(CERN)

“It’s great to see beam circulating in the LHC again,” said CERN Director General Rolf Heuer. “We’ve still got some way to go before physics can begin, but with this milestone we’re well on the way.”

The LHC circulated its first beams on 10 September 2008, but suffered a serious malfunction nine days later. A failure in an electrical connection led to serious damage, and CERN has spent over a year repairing and consolidating the machine to ensure that such an incident cannot happen again.

“The LHC is a far better understood machine than it was a year ago,” said CERN’s Director for Accelerators, Steve Myers. “We’ve learned from our experience, and engineered the technology that allows us to move on. That’s how progress is made.”

Recommissioning the LHC began in the summer, and successive milestones have regularly been passed since then. The LHC reached its operating temperature of 1.9 Kelvin, or about -271 Celsius, on 8 October. Particles were injected on 23 October, but not circulated. A beam was steered through three octants of the machine on 7 November, and circulating beams have now been re-established. The next important milestone will be low-energy collisions, expected in about a week from now. These will give the experimental collaborations their first collision data, enabling important calibration work to be carried out. This is significant, since up to now, all the data they have recorded comes from cosmic rays. Ramping the beams to high energy will follow in preparation for collisions at 7 TeV (3.5 TeV per beam) next year.

Particle physics is a global endeavour, and CERN has received support from around the world in getting the LHC up and running again.

“It’s been a herculean effort to get to where we are today,” said Myers. “I’d like to thank all those who have taken part, from CERN and from our partner institutions around the world.”

^1. CERN, the European Organization for Nuclear Research, is the world’s leading laboratory for particle physics. It has its headquarters in Geneva. At present, its Member States are Austria, Belgium, Bulgaria, the Czech Republic, Denmark, Finland, France, Germany, Greece, Hungary, Italy, Netherlands, Norway, Poland, Portugal, Slovakia, Spain, Sweden, Switzerland and the United Kingdom. India, Israel, Japan, the Russian Federation, the United States of America, Turkey, the European Commission and UNESCO have Observer status.

- CERN, the European Organization for Nuclear Research -

The researchers linked many powerful computer systems together to analyze enormous amounts of genetic data collected from all publicly available isolated strains of the H5N1 virus – the cause of avian flu. They then developed a new Web-based application that will allow health officials and the public visualize how the virus moved across the globe using Google Earth.

The green lines on this interactive map represent how pandemic influenza (H1N1) has moved from points in the United States to geographic locations across the globe. Screenshot taken using Google Earth.

The resulting visualizations, based on results of the data analysis, represent the most comprehensive map to date of how avian flu has been transmitted among sites in Asia, Africa and Europe.

But underlying those findings is a new way of analyzing genetic data that generates more complete information about the flu’s spread. The method, combined with the increasing availability of sequenced genomes of isolated flu strains, is expected to help public health officials make more knowledgeable predictions about how the H1N1 flu pandemic will evolve.

“We are taking into account more data but at the same time, we’re making simpler visualizations, allowing users to choose what they want to see,” said Daniel Janies, associate professor of biomedical informatics at Ohio State and senior author of the study.

“We’ve created an environment where people can avail themselves of flu information specific to their region of the world or their area of interest. We waded through all of the complexities so people in the public health realm who want to determine how a flu virus got from point A to point B can find that out, and we’ll have better public health outcomes as a result.”

The visualizations and application are available online at http://routemap.osu.edu.

The research appears online in the journal Cladistics.

The research environment has changed dramatically since 1997, when an avian flu outbreak in Hong Kong alerted health officials to its dangers to humans, Janies noted. The technology behind the Human Genome Project has improved to enable the rapid sequencing of numerous genomes, and avian flu’s broad transmission has encouraged scientists to place viral sequence data into the public domain. At the same time, computational power has continued to expand.

Janies and colleagues obtained high-quality avian flu sequences contained in the repositories at the National Institutes of Health’s GenBank and the Global Initiative on Sharing Avian Influenza Data (GISAID). They then focused on studying two genes within the virus whose mutations are believed to have the most impact on H5N1 behavior: hemagglutinin, which produces the protein that recognizes the host cell receptor, and neuraminidase, an enzyme that helps the virus escape one cell so it can enter other cells.

The researchers used 1,646 sequences of hemagglutinin and 1,335 of neuraminidase in this study.

Biologists construct what are called phylogenetic trees to trace evolutionary relationships among species or strains believed to share a common ancestor. These trees’ branching diagrams can be designed to track similarities in physical characteristics, for example, in the study of dinosaurs, for which genetic data cannot be easily recovered. Or, in the study of influenza, the trees can show how viral strains are related based on shared mutations.

In the past, scientists – including Janies – have selected a single phylogenetic tree to represent related viruses that share mutations. But in this paper, the researchers used the power of supercomputers to generate millions of trees representing relationships among these thousands of viruses. They then picked a pool of thousands of high-quality trees based on a scoring system in the bioinformatics field to use in their analysis of disease transmission.

The scientists then asked of these trees – what are the geographic connections between the isolated viral strains?

These resulting diagrams were then used as the basis for an interactive map that traces the genetic, geographic and evolutionary history of avian influenza over 12 years. The highly pathogenic lineage of avian flu that crossed Asia and Africa can be traced to an isolate taken from a goose in 1996. Little genetic data is available for H5N1 viruses isolated before that.

To avoid creating a complex map that looks like “spaghetti thrown on the screen,” Janies and colleagues also simplified the map’s design. Green lines represent transmission pathways most strongly supported by the research findings. Yellow lines indicate less certainty. Lines also are colored differently depending on whether they indicate an incoming or outgoing virus from a specific location. And users can search for specific transmission routes rather than seeing all transmission events on the map at once.

