2011 visualization challenge – illustration

As every year Science Magazine and the National Science Foundation present the winners of the International Science and Engineering Visualization Challenge.

illustration category

1°place: Tumor Death-Cell Receptors on Breast Cancer Cell

Cancer cells get the monster movie treatment. If Emiko Paul of Echo Medical Media’s illustration of breast cancer cells looks like something out of an H. P. Lovecraft short story, it’s no accident. “We wanted to show something that was dramatic and very active,” Paul says.

This image, modeled using 3D software then painted in Adobe Photoshop, depicts the war on cancer in a manner that makes clear who the bad guys are. Paul drew on microscopic images of breast cancer cells—seen here looking like creatures with long tentacles—for inspiration. But her illustration also depicts a possible weapon against these malignant tissues: an antibody developed by researchers at the University of Alabama, Birmingham, called TRA-8 (the green, globular structures). This molecule activates a protein on the surface of many cancer cells, which then triggers a chain of events that kills off those cells, much like a self-destruct switch. TRA-8, whose efficacy researchers are currently exploring, could be the garlic to cancer’s vampire.

2°place: Variable-Diameter Carbon Nanotubes

Nanostructures, as the name implies, are much too small to see. But using 3D modeling techniques and some guesswork, graphic artist Joel Brehm renders a handful of these ultrathin structures visible to the naked eye. Brehm’s illustration focuses on the work of his colleague, Yongfen Lu, an engineer at the University of Nebraska, Lincoln. Lu and colleagues employ lasers to develop new methods for crafting thin tubes made from carbon. But not just any tubes. His team’s method precisely varies the diameter and properties of these structures. The resulting tubes, seen here, widen, narrow, or even bulge out like pears along their length. These designs could improve transistors and sensors in a range of electronics, the team says.

The tricky part, Brehm says, was making the nanotubes look small even though they’d been blown up to poster size. To do that, he added a granular texture to the honeycombed stalks and also brightened their edges. Those small touches, he says, made the tubes look more like objects viewed through an electron microscope.

3°place: Exploring Complex Functions Using Domain Coloring

Mathematicians discover their hippie sides. Forgoing long strings of digits and variables, researchers at the Free University of Berlin have taken a tie-dye approach to visualizing math equations. This illustration represents one example of a complex function. Such functions are mathematical relationships that incorporate both real numbers and what experts call imaginary numbers, such as the square root of −1.

Unlike familiar sine waves or logarithmic curves, complex functions are four-dimensional, combining both inputs and outputs in two dimensions. To visualize these heady equations, Konstantin Poelke and his Ph.D. supervisor Konrad Polthier turned to and improved a technique called domain coloring. They assigned each complex number in their equation to a spot on a color wheel. The further numbers get from zero, the brighter they are (white regions, for instance, represent mathematical “singularities” that approach infinity). The result is like a topographic map, but it packs two dimensions of information (hue and brightness) into each point instead of the single dimension of altitude.

Such functions may fly right over the heads of many nonmath enthusiasts, Poelke says. But he hopes casual viewers will understand the basics of the relationships between the complex numbers shown here just by looking at the arrangement of the psychedelic shades.

4°place: Separation of a Cell (which is the people’s choice)

From films like Avatar to hand-held video games, 3D is all the rage. Textbook graphics are not catching on. In this illustration, Andrew Noske of the National Center for Microscopy and Imaging Research at the University of California, San Diego, and colleagues create a visualization of mitosis that hops off the page.

The new and tactile view of a cell undergoing division comes thanks to a specialized protein called MiniSOG. This molecule, which Noske’s team shows zipping toward the reader, is fluorescent and stands out crisply under an electron microscope. With some tweaking, it also binds tightly to a second protein closely associated with DNA. That gives scientists the ability to target and view in detail chromosomes as they peel apart during mitosis. The result is a far cry from the standard, flat images popular in biology textbooks, the team writes. And unlike the 3D glasses that accompany screenings of sci-fi films, this new visualization approach may be more than a gimmick, giving students a deeper look at a familiar phenomenon.

2011 visualization challange – photography

As every year Science Magazine and the National Science Foundation present the winners of the International Science and Engineering Visualization Challenge.

