Science Roundup -- The monthly review of Science highlights for AAAS members

This month in Science Roundup:


Catching Cosmic Clues
Introduction to special issue >>

In recent years, researchers have begun explorations at the boundaries between particle physics, astrophysics, and astronomy, building vast detectors on Earth and in space in hopes of capturing cosmic particles that will shed light on some of the universe’s deepest mysteries. A special section of the 5 Jan 2007 Science explored challenges and recent developments in this rapidly developing field of particle astrophysics. Six Perspectives and a News story looked at the physics of the Big Bang fireball, progress in the search for the mysterious dark energy and dark matter that make up much of the universe, as well as efforts to capture nearly massless particles called neutrinos from sources more distant than the sun, and to detect sources of high-energy cosmic and gamma rays. Whether particle astrophysics continues to flourish may depend on whether experiments currently in the works deliver any of these hoped-for discoveries. In connection with the special section, ScienceCareers.org profiled two young particle astrophysicists with a focus on their career paths.


Progress in Fuel Cells

One of the hurdles facing the realization of practical hydrogen-powered vehicles lies in the development of efficient fuel cells to convert hydrogen fuel into electrical energy. Two studies published in Science this month report progress in this area. Current automotive fuel cells employ the catalytic power of platinum nanoparticles. At the negative electrode, or anode, the platinum helps split hydrogen molecules into two protons and two electrons, the latter of which pass through a wire and power the vehicle. The electrons ultimately end up at the positively charged cathode and pass to oxygen molecules, causing them (again with the help of platinum) to split into negatively charged oxygen atoms that can pair up with protons from the anode to create water, a benign byproduct. Unfortunately, unwanted side reactions also occur at the cathode and the resulting oxides often bind to and block the platinum atoms or even strip them from the cathode surface, thereby reducing the cathode’s catalytic capacity. Now, a Report by Zhang et al. in the 12 Jan 2007 Science shows that adding tiny gold nanoclusters on top of conventional carbon-platinum cathodes inhibits their degradation during repeated electrochemical cycling -- like that required for braking and acceleration -- while leaving the overall oxygen-splitting activity of the platinum intact. And in another study in the 26 Jan issue (published online Science Express on 11 Jan), Stamenkovich et al. reports that alloying platinum crystals with nickel can increase the catalytic activity of a platinum surface 90-fold over conventional cathode catalysts used today. Science reporter R. F. Service discussed the promising findings in a related News story and podcast segment.


Connecting Nanoparticles

Nanoparticles can be used as building blocks to make a variety of materials including supercrystals and ionic liquids. But they lack the ability to bond along specific directions -- as atoms and molecules do -- which means that they cannot be joined together to maker larger structures like filaments or films. This is because nanoparticles are often coated with a capping layer of rodlike molecules to prevent further growth or clustering. This outer surface gives the particle a uniform chemistry so it cannot bond or be ordered in controlled directions. In a study reported in the 19 Jan 2007 Science DeVries et al. overcame this problem by placing chemical handles at opposite ends of the nanoparticles. The researchers effectively broke the symmetry of the spherical particles by bonding two different types of ligands, in this case thiol molecules, onto the poles of the spheres such that the ligands on one nanoparticle could freely bond with the ligands on other particles. Transmission electron microscopy confirmed the ability of these modified spheres to form linear chains ranging from 3 to 20 nanoparticles in length. Some chains even joined to produce a continuous free-standing film as large as a square centimeter across and 60 micrometers thick. The work could ultimately lead to a new class of nanopolymer materials with novel and exploitable properties.


Very-Low-Frequency Earthquakes

Improvements in the technology and density of seismic networks have enabled the detection of new rupture phenomena including nonvolcanic tremors, long-period volcanic events, and slow earthquakes. In a Report in the 26 Jan 2007 Science (published online 30 Nov 2006 ), Ito et al. described yet another type of seismic reverberation termed very-low-frequency earthquakes. Identified along the Nankai subduction zone off southwest Japan , these events have magnitudes of 3.1 to 3.5 and long periods of tens of seconds. The seismicity of the earthquakes accompanies and migrates with the activity of deep low-frequency tremors and slow slip events. The coincidence of these three phenomena should improve the detection and characterization of slow earthquakes, which are thought to increase the stress on the rupture zones of megathrust earthquakes. An accompanying Perspective by H. Dragert highlighted the study.


Understanding the Asthenosphere

Plate tectonic theory is based on the concept that the rigid plates of the lithosphere float or move over the weaker and ductile asthenosphere -- a layer that extends from about 60 to 220 kilometers below the oceans and 150 kilometers below continents. The softness of the asthenosphere -- as well as the observed slowdown of seismic waves as they pass through it -- could be explained by pockets of hydrous melt, but the mechanism that may cause melting has been unclear. According to a report in the 19 Jan 2007 Science , the water storage capacity of the mantle is key. Mierdel et al. showed that the asthenosphere coincides with a zone that marks the minimum solubility of water in mantle minerals (primarily olivine and orthoproxene). The minimum is due to a sharp decrease of water solubility in aluminous orthoproxene with temperature and pressure, whereas the water solubility of the more abundant mineral olivine continuously increases . The depth of the asthenosphere coincides with the point at which water comes out of solution and forms pockets of hydrous silica melt. As noted in an accompanying Perspective by N. Bolfan-Casanova, the new findings help explain "how mantle properties such as viscosity, melting, and differentiation are tied to its water storage capacity."


