This month in Science Roundup:
Celebrating Polar Science
Special Online Collection
Earth’s polar regions are priceless repositories of information about past climates, as well as harbingers of our planet’s future. This year, we enter the fourth International Polar Year (IPY) -- a multinational research initiative aimed at exploring the Arctic and Antarctica and the impact of polar change on global climate. In a special section of the 16 Mar 2007 issue, Science helped ring in the IPY with a look at some of the more vibrant research under way at the ends of the Earth. News and Review articles explored the influence of polar processes on sea-level rise and our planet’s ecological and biogeochemical cycles, the origins and impacts of Artic air pollution, some of the logistical challenges of polar research, and the contributions of indigenous Artic people to studies of climate change. A related podcast segment highlighted the complex dynamics of polar ice sheets in Antarctica and Greenland. And a collection of articles on ScienceCareers.org focused on scientists actively pursuing polar research.
Consequences of Shark Loss
The loss of large predators from ecosystems, often caused by human activities, can have effects that cascade through the rest of the food chain. In the oceans, fishing has disproportionately reduced the abundance of top predators, eliciting concern about their conservation and the indirect effects of their removal. In a Report in the 30 Mar 2007 Science, Myers et al. documented the magnitude of the decline of large sharks in the northwest Atlantic -- primarily due to overexploitation -- and the consequences of those declines on the food web. The team analyzed a compilation of independent research surveys and fisheries records and found that sharp declines in 11 species of large sharks over the past 35 years have resulted in dramatic increases in 12 out of 14 elasmobranch prey species, which include rays, skates, and small sharks. The abundance of one of these prey species, the cownose ray, has increased 20-fold since 1970. Enhanced predation by that ray species on its bay scallop prey has caused the collapse of a century-old scallop fishery in North Carolina and may hurt other bivalve fisheries. This cascade could potentially extend to seagrass habitat, exacerbating stresses on already highly degraded coastal ecosystems. Senior author C. Peterson discussed the study and its implications for resource management practices in a segment of the 30 Mar podcast.
Sediment and Ice Sheet Stability
It has long been argued that a rise in sea level or a change in ice sheet thickness can result in ice sheet instability that may in turn lead to an increase in the overall rate of sea-level rise. But the relative importance of the different causes of ice sheet change remains uncertain. Two Reports in the 30 Mar 2007 Science (published online 2 Mar) examined how sedimentation at the grounding line of ice streams-- the most distal point at which an ice sheet rests on the ground and beyond which it floats on water -- might affect ice sheet stability. Anandakrishnan et al. used radar surveys to show that rapid sedimentation has been occurring at the grounding line of the Whillans Ice stream, a major drainage outlet of the West Antarctic Ice Sheet. The observed sediment "wedge" is likely to have formed during a pause in the overall retreat of the ice sheet. Alley et al. used the radar data to model how the sedimentation process affects ice sheet stability. Results from three models indicate that the sediment wedge causes the ice sheet to thicken at the grounding line, thereby stabilizing it to small changes in sea-level rise, up to a few meters. This implies that the rapid increases in ice loss that have recently been documented at the margins of the Antarctic and Greenland ice sheets are due to dynamic responses to climate warming as opposed to sea-level change. However, large sea-level increases, in the range of tens of meters, could overwhelm the wedge’s stabilizing effects. An accompanying Perspective by J. B. Anderson highlighted the studies.
