could have a major impact on human health", one of the authors said.

The study also found that the scale of these hydrocarbons in the air was far in excess of the levels expected by government, which are based on data from car manufacturers' emissions tests.

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