Science Roundup

This month in Science Roundup:

 

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Life in Cities
Special Online Collection

By 2030, nearly 5 billion people, or 60% of the world’s projected population, will live in cities. As described in a special section of the 8 Feb 2008 Science, these hot spots of production, consumption, and creative thinking present both the problems and solutions to the sustainability challenges that face an increasingly urbanized world. A series of News articles offered an on-the-ground look at how cities are tackling specific problems from poverty and poor sanitation to traffic jams and air pollution. Reviews and Perspectives examined how cities evolve, and the impacts of urbanization on the environment, human health, economic growth, and the demographics of the developing world. A related podcast segment discussed the tradeoffs between urban living and human reproduction, and an accompanying online video introduction highlighted the challenges, prospects, and science of urban transformation.


Power Walking

As we walk, we expend energy not only in pushing off with our planted leg, but also when our other leg decelerates as it makes contact with the ground -- energy that could be harvested for other uses, according to a new study. In a Report in the 8 Feb 2008 Science, Donelan et al. described the development of a knee-mounted mechanical device that can covert the expended mechanical energy of the deceleration step of walking into electrical power. The so-called "biomechanical energy harvester" consists of an aluminum chassis and generator mounted on a customized orthopedic knee brace, and weighs about 1.5 kg. Embedded sensors detect the angle and velocity of the wearer’s leg, switching the device on only during the braking phase of each swing -- analogous to regenerative braking in hybrid cars, where energy normally dissipated during braking drives a generator instead. The team reported that volunteers walking with one device on each leg produced an average of 5 watts of electricity -- enough to power 10 cell phones. The ability to produce substantial electricity with little effort makes this technology attractive for powering prosthetic limbs or other portable medical devices. A related ScienceNOW story by D. Powell highlighted the innovation.


Ovulation Control

In mammals, the ability of a female to remain fertile depends on the continuous activation of oocyte-containing follicles from their dormant state in the ovary. Menopause, or the natural end of the female reproductive cycle, occurs when the primordial follicle pool has been exhausted. However, the molecular mechanisms underlying follicle activation have been poorly understood. Now, in a Report in the 1 Feb 2008 Science, Reddy et al. report that Pten, a gene best known for its role as a tumor suppressor, plays a vital role in regulating this process. The researchers showed that in genetically engineered mice lacking PTEN in their oocytes, the entire pool of immature eggs is activated prematurely, depleting the supply of mature, fertilizable eggs by early adulthood -- a situation similar to that of premature ovarian failure in humans. As noted in a related News story by J. Marx, whether mutations in PTEN or in other proteins that cooperate with PTEN are involved in human ovarian problems remains to be determined. If so, the new findings may aid the design of improved fertility treatments.


Microbial Balance in the Gut

The relationship between an animal host and the complex mixture of microbes it carries in its gut is a delicate one. Among the critical functions of microbiota are extracting nutrients from food, and protecting the gut lining from injury. On the flip side, damage to the gut microbe community has been implicated in maladies such as inflammatory bowel disease. In a Research Article in the 8 Feb 2008 Science (published online 24 Jan 2008), Ryu et al. offered new insights into how gut-microbe homeostasis is maintained. Using the fruit fly as a model -- as it has a much simpler intestinal microbial community than our own -- the researchers showed that bacteria normally resident in the gut provoke an innate immune response, but that the response is muted through the action of the gene Caudal. This gene, well known for its role in the development of the gastrointestinal tract, blocks the production of harmful antimicrobial peptides that could otherwise kill off beneficial gut bacteria. In contrast, inhibiting Caudal expression led to increased production of antimicrobial peptides, which wiped out a common gut microbe, leaving a pathogenic strain that eventually destroyed cells in the intestinal lining and caused host mortality. An accompanying Perspective by N. Silverman and N. Paquette noted that the new results demonstrate the important role that gut microbiota play in their own proper maintenance and the critical role that properly regulated host immune responses play in supporting these microbes.


