This month in Science Roundup:

• Plant-Microbe Interactions
• Living Counters
• Safer Drug Target for Alzheimer's
• African Population History
• Imaging with Infrared
• Ovulation Signals
• Death Mirroring Life
• MESSENGER's Second Mercury Flyby
• Future Fuels
• Advances in Optical Lithography
• Ice and Climate Complexities
• Slab Tears
• In Science Signaling

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Plant-Microbe Interactions
Introduction to Special Issue

Plants, like animals, live immersed in a thriving community of microbes. The diversity of fungi, bacteria, and other microorganisms with which plants interact bring both plague and benefit. A special section of the 8 May 2009 Science highlighted recent advances in our understanding of the biochemistry, signaling, and ecosystem dynamics that shape how microbes and plants interact. A series of Perspectives looked at innate immunity in plants, which is their first line of defense against potentially dangerous microbes; the role of chemical diversity in plant defense; cross-talk between plant hormonal and defense signaling pathways; how plants form and maintain mutually beneficial interactions with microbes; and the need for improved models of host-pathogen coevolutionary interactions to help researchers predict the long-term consequences of different types of human interventions on disease. A related Editorial discussed how a deeper understanding of plant-microbe interactions is likely to benefit efforts to improve plant health and productivity in agricultural settings in the coming decades.


Living Counters

Synthetic biologists take much of their inspiration from computing and electrical engineering, attempting to gain programmability in cells using analogous genetic circuits. Engineered biological counters would enable many applications, such as regulating cell death after a specified number of cell divisions, noninvasive monitoring of aging, and recording the frequency of environmental events. In the 29 May 2009 Science, Friedland et al. reported an important step toward the construction of such genetically encoded counters. The team constructed two complementary synthetic genetic counters in E. coli that can count up to three induction events (the counters trigger the expression of a desired protein following the processing of two or three input signal pulses). These molecular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers. Similar devices may find application in multi-event processes of cell biology, bioengineering, and, potentially, therapeutics. An accompanying Perspective by C. D. Smolke noted that important next steps include developing circuits that can report on intermediate states, as well as the final state, and circuits that allow counters to distinguish between continuous and transient signals.


Safer Drug Target for Alzheimer's

Accumulation of the amyloid-beta (A-beta) protein in the brain is one the hallmarks of Alzheimer's disease and is thought to trigger a pathological cascade that ultimately results in neuronal dysfunction and neurodegeneration. Therapies for the disease have therefore largely focused on preventing or slowing A-beta aggretation, or breaking up toxic A-beta aggregates. The gamma-secretase enzyme complex is responsible for the final cleavage of A-beta from its precursor protein, but the development of clinically useful inhibitors has proven challenging. That's because the enzyme complex cleaves not only the A-beta precursor, but also several important signaling proteins including Notch1, which is important for controlling processes such as cell growth, differentiation, and proliferation. As a result, treatment of mice with general gamma-secretase inhibitors leads to various toxic side effects including abnormalities in the skin and gastrointestinal and immune systems (see the related Perspective by T. E. Golde and T. L. Kukar). Now, in a Report in the 1 May 2009 Science, Serneels et al. show that selective removal of the Aph1B component of the gamma-secretase complex in a mouse model of Alzheimer's decreases the formation of A-beta plaques and improves behavioral deficits without the harmful side affects observed when targeting gamma-secretase more generally. Drugs that specifically inhibit this component may therefore be useful in treating the disease. The results may also have implications for the treatment of various cancers in which gamma-secretase is known to play role.