The maps represent scientists’ best approximation of avian flu transmission based on the information available, Janies explained. Without access to every complete genome of every flu virus that ever infected a bird or human, researchers can never fully track evolutionary relationships, genetic histories and specific locations of each outgoing and incoming viral transmission.

Daniel Janies

“Collect and share as much data as possible and let the data tell the story,” he said. “We’re honest about the uncertainty our results may have – but even with partial data, we can infer much about a virus in an area based on its sources.”

The method has already been applied to studies of the H1N1 flu currently infecting millions of people in the United States. International cooperation spearheaded by the NIH, GISAID and the Centers for Disease Control and Prevention has resulted in ready availability of H1N1 sequences for study.

“With what we have so far, we can see the spread of H1N1 out of the United States and all over the world. There is a different dynamic, in that this is a virus carried by humans, who are cosmopolitan and moving both ways,” Janies said. “It’s also a virus that has been transmitted all over the world in a matter of months, and it’s still similar to its ancestors.”

H5N1, on the other hand, has been creeping across Asia and into Europe and Africa for more than a decade and picked up mutations along the way, he noted. While H1N1 has spread more quickly, it is far less deadly to humans than H5N1 – meaning it is still useful for the world to keep an eye on avian flu, Janies said.

His group’s visualizations will help make that possible.

The computing power used in this study was supplied by the Ohio Supercomputer Center and the Ohio State University Medical Center. The research is funded by the U.S. Army Research Laboratory and Office, Ohio State’s Department of Biomedical Informatics and the Mathematical Biosciences Institute (MBI) at Ohio State.

Janies conducted the work with Rasmus Hovmöller, Boyan Alexandrov and Jori Hardman of Ohio State’s Department of Biomedical Informatics. Hovmöller is also an investigator in the MBI.

Written by Emily Caldwell – Ohio State University

Screen shot from TowerMadness, a 3D iPhone game created by UC San Diego computer science students, past and present. (University of California, San Diego)

Three current and former UC San Diego computer science students created TowerMadness, the cheat-resistant 3D game which challenges players to repel alien onslaughts by constructing defensive towers in strategic locations. A multi-touch interface allows TowerMadness players to zoom in and around the visually-detailed 3D action.

The game’s cheat resistance is rooted in a unique online replay feature. In particular, the developers built a proprietary replay verification system that automatically replays high-scoring games and checks that players legitimately scored as many points as their devices are reporting.

“The replays allow us to verify that the games submitted to our servers are genuine, keeping the online global scoring fair and fun for everyone,” said Iman Mostafavi, a computer science Ph.D. student at the UC San Diego Jacobs School of Engineering and one of the game’s three developers.

Each replay is a tamper-resistant, highly compact recording of a player’s actions over the course of a game.

“We’ve already thwarted several attempts at cheating,” said co-developer Volker Schönefeld, a former visiting graduate student to UC San Diego’s computer science department who is completing his doctoral degree at RWTH Aachen University, in Aachen Germany.

The replays are significantly smaller than a video of the same length and can be transmitted over the Internet in seconds.

TowerMadness’ replay features grew out of the technology Schönefeld pioneered in 2003 for Waaagh!TV, his e-Sports broadcasting company. Waaagh!TV develops software that allows thousands of users to simultaneously watch live online matches of the popular computer game Warcraft III.

In addition to cheat resistance, the replay feature allows TowerMadness players to show off their strategies and learn new ones by watching completed games. Anyone with a copy of TowerMadness can watch the replays.

The game includes additional online features supported by Google’s App Engine cloud computing platform. Players can compete globally for high scores, download free additional game content, and share their games on Twitter and Facebook.

Schönefeld and Mostafavi, along with Arash Keshmirian, a UC San Diego computer science BS/MS alumnus, began developing TowerMadness in their spare time shortly after Schönefeld’s first visit to the department in 2008. “With our shared interest in building apps for the platform, combined with many years of experience in developing computer graphics software, I knew we could push the iPhone’s capabilities to a level where only experienced developers could compete. This would be an important differentiator in an already crowded marketplace,” said Keshmirian, who is now an entrepreneur and consultant based in Silicon Valley.

On May 15, 2009, after nearly six months of development, TowerMadness scored a preview feature on the holy grail of iPhone gaming Touch Arcade, which fueled widespread anticipation for the release. The game went live on May 23rd, and news and reviews of the game began appearing on numerous blogs, web sites, and media around the world. Several days later, TowerMadness won an award from the prominent mobile gaming web site Pocket Gamer.

Another big visibility boost came when Apple picked TowerMadness for a prized high-profile spot on the iTunes App Store itself—the Featured Apps section.

“In a sea of over 50,000 apps, visibility is paramount. Being put in the spotlight by Apple early on has been a tremendous boon,” according to the developers. Only a month since its launch, players have submitted well over 150,000 rounds of TowerMadness to the online leaderboards.

Much of the cutting-edge 3D graphics, programming and gaming know-how that is helping to make TowerMadness popular was developed, strengthened or nurtured at UC San Diego. The UCSD Department of Computer Science and Engineering (CSE) and the UC San Diego Division of Calit2 (California Institute of Telecommunications and Information Technology) played particularly important roles.

The trio’s company, Limbic Software, plans to continue releasing downloadable content and updates for TowerMadness. Hoping to bring the excitement of competitive gaming to mobile gamers, the game will soon allow players to compete for real prizes. The team is also working hard towards the release of their upcoming second game.

The TowerMadness web site http://www.towermadness.com features more information, screenshots, and videos.