Modern Human Migrations

Researchers disagree about whether the ancestors of modern humans spread out of Africa and into Eurasia as early as 100,000 years ago or as recently as 50,000 years ago. Although recent genetic studies have supported a late exodus, the dearth of human fossils from sub-Saharan Africa has made it particularly difficult to discern when modern humans left there and where they went. Now, two Reports in the 12 Jan 2007 Science lend fresh support to the recent-dispersal hypothesis. Grine et al. dated a skull first discovered in 1952 from Hofmeyr, South Africa, to about 36,000 years ago based on luminescence data and uranium-series dating methods. The skull looks more like fossils of modern humans who lived in Europe and Asia about 36,000 years ago than fossils of Africans or Europeans from the past 10,000 years, which suggests that the specimen is closely related to the modern humans who first emigrated from sub-Saharan Africa to populate Europe and Asia . Dr. Grine discussed the exciting find in a related podcast segment.

In a second study, Anikovich et al. unearthed stone, ivory, and bone artifacts -- probably representing modern humans -- from archaeological sites on the Don River in Russia , about 400 kilometers south of Moscow . Radiocarbon and luminescence dating and paleomagnetic data date the artifacts to about 45,000 to 42,000 years ago. These results imply that modern humans appeared on the central plain in Eastern Europe as early as anywhere else in northern Eurasia . As noted in an accompanying Perspective by T. Goebel, "other events in the missing years of modern human evolution must await new fossil and archaeological discoveries as well as continued DNA sampling of the world’s living populations."


Wandering Minds

It has happened to all of us: one minute you are listing to a seminar, and the next you are thinking about what’s left in your refrigerator and that strange women in front of you at the coffee shop this morning. Despite the preponderance of daydreaming during everyday life, little is known about its neural underpinnings. In a Report in the 19 Jan 2007 Science Mason et al. used functional magnetic resonance imaging (fMRI) to investigate how the brain spontaneously produces the images, voices, thoughts, and feelings that constitute so-called stimulus-independent thought. Reasoning that minds wander more when the job at hand is not very demanding, t he team followed the brain activity of subjects performing practiced, monotonous tasks as well as novel, more challenging ones. As expected the subjects reported a greater tendency of their minds to wander during the monotonous tasks. The imaging results further revealed that mind-wandering is associated with activity in the default network -- a network of cortical regions that are active when the brain is "at rest." The new work suggests that activity in the default network is necessary to generate spontaneous thoughts, but leaves open the question of why minds wander at all. A related Science NOW story by G. Miller highlighted the study.


Climate Change and Fish Physiology

Climate change is projected to affect individual organisms, the size and structure of their populations, as well as the structure and functioning of whole ecosystems. Nevertheless, distinguishing direct causal relationships between environmental temperature and species distribution patterns remains difficult. Now, a Report by Pörtner and Knust ( http://www.sciencemag.org/cgi/content/short/315/5808/95 ) in the 5 Jan 2007 Science shows how physiological studies can aid our understanding of how temperature determines the geographical range of animals. The team compared field observations and laboratory data on a North Sea and Baltic Sea fish species called the eelpout, and contend that the observed decrease in their size abundance can be explained by the fish’s physiological responses to hot summers and coincident warmer water temperatures. Eelpout need more oxygen at higher temperatures, yet the concentration of dissolved oxygen in sea water declines with increased temperature. Consequently, there is a critical temperature beyond which the animals’ cardiorespiratory system can no longer deliver sufficient oxygen for key functions including muscular activity, growth and reproduction. The researchers argue that warmed water in the North Sea is pushing the eelpout to this limit and could thereby influence the long-term fate of the population. An accompanying Perspective by T. Wang and J. Overgaard highlighted the study.


Not-So-Silent SNP

Each amino acid in a protein is encoded by a triplet code of DNA bases, with most amino acids being represented by more than one codon (referred to as synonymous codons). Synonymous codon substitutions result from small genetic changes called single-nucleotide polymorphisms (SNPs). Because these SNPs do not change the amino acid composition of the protein product, they are termed "silent" and have largely been assumed to exert no discernible effect on gene function or genotype. Now, a Report by Kimchi-Sarfaty et al. in the 27 Jan 2007 Science (published online 21 Dec 2006 ) shows that silent SNPs can indeed affect protein folding, and consequently, function. The researchers looked at the human multidrug resistance 1 ( MDR1 ) gene, which encodes a transmembrane protein pump that transports anticancer and other drugs out of cells. The team found that a relatively common SNP that changes the codon ATC to ATT (both of which encode the amino acid isoleucine) -- in combination with two other polymorphisms -- changes the conformation of the protein and also underlies its altered drug and inhibitor interactions. As noted in an accompanying Perspective by A. A. Komar (also published online 21 Dec), the study opens up a new avenue of research and suggests that silent SNPs might contribute to the development and progression of certain diseases.