African Population History

Africa is the birthplace of modern humans, but genetic studies have so far tended to under-represent African populations. As a result, the extent of genetic diversity and the genetic relationships among the continent's diverse populations have been unclear. Now, in a Research Article in the 22 May 2009 Science (published online 30 Apr), Tishkoff et al. provide details of the largest study yet of African genetic diversity. The team analyzed DNA from blood samples collected over a decade from 113 geographically diverse African populations and found that they can be traced back to 14 ancestral groups that often correlate with self-described ethnicity and shared cultural and/or linguistic properties (see the related News story by A. Gibbons in the 1 May issue). The data reveal high levels of mixed ancestry in most populations, reflecting historical migration events across the continent. The data also provide evidence for shared ancestry among geographically diverse hunter-gatherer populations including Pygmies and Khoesan speakers of southern Africa. Analysis of DNA from African Americans revealed that their ancestry is predominantly (~71%) from populations in western Africa, 13% European, and 8% from other African populations, although admixture levels varied considerably among individuals. In a related podcast interview lead author Sarah Tishkoff explained how the findings will be informative for further studies aimed at reconstructing human evolutionary history, understanding African-American ancestry, and for identifying genetic risk factors for disease in Africa.


Imaging with Infrared

Proteins from jellyfish and corals that fluoresce in the visible wavelength range have revolutionized optical imaging of cells. However, these wavelengths are absorbed by hemoglobin, water, and lipid, thus hindering the use of these proteins for deep-tissue imaging. In a Report in the 8 May 2009 Science, Shu et al. described the engineering of a bacterial protein that can emit infrared light, thus opening the door to new imaging applications (see the related ScienceNOW story by R. F. Service). The new protein is a modified version of a phytochrome from Deinococcus radiodurans -- a bacterium renowned for its ability to survive huge doses of radiation. The phytochrome normally absorbs deep-red light at the far end of the visible spectrum and then uses that energy to send a signal to the cell to turn on particular genes. By tinkering with the DNA that encodes the protein, the teams created a protein that instead uses its energy to create infrared light. The resulting infrared fluorescent proteins are expressed well in mammalian cells and in mice. Because infrared can pass through tissue more easily than visible light can, the advance should allow researchers to trace individual molecules throughout the bodies of mice and other small, live animals. Lead author of the study, Xiaokun Shu, discussed the work in a related podcast interview.


Ovulation Signals

In mammals, female reproductive success depends on the growth of ovarian follicles, differentiation and proliferation of granulosa cells -- ovarian cells that support the oocyte or egg -- as well as oocyte maturation and ovulation. Failure to initiate or complete follicle development, or defects in the oocyte, will result in infertility. In a Report in the 15 May 2009 Science, Fan et al. described the cellular signaling pathways in the mouse ovary that support follicle maturation and, ultimately, the release of a mature egg. Luteinizing hormone (LH), released in monthly surges by the pituitary gland, binds to its receptors on granulosa cells and plays a critical role in ovulation and oocyte maturation. In the new study, the researchers show that mitogen-activated protein kinases MAP1 and MAP 3 and (also known as ERK1/2) are essential downstream targets of this hormonal signal. Engineered mice incapable of expressing ERK1/2 in their granulosa cells displayed multiple disrupted ovarian processes, including prolonged follicle development and failure of oocytes to mature. The team also provided evidence that the transcription factor C/EBPbeta is a critical downstream mediator of ERK1/2 activation. As noted in an accompanying Perspective by R. Duggavathi and B. D .Murphy, these findings could help elucidate the underlying causes of ovarian pathologies and lead to therapies for female infertility.


Death Mirroring Life

The accuracy with which fossil assemblages represent the actual composition of ancient ecological communities is often uncertain, especially during periods of rapid population and environmental change. One way to assess the degree of fidelity between living and dead assemblages is to compare modern living communities and the records they leave behind them in real time. In a Report in the 22 May 2009 Science, Western and Behrensmeyer presented their results of just such a study. Using live population counts and bone surveys, the team tracked correlations between dead and living populations of 15 herbivorous species (14 mammals and ostrich) in the Amboseli reserve in southern Kenya over 40 years (1964 to 2004). Over this time period, dense woodlands and bushlands gave way to open grassland and large swamps, the abundance of grazing animals increased relative to browsers, and species richness declined. The team found that the relative abundance of species recorded in the bone assemblages accurately tracked these changes in community composition and habitat over intervals as short as 5 years and that the aggregated bone sample provides an accurate record of community structure time-averaged over four decades. The findings thus lay the groundwork for integrating paleobiological and contemporary ecological studies across evolutionary and ecological time scales.