Before developing TowerMadness, Iman Mostafavi worked on various visualization projects at Calit2, including some that matured into StarCAVE, a five-sided virtual reality room where scientific models and animations are projected in stereo on 360-degree screens surrounding the viewer, and onto the floor.

Mostafavi also develops algorithms for improving the quality and utility of 3D models that represent biological data gleaned from biological images taken by electron microscopes. Mostafavi performs this work at the National Center for Microscopy and Imaging Research (NCMIR) at UC San Diego, which develops state-of-the-art 3D imaging and analysis technologies to help biomedical researchers understand biological structure and function relationships in cells and tissues.

Mostafavi also collaborated on UC San Diego interactive artwork, shown at SIGGRAPH 2007, that explored new ways of representing nature in the era of metagenomics.

At UC San Diego, Keshmirian developed physically-based simulations of light transport to produce realistic images of various phenomena, such as light passing through plant leaves. Keshmirian’s 2008 thesis, with advisor, computer science professor Henrik Wan Jensen, describes a new, and significantly more complete model for the simulation of light within camera lenses. The techniques can be used to artificially produce many of the effects observed when taking photographic pictures in the real world, thereby enhancing simulated images. Keshmirian was also the editor of the photography department at the UCSD Guardian, the university’s official student-run newspaper.

“Having the opportunity to take two completely different perspectives on photography: scientific and artistic, was a real boon for both my research and my art,” remarks Keshmirian. Keshmirian’s creative eye helped him develop the quirky-cute visual style for TowerMadness.

During his six month stay at the computer science department at UC San Diego, Schönefeld worked on his Master’s thesis, the topic of which is the mathematical analysis of physically-based simulation of light as it travels through a virtual scene. Schönefeld performed this research under the supervision of computer science professor Henrik Wann Jensen.

TowerMadness Gameplay: Tutorial and Easy Map

By Daniel Kane – University of California, San Diego

Pioneer-Venus visible-light image, and Magellan radar view of Venus. Credit: NASA/JPL/RPIF/DLR.

“Carrying out these observations was a great challenge, as SCIAMACHY was not actually designed for such measurements,” Dr. Manfred Gottwald, responsible for SCIAMACHY at the DLR Remote Sensing Technology Institute (Institut für Methodik der Fernerkundung; IMF), said. “We were surprised how excellently everything worked despite that,” his colleague at the institute, Dr. Sanders Slijkhuis, the specialist responsible for calibrating the instrument, added.

SCIAMACHY on Envisat, Venus Express and COROT complement one another

The Venus observations by SCIAMACHY are useful in two respects. On the one hand, they support the in-situ measurements by the Venus Express space probe of the European Space Agency (ESA), which has been orbiting our neighbouring planet since 2006. Venus Express is studying the dense atmosphere of Venus with great precision using the SPICAV and VIRTIS spectrometers. SCIAMACHY and Venus Express are observing Venus under different viewing geometries and lighting conditions, so that their results complement one another well. In addition, SCIAMACHY’s Venus observations are a further test of the way that an Earth-like planet presents itself spectrally when observed from a great distance.

Since the first extra-solar planets – that is, planets orbiting stars other than our Sun – were discovered in the mid-1990s, the search for Earth-like companions of stars similar to the Sun, in other words a ’second Earth’, has been one of the great challenges in astronomy. Currently, however, most of the so-called exoplanets that have been found are giant gas planets rather like Jupiter. In 2008, researchers succeeded for the first time in discovering a possible Earth-like exoplanet using the CoRoT (Convection, Rotation and Planetary Transits) space telescope, a project in which the DLR is also involved (see article CoRoT discovers extrasolar rocky planets in the right column). But in the near future, small Earth-like planets could also come within reach using improved telescopes. However, they will always appear as small dots due to the enormous distances involved. The spectral analysis of the central star’s light when scattered by the exoplanets and their own thermal radiation emissions could provide information as to whether they might be suitable for harbouring life. Hence, observations of the known planets in our solar system provide an excellent experimental environment for gaining experience with regard to the interpretation of spectral signatures of Earth-like bodies.

Earth observation satellite ENVISAT. Credit: ESA.

DLR planetary researchers pleased about interdisciplinary approach

The observations of Venus, with its hot and hostile environment – surrounded by a dense carbon dioxide atmosphere – can provide outstanding comparative data in our immediate cosmic neighbourhood for the analysis of the atmosphere of exoplanets. “As planetary researchers, we are of course very pleased about these additional measurements from a mission whose aim is actually Earth observation,” Prof. Tilman Spohn, Director of the DLR Institute of Planetary Research (Institut für Planetenforschung) in Berlin-Adlershof, says. He adds: “It is excellent that these data from SCIAMACHY were picked up. They help us to evaluate the data supplied by our experiments on the planetary missions.”

“We are very impressed by the SCIAMACHY observations,” Prof. Heike Rauer, also from the DLR Institute of Planetary Research and the leader of the project through which DLR is involved in the search for exoplanets with CoRoT, said happily. “The new results illustrate excellently what atmospheric signatures would be expected if a Venus-like exoplanet were discovered.” Future satellites could then search for signs of a biosphere, the zone where organisms can live, on such planets. Scientists from the DLR Remote Sensing Technology Institute in Oberpfaffenhofen have been working with the researchers from the DLR Institute of Planetary Research in Berlin-Adlershof for some time in the search for what are known as ‘biomarkers’ – components in the atmosphere or on the surface of planets that have been created through the metabolic activity of life forms.

