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Welcome to dxomark.com (beta), a free resource dedicated to RAW-based camera image quality
DxO Labs created dxomark.com for members of the digital photographic community who are passionate about image quality – professional photographers, advanced amateurs, photography reviewers and imaging media journalists. While other websites publish information about JPEG image quality, only DxO Labs provides the first publicly-accessible database of objective and in-depth RAW sensor image quality measurements.
Image Quality Evaluation, our core expertise
Whatever your digital imaging system - from cameraphones to D-SLR cameras, from webcams to medical imaging systems, from consumer digital still cameras to video surveillance systems – DxO Labs products and services can help maximize their image quality.
DxO Labs excels in the scientific and technical expertise needed for measuring the key imaging properties and optical defects of digital imaging systems.
DxO Labs delivers its image quality evaluation solution competence and know-how through integrated solutions in the DxO Analyzer product line.
Unique products and solutions
DxO Analyzer addresses the needs of all industries that require imaging performance tests and measurement. DxO Analyzer includes everything that you need to reliably measure and analyze the imaging performance of any type of image capture device: testing protocols and methodologies, laboratory specifications and installation guidelines, data management and analysis software.
Support and customized services
We can assist you in acquiring the expertise you need to establish your own image quality testing capabilities quickly and smoothly. We know that building an efficient, comprehensive image quality testing facility is time consuming and costly, DxO Labs offers customized training and support in image quality evaluation to our clients to ensure that you spend more time analyzing the results than obtaining them. We help you to efficiently integrate DxO Analyzer solution within your operations.
As a complement to the on-site support we provide our clients, we also offer image quality evaluation services in our own labs. We deliver in-depth analysis and diagnostic reports on cameraphones, digital camera modules or camera components (optics, sensor, image processor) for our customers. These services are extremely valuable for companies undertaking in-depth analyses for the selection of third-party components, or who are evaluating new camera module technologies or architectures.
DxOMark Sensor ranks cameras based on real-life photographic scenarios
Objective measurements of RAW images are an essential basis for any analysis of digital cameras, but such measurements were neither possible nor available until now. DxO Labs has developed a new scale for digital camera image quality performance, called DxOMark Sensor, to serve as an additional tool to help photographers rank and compare digital cameras.
This scale is based on three underlying metrics, Color Depth, Dynamic Range and Low-Light ISO, each one tied to a real-life photographic scenario: landscape, studio & portrait, and photojournalism & sport.
Read more on the logic behind the DxOMark Sensor scale architecture.
This interactive graph shows the ranking for approximately 50 currently-available digital cameras on the DxOMark Sensor scale and its three metrics (click on the different tabs to view the performance and ranking of cameras versus each metric). You can switch the x-axis for time, price range, or resolution, as well as filter the ranking by brand, resolution, sensor size, time and price (USD). You can also access the comprehensive set of RAW-based measurement data, curves, and plots for any given camera by clicking on its product sheet (left column).
A website for people who are passionate about image quality
dxomark.com (beta version) is a new website featuring the first database of objective digital camera image quality measurements entirely accessible via the internet. In addition to the Image Quality Database itself, dxomark.com proposes a new scale, the DxOMark Sensor scale, that enables to rank digital camera with a single number: an easy tool for photographers to evaluate and compare models. Four principal characteristics make the DxOMark Sensor scale and the Image Quality (IQ) Database uniquely valuable to members of the photographic community who are passionate about image quality:
RAW sensor-based
All published measurements are RAW sensor-based and performed prior to any digital image processing (camera- or PC software-based). As RAW format is considered the equivalent of a film negative by analogy to traditional photography, it is the format by which camera body performance is most effectively evaluated, as it does not depend on the camera optics nor on the quality of the RAW conversion applied.
Reproducible
All measurements are objective, conforming on the one hand to ISO standards (ISO), and on the other hand to accepted scientific methodology, thanks to DxO Analyzer. As the only solution on the market that takes measurements directly from RAW images using automated processing to ensure fully-reproducible results, DxO Analyzer is the tool of reference for the imaging industry and photography reviewers.
DxO Labs, the creator of DxO Analyzer, is the world leader in image quality measuring tools. In addition to serving as technical editor for the Camera Phone Image Quality (CPIQ) Initiative Group of the International Imaging Industry Association (I3A), with which it also participates in defining the standards for cameraphone image quality, DxO Labs also contributes solutions to such difficult technological challenges as finding ways to scientifically measure perceived image quality attributes such as preservation of texture and color richness.
Normalized data
The DxOMark Sensor scale results and the IQ Database measurements are painstakingly and exhaustively obtained across the entire range of sensor functioning parameters, describing the performance of the camera body for all its functional modes, white balance, and ISO settings. These measurements are furnished both as raw data, but also as normalized data so as to permit fair comparison between camera bodies with different resolutions, number or size of pixels, and/or sensitivity.
The DxOMark Sensor scale
The IQ Database could not be used easily without a global scale of measuring, evaluating, and comparing camera body quality. This is why DxO Labs has also invented the DxOMark Sensor scale, which aggregates the measurements of the IQ Database in a simple and logical manner.
One of the innovations of DxOMark Sensor scale is that it was conceived and built on three principal photographic uses:

• Studio and portrait photography
• Landscape photography
• Photojournalism and sports photography

These three cases were chosen because of their particular relationships to three fundamental aspects of image quality: color richness, dynamic range, and noise level. In other words, each of these cases relies heavily on one of these attributes: studio/portrait photography depends on full color richness; landscape photography concerns itself principally with capturing the full dynamic range of a naturally-lit setting; and photojournalists and sports photographers rely on their cameras to capture moment-to-moment details with the best signal-to-noise ratio possible. Generalizing from these three selected can arguably provide the basis for evaluating all other kinds of photography.

DxOMark Sensor scale, metrics, and measurement data technologies
This website presents a large set of measurement data built over time in the testing laboratories at DxO Labs. Our imaging experts have developed a thorough understanding of the technologies and methods involved in measuring the parameters of digital camera image quality. Indeed, the strength of DxO Labs’ industry-leading image quality evaluation solution, DxO Analyzer, lies in its precisely-described test protocols in tandem with strict control of all physical parameters that might influence measurements.
In keeping with accepted scientific protocols, all measurements can be repeated independently under the same bias-free conditions. This ensures that DxO Labs' measurements and its DxOMark scale are objective and reliable metrics to help photographers evaluate digital camera image quality performance.
This section contains a number of articles describing some of the technologies, methods, and tools that we have developed:
“Defining the measurements” provides descriptions and definitions for all the image quality measurements reported for the set of tested cameras: ISO sensitivity, noise, signal-to-noise ratio, dynamic range, tonal range and color sensitivity.
“Echaracteristics of noise” details the phenomena that create and influence noise within an image sensor, and how noise varies with changes in light levels.
"Overview of DxO Labs image quality testing protocols" describes in detail the methods and tools used to measure camera image quality performance.

DxOMark website was conceived primarily to give photographic reviewers and expert photographer previously unavailable, internet-accessible information about digital camera RAW sensor performance.
In-depth technical analyses and reviews of photographic equipment rely on user-based tests, subjective evaluations, and objective performance measurements on JPEG and RAW images. Some of these measurements are available today, but only in JPEG form. Also, global evaluations depend largely on the individual reviewer, and so are very difficult to compare.
Until now, only partial IQ measurements have been available, and only for JPEG performance rather than for RAW sensor performance. Furthermore, such measurements are difficult for the non-expert to interpret.
DxOMark fills the gap by bringing to the community some of the key missing elements needed to perform objective and exhaustive digital camera image quality evaluation.
Because of its leading position in the image quality industry, DxO Labs has made a large investment both technologically and in human expertise to create a precise system of sensor performance measurement. (While manufacturers have this information, clearly they are not in a position to disseminate it for reasons of confidentiality and competition.)
DxO Labs' aim is to see its DxOMark website become the site of information transmission and discussion about all aspects of digital camera image quality.
Because our focus is on only certain objectively-measured aspects of digital image quality, and not on other fundamental aspects of cameras such as ergonomics, breadth and depth of functionality, value for money, etc., the DxOMark website site does not in any way attempt to replace the many and often excellent photography sites and journals that review cameras.
Our sole ambition is to furnish those photography reviewers and professionals who are our Expert Partners with a solid and quantifiable basis for the articles and reviews that they write. The information on the DxOMark website can be freely used by our partners so long as they refer to DxOMark website as their source and provide explicit links to our site. (Our partners, of course, will be referenced on our site.)
We desire to bring together a photographic community dedicated to promoting digital image quality. DxO Labs is publishing its objective, scientific digital camera measurements with the goal of increasing interest—not just for our own DxOMark website, but also in our participants’ sites and publications.