MESSENGER's Second Mercury Flyby

In October 2008, the spacecraft MESSENGER made its second of three scheduled flybys of Mercury before it settles into the planet's orbit in 2011. These flybys, together with observations collected by Mariner 10 in the mid-1970s, now provide a near-global look at the planet. Four Reports in the 1 May 2009  Science described observations from MESSENGER's second flyby and new insights into Mercury's outer atmosphere and its surface. Two reports examined the complexity of Mercury's magnetosphere, formed by solar wind interaction with the planet's magnetic field (see the related Perspective by K.-H. Glassmeier). Slavin et al. reported observations of intense magnetic reconnection -- a process in which the interplanetary magnetic field lines join the magnetospheric field lines, transferring energy from the solar wind into the magnetosphere -- 10 times as intense as that on Earth. McClintock et al. reported on the detection of magnesium in Mercury's tenuous exosphere, which presumably derived from surface materials, as well as differing spatial distributions of magnesium, calcium, and sodium atoms. Turning to the surface of Mercury, Denevi et al. looked at the mechanisms that have shaped the planet's crust, which likely formed by eruption of magmas of different compositions over a long period of time. And Watters et al. described the well-preserved Rembrandt Impact Basin, which is the second largest known on the planet. The basin is only partially flooded by volcanic plains and shows a unique pattern of radial and concentric tectonic features, some of which result from Mercury's contraction as its interior cooled over time.


Future Fuels

The escalating monetary and political costs of imported petroleum, as well as growing concerns over the environmental impact of greenhouse gas production, have accelerated efforts to develop more environmentally friendly transportation fuels. Biomass has been promoted as an important source of power for automobiles, either to generate electricity for electric vehicles, or to make ethanol for combustion vehicles. In a Report in the 22 May 2009 Science (published online 7 May), Campbell et al. examined each approach's demands on land use, using a lifecycle assessment model, for a range of energy feedstocks, conversion methods, and vehicle types. The team found that in nearly all cases, bioelectricity would have a significantly higher net transportation efficiency per unit area of cropland used than bioethanol, owing to the greater efficiency of electric engines. Bioelectricity would also result in greater greenhouse gas offsets (listen to the related podcast interview with lead author Elliot Campbell). In a related Policy Forum, Ohlrogge et al. argued that "replacement of gasoline by bioelectricity in cars and with diesel engines in heavier vehicles may be the best route to the goal of reducing petroleum consumption and carbon dioxide emissions."


Advances in Optical Lithography

Microscopists have achieved fluorescence imaging at subwavelength resolution by focusing one beam of light in a halo around another beam, thereby quenching the glow of fluorescent dyes in all but the very center of the illuminated spot. Three studies in the 15 May 2009 Science (published online 9 Apr) have adapted this approach to photolithography, the process used to pattern the formation of electronic circuits on microchips. The new approach allows small feature sizes to be created more easily and inexpensively than with traditional approaches. Scott et al. developed a two-color irradiation scheme in which a central beam of one wavelength activates polymerization initiators, and a surrounding halo-shaped beam of a second wavelength halts polymerization in the surrounding area, thus enabling fine-detailed patterning in the center of the "halo". Li et al.  found that use of a different initiator molecule allowed both beams to share the same wavelength (800 nanometers), with a relatively weak quenching beam lagging slightly behind an intense initiating beam. Both of these techniques produced three-dimensional features honed to subwavelength dimensions. Finally, Andrew et al. described a method that involves placing a thin film on top of the light-sensitive template being patterned. Upon absorbing an ultraviolet etching beam, molecules in the film isomerized to a transparent layer, but then returned to the initially opaque form upon absorption of visible light. Applying an interference pattern with ultraviolet peaks superimposed on visible nodes restricted etching to narrow regions in the center of these nodes, yielding lines of subwavelength width. An accompanying Perspective by J. W. Perry highlighted the studies.