Understanding HIV Evolution
One of the reasons that human immunodeficiency virus (HIV) is so insidious stems from its ability to rapidly mutate and thus evade recognition by host immune cells (T cells) and antibodies. In 2002, researchers showed that polymorphisms in genes that encode host immune proteins responsible for "presenting" viral peptides to T cells have a strong influence on how the virus evolves. That is to say, variations in an HIV-infected patient’s immune response genes often correlated with specific "immune escape" mutations in the virus’s genomic sequence. But a Report in the 16 Mar 2007 Science now reveals that HIV sequence variability may not be as predictable as previously thought. By applying statistical approaches that account for the phylogenetic relationships among HIV sequences, Bhattacharya et al. showed that many of the apparent associations between viral mutations and host immune gene variations are not the result of immune escape, but rather reflect subtypes of viruses that are historically and geographically related. Senior author B. Korber talked about the work in the 16 Mar podcast and a Perspective by P. Klenerman and A. McMichael discussed the implications for the study of other viruses such as hepatitis C, and for strategies for vaccine development
Insight into Hurricane Intensity
Although forecasts of hurricane tracks and landfall locations have improved in recent decades, forecasting of hurricane intensity -- how strong the wind will be at landfall -- has not. This is because changes of storm intensity are connected with small-scale, rapidly evolving cloud and precipitation patterns that occur internal to the storm, typically while it is still over the ocean, and are thus difficult to observe. In a Research Article in the 2 Mar 2007 Science, Houze et al. offered important insights into a key component of hurricane intensity change. Using high-resolution airborne radar observations of wind speed and direction, temperature, humidity, and pressure, the researchers documented --and developed a conceptual model for -- the eyewall-replacement cycle in Hurricane Rita, which pummeled the U.S. Gulf Coast in 2005. The eyewall is a circular region of heavily precipitating cloud that encircles the relatively calm "eye" of the storm and is where the strongest winds occur. During eyewall replacements, a new (outer) ring of clouds envelops the original (inner) eyewall, creating a new larger-diameter eyewall and reducing the intensity of the storm. This new eyewall can subsequently contract thereby reintensifying the storm, and the whole process may repeat itself over the storm’s lifetime. Understanding the replacement mechanisms is therefore vital to predicting changes in hurricane intensity. An accompanying Perspective by H. E. Willoughby highlighted the study.
An Ancient Solar Observatory
Evidence of systematic astronomical observations, and the nature and context of those observations, can shed light on the ways in which ancient people marked time or otherwise attempted to order their world. Archaeological sites as well as written and spoken records document that the Incas were making careful solar observations about 500 years ago. Now, a Report by Ghezzi and Ruggles in the 2 Mar 2007 Science describes an astronomical observatory in the coastal desert of Peru that predates Incan civilization by almost two millennia. The group of stone structures, known as the Thirteen Towers, lies within Chankillo -- a 2300-year-old massive ceremonial complex whose best-known feature is a hilltop temple-like structure fortified with concentric walls. The small rectangular towers run north to south along a low ridge to the east of this main structure. The team discovered two likely observation points constructed about 200 meters away from and on opposite sides of the line of towers. Notably, when viewed from these locations, the spread of the towers along the horizon marks the annual rising and setting positions of the Sun such that on the winter and summer solstices, the sun rises and sets over the towers on the opposite end of the line. The Chankillo towers thus provide evidence of early solar observations and suggest that Sun worship may have been an important facet of this early Andean culture. Science correspondent C. C. Mann highlighted the work in a related News story and podcast interview.
Sleep, Smell, and Memory
What are our brains up to while we sleep? Experiments with rodents and people showing a correlation between neural activity in the hippocampus during sleep and subsequent memory performance support the notion that the sleeping brain replays experiences from the day to strengthen newly acquired memories. In a study reported in the 9 Mar 2007 Science, Rasch et al. investigated whether artificially boosting memory-related neural activity -- in this case through odor cues -- can actually improve memory performance. The team had volunteers play a video version of the card game Memory, in which they had to learn and remember the locations of pairs of cards bearing the same image. During the learning phase of the game, subjects were exposed to the scent of roses. That same night, while the volunteers were in deep, so-called slow-wave sleep, the rose scent was re-introduced to some players to facilitate "reactivation" of memories from the learning session. Although they didn’t remember smelling roses in their sleep, the subjects who got the fragrant prompt remembered the matched pairs better the next day, getting 97% correct compared to 86% for subjects who weren’t exposed to the scent while sleeping. Functional magnetic resonance (fMRI) imaging confirmed significant hippocampal activation in response to odor re-exposure. In contrast, other subjects exposed to the scent during lighter REM sleep or while awake, did not show improved memory performance. A related News Focus by G. Miller discussed the new work, as well as other hypotheses about the functions of sleep.