Predation and Ecosystem Dynamics

Top predator species in marine and terrestrial ecosystems are among the fastest disappearing elements of biodiversity, and understanding their role in local ecosystem functioning may help to predict the effects of their loss. In a Report in the 15 Feb 2008 Science, Schmitz showed that predators, by affecting prey behavior, can change both plant diversity and productivity in a grassland ecosystem. In a unique 3-year experiment set in a meadow in northeastern Connecticut, the author established 14 caged plots containing plants, grasshopper herbivores, and predatory spiders -- with half the plots containing "sit and wait" ambush spiders and the other half containing actively roaming spiders. Schmitz found that in plots where actively hunting spiders reigned, their grasshopper prey roamed freely to feed on the plants, reducing plant diversity but boosting aboveground net primary production and nitrogen mineralization. In experimental plots containing "sit and wait" spiders, however, grasshoppers altered their feeding strategy to avoid the lurking predators, with opposite effects on plant diversity, growth, and nitrogen mineralization. The experiment shows that the mechanisms by which predators hunt their prey are relevant to our understanding of how predators affect ecosystems and the development of effective conservation measures. An accompanying Perspective by S. Naeem highlighted the contribution of the study to efforts to better understand what governs ecosystem "greenness."


Learning with Regret

Much of human learning in social settings is interactive in nature: What an individual learns is affected by what other individuals are learning at the same time. Economic games represent a widely accepted paradigm for representing interactive decision-making, and in a Report in the 22 Feb 2008 Science, Marchiori and Warglien explored the how well neural networks can model and predict human interactive learning in repeated games. Their basic assumption was that players modify their behavior by looking backward to what might have been their best move, once they know what the other player’s move was. The researchers found that even very simple learning networks, driven by such regret-based feedback, accurately predicted observed human behavior in 21 different games. Introducing an approximation of regret dramatically improved the performance of the neural network and allowed more precise prediction of human behavior than established models of learning. An accompanying Perspective by M.D. Cohen noted that "[the] approach extends a recent emphasis on obtaining useful approximations of actual choice behavior, which is a different goal from the exact explication of neurological mechanisms sought by psychologists."


Inhibiting Infection by Chelation

Tissue abscesses form when invading bacteria meet cells of the immune system, most notably neutrophils. These abscesses help confine the spread of infection by restricting microbial growth and dissemination to neighboring tissues, but the specific host factors involved in the process have not been well defined. In a Report in the 15 Feb 2008 Science, Corbin et al. identified an abundant neutrophil protein, calprotectin, as an important inhibitor of bacterial growth inside abscesses. This protein is known to be involved in signaling to other immune cells after tissue damage and/or inflammation. According to the new study, calprotectin also defends against infection by chelating manganese and zinc ions -- metals required by the human pathogen Staphylococcus aureus for growth and for counteracting immune attack. The researchers showed that infected mice lacking calprotectin had elevated metal levels and increased bacterial growth in tissue abscesses. Inhibition of bacterial nutrient uptake may thus represent a promising new area of research for the design of antimicrobial therapeutics. As noted in an accompanying Perspective by R.P. Novick, however, whether it is possible to reduce an essential trace metal to a concentration low enough to block bacterial growth without also compromising the functions of host cells remains to be seen.


Clues to Exosome Formation

Cellular proteins and fats tagged for disposal are typically either digested in organelles called lysosomes, or released outside the cell in small membrane-bound vesicles called exosomes. Exosomes are thought to play key roles in cell-to-cell communication, antigen presentation, and the pathogenesis of retroviral infections like HIV, but how they form has been unclear. Now, in a Report in the 20 Feb 2008 Science, Trajkovic et al. explain that lipid components in the membrane of endosomes -- compartments within the cytoplasm that hold cellular waste --selectively collect cargo destined for exosomes or lysosomes in distinct membrane subdomains. The researchers showed that subsequent invagination of the endosomal membrane to form exosomes does not depend on budding machinery known to be required for forming lysosome-destined vesicles. However, exosome formation does appear to require ceramide, one of the components of the membrane lipid sphingomyelin. Exosomes purified from cell culture medium were enriched in ceramide, and inhibition of the enzyme that produces ceramide results in reduced exosome secretion. An accompanying Perspective by M. Marsh and G. van Meer noted that it is not clear whether all exosomes are formed through the same molecular mechanism, or if different mechanisms are used for different types of exosome cargo -- but that the new work suggests that a better understanding of lipid metabolism may provide new vistas in exosome research.