The intention is to make further use of the SCIAMACHY measurements in the ‘Planetary Evolution and Life’ Helmholtz Alliance. This international research network is investigating the question, among other things, as to what conditions must prevail on a planet in order for life to develop. Here, the data offer a realistic background for modelling the radiation transport in the atmospheres of Earth-like planets.

Additional measurements of spectra in various phases of Venus are planned with SCIAMACHY. In addition, studies are underway as to how the other bright planets of our solar system, Mars, Jupiter and Saturn, can also be used as extraterrestrial objects of investigation.

Venus – bright, small and “difficult to measure”

Relative positions of Earth and Venus, March and June 2009. Credit: DLR/NASA-JPL Solar System Simulator.

Venus, with its 12 100-kilometre diameter, is almost as large as our home planet.  Seen from Earth, it appears as the brightest celestial body after the Sun and Moon – but with a subtended angle of less than one minute of arc (one sixtieth of a degree) it looks relatively small. As a consequence, in order to keep this small ‘Venusian disc’ in SCIAMACHY’s field of view long enough to perform the observations, the instrument configuration had to be changed substantially. Due to the arrangement of SCIAMACHY’s observation windows, Venus only appears above Earth’s horizon briefly after rising – a process which is repeated 14 to 15 times per day as a result of Envisat’s orbit of the Earth. Precise planning as well as chronologically exact measurements finally enabled the derivation of Venus spectra on the basis of the solar radiation reflected and scattered by the planet’s atmosphere. Both in March and in June 2009 SCIAMACHY recorded Venus spectra during several orbits of Earth (see PDF download ‘SCIAMACHY spectra of Venus’ in the right column).

As an inner planet, Venus moves faster around the Sun than Earth. Therefore, the relative positions of Earth, Venus and Sun changed significantly between March and June 2009 (see image). In March 2009, Venus was close to what is known as its ‘inferior conjunction’, directly between Earth and the Sun. Seen from Earth, it presented mainly its dark side and only a thin crescent of the sunlit planetary disc was visible. At this time, the distance of Venus from Earth was only 43 million kilometres. In June 2009, by contrast, the Sun, Venus and Earth formed an almost right-angled triangle. Although the distance between Venus and Earth had grown to 127 million kilometres, more than 50 percent of Venus’ disc now lay in sunlight when seen from Earth.

SCIAMACHY on Envisat

ESA’s Envisat Earth observation satellite has been orbiting Earth since 2002 and supplies valuable information about the state of Earth. The SCIAMACHY atmospheric instrument on board Envisat, designed under the lead management of  DLR together with Dutch and Belgian partners, measures the solar radiation scattered back from Earth’s surface and atmosphere from the ultraviolet to the near-infrared parts of the spectrum. These measurements can be used to determine the atmospheric concentration of many different trace gases, which are important with regard to air quality, the greenhouse effect and ozone chemistry. SCIAMACHY is the first and currently the only satellite instrument in the world to carry out measurements of such complexity. The project is managed by DLR and the Netherlands Space Office (NSO). The Institute of Remote Sensing and Environmental Physics (IFE/IUP) of the University of Bremen is responsible for the scientific management the project.

German Aerospace Center (Deutsches Zentrum für Luft- und Raumfahrt; DLR)

A new study conducted at Georgia Tech found that sandfish (shown here) place their limbs against their sides and create a wave motion with their bodies like snakes to swim through sand. (Georgia Tech Photo: Gary Meek)

“When started above the surface, the animals dive into the sand within a half second. Once below the surface, they no longer use their limbs for propulsion—instead, they move forward by propagating a traveling wave down their bodies like a snake,” said study leader Daniel Goldman, an assistant professor in Georgia Tech’s School of Physics.

With funding from the National Science Foundation and the Burroughs Wellcome Fund, the research team used high-speed X-ray imaging to visualize sandfish—formally called Scincus scincus —burrowing into and through sand. The team used that information to develop a physics model of the lizard’s locomotion.

The sandfish used in this study inhabits the Sahara desert in Africa and is approximately four inches long. It uses its long, wedge-shaped snout and countersunk lower jaw to rapidly bury into and swim within sand. The sandfish’s body has flattened sides and is covered with smooth shiny scales, its legs are short and sturdy with long and flattened fringed toes and its tail tapers to a fine point.

• Watch a video of a sandfish using its limbs to run on the surface and rapidly bury into the interior of granular media here.




• Watch a video of a sandfish slither like a snake through granular media here.




• Watch a video of a sandfish swim through granular media with opaque markers on its body that clearly show that its limbs are held close to its body during swimming here.

To conduct controlled experiments with the sandfish, Goldman and graduate students Ryan Maladen, Yang Ding and Chen Li built a seven-inch by eight-inch by four-inch-deep glass bead-filled container with tiny holes in the bottom through which air could be blown. The air pulses elevated the beads and caused them to settle into a loosely packed solid state. Repeated pulses of air compacted the material, allowing the researchers to closely control the density of the material.

Georgia Tech graduate student Ryan Maladen (left) and physics assistant professor Daniel Goldman set up the high-speed X-ray imaging system to record the movements of sandfish below the sand surface. (Georgia Tech Photo: Gary Meek)

Since a sandfish might encounter and need to move through different densities of sand in the desert, the researchers tested whether sandfish locomotion changed when burrowing through media with volume fractions of 58 and 62 percent—typical values for desert sand.

“Since loosely packed media is easier to push through and closely packed is harder to push through, we thought there should be some difference in the sandfish’s locomotion,” said Goldman. “But the results surprised us because the density of the granular media did not affect how the sandfish traveled through the sand; it was always the same undulatory wavelike pattern.”