Ice and Climate Complexities

Two studies reported in Science this month turned to glaciers for clues to past climate dynamics and future sea-level rise.

-- Schaefer et al. (1 May 2009) investigated how Earth's climate has evolved over the past few millennia, with particular attention to how climate in the northern half of the globe has changed with respect to climate in the southern half. Their chronology of glacial movement in New Zealand's Southern Alps over the last 7000 years, compared to similar records from the Northern Hemisphere, revealed clear differences in glacier histories between hemispheres, likely owing to regional controls. Thus, neither of the two popular arguments -- that the hemispheres change in phase or that they change in an anti-phase manner -- appear to be correct. An accompanying Perspective by G. Balco highlighted the Report.

-- Bamber et al. (15 May 2009) assessed how a rapid collapse of the West Antarctic Ice sheet, which glaciologists have proposed is unstable, would contribute to sea-level rise (see the related Perspective by E. R. Ivins). They determined that collapse of the ice sheet would raise sea level by about 3.2 meters, on average, with the maximum increase concentrated along the Atlantic and Pacific seaboards of the United States. Although this is only about half as much as previously estimated, the impact on coastal areas would still be devastating.


Slab Tears

At mid-ocean ridges, magma rises into the upper mantle and crust and then spreads away from the ridge and cools, forming the stiff oceanic lithosphere. As it moves away from the ridge, the lithosphere becomes cooler and denser, and ultimately descends back into the mantle in slabs through the process of subduction. Recent seismic data have shown that some slabs penetrate deep into the mantle whereas others bend and become horizontal at 670 kilometers near a prominent phase boundary. A Report in the 29 May 2009 Science now shows that subduction can also cause vertical tearing of slabs of oceanic lithosphere. Obayashi et al. presented seismic tomographic data that provide a detailed view of tearing at the junction of the Izu-Bonin and Japan slabs in the western Pacific. The slabs are joined together, but oriented in slightly different directions. The vertical tear the team observed seems to be generated by resistance at the bottom of the upper mantle, where the slabs bend and start to flatten. The geometry of the gash should help researchers better understand the past evolution of this plate boundary. An accompanying Perspective by G. Nolet highlighted the Report.

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In Science Signaling

Complex Crosstalk

Traditionally, signaling pathways are investigated by measuring the responses of cells to a single factor. Although this approach provides valuable information on the signaling pathways stimulated by that ligand in vitro, the situation in vivo is often much more complex. In a Research Article in the 19 May 2009 issue, Hsueh et al. measured the cytokines secreted by macrophages in response to three-, four-, and five-way combinations of ligands and then mathematically analyzed the differences between the outcomes predicted from lower-order combinations and the measured outcomes. They found that despite the high number of possible interactions among the stimulated signaling pathways, a modest number of responses were observed. In addition, they also uncovered some unpredicted signaling outcomes, which should help in the future modeling of responses of cells in different contexts.

Also in Science Signaling this month:
-- Balamotis et al. reported on the effect of transcription factor binding interactions on transcriptional activation kinetics in response to signaling (5 May 2009)
-- Parker highlighted recent research on a signal that primes the systemic immune response in plants (12 May 2009)
-- Golebiowski et al. analyzed the targets and dynamics of SUMOylation in cultured cells in response to heat shock (26 May 2009)

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Image credits (in order of appearance): T. Boller, S. Y. He, Science 324, 742 (2009), Tishkoff et al., Science 324, 1035 (2009); Science cover, 1 May 2009; Jonathan Bamber