http://www.dxomark.com/

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As economic conditions and consumer spending continue to deteriorate, semiconductor executives offer views on 2009 revenue growth that continue to turn more pessimistic, and anticipate a steep decline in profitability over the next 12 to 18 months, according to a recent global survey of semiconductor company executives conducted by KPMG LLP, the U.S. audit, tax and advisory firm. In addition, the majority of executives see R&D and CapEx investment decreasing significantly next year, and see significant workforce contraction in a period where the need for critical workforce skills is high.
KPMG's global survey, conducted in collaboration with the Semiconductor Industry Association in October and November, surveyed 85 senior level executives at the semiconductor companies, including device, foundry and fabless manufacturers. According to the results, the growth projections are much more pessimistic this year compared to last year and continued to regress during the response solicitation period, as market and industry conditions continue to deteriorate at an accelerating rate.
In fact, when comparing responses from November to October, it was clear that executive sentiment on industry performance became decidedly more volatile. Fifty-two percent of those surveyed in November expect revenue to decline, including 39 percent who see a decline of greater than six percent. That is in stark contrast to October results when 60 percent of execs projected revenues to increase.
These views represent a major decline compared to 99 percent who expected revenue growth last year, with approximately half (52 percent) estimating growth in excess of 10 percent.
The KPMG study found that execs are also clearly expecting negative trends on profitability. In fact an already stark outlook from October respondents turned even more negative in November. When asked to project profitability over the next 12 to 18 months, 61 percent surveyed in October said profits would decline, including 20 percent who project a decrease of more than 10 percent, while 69 percent of November respondents see a decline with 33 percent estimating losses of more than 10 percent.
"Semiconductor execs are grappling with profitability outlooks while dealing with the dynamics of a depressed economy, pricing pressures, diminished consumer spending, and workforce issues" said Gary Matuszak, leader of KPMG's global Information, Communications, and Entertainment (ICE) practice. "Executives are clearly telling us that the negative industry trends we began to see in September are expected to deteriorate further, and these companies will need to become more efficient in managing costs - especially with tight credit markets."
According to executives, the negative profitability trend is expected to extend beyond the short-term, with 47 percent of overall respondents saying they see global semiconductor profitability as volatile, unpredictable or declining over the next three years.
The anticipated decline in profits and revenue growth are expected to have a significant impact on the global semiconductor workforce. KPMG found that 70 percent of executives surveyed in November expect their companies to decrease their global workforce in the next 12 months, including 40 percent who see a decrease of more than six percent. Only 16 percent say they will expand the global workforce. This outlook is much more negative than the views of the executives surveyed in October, when only 38 percent said they see workforce contraction at their companies.
Investment will fall, but greentech and workforce skills are top of mind
While the executives surveyed indicated some hope of revenue growth opportunities in consumer, computing and hand held wireless markets, the current decline in consumer electronic and handset spending will mute even these growth opportunities in the short term. In addition, KPMG's survey found that green semiconductor products are expected to become a larger part of the revenue stream. However, the current economic conditions make it harder to predict consumer spending, lending uncertainty to bottom line profits in the near-term. This uncertainty can be seen in the negative views expressed on the anticipated CapEx and R&D spending compared to previous years.
In fact, only 28 percent of executives surveyed by KPMG in November indicated that they expect R&D spending to increase in the next fiscal year - down significantly from the 75 percent response to the same question in KPMG's 2007 survey. Conversely, 48 percent see R&D investment falling, including 20 percent who anticipate the decrease will be in excess of 10 percent.
While R&D spending is expected to decrease, executives did indicate that investment in green semiconductor product initiatives will continue to grow over the next two to three years. In fact, 77 percent see their companies increasing their R&D investment in greentech, including 49 percent who see that investment increasing by more than 10 percent. This investment direction coincides with executive views on customer interest in green products as well as how large a portion of revenue streams green semiconductor products will become. Seventy-six percent of execs surveyed said their customers have extremely high interest in green semiconductor products. In addition, 54 percent of executive surveyed estimate that green products account for less than 20 percent of current revenue, however, 84 percent of executives see green products accounting for more than 20 percent of revenues in five years. Thirty-six percent of execs see more than 60 percent of their companies' revenues coming from green products in five years.
Three key geographic markets are expected to see the bulk of R&D investment over the next three years, including the U.S., Europe and China. Forty-four percent of execs said the U.S. would be the top allocation market followed by Europe with 14 percent and China with 10 percent of responses.
Further indicating the ongoing volatility in the semiconductor industry, KPMG found that 52 percent of November respondents expect CapEx spending to plummet, with 36 percent anticipating a decrease of greater than 10 percent. In October only 38 percent expected CapEx to decrease.
Interestingly, in an economic climate where workforce contraction is expected, 76 percent of executives indicated that the availability of a skilled workforce was very important in determining the allocation of CapEx spending. Over the next three years critical workforce skills are expected to be hired from several key markets, including 28 percent from the U.S., 23 percent from China, 12 percent from Korea and 11 percent from Taiwan.
"Despite poor conditions and reduced spending, these companies need to place an emphasis on R&D in an effort to foster innovation and identify broader application markets for semiconductors," added Matuszak. "Another element of that growth investment will be targeted at ensuring a skilled workforce, which becomes increasingly important as the competition intensifies."
KPMG LLP, the audit, tax and advisory firm, is the U.S. member firm of KPMG International. KPMG International's member firms have 123,000 professionals, including more than 7,100 partners, in 145 countries.