For a given wave frequency, the swimming speed depended only on the frequency of the wave and not on the density. Unexpectedly though, the animals could swim a bit faster in closely packed material by using a higher frequency range. The team also varied the diameter of the glass beads, but still observed similar wavelike motion.

By tracking the sandfish in the X-ray images as it swam through the glass beads, Goldman was able to characterize the sandfish’s motion—called its kinematics—as the form of a single-period sinusoidal wave that traveled from the head to the tail.

“The large amplitude waves over the entire body are unlike the kinematics of other undulatory swimming organisms that are the same size as the sandfish, like eels, which propagate waves that start with a small amplitude that gets larger toward the tail,” explained Goldman.

After collecting the experimental data, Goldman’s team developed a physics model to predict the speed at which sandfish swim through sand. The model was inspired by the resistive force theory, which allowed the researchers to partition the body of the sandfish into segments, each of which generated thrust and experienced drag when moving through the granular environment.

“When you balance the thrust and drag, you get motion at some velocity, but we needed to determine the forces on the animal segments because we don’t have the appropriate equations for drag force during movement through granular media,” explained Goldman.

To establish these equations, the researchers measured the granular thrust and drag forces on a small stainless steel cylindrical rod, thus allowing them to predict the wave efficiency and optimal kinematics. They found that the faster the sandfish propagate the wave, the faster they move forward through granular media—up to speeds of six inches per second. This speed allows the animal to escape predators, the heat of the desert surface and quickly swim to ambush surface prey they detect from vibrations.

Georgia Tech researchers developed a physics model of sandfish locomotion through granular media. They found that media density did not affect the lizard’s motion—it was always the same snakelike movement. (Georgia Tech Photo: Gary Meek)

“The results demonstrate that burrowing and swimming in complex media like sand can have intricacy similar to that of movement in air or water, and that organisms can exploit the solid and fluid-like properties of these media to move effectively within them,” noted Goldman.

In addition to having a biological impact, this study’s results also have ecological significance, according to Goldman. Understanding the mechanics of subsurface movement could reveal how the actions of small burrowing organisms like worms, scorpions, snakes and lizards can transform landscapes by their burrowing actions. This research may also help engineers build sandfish-like robots that can travel through complex environments.

“If something nasty was buried in unconsolidated material, such as rubble, debris or sand, and you wanted to find it, you would need a device that could scamper on the surface, but also swim underneath the surface,” Goldman said. “Since our work aims to fundamentally understand how the best animals in nature move in these complex unstructured environments, it could be very valuable information for this type of research.”

This material is based upon work supported by the National Science Foundation (NSF) under Award No. PHY-0749991 and the Burroughs Wellcome Fund. Any opinions, findings, conclusions or recommendations expressed in this publication are those of the researcher and do not necessarily reflect the views of the NSF.

Related Links

• Daniel Goldman
• Georgia Tech School of Physics

By Abby Vogel – Georgia Institute of Technology

The isotopic analysis of a bone from one of the earliest modern humans in Asia, the 40,000 year old skeleton from Tianyuan Cave in the Zhoukoudian region of China (near Beijing), by an international team of researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig, the Graduate University of Chinese Academy of Sciences and the Institute of Vertebrate Paleontology and Paleoanthropology in Beijing, the University of British Columbia in Vancouver and Washington University in Saint Louis has shown that this individual was a regular fish consumer (PNAS, 07.07.2009).

Fig.: Lower mandible of the 40 000 year old human skeleton, found in the Tianyuan Cave near Beijing. Analyses of collagen extracted from this bone prove that this individual was a regular consumer of fish. Image: Hong Shang / Chinese Academy of Sciences, Beijing

Freshwater fish are a major part of the diet of many peoples around the world, but it has been unclear when fish became a significant part of the year-round diet for early humans. Chemical analysis of the protein collagen, using ratios of the isotopes of nitrogen and sulphur in particular, can show whether such fish consumption was an occasional treat or part of the staple diet.

The isotopic analysis of the diet of one of the earliest modern humans in Asia, the 40,000 year old skeleton from Tianyuan Cave near Beijing, has shown that at least this individual was a regular fish consumer. Michael Richards of the Max Planck Institute for Evolutionary Anthropology explains “Carbon and nitrogen isotope analysis of the human and associated faunal remains indicate a diet high in animal protein, and the high nitrogen isotope values suggest the consumption of freshwater fish.” To confirm this inference the researchers measured the sulphur isotope values of terrestrial and freshwater animals around the Zhoukoudian area and of the Tianyuan human.

Since fish appeared on the menu of modern humans before consistent evidence for effective fishing gear appeared, fishing at this level must have involved considerable effort. This shift to more fish in the diet likely reflects greater pressure from an expanding population at the time of modern human emergence across Eurasia. “This analysis provides the first direct evidence for the consumption of aquatic resources by early modern humans in China and has implications for early modern human subsistence and demography”, says Richards.

Original work:

Yaowu Hu, Hong Shang, Haowen Tong, Olaf Nehlich, Wu Liu, Chaohong Zhao, Jincheng Yu, Changsui Wang, Erik Trinkaus, Michael P. Richards
Stable Isotope Dietary Analysis of the Tianyuan 1 Early Modern Human
PNAS. July 7, 2009. Vol. 106, No. 27

Max Planck Society

A new prostate cancer “homing device” could improve detection and allow for the first targeted treatment of the disease.

This image depicts transporter molecules carrying therapeutic drugs to PSMA targets on a prostate cancer cell. A Purdue research team designed a molecule that finds and penetrates prostate cancer cells and can transport drugs or imaging agents into the cell. (Image courtesy of Low laboratory)

A team of Purdue University researchers has synthesized a molecule that finds and penetrates prostate cancer cells and has created imaging agents and therapeutic drugs that can link to the molecule and be carried with it as cargo.