Optical microscopes are invaluable tools for the study of materials and biological structures. However, their spatial resolution is limited by the diffraction of light waves -- a value on the order of 200 nanometers. In the 23 Mar 2007 Science, two research teams described the development of metamaterial "superlenses" that can magnify objects smaller than the diffraction limit of light. Liu et al. used curved nanoscale multilayers of silver and aluminum oxide to create a half-cylindrical shaped superlens with a negative refractive index, meaning that light passing through it bends the opposite way to what is normally expected. The lens projects the image of the object placed in it onto a far-field surface, where it can be viewed with a conventional microscope. The team showed that the lens can clearly resolve a pair of 35-nm-wide lines spaced just 150 nm apart. The superlens technology developed by Smolyaninov et al. achieved a resolution on the order of 70 nanometers and consists of concentric circles of a polymer with alternating positive and negative refraction indices deposited on a gold film. To see an object inside the innermost circle, the sample is illuminated with light. This excites waves of electrons called plasmons in the gold film, which radiate into the superlens structure. The magnified image of the object can then be seen at the outermost circle with a conventional microscope. Both studies demonstrate the potential utility for superlenses in biomolecular imaging and nanolithography.
The transition from aquatic to terrestrial locomotion was a key development in vertebrate evolution. Because salamanders swim in the same manner as primitive fish (such as lampreys), but walk with a waddling gait similar to alligators and their ancient relatives, they are considered key animals for understanding the evolutionary switch from swimming to walking. In a Report in the 9 Mar 2007 Science, Ijspeert et al. presented a theoretical model to show how a primitive neural circuit for swimming can be extended to explain salamander locomotion. The model explains the transition from one mode of locomotion to the other, the switch between traveling and standing waves of body undulations, the coordination between body and limbs during walking, and the control of speed and direction. To validate the model, the team built an 85-cm-long robot designed to mimic the kinematic structure of salamanders. With four rotating legs and six moveable body joints, and powered by 10 motors instead of muscles, the robot is capable of producing (and switching between) swimming, serpentine crawling, and walking gaits. As noted in an accompanying News story by E. Pennisi, the study demonstrates how robotics can be used to test biological models and is likely to stimulate future collaborations.
Earliest Remnants of Plate Tectonics
Earth’s crust is continually being formed and recycled at mid-ocean ridges, where plates move apart and hot magma wells up from below, and above subduction zones, where one plate slides underneath another and can cause plate edges to grow by accretion. But scientists have long debated when these plate tectonic processes actually began: early in Earth’s history or much later in its 4.5 billion-year existence? In a Report in the 23 Mar 2007 Science, Furnes et al. described telltale evidence from an oft-studied cluster of ancient rocks in southwest Greenland. Poring over an area known as the Isua supracrustal belt, the team discovered a banded rock structure called a sheeted dike complex. These structures are the hallmark of ophiolites -- pieces of ocean crust that have been uplifted and stranded on land. Built like a stack of cards, sheeted dikes are composed entirely of the thin sheets of once-molten rock injected into the crests of mid-ocean ridges as the newly formed plates spread away from the ridge. The Isua rocks date to 3.8 billion years ago, thus making them the oldest known example of oceanic crust formed by sea-floor spreading. An accompanying News story by R. A. Kerr highlighted the Report.
Defending Against Phage
Even simple organisms like bacteria are under a constant threat of invasion by pathogens. In a Report in the 23 Mar 2007 Science, Barrangou et al. identified a new defense mechanism by which bacteria do battle with viruses called bacteriophage -- and that involves the acquisition of DNA sequences from the very phage that threaten them. Clustered regularly interspaced short palindromic sequences, or CRISPR sequences, are widely distributed throughout bacterial genomes, and spacer sequences within these regions have been found to resemble sequences in phage and as well as plasmids. Working with the bacterium *Streptococcus thermophilus*, commonly used to make yogurt and cheese, the researchers found that infection of the bacteria with phage led to integration of viral sequences as new spacers into CRISPR regions and that this process conferred resistance to further infection by the phage strains that contributed to the spacer sequences. This system of bacterial immunity likely works in a manner akin to RNA interference, whereby the spacers make short RNA sequences that can bind to complementary sequences in viral transcripts and thus prevent viral gene expression. The team also found that addition and deletion of the spacers altered bacterial sensitivity to phage and that at least one CRISPR-associated gene is necessary for the resistance mechanism. A related News story by J. Marx noted that the work could help the food and biotechnology industries, which rely on bacterial cultures to make dairy products and proteins for human medicine.