http://edageek.com/2008/12/19/kpmg-study/

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The UN Environment Program estimates that there are 46,000 pieces of plastic litter in every square mile of ocean, and a swirling vortex of trash twice the size of Texas has spawned in the North Pacific.

Plastic bags, once icons of customer convenience, cost more than 1.6 billion barrels of oil per year and leave the environment to foot the bill. Each year the world produces 500 billion bags, and they take up to 1,000 years to decompose. They take up space in landfills, litter our streets and parks, pollute the oceans and kill the wildlife that eat them.
Eco-friendly legislation that targets the production and distribution of plastic bags has been introduced in Israel, San Francisco, Ireland and China. Addiionally, a recent scientific discovery (see below) offers a potential long-term solution to the global plastic crisis.

Since stories have started surfacing more recently, many have wondered, if the rumors are true. Are there really 'continents', or massive floating garbage patches residing in the Pacific? Apparently, the rumors are true, and these unsightly patches are reportedly killing marine life and releasing poisons that enter the human food chain, as well. However, before you start imagining a plastic version of Maui, keep in mind that these plastic patches certainly aren't solid surfaced islands that you could build a house on! Ocean currents have collected massive amounts of garbage into a sort of plastic "soup" where countless bits of discarded plastic float intertwined just beneath the surface. Indeed, the human race has really made its mark. The enormous Texas-sized plastic patch is estimated to weigh over 3 million tons.
But if there is an unfathomably massive collection of plastic junk out there, then why doesn't everyone already know about it, and why aren't we doing something about it?
Well, there are several reasons. First, no one is keen to claim responsibility for these monstrosities, which exists in one of the most remote spots on the planet. It's easier to ignore than to deal with, at least in the short term. Most of the plastic is floating just below the surface where explorers, researchers, and scientists can get a good close-up view, but it is nearly impossible to see the massive quantities of submerged trash in photographs taken from great distances. This makes it easier for naysayers to disregard the problem as a mere myth, in spite of all of the well-documented research to the contrary. Clean up seems nearly impossible at this point, so even those who are well aware of the situation have adopted the famous ostrich cliche of burying their heads in the sand. Even so, this polluted, chemical filled junk is finding it's way onto our dinner tables.
Sadly, marine researcher Charles Moore at the Algalita Marina Research Foundation in Long Beach says there’s no practical fix for the problem. He has been studying the massive patch for the past 10 years, and said the debris is to the point where it would be nearly impossible to extract.
"Any attempt to remove that much plastic from the oceans - it boggles the mind," Moore said from Hawaii, where his crew is docked. "There's just too much, and the ocean is just too big."
The trash collects in this remote area, known as the North Pacific Gyre, due to a clockwise trade wind that encircles the Pacific Rim. According to Moore the trash accumulates the same way bubbles clump at the center of hot tub.
Ian Kiernan, the Australian founder of Clean Up the World, started his environmental campaign two decades ago after being shocked by the incredible amount of rubbish he saw on an around-the-world solo yacht race. He'll says he’ll never be able the wipe the atrocious site from his memory.
"It was just filled with things like furniture, fridges, plastic containers, cigarette lighters, plastic bottles, light globes, televisions and fishing nets," Kiernan says. "It's all so durable it floats. It's just a major problem."
Kiernan says it’s killing wildlife in a vicious cycle. Holding an ashtray filled with colorful pieces of plastic he told The Sydney Morning Herald, "this is the contents of a fleshy-footed shearwater's stomach. They go to the ocean to fish but there ain't no fish - there's plastic. They then regurgitate it down the necks of their fledglings and it kills them. After the birds decompose, the plastic gets washed back into the ocean where it can kill again. It's a form of ghost fishing, where it goes on and on."
A Dutch study in the North Sea of fulmar seabirds concluded 95 per cent of the birds had plastic in their stomachs. More than 1600 pieces were found in the stomach of one bird in Belgium.
The United Nations Environment Program says plastic is accountable for the deaths of more than a million seabirds and more than 100,000 marine mammals such as whales, dolphins and seals every year.
Since his first encounter with the gyre in 1997, Moore created the Algalita Marine Research Foundation to help study the problem. Canadian filmmaker Ian Connacher joined Moore last year to film the garbage patch for his documentary, I Am Plastic.