Photography:

1° place: Metabolomic Eye

Eyeballs—now in Technicolor. This photo graph, taken by neuroscientist Bryan Jones of the University of Utah’s Moran Eye Center (MEC) in Salt Lake City, may look like a piece of candy. But it’s actually a metabolic look at the wide diversity of cells in the mouse eye—in all, 70 different types of cells, from muscles to retina, each colored a unique shade.

To map out the tissues in this mouse’s eye, Jones turned to a technique called computational molecular phenotyping (CMP). This approach, pioneered by Robert Marc, also at MEC, takes advantage of the unique array of molecules in all cells in a tissue. “Within a cell type, there is a very narrowly regulated fingerprint that defines who that cell is and what that cell does,” Jones says. In this case, he probed the relative concentrations of several common organic molecules.

Using a tool that cuts into biological material on the microscopic scale, Jones shaved into the eye, creating serial 120-nanometer-thick slices, thinner than the wavelength of light—much like licking a gobstopper, he says. Jones then stained those layers with specialized antibodies that bind to three molecules: taurine, glutamine, and glutamate, which he assigned to red, green, and blue color channels on a computer. The unique distributions of these molecules can be seen here in rainbow color. Muscle cells, located at the left edge of the image, look pale yellow, whereas scleral tissue, surrounding the entire orb, shows up green in this image.

In order to study the molecular fingerprints of specific tissues, scientists previously had to grind up entire organs and analyze the cells all together. That turned what might be a metabolically diverse organ into a homogenous mess, Jones says. But CMP highlights a tissue’s complexity. “There’s incredible diversity in a cell population normally thought to be homogenous.” And mammal eyes aren’t even the most complex retinas out there, he adds. Goldfish eyes, for instance, contain more than 200 separate cell types.

The photograph is certainly eye-catching, says challenge judge Alisa Zapp Machalek. “It was just what we were looking for,” she says. “It was the perfect balance between a beautiful picture that tingles the eyeballs and something that is incredibly informative.”

2° place: Microscopic Image of Trichomes on the Skin of an Immature Cucumber

No, this photograph doesn’t depict alien slugs stripped from a science-fiction film—just the surface of a young cucumber. It’s a new perspective on an old vegetable. To take this close-up, vibrant shot, photographer Robert Belliveau employed a polarizing microscope. Unlike normal light microscopes, which use unpolarized light, these zooming tools adopt plane-polarized light and record the refraction of light as it passes through small objects to produce a sharp, colorful image.

The structures shown here at 800× magnification are trichomes. They coat the surface of still-growing cucumbers and look, to the naked eye, like a thin film of hair. That fuzziness, however, belies the structures’ nasty streak. The tips of trichomes taper to a point that can pierce the mouths of predators, and their bulbous bases are filled with bitter-tasting and toxic molecules called cucurbitacins. It’s a dangerous and strange landscape that humans normally don’t get to see, says Belliveau, who has also turned his microscope on tomatoes and many other edible plants. “The microscopic world of plants, especially fruits and vegetables, is such an exotic world,” he says. “It’s actually otherworldly.”

3° place: The Cliff of the Two-Dimensional World

This landscape, which looks like a red-rock bluff straight out of Utah, isn’t a geologic feature. Instead, it’s a nanostructured material made from ultrathin layers of titanium-based compounds and seen under an electron microscope.

To construct the small outcropping, Babak Anasori and colleagues at Drexel University in Philadelphia used a technique called exfoliation. They placed Ti3AlC2 powders in a solution of hydrofluoric acid and stripped away the aluminum atoms. What remained were stacked layers of Ti3C2, seen here in false color, resembling stratigraphic mineral layers. These exfoliated layers, which the team dubbed MXenes, are so thin they are two-dimensional. In other words, each strip is only five atomic layers thick. The team is the first to render such materials in 2D. The MXenes could be used in energy storage devices, sensors, solar cells, and other applications, the team writes. And they could give the majesty of Arches National Park in Utah some nanoscale competition.

Panorama of the east coast

This Jan. 29 panorama of much of the East Coast, photographed by one of the Expedition 30 crew members aboard the International Space Station, provides a look generally northeastward: Philadelphia-New York City-Boston corridor (bottom-center); western Lake Ontario shoreline with Toronto (left edge); Montreal (near center). An optical illusion in the photo makes the atmospheric limb and light activity from Aurora Borealis appear “intertwined.”