A radioimaging application used for body scans is expected to enter clinical trials this fall, and an optical imaging application used to measure prostate cancer cells in blood samples is already in clinical trials.

Philip Low, the Ralph C. Corley Distinguished Professor of Biochemistry who led the team, said a targeted treatment could be much more effective in treating cancer and would greatly reduce the harmful side effects associated with current treatments.

“Currently none of the drugs available to treat prostate cancer are targeted, which means they go everywhere in the body as opposed to only the tumor, and so are quite toxic for the patient,” said Low, who is a member of the Purdue Cancer Center. “By being able to target only the cancer cells, we could eliminate toxic side effects of treatments. In addition, the ability to target only the cancer cells can greatly improve imaging of the cancer to diagnose the disease, determine if it has spread or is responding to treatment.”

Prostate cancer is the most common cancer, other than skin cancers, and is the second leading cause of cancer death in American men, according to the American Cancer Society. It is estimated that about 192,280 new cases will be diagnosed and 27,360 men will die of prostate cancer in the United States this year.

The molecule Low’s team created attaches to prostate-specific membrane antigen, or PSMA, a protein that is found on the membrane of more than 90 percent of all prostate cancers. It also is found on the blood vessels of most solid tumors and could provide a way to cut off the tumor blood supply, Low said.

“A lot of new drugs are being designed to destroy the vasculature of solid tumors, and, if they could be linked to this new targeting molecule, we could have a two-pronged attack for prostate cancer,” he said. “We could not only kill the prostate cancer cells directly, we could also destroy the vasculature that feeds the tumors.”

There also is potential for the targeting molecule to be used to attack the vasculature of solid tumors of other types of cancers, Low said.

Two papers detailing the work of the Purdue team were published in the June 1 issue of Molecular Pharmaceutics. Endocyte Inc. funded the work.

The team’s animal study data shows an ability to eliminate human prostate cancer cells in mice with no evidence of collateral toxicity in normal tissue.

Sumith Kularatne, a graduate student in Purdue’s chemistry department and first author of both papers, compared the targeting molecule to a homing device.

“The molecule acts like a homing device for prostate cancer,” he said. “PSMA, which is found only on prostate cancer cells and tumor blood vessels, acts as the homing signal that the molecule targets. The molecule and its cargo go only to cancerous tissue, leaving healthy tissue unharmed.”

Philip Low, the Ralph C. Corley Distinguished Professor of Biochemistry at Purdue, and graduate student Sumith Kularatne, in foreground, examine the uptake of an imaging agent in prostate cancer cells. Low led a research team that designed a molecule to find and penetrate prostate cancer cells and has created imaging agents and therapeutic drugs that can link to the molecule and be carried with it as cargo. (Purdue University photo/Andrew Hancock)

Once the molecule reaches the PSMA protein, it binds to it. The molecule is designed with a specific shape that fits with the protein like a key to a lock, Kularatne said. The molecule and its cargo are then carried inside the cell with the protein as it goes through its normal cycle.

In 1995 Low developed a similar method to infiltrate cancer cells by attaching treatments to the vitamin folate, which many cancers rapidly consume. This method provided a “Trojan Horse” entry of large treatment molecules that otherwise would not be able to enter cancer cells.

Low was inspired to find a similar way to target prostate cancer, which does not have the same appetite for folate, he said.

A clinical trial of the radioimaging application is expected to begin at the Indiana University Medical Center in the fall through a collaboration between the Purdue Cancer Center and the Indiana University Cancer Center with additional support from Endocyte Inc.

A radioimaging agent linked to the targeting molecule will be injected into prostate cancer patients and pictures will be taken using a special camera that detects radioactivity. The pictures show where the cancer is present to help doctors determine if it has metastasized, or spread, to any other areas of the body. It also will help doctors decide on the best course of treatment, Low said.

There is currently only one radioimaging agent for prostate cancer approved by the Food and Drug Administration.

“The current imaging capabilities available for prostate cancer are very poor,” Low said. “The existing imaging agent is limited because of its large size, which is difficult to get into a solid tumor. Also it seeks out a target located inside the cancer cell and is only able to mark injured cells that are falling apart as opposed to actively growing cancer cells.”

The targeting molecule and radioimaging agent combination designed by Low’s group is more than 150 times smaller than the existing agent and has much easier penetration through a solid tumor to reach all of the cells inside, he said. It also has the advantage of targeting an area of PSMA exposed on the outside of cancer cells.

Already in clinical trials is an optical imaging application that involves attaching a fluorescent dye to the targeting molecule and mixing it with a patient’s blood sample. Circulating prostate cancer cells in the sample fluoresce and are easily measured to help in diagnosing patients with prostate cancer. Researchers also are investigating whether this could be used to evaluate a patient’s response to therapy, Low said.

Low’s research group modeled the targeting molecule after a naturally occurring molecule that strongly binds to PSMA, called DUPA. Several alterations were necessary to create a molecule that fit the needs of a homing device and delivery vehicle, Kularatne said. The team created an area on the molecule that would link to various imaging or therapeutic agents to bring them along as cargo and created a spacer that would stretch the molecule so that its cargo would not keep it from properly fitting into the binding site. The spacer also was designed to improve binding of the targeting molecule to PSMA.

In addition to Low and Kularatne, co-authors of the papers include Endocyte researchers Kevin Wang and Hari-Krishna R. Santhapuram, graduate student in medicinal chemistry Zhigang Zhou, graduate student in chemistry Jun Yang, and professor of medicinal chemistry and molecular pharmacology Carol B. Post.