"The most menacing part is those little bits of plastic start looking like food for certain animals, or the filter feeders don't have any choice, they just pick them up," noted Connacher.
Perhaps an even bigger problem is hiding beneath the surface of the islands of garbage. Greenpeace reports that about 70 per cent of the plastic that makes it to the ocean sinks to the bottom, where it then smothers marine life on the ocean floor. Dutch scientists have found 600,000 tons of discarded plastic on the bottom of the North Sea alone.
A study by the Japanese geochemist Hideshige Takada and his colleagues at Tokyo University in 2001 found that plastic polymers soak up the resilient poisons such as DDT and polychlorinated biphenyls. The researchers found that non-water-soluble toxic chemicals can be found in plastic in levels as high as a million times their concentration in water. As small pieces of plastic are mistaken for fish eggs and other food by marine life, these toxins end up at the dinner table. But even without the extra toxins, eating plastic is hazardous to health.
It is estimated that 80 per cent of plastic found at sea is washed out from the land. The journal Science last year predicted seafood stocks would collapse by 2048 if overfishing and pollution continued. If the seafood stocks collapse, a lot of humans will follow. So, is there anything we can do to prevent this?
Greenpeace says embracing the three Rs - reduce, re-use and recycle - would help tackle the problem. Plastic recycling is lagging well behind paper and cardboard. Part of the reason is because many people aren’t even sure what recycling options exist in their area. But there are other challenges for plastic recycling too. Some plastics release toxic chemicals into the atmosphere, and are more expensive to recycle than to simply create a new product from petrochemicals.
The widespread use of bioplastics could largely reduce the amount of plastic strewn around the world. Traditional petrochemical-based plastics are non-degradable and non-renewable; degradable plastic breaks into smaller pieces in UV light but remains plastic. Then there are two kinds of biodegradable plastic that break down in compost - one from a petrochemical resource, the other from a renewable resource such as corn or wheat, which is known as bioplastic. Bioplastic is by far the most environmentally friendly option. Dr Katherine Dean, of the CSIRO, says corporate firms are now becoming increasingly interested in bioplastics.
"When oil prices soared in 2005, that changed a lot of people's perspective, because bioplastic became quite cost-competitive," she says. "All of a sudden it wasn't just about doing the right thing."
The company Plantic Technologies, has developed biodegradable plastic for everything from food and beverage packaging to medical, agricultural and sporting applications. The chief executive of Plantic, Grant Dow, says once composted, the plastic would become nothing more than carbon dioxide and water.
"For all intents and purposes, it looks like plastic and feels like plastic and does the same thing as plastic in the application," he says.
"It will only biodegrade in the presence of heat, moisture and bacteria, so it will sit in your cupboard pretty much indefinitely, but when the bacteria get to it in compost, that's it. It's gone."
While parts of our oceans have already become inhospitable soups of plastic and plankton, we can at least mitigate the future consequences by making smart individual choices. Experts say the best way to mitigate the damage down the road is by buying less products that contain plastics or plastic packaging, recycling, lobbying for safer bio-degradable plastics, and by purchasing reusable cloth grocery bags among other strategies.
That said, a solution to the world's plastic crisis may have a possible long-term solution: a Waterloo, Canada teenager, Daniel Burd, has found a way to make plastic bags degrade faster -- in three months, he figures. Burd recently won the top prize at the Canada-Wide Science Fair in Ottawa. He came back with a long list of awards, including a $10,000 prize, a $20,000 scholarship, and recognition that he has found a practical way to help the environment.
Burd’s discovery isolated two strains of bacteria (Sphingomonas and Pseudomonas) that work together to consume polyethelene plastic at record rates, yielding a culture that rendered plastic bags 43% decomposed after six weeks, with the only outputs being water and an infinitesimal amount of carbon dioxide. The system is cheap, energy efficient, and easily scalable for industrial applications. “All you need," Burd says "is a fermenter . . . your growth medium, your microbes and your plastic bags."
Burd's discovery will not solve the whirling vortexes of plastic garbage in the North Pacific, but with an infrastructure in place to harness Burd's innovation, there's hope to prevent future damage to the planet.