Quantum Matter
Special Online Collection

In the quantum world, solids, liquids, and electrons can flow without dissipation; exotic phases of matter can emerge; and objects can be entangled and be in multiple places at once. As explained in a special section of the 29 Feb 2008 Science, experimentalists and theorists have been exploring the curious quantum regime for some time, studying how individual particles and ensembles of particles behave, in attempts to unravel the underlying physics producing these exotic properties and phases. Six Perspectives provided a taste of some of the topics that occupy the world of quantum matter, including the theoretical basics of quantum gases and liquids, supersolidity, and quantum critical electron systems. Developments made in the quantum world are also carrying over to applications from quantum computing to the use of quantum optics in areas such as secure communication and cryptography. A related News Focus described current research in Fermi condensates, ultracold gases composed of fermionic atoms (atoms that have an odd number of protons, neutrons, and electrons), which may help researchers model the properties of materials such as high-temperature superconductors and the interiors of neutron stars.


A Solar System Like Ours

Searches for extrasolar planets have uncovered a diversity of planetary systems, all of them very different from our own. Most of the discoveries have been of bodies with masses much larger than the heaviest objects of our solar system, largely because methods of detecting them are only sensitive to massive orbiting objects. Now, in a Report in the 15 Feb 2008 Science, Gaudi et al. report the discovery of a multi-planet system that bears a striking resemblance to our own solar system. Using a new and powerful technique called gravitational microlensing, in which light from distant stars is bent by the planetary system on its way to earth, the team detected a system consisting of a star calculated to have only half the mass of the sun, and two giant planets that look like scaled down versions of Jupiter and Saturn. The ratio of the planets’ masses and the ratio of their distances from the star are similar to those of Jupiter and Saturn. And the ratio of the larger planet’s mass to that of the star is close to the Jupiter-sun ratio. An accompanying News story by R.A. Kerr and a podcast interview with lead author Dr. B.S. Gaudi highlighted the discovery.


Climate Change and Food Security

Some of the most profound impacts of climate change over the next few decades will be on agricultural and food systems. In a Report in the 1 Feb 2008 Science, Lobell et al. used statistical crop models and climate change projections for 2030 to analyze the climate risks for crops in 12 food-insecure regions worldwide. Together, these regions are home to nearly 95% of the world’s malnourished individuals. The results indicate that South Asia and Southern Africa are two regions particularly at risk for harmful impacts on several crops, but that uncertainties vary widely by crop. Because climate impacts are also likely to vary within individual regions according to differences in natural and technological resources, management, and other factors, prioritizing adaptation needs will ultimately depend on how investing institutions perceive the risks. A related Perspective by by M.E. Brown and C.C. Funk discussed measures that could help farmers adapt to climate change, including use of fertilizer and higher-yielding crop varietals, improved environmental monitoring and local governance, and crop insurance programs.


Bioinspired Polymer Films

Nature has found ways to take weak or brittle starting materials and make them stronger and tougher composites, for instance, by combining biopolymers and ceramic building blocks to create materials like bone, teeth, and the nacreous layer of mollusk shells (also known as mother of pearl). Scientists have also been able to create sturdy composite materials, but have not been able to achieve the same level of sophistication as hybrid materials built up by living organisms. Now, in a Report in the 22 Feb 2008 Science, Bonderer et al. have applied some of the structural concepts found in biological materials to design and fabricate platelet-reinforced hybrid films that are both strong and ductile. By sequentially depositing ceramic plates less than 1 millimeter thick in a ductile polymer matrix, the researchers created a layered nacre-like material with high tensile strength and flexibility. A related Perspective by C. Ortiz and M.C. Boyce highlighted the new work as well as other efforts to mimic the mechanical design principles of seashells, noting that such bioinspired materials could transform fields from civil engineering to aeronautics.


Building with DNA

DNA is the molecule of life. Techniques for its manipulation are the foundation of the biotechnology industry -- and in recent years it has become the molecule of choice for nanotechnologists. DNA’s power lies in the specificity of the interactions between its complementary nucleotide bases (A’s and T’s, C’s and G’s), which means that researchers can control the interactions between single DNA strands through the design of their base sequences. In a Report in the 1 Feb 2008 Science, Kufer et al. reported the use of this versatile molecule to assemble materials from the bottom up. Their method, which combines the selectivity of DNA hybridization with the precision of the atomic force microscope (AFM), used light-emitting molecules called fluorophores as building blocks. The fluorophores were first linked to short single-stranded DNA molecules, which served as molecular handles. Using an AFM tip bearing a complementary DNA strand, the team was able to pick up these building blocks from a "depot" area and precisely deposit them on a "target" area to create basic geometrical structures. The transfer process can be repeated up to 5000 times with less than 10% loss of transfer efficiency. As noted in an accompanying News story by R.F. Service, the technique is likely too slow to assemble large amounts of materials, but could help researchers put chains of molecules together to answer questions such as how different enzymes work together in a series.