Organic Meat Not Free of Drug-Resistant Bacteria

If you’re paying premium prices for pesticide- and antibiotic-free meat, you might expect that it’s also free of antibiotic-resistant bacteria. Not so, according to a new study. The prevalence ofone of the world’s most dangerous drug-resistant microbe strains is similar in retail pork products labeled “raised without antibiotics” and in meat from conventionally raised pigs, researchers have found.

Methicillin-resistant Staphylococcus aureus (MRSA), a drug-resistant form of the normally harmless S. aureus bacterium, kills 18,000 people in the United States every year and sickens 76,000 more. The majority of cases are linked to a hospital stay, where the combination of other sick people and surgical procedures puts patients at risk. But transmission also can happen in schools, jails, and locker rooms (and an estimated 1.5% of Americans carry MRSA in their noses). All of this has led to a growing concern about antibiotic use in agriculture, which may be creating a reservoir of drug-resistant organisms in billions of food animals around the world.

Tara Smith, an epidemiologist at the University of Iowa College of Public Health in Iowa City who studies the movement of staph bacteria between animals and people, wondered whether meat products might be another mode of transmission. For the new study, published this month in PLoS ONE, she and colleagues bought a variety of pork products—395 packages in all—from 36 different stores in two big pig farming states, Iowa and Minnesota, and one of the most densely populated, New Jersey.

In the laboratory, the team mixed meat samples “vigorously” with a bacterial growth medium and allowed any microbes present to grow. MRSA, which appears as mauve-colored colonies on agar plates, was genetically typed and tested for antibiotic susceptibility.

The researchers found that 64.8% of the samples were positive for staph bacteria and 6.6% were positive for MRSA. Rates of contamination were similar for conventionally raised pigs (19 of 300 samples) and those labeled antibiotic-free (seven of 95 samples). Results of genetic typing identified several well-known strains, including the so-called livestock-associated MRSA (ST398) as well as common human strains; all were found in conventional and antibiotic-free meat.

Smith says she was surprised by the results. In a related investigation, which has not been published, her group tested pigs living on farms and found that antibiotic-free pigs were free from MRSA, whereas the resistant bug is often found on conventional pig farms.

The study reveals an important data point on the path from farm to fork, yet the source of the MRSA on meat products is unknown, Smith says. “It’s difficult to figure out.” Transmission of resistant bugs might occur between antibiotic-using and antibiotic-free operations, especially if they’re near each other, or it could come from farm workers themselves. Another possibility is that contamination occurs at processing plants. “Processing plants are supposed to be cleaned between conventional and organic animals,” she says. “But how well does that actually happen?”

In another recent study, researchers from Purdue University in West Lafayette, Indiana, found that beef products from conventionally raised and grass-fed animals were equally likely to be contaminated by antibiotic-resistant Escherichia coli. In a second study by the same group, poultry products labeled “no antibiotics added” carried antibiotic-resistant E. coli and Enterococcus (another bacteria that causes invasive disease in humans), although the microbes were less prevalent than on conventionally raised birds.

“The real question is, where is it coming from, on the farm or post-farm?” says Paul Ebner, a food safety expert who led the Purdue studies. And the biggest question of all, he says, “Is it impacting human health?”

“There’s a tremendous amount of interest in this issue—feeding antibiotics to food animals,” says Ellen Silbergeld, an expert on health and environmental impacts of industrial food animal production at the Johns Hopkins Bloomberg School of Public Health in Baltimore, Maryland. “Thus, determining when amending that practice makes a difference is important.”

“The definitive study would take every bacterium and follow that along until it gets in humans—from food supply to causing a certain disease,” Smith says. “It would be a huge and costly study that no one’s going to do, but that’s what the meat producers” say is missing.” Meanwhile, Smith says she will continue her investigations of MRSA, one potential transmission point at a time.

Stunning image of the earth

Blue Marble

A ‘Blue Marble’ image of the Earth taken from the VIIRS instrument aboard NASA’s most recently launched Earth-observing satellite – Suomi NPP. This composite image uses a number of swaths of the Earth’s surface taken on January 4, 2012. The NPP satellite was renamed ‘Suomi NPP’ on January 24, 2012 to honor the late Verner E. Suomi of the University of Wisconsin.

Suomi NPP is NASA’s next Earth-observing research satellite. It is the first of a new generation of satellites that will observe many facets of our changing Earth.

Suomi NPP is carrying five instruments on board. The biggest and most important instrument is The Visible/Infrared Imager Radiometer Suite or VIIRS.

for see the original image

The great Arctic oil race begins

Conservationists fear spills in icy waters as Norway awards oil-production licences.