http://www.dailygalaxy.com/my_weblog...re-a-natu.html

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A team led by a Purdue University researcher has achieved images of a virus in detail two times greater than had previously been achieved.
Wen Jiang, an assistant professor of biological sciences at Purdue, led a research team that used the emerging technique of single-particle electron cryomicroscopy to capture a three-dimensional image of a virus at a resolution of 4.5 angstroms. Approximately 1 million angstroms would equal the diameter of a human hair.
"This is one of the first projects to refine the technique to the point of near atomic-level resolution," said Jiang, who also is a member of Purdue's structural biology group. "This breaks a threshold and allows us to now see a whole new level of detail in the structure. This is the highest resolution ever achieved for a living organism of this size."
Details of the structure of a virus provide valuable information for development of disease treatments, he said.
"If we understand the system - how the virus particles assemble and how they infect a host cell - it will greatly improve our ability to design a treatment," Jiang said. "Structural biologists perform the basic science and provide information to help those working on the clinical aspects."
A paper detailing the work was published in the Feb. 28 issue of Nature.
Roger Hendrix, a professor of biological sciences at the University of Pittsburgh, said what is learned about viruses can be applied to many other biological systems.
"Understanding the proteins that create the structure of a virus gives us insight into the tiny biological machines found throughout our bodies," he said. "Getting to 4.5 angstrom using this technique is a watershed of sorts because it is the first time we can actually trace the polypeptide chain - the backbone of proteins. Now we can see the tiny gears and levers that allow the proteins to move and interact as they carry out their intricate biological roles."
The imaging technique, called cryo-EM, has the added benefit of maintaining the sample being studied in a state very similar to its natural environment. Other imaging techniques used regularly, such as X-ray crystallography, require the sample be manipulated.
"This method offers a new approach for modeling the structure of proteins in other macromolecular assemblies, such as DNA, at near-native states," Jiang said. "The sample is purified in a solution that is very similar to the environment that would be found in a host cell. It is as if the virus is frozen in glass and it is alive and infectious while we examine it."
In addition to Jiang, Matthew L. Baker, Joanita Jakana and Wah Chiu from Baylor College of Medicine, and Peter R. Weigele and Jonathan King from Massachusetts Institute of Technology worked on the project, which was funded by the National Institutes of Health and the National Science Foundation.
The team obtained a three-dimensional map of the capsid, or protein shell, of the epsilon15 bacteriophage, a virus that infects bacteria and is a member of a family of viruses that are the most abundant life forms on Earth, Jiang said.
Other methods of determining the structure could not be used for this family of virus. None had been successfully crystallized, and the complexity of members of this family had prevented evaluation through the genome sequence alone.
"This demonstration shows that cryo-EM is doable and is a major step in reaching the full potential of this technique," he said. "The goal is to have it reach a 3 to 4 angstrom resolution, which would allow us to clearly see the amino acids that make up a protein."

