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Volume 5, Issue 20
July 8, 2005
Circulation 17,351

Friday FYI

Newsletter from the Office of the Vice President for Research and Graduate Education - U. T. Dallas

Other News

Protein Structure Initiative Advances to Rapid Production Phase

With the announcement of 10 new research centers, the Protein Structure Initiative (PSI) launches the second phase of its national effort to find the three-dimensional shapes of a wide range of proteins. This structural information will help reveal the roles that proteins play in health and disease and will help point the way to designing new medicines.

Selection of the centers, slated to receive about $300 million over the next five years, marks the second half of the decade-long initiative funded largely by the National Institute of General Medical Sciences (NIGMS), part of the National Institutes of Health.

When the PSI established its pilot centers beginning in 2000, its goal was twofold: to develop innovative approaches and tools, such as robotic instruments, that streamline and speed many steps of generating protein structures, and to incorporate those new methods into pipelines that turn DNA sequence information into protein structures.

Now, the focus shifts to a production phase during which the new centers will use methods developed during the pilot period to rapidly determine thousands of protein structures found in organisms ranging from bacteria to humans. These efforts will facilitate structure determination on a much larger number of proteins through computer modeling.

The PSI production phase includes two types of centers. Four large-scale centers, established during the pilot phase, expect to generate between 3,000 and 4,000 structures. Six specialized centers will develop novel methods for quickly determining the structures of proteins that traditionally have been difficult to study. These include small protein complexes; proteins that attach to a cell’s outer envelope, or membrane; and many proteins from higher organisms, including humans.

While both sets of centers are charged with developing new methods for handling these more difficult proteins, the specialized centers will focus particularly on this task.

As before, the PSI centers will submit their structures and related findings to the Protein Data Bank (http://www.rcsb.org/pdb/), an NSF- and NIH-supported public repository of three-dimensional biological structure data.

From this repository, researchers can access a wealth of PSI-generated information that may help them better understand the function of proteins, predict the shapes of unknown proteins, identify new targets for drug development, and even compare protein structures from normal and diseased tissues.

The large-scale centers are:

The specialized centers are:

[ FYI Index ]

International Conference Creates Strategy to Fight Avian Influenza

International animal and human health experts Wednesday unveiled a multi-point plan designed to reduce the risk of the H5N1 avian influenza virus spreading from poultry to humans, and appealed to the international community to come forward with funds to make it work and help stave off the risk of an influenza pandemic.

The strategy was drawn up at a three-day conference in Kuala Lumpur, Malaysia, attended by experts from around Asia, as well as by senior representatives of the UN Food and Agriculture Organization (FAO), the World Organization for Animal Health (OIE) and the World Health Organization (WHO).

The plan will be the basis for urgent actions by affected states and will be made available to the international community to help donors focus on the areas of highest need.

The conference took place against the backdrop of a growing threat from the avian influenza H5N1 virus, which has so far infected 108 people in Asia, killing 54 of them and raising fears of an influenza pandemic. The virus, which delegates were told is taking an ever-tightening grip in a number of Asian countries, has so far led to the slaughter of over 140 million chickens in an attempt to halt its spread.

The meeting agreed that the avian influenza situation in Asia was extremely serious but determined that there was still a window of opportunity to ward off a pandemic.

Delegates concluded that priority should be given to the situation in small-scale and backyard farms, the scene of the majority of human cases since the avian influenza outbreak became known in early 2004. Recommendations covering this type of small-scale farming included:

“We agreed that it is vital to urgently change or even end a number of farming practices that are dangerous to humans,” said Dr Joseph Domenech, Chief Veterinary Officer with the FAO. “These include the way chickens, ducks and pigs are raised in close proximity to each other, often with no barriers between them and humans. Another area of concern is wet markets, where animals are often slaughtered in unsanitary conditions. These activities constitute a high risk to people who are exposed to contaminated animals or products, such as blood, faeces, feathers and carcasses.”

These practices increase the danger of an interspecies transmission of avian viruses, with the risk of an exchange of genetic material and the emergence of a new virus that could endanger human health.

An FAO and OIE strategy for the control of avian influenza in Asia will cost around $100 million to support surveillance, diagnosis and other control measures, including vaccination. “Without international support, poor countries will not be able to battle bird flu,” said Dr Domenech.

WHO estimates the cost of an effective response on the public health front at about $150 million, mainly for capacity building in affected countries, including emergency support in the areas of laboratory diagnosis, vaccine development, surveillance and public education. Some of the funds would be earmarked for antiviral drugs and personal protective equipment for people most at risk of infection.

[ FYI Index ]

NASA's Deep Impact Generates its own Spectacular Photo Flash

The hyper-speed demise of NASA's Deep Impact probe generated an immense flash of light, which provided an excellent light source for the two cameras on the Deep Impact mothership. Deep Impact scientists theorize the 820-pound impactor vaporized deep below the comet's surface when the two collided at 1:52 am July 4, at a speed of about 10 kilometers per second (6.3 miles per second or 23,000 miles per hour).

"You can not help but get a big flash when objects meet at 23,000 miles per hour," said Deep Impact co-investigator Dr. Pete Schultz of Brown University, Providence, R.I. "The heat produced by impact was at least several thousand degrees Kelvin and at that extreme temperature just about any material begins to glow. Essentially, we generated our own incandescent photo flash for less than a second."

The flash created by the impact was just one of the visual surprises that confronted the Deep Impact team. Preliminary assessment of the images and data downlinked from the flyby spacecraft have provided an amazing glimpse into the life of a comet.