“The race is on for positions in the new oil provinces.” That starting-gun quote was fired last week by Tim Dodson, executive vice-president of the Norwegian oil and gas company Statoil. The ‘new oil provinces’ are in the Arctic, which brims with untapped resources amounting to 90 billion barrels of oil, up to 50 trillion cubic metres of natural gas and 44 billion barrels of natural gas liquids, according to a 2008 estimate by the US Geological Survey. That’s about 13% of the world’s technically recoverable oil, and up to 30% of its gas — and most of it is offshore.

Oil companies see an opportunity to sate the world’s demand for fossil fuels. Green groups and many scientists, however, are horrified by the prospect of drilling and production in remote, often ice-choked waters, where spills would be harder to control and clean up than in warmer regions. Memories of the devastating environmental impact of the Exxon Valdez accident in 1989 in Alaska’s Prince William Sound are still all too fresh — like the oil that can still be found in the area’s beaches.

At last week’s Arctic Frontiers conference in Tromsø, Norway, the oil industry insisted that it will be cautious and responsible in extracting oil and gas in the region, and it rolled out an initiative to develop ways of coping with any accidents. Dodson told the meeting that “technology will be there to clean it up”.

Statoil already operates the world’s most northerly liquefied natural-gas production facility near Hammerfest, which draws gas equivalent to about 48,000 barrels of oil a day from the Snøhvit field in the Arctic waters off Norway. By 2020, the company hopes to extract one million barrels of oil equivalent a day from new wells in the Arctic. It is planning exploratory drilling later this year, for example, in the Skrugard and Havis gas fields that were discovered in the Barents Sea last year.

The Norwegian government is happy with Statoil’s bold plans. Norway is currently the world’s second-largest gas exporter, with production continuing to rise, but it is looking to the Arctic to offset a one-third decline in production at its oil fields farther south since 2000. “If we don’t invest, we might lose another third within the next decade,” says Ola Borten Moe, Norway’s minister of petroleum and energy.

On 17 January, Moe awarded 26 production licences for developed offshore oil areas in the Norwegian and Barents Sea to companies including Statoil, Total, ExxonMobil and ConocoPhillips. And the settlement in 2010 of a long-running row between Norway and Russia over their Arctic maritime boundary will allow more exploration in formerly disputed parts of the Barents Sea (see ‘Frozen fuels’). “There’s an ocean of new opportunities that we will grasp with both hands,” says Moe.

The resource rush is alarming critics. A group of 573 scientists, for example, wrote last week to US President Barack Obama, urging caution in authorizing new oil and gas activity in the Arctic Ocean north of Alaska. The open letter, coordinated by the Pew Environment Group, a conservation organization headquartered in Washington DC, argues that more research is needed to assess the potential impact on the region’s environment and ecosystems before going ahead with more drilling.

The industry holds that Arctic oil and gas development can be done in an environmentally sustainable manner despite the challenges. “We realize that there are huge issues when working in the cold and darkness and in the presence of sea ice in areas at great distance from any infrastructure,” says Joseph Mullin, a London-based programme manager at the International Association of Oil and Gas Producers. Mullin will oversee a four-year, US$20-million research programme to address those issues, launched at the Tromsø conference by nine major oil companies.

The initiative, which is open to academic collaborators, will include research on the environmental effects of Arctic oil spills, spill trajectory modelling and remote sensing, and oil recovery techniques in sea-ice areas. It will also test Arctic clean-up technologies in a number of controlled oil releases. “You’d like to have a variety of spill-response options in the tool box before you venture out there,” says Mullin.

The leading Russian oil and gas companies, Gazprom and Rosneft, have so far stayed clear of the initiative, adding to concerns about their compliance with national and international safety standards.

In December 2011, for example, at least 37 people were killed when an oil rig under contract to Gazprom capsized off Sakhalin Island in Russia’s Arctic Ocean, resulting in a fine for the company.

And according to Vladimir Chuprov, a Moscow-based energy expert who works for Greenpeace, emergency contingency plans for the Prirazlomnoye oil platform in the Russian Barents Sea, where commercial drilling is to start this year, have not been publicly released, despite being required by Russian regulators.

But even companies with better safety records should avoid the Arctic, say Chuprov and other environmentalists. “In our view no company is ready for offshore oil projects in the Arctic Ocean,” he says.