In electron microscopy, a beam of electrons takes the place of the light beam used in a conventional microscope. The use of electrons instead of light allows the microscope to "see" in much greater detail.
Cryo-EM cools specimens to temperatures well below the freezing point of water. This decreases damage from the electron beam and allows the specimens to be examined for a longer period of time. Longer exposure time allows for sharper, more detailed images.
Researchers using cryo-EM had obtained images at a resolution of 6-9 angstroms but could not differentiate between smaller elements of the structure spaced only 4.5 angstroms apart.
"There are different elements that make up the protein building blocks of the virus," Jiang said. "It is like examining a striped blanket. From a distance, the stripes blur together and the blanket appears to be one solid color. As you get closer you can see the different stripes, and if you use a magnifying glass you can see the strands of string that make up the material. The resolution needs to be smaller than the distance between the strands of thread in order to see two separate strands.
"By being able to zoom in, researchers were able to see components that blurred together at the earlier achieved resolution."
Cryo-EM requires high-end electron microscopes and powerful computing resources. The research team used the Baylor College of Medicine's cryoelectron microscope. It is expected that Purdue will install a state-of-the-art cryoelectron microscope in 2009.
In 2006 Purdue received a $2 million grant from the National Institute of Health to purchase the microscope. It will be installed in Hockmeyer Hall of Structural Biology, expected to open in 2009.
Computer programs are used to extract the signal from the microscope and to combine thousands of two-dimensional images into an accurate three-dimensional image that maps the structure of the virus. This requires use of a large data set and could not have been done without the resources of Purdue's Office of Information Technology, or ItaP, Jiang said.
Jiang used Purdue's Condor program - which links computers including desktop machines and large, powerful research computers - to create the largest distributed computing network at a university.
"ITaP provided us with computational power at the supercomputer scale that was necessary for this work," he said. "Purdue's Condor program allowed us to take advantage of the power of 7,000 computers. This was a critical element to our success."
Jiang plans to continue to refine every step of the process to improve the capabilities of the technique and to examine more medically relevant virus species.
Purdue's structural biology group studies a diverse group of problems, including cellular signaling pathways, RNA catalysis, bioremediation, molecular evolution, viral entry, viral replication and viral pathogenesis. Researchers use a combination of X-ray crystallography, electron cryomicroscopy, NMR spectroscopy, and advanced computational and modeling tools to study these problems.
Writer: Elizabeth K. Gardner, (765) 494-2081,ekgardner@purdue.edu
Source: Wen Jiang, (765) 496-8436, jiang12@purdue.edu
Purdue News Service: (765) 494-2096; purduenews@purdue.edu
IMAGE CAPTION:
Shown is an image of bacteriophage Epsilon15 studied by Wen Jiang, an assistant professor of biological sciences at Purdue. The bacteriophage is shown at a resolution of 4.5 angstrom - the highest resolution achieved for a living organism of this size. (Graphic/Wen Jiang lab)