Earthquake Cascades

Earthquakes of all sizes can trigger other earthquakes. A mainshock (the largest earthquake in a sequence) causes aftershocks, which in turn activate their own local aftershock sequences. Determining how and to what extent any two quakes are connected within this cascade of activity has been a long-standing challenge for seismologists. According to a Report by Marsan and Lengliné in the 22 Feb 2008 Science, the probability of directly and indirectly triggering aftershocks can be estimated without an a priori model. Instead, the team showed that an algorithm based on two simple assumptions can decipher a complex seismicity time series to reveal the underlying triggering influences exerted by earthquakes of all sizes. Using this model, the researchers analyzed seismicity in southern California between 1984 and 2002 and found that large regional earthquakes have a short and direct influence in comparison to the overall duration of aftershock sequences. Relative to these large mainshocks, small earthquakes have a disproportionate effect on triggering. The results thus suggest that cascade triggering is a key component in earthquake interactions.


Brevia Highlights

This month in Science’s Brevia section:
-- Atkinson et al. (1 Feb 2008) used vocabulary data from three of the world’s major language groups -- Bantu, Indo-European, and Austronesian -- to show that up to one-third of their words arose in rapid evolutionary bursts.
-- Chen et al. (8 Feb 2008) explained that in order to play the high range of the saxophone, players learn to tune the second resonance of their vocal tract to the desired note.
-- Chan et al. (15 Feb 2008) reported on extreme oxygen deficits in the northern California Current system, which caused widespread anoxia during 2006 (listen to the related podcast segment)
-- Futahashi and Fujiwara (22 Feb 2008) showed that in swallowtail butterflies, a hormone regulates a dramatic developmental shift as young caterpillars, which mimic bird droppings, grow into green cryptic larva.
-- Christner et al. (29 Feb 2008) reported that bacteria and other biogenic aerosols are ubiquitous in the nuclei of ice particles that grow and form snowflakes ( listen to the related podcast interview with the lead author).

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In Science Signaling

(Note: Science’s STKE changed its name to Science Signaling starting with the first issue in January 2008. For more information see the Science Magazine website.)

Surviving Stress

Although the ultimate outcome of prolonged exposure of cells to stress is often death, the early response appears to be the activation of survival pathways that are likely to give the cell an opportunity to repair low-level damage. How these stress-initiated survival mechanisms influence proteins that comprise the core cell death machinery has remained unclear. In a Perspective in the 19 Feb 2008 issue, M.E. Guicciardi and G.J. Gores highlighted two recent studies that identified new players and mechanisms that integrate stress responses and cell death. In the liver, p53-mediated induction of the gene that encodes insulin-like growth factor–binding protein-1 (IGFBP1) attenuates the cell death response by preventing the formation of a complex between p53 and the proapoptotic protein BAK. At the mitochondria in three unrelated cell lines, withdrawal of growth factors or nutrients promotes the stability of a certain protein complex that ultimately raises the threshold of another protein signal required to trigger cell death. The studies demonstrate that the cell’s initial adaptive response to stress is to survive and not to die. This response probably allows time for the cell to repair low-level damage, and survival is ultimately achieved by altering the activity of Bcl-2 proteins, which constitute the core cell death machinery.

Also in Science Signaling this month:
-- F.P.G. Van Horck and C.E. Holt discussed how mutual interactions between the cytoskeleton and local translation may mediate growth cone steering response (26 Feb 2008)
-- R. Iyengar provided lecture notes and slides for a class on mathematical modeling of mammalian signaling pathways (19 Feb 2008)
-- H.C. O’Neill and B.J.C. Quah discussed how the secretion of small vesicles by bacterially infected macrophages helps promote inflammation (12 Feb 2008)
-- M.C. Boersma and M.K. Meffert highlighted recent evidence of novel roles for the NF-kappaB signaling pathway in regulating neuronal function (12 Feb 2008)

This month’s Science Roundup is sponsored by:

 Special Offer:
Fashion Breakthrough of the Year!

Now you can order a t-shirt like the one featured on the 21 Dec 2007 Issue of Science. Sneak a peek at www.promo.aaas.org/geneshirt.