At a news conference held later on July 4, Deep Impact team members displayed a movie depicting the final moments of the impactor's life. The final image from the impactor was transmitted from the short-lived probe three seconds before it met its fiery end.

The Deep Impact scientists are not the only ones taking a close look at their collected data. The mission's flight controller team is analyzing the impactor's final hours of flight. When the real-time telemetry came in after the impactor's first rocket firing, it showed the impactor moving away from the comet's path.

The Deep Impact mission was implemented to provide a glimpse beneath the surface of a comet, where material from the solar system's formation remains relatively unchanged. Mission scientists hoped the project would answer basic questions about how the solar system formed, by providing an in-depth picture of the nature and composition of the frozen celestial travelers known as comets. The University of Maryland is responsible for overall Deep Impact mission science, and project management is handled by JPL. The spacecraft was built for NASA by Ball Aerospace & Technologies Corporation, Boulder, Colo.

[ FYI Index ]

Ancient Footprints Discovered in Mexico

Scientists have unearthed human footprints in central Mexico which they claim are around 40,000 years old, shattering previous theories on how humans first colonized the Americas.

The researchers hope that their preliminary findings will eventually help shed light on one of the most contentious debates in American history: who was there first and how did they get there?

An international team of geoarchaeologists, led by Dr Silvia Gonzalez from Liverpool John Moores University (LJMU) in the United Kingdom, finally completed dating the footprints, found in 2003, earlier this year. The footprints were found in an abandoned quarry by Dr Gonzalez, Professor David Huddart (LJMU) and Professor Matthew Bennett ( Bournemouth University) in September 2003 and have been subsequently studied by a multinational team of scientists.

The first stage of their research focused on analyzing 269 footprints, both animal and human, found close to the Cerro Toluquilla volcano in the Valsequillo Basin, near the city of Puebla, 130 km southeast of Mexico City.

Further sites in the area with footprints have been identified in the Valsequillo Basin. Now Gonzalez and her research team will carry out more extensive investigations to corroborate their initial findings and also calculate the height, pace and stride of the human population present 40,000 years ago. Such research would also give a better understanding of the relationship that these early Americans had with megafauna, such as mammoths, camels and other large animals.

The footprints were preserved as trace fossils in volcanic ash along what was the shoreline of an ancient volcanic lake. Climate variations and the eruption of the Cerro Toluquilla volcano caused lake levels to rise and fall, exposing the Xalnene volcanic ash layer.

The geoarchaeologist suggests that the early Americans walked across this new shoreline, leaving behind footprints that soon became covered in more ash and lake sediments. The trails became submerged when the water levels rose again, so preserving the footprints.

Now as hard as concrete, the Xalnene ash is used locally as a building material. Dr Gonzalez and her research team were able to see the footprints without carrying out any excavation as quarry workers had already removed between 2-3metres of lake sediments that had been deposited on top of the volcanic ash.

The team’s findings pose serious challenges to considered wisdom on the settlement of the continent. Gonzalez, working as part of the Natural Environment Research Council’s ‘Environmental Factors in the Chronology of Human Evolution and Dispersal (EFCHED) research program, said: “We think there were several migration waves into the Americas at different times by different human groups.”

This debate has been running for more than a century. The traditional view –known as the Clovis First Model – is that settlers crossed the Bering Straits, from Russia to Alaska, at the end of the last ice age – around 11,500 to 11,000 years ago. Evidence for this theory comes from Clovis Points – tools used to hunt mammoths and mastodonts – found from many locations in the American continent.

The discovery of human footprints in the Valsequillo Basin of Central Mexico challenges this model, providing new evidence that humans settled in the Americas as early as 40,000 years ago.

The Mexican Footprint research is vitally important for the study of the settlement of the Americas as it provides extensively validated data that directly challenges current theories on the peopling of the Americas. It also re-confirms the importance of Central Mexico as one of the most important areas for the study of early human occupation.

The footprints were mapped and scanned using laser technology and have been reproduced at the University of Bournemouth using rapid proto-typing technology, allowing excellent visualization. This technology has been used to produce physical models of the footprints with sub-millimetre precision.

Ancient human and animal prints are a rarity due to the special conditions required for their preservation. The discovery of the Valsequillo Basin footprints is an important addition to the global archive of human prints.

The footprints are indisputably human because they have some unique characteristics, including:

[ FYI Index ]

Venomous Mammal Find a First: Alberta Paleontologist

A small, fossilized mammal had what appears to be poisonous fangs that allowed it to bite like a snake – the first such find in an extinct mammal, Canadian researchers say.

Vertebrate paleontologist Richard Fox of the University of Alberta in Edmonton found the specimen in 1991. Now Fox and his research team say the extinct, mouse-sized creature was built to deliver venom.

The world is home to few living mammals with venom delivery systems: the duck-billed platypus, the Caribbean solenodon, and a few rat-like shrews.

Scientists concluded that mammals long ago lost the ability to release venom to defend themselves or find food, given how few mammalian species still use the strategy.

The 60-million-year-old fossil of the mouse-sized creature, called Bisonalveus browni, has a deep groove in its upper canine. The length of the tooth may have allowed it to act like a piercing fang, like those found in modern venomous snakes,

An article on the find appears in the current issue of the journal Nature.

The fossil teeth were found at two sites in the Paskapoo Formation of central Alberta, an area rich in well-preserved mammalian fossils.

The study shows how even after scientists work on a research project for years, uncovering one small piece of information can lead to new discoveries, Fox said.

The Natural Sciences and Engineering Research Council of Canada and the University of Alberta sponsored the research.

 

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