UK sets sights on gene therapy in eggs

Public consultation and safety assessment would pave the way for embryo manipulation to treat genetic diseases.

Britain has set out a road map towards the first clinical tests of reproductive techniques that combine parents’ genes with DNA from a third party. The approach raises ethical questions, but could spare children from inheriting some rare diseases, including forms of muscular dystrophy and neurodegenerative disorders that affect around 1 in 5,000 people.

These conditions are caused by defects in the mitochondria, the ‘power packs’ of the cell, which are inherited from a child’s mother through the egg. Experiments on primates, and with defective human eggs, have already shown that genetic material can be removed from an egg that has faulty mitochondria and transferred to a healthy donor ovum, leaving the flawed mitochondrial DNA behind. In principle, the resulting egg could then develop into a healthy child carrying both the parents’ nuclear genes and mitochondrial DNA from the donor. But the work amounts to genetic modification of embryos — which is currently illegal in the United Kingdom — and also involves destroying fertilized eggs.

On 19 January, the UK government’s Human Fertilisation and Embryology Authority (HFEA) announced a public consultation on the process, the first step towards making it legal. Simultaneously, the country’s biggest biomedical charity, the Wellcome Trust, said that it would fund preclinical experiments to gauge the safety of the techniques. An independent bioethical review is also in progress. “It’s a wonderful example of how regulation should work, because it’s saying let’s see the science, let’s see the bioethics, let’s find out what the public thinks,” says Peter Braude, a reproductive biologist at King’s College London.

Two procedures are being developed: pronuclear transfer and maternal spindle transfer (seethe image above). US researchers have already used maternal spindle transfer to produce two healthy rhesus monkeys. Meanwhile, neurologist Douglass Turnbull of Newcastle University, UK, and his team have performed pronuclear transfer on defective human eggs, and found that normal development occurred in a small minority.

In 2011, Braude co-authored a report for the HFEA that concluded that the nuclear transfer procedures seem safe on the basis of current research. The report outlined several studies that it deemed “critical” before either procedure could be used to create a child. These include experiments on healthy human eggs, and proof that the pronuclear transfer technique can conceive healthy monkeys.

The Wellcome Trust has now awarded Turnbull £4.4 million (US$6.8 million), which his university has topped up with another £1.4 million, to perform the procedures on healthy human eggs. Turnbull and his team hope to determine whether the embryos can safely reach the 100-cell blastocyst stage, when implantation occurs. Yet they have no plans to test pronuclear transfer in monkeys, and it is unclear who would conduct such experiments.

Shoukhrat Mitalipov, a reproductive biologist at Oregon Health and Science University near Portland, who led the work on rhesus monkeys, says that his lab uses the maternal spindle transfer technique because it is easier to perform. Mitalipov has begun experiments on human eggs in a privately funded lab. Such work is barred from receiving federal funds because it involves the destruction of human embryos.

No scramble

Turnbull is agnostic about which, if any, procedure is likely to reach the clinic first. One technique may prove more efficient than the other, or may shuttle fewer mutant mitochondria to the donor egg. “We’ve got to be careful that this is not a race,” Turnbull says. Taking the technique beyond the lab would also require a change in the law. Nuclear transfer procedures are banned under the UK Human Fertilisation and Embryology Act, but the government could amend the law for procedures used to treat mitochondrial diseases.

Meanwhile, the Nuffield Council on Bioethics in London has begun an independent review of the procedures. Science writer Geoff Watts, chairman of the working group behind the review, believes that it will inform the government’s decision. It will consider issues such as whether the procedures should be used to conceive only males, who will not pass on any donor mitochondria to their children. The council says that it will deliver a report in the summer.

Braude worries that, outside the United Kingdom, “somebody will be a cowboy” and attempt the procedures without regulatory oversight. Yet government hurdles could prevent the techniques from being adopted quickly elsewhere. In Australia, for example, a government review in 2011 recommended continuing a ban on such techniques. In the United States, the Food and Drug Administration would be responsible for approving them. Such restrictions, combined with the US ban on federal funding of human embryo work, mean that the first clinical trials of nucleus-swapping procedures will almost certainly occur in the United Kingdom.

“We’ve moved to the stage where we think that the preliminary evidence is very supportive,” says Turnbull, “and we think it’s a very good idea that they consider this.”