Low is the chief science officer for Endocyte, a Purdue Research Park-based company that develops receptor-targeted therapeutics for the treatment of cancer and autoimmune diseases. Endocyte holds the license to many of Low’s drug-targeting technologies.

Papers:

Prostate-Specific Membrane Antigen Targeted Imaging and Therapy of Prostate Cancer Using a PSMA Inhibitor as a Homing Ligand
Sumith A. Kularatne, Kevin Wang, Hari-Krishna R. Santhapuram, and Philip S. Low

Design, Synthesis, and Preclinical Evaluation of Prostate-Specific Membrane Antigen Targeted ^99mTc-Radioimaging Agents
Sumith A. Kularatne, Zhigang Zhou, Jun Yang, Carol B. Post, and Philip S. Low

By Elizabeth K. Gardner – Purdue University

Color melon flesh is full of nutrients. Plant breeders may develop even better varieties now that the melon genome with hundreds of DNA markers has been mapped . (Texas AgriLife Photo by Kathleen Phillips)

Plant breeders now have a better chance to pinpoint such traits for new varieties, because the melon genome with hundreds of DNA markers has been mapped by scientists with Texas AgriLife Research. That means tastier and healthier melons are likely for future summer picnics.

“This will help us anchor down some of the desirable genes to develop better melon varieties,” said Dr. Kevin Crosby, who completed the study with Drs. Soon O. Park and Hye Hwang. “We can identify specific genes for higher sugar content, disease resistance and even drought tolerance.”

The results are reported in the Journal of the American Society of Horticultural Sciences.

Melons are fleshy, edible cucurbits grown worldwide in a multitude of varieties. Not only are they economically important, the scientists noted, but they are a favorite among consumers internationally.

The average person in the U.S. eats about 25 pounds of melon every year, according to the Agricultural Marketing Resource Center at Iowa State University.

Scientists from France and Spain already had completed partial maps of segments of the melon DNA sequence. The Texas researchers connected those segments with new findings in their study to complete the entire melon genome map.

For the study, the Deltex ananas melon was crossed with a wild melon called TGR 1551. More than 100 of the offspring from that cross were grown in the AgriLife Research greenhouses at Weslaco, Crosby noted.

DNA was extracted from leaf tissue collected 21 days after planting. Results from these tests were integrated into partial maps created by other researchers.

Previous knowledge of melon DNA was like two sets of directions – one from Miami to Houston and the other from El Paso to Los Angeles. That would make one wonder how to get from Houston to El Paso. The study by Crosby’s group, in essence, devised the path from Miami to LA and all points between.

In addition to the complete map, the researchers located genetic markers linked to fruit sugars, ascorbic acid (vitamin C) and male sterility, which is useful for developing hybrid varieties.

The trio said the genetic map will be helpful for future studies in identifying fruit sweetness, quality, size, shape and resistance to disease.

By Kathleen Phillips – Texas A&M AgriLife

Noctilucent clouds observed from Donnelley Dome near Fairbanks, Alaska, resulting from a post-space shuttle plume in August 2007. M.J. Taylor and C.D. Burton / Utah State University

The research, accepted for publication (June 24) by the journal Geophysical Research Letters, published by the American Geophysical Union, connects the two events by what followed each about a day later: brilliant, night-visible clouds, or noctilucent clouds, that are made up of ice particles and only form at very high altitudes and in extremely cold temperatures.

“It’s almost like putting together a 100-year-old murder mystery,” said Michael Kelley, the James A. Friend Family Distinguished Professor of Engineering at Cornell, who led the research team. “The evidence is pretty strong that the Earth was hit by a comet in 1908.” Previous speculation had ranged from comets to meteors to black holes.

The researchers contend that the massive amount of water vapor spewed into the atmosphere by the comet’s icy nucleus was caught up in swirling eddies with tremendous energy by a process called two-dimensional turbulence, which explains why the noctilucent clouds formed a day later many thousands of miles away.

Noctilucent clouds are the Earth’s highest clouds, forming naturally in the mesosphere at about 55 miles over the polar regions during the summer months when the mesosphere is around minus 180 degrees Fahrenheit (minus 117 degrees Celsius).

The space shuttle exhaust plume, the researchers say, resembled the water vapor from the comet. A single space shuttle flight injects 300 metric tons of water vapor into the Earth’s thermosphere, and the water particles have been found to travel to the Arctic and Antarctic regions, where they form the clouds after settling into the mesosphere. The thermosphere is the layer of the atmosphere above the mesosphere.

Kelley and collaborators saw the noctilucent cloud phenomenon days after the space shuttle Endeavour (STS-118) launched on Aug. 8, 2007. Similar cloud formations had been observed following launches in 1997 and 2003.

Following the 1908 explosion, known as the Tunguska Event, the night skies shone brightly for several days across Europe, particularly Great Britain — more than 3,000 miles away. Kelley said he became intrigued by the historical eyewitness accounts of the aftermath, and concluded that the bright skies must have been the result of noctilucent clouds. The comet would have started to break up at about the same altitude as the release of the exhaust plume from the space shuttle following launch. In both cases, water vapor was injected into the atmosphere.

The scientists have attempted to answer how this water vapor traveled so far without scattering and diffusing, as conventional physics would predict.

“There is a mean transport of this material for tens of thousands of kilometers in a very short time, and there is no model that predicts that,” Kelley said. “It’s totally new and unexpected physics.”

This “new” physics, the researchers contend, is tied up in counter-rotating eddies with extreme energy. Once the water vapor got caught up in these eddies, the water traveled very quickly — close to 300 feet per second.