http://news.uns.purdue.edu/x/2008a/0...angNature.html

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This artist's conception depicts the structure of a "molecular motor" that packages DNA into the head segment of the T4 virus. Researchers at Purdue and The Catholic University of America have determined the atomic structure of this motor, which is made of two ringlike structures, and both of these discs contain five segments made of a protein called gp17. The image shows a cross section of the virus head, or capsid, and an artist\'s interpretation of the motor as it packages DNA into the virus. The hands represent the five segments of the ringlike structures. Each hand takes a turn grabbing the DNA and moving it into the head until the head is full. Credit: The journal Cell, Dec. 26, 2008; Steven McQuinn, independent science artist, and Venigalla Rao, The Catholic University of America.) Researchers have discovered the atomic structure of a powerful "molecular motor" that packages DNA into the head segment of some viruses during their assembly, an essential step in their ability to multiply and infect new host organisms. The researchers, from Purdue University and The Catholic University of America, also have proposed a mechanism for how the motor works. Parts of the motor move in sequence like the pistons in a car's engine, progressively drawing the genetic material into the virus's head, or capsid, said Michael Rossmann, Purdue's Hanley Distinguished Professor of Biological Sciences. The motor is needed to insert DNA into the capsid of the T4 virus, which is called a bacteriophage because it infects bacteria. The same kind of motor, however, also is likely present in other viruses, including the human herpes virus. "Molecular motors in double-stranded DNA viruses have never been shown in such detail before," said Siyang Sun, a postdoctoral research associate working in Rossmann's lab. Findings are detailed in a paper appearing online on Dec. 24 in the journal Cell. The lead authors are Sun and Kiran Kondabagil, a research assistant professor at Catholic University of America working with biology professor Venigalla B. Rao. "This research is allowing us to examine the inner workings of a virus packaging motor at the atomic level," Rao said. "This particular motor is very fast and powerful." Other researchers have determined that the T4 molecular motor is the strongest yet discovered in viruses and proportionately twice as powerful as an automotive engine. The motors generate 20 times the force produced by the protein myosin, one of the two proteins responsible for the contraction and strength of muscles. The virus consists of a head and tail portion. The DNA-packaging motor is located in the same place where the tail eventually connects to the head. Most of the motor falls off after the packaging step is completed, allowing the tail to attach to the capsid. The DNA is a complete record of a virus's properties, and the capsid protects this record from damage and ensures that the virus can reproduce by infecting a host organism. Sun determined that the packaging motor is made of two ringlike structures, and both of these discs contain five segments made of a protein called gp17, for gene product 17. The researchers determined the atomic structure of these protein segments using a procedure called X-ray crystallography. They also used another technique called cryo-electron microscopy, which enabled them to see a more distant, overall design of the motor's ringlike structure. Sponsored Links (Ads by Google) One disc sits on top of the other, and each of the five segments of the top disc shares a gp17 protein with a corresponding segment in the bottom disc. The gp17 proteins have two segments, or domains, one segment in the lower disc and the other segment in the upper disc. The lower disc first attaches to the DNA and is then drawn upward by the upper disc, pushing the DNA into the virus's capsid in the process. The top disc of the motor pulls the lower disc upward using electrostatic forces generated between oppositely charged objects, Rossmann said. "These findings determined the relationship between the motor and DNA," Rossmann said. The research data also showed that the motor is dynamic and apparently exists in two states: relaxed and tensed, the latter likely occurring when the top disk has attracted the lower disc. Researchers at Catholic University of America supplied the gp17 and other materials, and the Purdue researchers studied the structure of the materials. "By combining the structural data and the biochemical data of our colleagues at the Catholic University of America, we were jointly able to come up with a hypothesis of how this motor works," Rossmann said. Because herpes and other viruses contain similar DNA packaging motors, such findings could someday help scientists design drugs that would interfere with the function of these motors and mitigate the result of some viral infections. The findings also could have other future applications, such as developing alternatives to current antibiotics, creating methods to deliver genetic material to patients for gene therapy or creating tiny "nanomotors" in future machines. "But this is very basic research, and it's far too soon to talk more about possible practical applications of this knowledge," Rossmann said.
Provided by Purdue University.


http://www.physorg.com/news149344139.html

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