Copy Number and Autism
Autism is one of a group of developmental disorders called autism spectrum disorders, characterized by language impairments, social deficits, and repetitive behaviors. To date, the majority of studies aimed at mapping genes involved in the disease have focused on the 10% of cases that seem to be inherited. Now a Report published online ScienceExpress on 15 Mar offers genetic clues to the other 90% of autism cases -- the so-called sporadic cases, in which only one person in a family is afflicted. Sebat et al. analyzed the DNA from 264 families, including 118 "simplex" families containing a single child with autism, 47 "multiplex" families with multiple affected siblings, and 99 control families with no diagnoses of autism. The researchers found that 10% of patients with sporadic autism showed spontaneous copy number variations (CNVs) -- variations in the number of copies of certain genome regions that were not present in their parents. In contrast, copy number variants turned up in just 2% of patients with apparent inherited autism and only 1% of controls. Interestingly, none of the genomic variants were observed more than twice and most were seen only once. These results suggest that many different genetic defects can contribute to autism. A ScienceNOW story by E. Stokstad highlighted the study.
Electronic Structure and Superconductivity
High-temperature superconductors -- layered materials containing planes of copper and oxygen atoms -- can conduct electricity without any resistance and temperatures as high as 138 K. Some two decades after the discovery of these materials, physicists have yet to pin down how they actually work. In a Research Article in the 9 Mar 2007 Science (published online 8 Feb), Kohsaka et al. offered new details about the electronic structure of two families of cuprates (copper oxides) that could help researchers understand the mechanism by which currents flow without resistance in superconductors. Using scanning tunneling spectroscopy -- a technique that measures the quantum mechanical probability of adding or removing an electron at a specific location at a given energy -- the team was able to probe the spatial distribution of the electron motions in these materials. The patterns they revealed can be viewed as the quantum analog of stop-and-go traffic, with the electrons self-organizing into one-dimensional "highways" (which appear as stripes in the spectroscopy images) where they move relatively freely, separated by areas where electron traffic is jammed. The authors argue that the electronic superstructure, which forms narrow stripes with a spatial period of four unit cells, is an intrinsic property of the cuprates and is the precursor parent phase to the onset of superconductivity. An accompanying Perspective by J. Zaanen highlighted the study.
In Science’s STKE
Unconventional Roles of NADPH Oxidase
White blood cells called neutrophils form an early line of defense against bacterial infection. Armed with enzymes and other antimicrobial molecules, these cells engulf and digest pathogens by phagocytosis. The NADPH oxidase NOX2 -- an enzyme complex that generates noxious reactive oxygen species (ROS) -- plays a central role in mediating bacterial killing by neutrophils. However, this complex plays other less-well known, but important roles in neutrophil physiology. In a Perspective in the 27 Mar 2007 issue, Steinberg and Grinstein discussed these underappreciated functions, which include cell signaling, ion homeostasis, and cell death. The authors highlighted recent work implicating ROS produced by NADPH oxidase in the formation of neutrophil extracellular traps or NETs. These structures consist of fibers of chromatin decorated with granular proteins and are able to simultaneously trap and kill various extracellular pathogens by providing a highly concentrated supply of antimicrobial compounds.
Also in STKE this month:
--de Candia et al. described virtual-cell software that allows the execution and spatiotemporal analysis of in silico chemotaxis experiments (20 Mar 2007)
--Wang discussed the dynamic nature of focal adhesions, which provide physical linkages between the interior of an adhesive cell and the extracellular matrix (13 Mar 2007)
--Stelling reviewed "An Introduction to Systems Biology," a book that looks at the design principles of biological control circuits (6 Mar 2007)