Genome of an STD Pathogen

Trichomonas vaginalis is a single-celled human parasite that causes trichomoniasis, a common but often overlooked sexually transmitted disease, with some 170 million cases occurring annually worldwide. Although the disease can persist without major symptoms, acute infections can cause pelvic inflammation, increased risk of HIV infection, and pregnancy complications such as premature birth. In a Research Article in the 12 Jan 2007 Science , Carlton et al. reported the draft genome sequence of T. vaginalis . The team predicts that the organism’s massive ~160-megabase genome, about two-thirds of which consists of repeats and transposable elements, encodes about 60,000 protein-coding genes -- one of the highest coding capacities among known eukaryotes. Amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may reflect adaptations of the pathogen during its transition from an enteric environment (the habitat of most related parasites) to the urogenital tract. The increased genome size, and hence cell volume, might provide the parasite with a selective advantage for the engulfment of bacteria and host epithelial and blood cells. As noted by Dr. Jane Carlton in a segment of the 12 Jan podcast , the genome sequence offers new insights into the evolution of this intriguing parasite, as well as potential leads for the development of new therapies and novel methods for diagnosis.


Three-Way Symbiosis

Fungi commonly grow within plant tissues and in some cases enable the plant to adapt to extreme environments. In 2002, for example, researchers reported that a mutualistic heat-tolerant fungus is key to the survival of grasses in the hot spots of Yellowstone National Park -- where soil temperatures can reach as high as 50 degrees Celsius (about 120 degrees Fahrenheit). Now, a Report by Márquez et al. in the 26 Jan 2007 Science reveals that this symbiotic relationship actually depends on a previously unknown third partner -- a virus that infects the fungus. The team discovered the virus by virtue of its double-stranded RNA, which showed only some sequence similarity to other RNA viruses. They further showed that fungal isolates cured of the virus are unable to confer heat tolerance to the host plant, but that heat tolerance is restored after the virus is reintroduced. Dr. Roossinck, senior author on the study, discussed the new work in a segment of the 26 Jan podcast and hopes it will help others think about viruses as something other than agents of disease.


Nodulation Signals

A number of plant species have developed an intimate association with nitrogen-fixing bacteria (rhizobia) that provide the plants with a reliable source of nitrogen. Central to this symbiotic interaction is the formation of unique organs on plant roots called nodules, which house the bacteria and provide a suitable environment for nitrogen fixation. Two Reports in the 5 Jan 2007 Science (both published online 16 Nov 2006 ) provided new insight in the mechanisms underlying nodule formation. Using genetic approaches, Murray et al. and Tirichine et al. showed that a signaling pathway involving the plant hormone cytokinin is required for the cell divisions that initiate nodule development. A gain-of-function mutation in the cytokinin receptor leads to spontaneous formation of nodules in the absence of rhizobia or rhizobial signal molecules, whereas loss-of-function mutations result in too few nodules, despite aggressive formation of membrane projections called infection threads, which enable bacterial invasion. As noted in an accompanying Perspective by G. E. D. Oldroyd, cytokinins are also used by plants that do not form nodules in diverse developmental pathways, including the regulation of root and shoot branching. Further understanding of the details of cytokinin signaling in legumes may therefore shed light on the possibility of transferring the nodulation process to agriculturally important plant species, thereby reducing their dependence on industrial nitrogen fertilizers.


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In Science ’s STKE


Unstructured, Multifunctional Domains

Complexes of multiple protein molecules act together as tiny molecular machines to perform a diverse array of cellular functions. Hundreds of these protein assemblies and many of the interactions between them have been identified, but less is known about the subtleties of complex formation, evolution, or regulation. Two Perspectives published in Science ’s Signal Transduction Knowledge Environment (STKE) this month highlighted the importance of protein modularity in complex organization and of unstructured domains in proteins as sites for interaction with multiple partners. In the 16 Jan 2007 issue, Neduva and Russell focused on a recent study of the Ldb1 transcriptional complex, which plays a central role in mammalian head development. Researchers identified a proline-rich but otherwise unstructured module of a key component of this complex that is likely responsible for transcriptional activation, but is curiously mobile, occurring in different proteins in different species. And in the 23 Jan issue, Heximer and Blumer reviewed three recent studies demonstrating that an unstructured N-terminal domain allows RGS2, a known regulator of G protein signaling, to interact with unexpectedly diverse classes of protein partners (including channels, scaffolds, and kinases), and thus serve as a key point of integration for multiple intracellular signaling pathways.

Also in STKE this month:

--STKE editors compiled a list of the most important signaling breakthroughs of 2006 , from structural and functional revelations to approaches for the global analysis of signaling pathways ( 2 Jan 2007 )
-- Hoffman reviewed the current understanding of G protein signaling in fungi ( 23 Jan 2007 )
-- Naranjo and Mellström discussed how three transcription factors act outside the nucleus to regulate calcium homeostasis ( 30 Jan 2007 )