Scientists have long tried to study the wind structure in these upper regions of the atmosphere, which is difficult to do by such traditional means as sounding rockets, balloon launches and satellites, explained Charles Seyler, Cornell professor of electrical engineering and paper co-author.

“Our observations show that current understanding of the mesosphere-lower thermosphere region is quite poor,” Seyler said.

The paper is also co-authored by Clemson University physicist Miguel Larsen, Ph.D. ‘79, a former student of Kelley. The work performed at Cornell was funded by the Atmospheric Science Section of the National Science Foundation.

On July 1, Kelley will give a lecture, “Two-dimensional Turbulence, Space Shuttle Plume Transport in the Thermosphere, and a Possible Relation to the Great Siberian Impact Event,” at a plenary session of the annual meeting of Coupling, Energetics and Dynamics of Atmospheric Regions in Santa Fe, N.M.

The paper is available at: http://www.agu.org/journals/gl/papersinpress.shtml.

By Anne Ju – Cornell University - Cornell Chronicle Online

The huge Aletsch Glacier, as seen from Eggishorn, with a view up to the Jungfraujoch and the Mid-Aletsch Glacier (Image: F. Funk-Salamí)

The earth’s glaciers are one of the “uncertain” factors in climate forecasts. It is difficult to precisely calculate the ice volume, making its effects – such as a rising sea level – unpredictable. However, melting glaciers do not only contribute to a rising sea level. They cause a reduction in freshwater supplies and change the landscape and ecosystems forever. Switzerland is also affected: Swiss glaciers have reduced dramatically in size over the past twenty years, particularly during the past ten years, which has been the warmest decade of the past 150 years.

A new method of calculation can now more accurately determine just how much ice the Swiss glaciers have lost. The process was developed by Martin Funk, professor and head of the Department for Glaciology at the Laboratory for Hydraulics, Hydrology and Glaciology (Versuchsanstalt für Wasserbau, Hydrologie und Glaziologie – VAW) and his team at ETH Zurich, in order to estimate the total ice volume of the Swiss glaciers. Knowing the exact volume is important to be able to put the observed change in the right context. Previously, however, the volume of only very few glaciers was known reliably. For these glaciers, it was possible to determine the ice thickness and the approximate volume through drillings or echo-sounding examinations. The researchers were able to calibrate their new process on these glaciers.

Estimation based on mass conservation

Up until now, glacier volumes were calculated based on empirical relationships between glacier area and volume, according to Daniel Farinotti, postgraduate student studying under Funk. The scientists developed their method of calculation based on the law of mass conservation for glaciers. This states that the surface mass budget must be balanced by the flow of ice and the changes in the thickness of the glacier’s ice. The ice volume is ultimately calculated using the glacier’s topography and the estimated area spread of the surface mass budget. The ice flow is first determined using the basic laws of glacial mechanics, including the geometry of the glacier surface, which in turn is used to calculate the thickness of the ice. Unlike previous estimation methods, the newly developed method does not just give indications on the ice volume of the glacier, but also the spread of the ice’s thickness. This also allows the topography of the glacial bed to be determined.

Large glaciers are decisive

The scientists have now applied their method to 59 Swiss glaciers, which were larger than three square kilometres in 1999, and three smaller glaciers for which thickness measurements were already available. For the approximately 1400 remaining glaciers, the scientists deduced the ice volume using an empirical volume-area approach. Their calculations showed that the ice volume amounted to 74 cubic kilometres in 1999, with a possible deviance of 9 cubic kilometres. All of the Swiss glacial ice masses would therefore easily fit into Lake Geneva – which has a water volume of 89 cubic kilometres.

The researchers further calculated an average ice thickness of seventy metres. They were also able to show that 88 percent of the ice mass is contained in the 59 largest glaciers, of which 24 percent are in the Aletsch region alone. “The area of the Great Aletsch Glacier is roughly the same as the total area of all Swiss glaciers less than one square kilometre in size. Their total ice volume, however, is twenty times smaller than the Great Aletsch Glacier. Scientists maintain that in order to provide a more accurate estimation of the regional ice volume, it is vital to carry out further thickness measurements on the largest glaciers in Switzerland, as these are obviously particularly consequential when calculating the volume.

Scientists calculated the development of the size of the glaciers over the past ten years by using an average mass timeline. “The timeline took an average from around 30 glaciers where we have data on changes in volume”, states Farinotti. This showed that the heat wave in 2003 was responsible for 2.6 of the total of 9 cubic kilometres of ice lost.

Glaciers have been shrinking since 1850

The development of the Swiss glaciers has been observed and documented since 1880. The current calculations are based on data recorded in 1999 at the time when the survey of Swiss glaciers was last updated with satellite images combined with a geographic information system and a digital contour model. The last time this was done was in 1973. Based on these data, calculations on the volume of Swiss glacial ice were between 74 and 67 cubic kilometres. “Although these figures are similar to ours, they are based on much less accurate data. The fact that a considerable amount of ice has melted since then suggests that the ice volume for 1973 was somewhat underestimated”, states Farinotti.

Since the last minor ice age, which ended around 1850, the area covered by glaciers has been shrinking. In 1999, around 1063 square kilometres remained.

References:

Farinotti D, Huss M, Bauder A, Funk M & Truffer M.: A method to estimate ice volume and ice thickness distribution of alpine glaciers. Journal of Glaciology (2009), 55, 422-430.

Farinotti D, Huss M, Bauder A & Funk M: An estimate of the glacier ice volume in the Swiss Alps. Global and Planetary Change (2009).

By Simone Ulmer – ETH Zürich