This Week in Science

Science  22 Apr 2005:
Vol. 308, Issue 5721, pp. 464
  1. Modeling Signaling Networks


    The prediction of causal influences between components of a signaling network requires detailed modeling from large data sets. Single-cell measurements of the phosphorylation state of a panel of signaling proteins with phospho-specific antibodies after various treatments that influenced cellular signaling provided sufficient data so that Sachs et al. (p. 523; see the Perspective by Brent and Lok) could apply a Bayesian network inference algorithm to map a signaling network and infer causal influences between the components of the network. Known connections were reproduced, and a newly discovered connection was experimentally tested and found indeed to be of biological relevance.

  2. Funneling Fast Solar Winds

    The Sun emits a solar wind that bends and distorts the ionized tails of comets and influences the behavior of Earth's ionosphere. Much of this solar wind consists of an energetic “fast” component whose origin within the solar furnace is not well understood. Tu et al. (p. 519) used Doppler imagery and magnetic mapping to construct three- dimensional maps of funnels near the surface that are believed to be the source of the fast solar wind. The correlation of ultraviolet emission and magnetic field structure can pinpoint where in the solar atmosphere the fast solar wind is generated.

  3. Microbial Metagenome Analysis

    The volume of sequence required to assemble representative whole genomes from complex microbial communities in environmental samples is enormous: up to 100 megabases of sequence is needed to draft a single genome at eightfold coverage, which is feasible for a predominant species, but near impossible for rare species. Tringe et al. (p. 554) took the alternative strategy of analyzing the gene content of samples from disparate environmental microbial communities. Distinctive metabolic hallmarks indicated selection pressures within the respective habitats. For example, cellobiose phosphorylase was only found in the soil sample but not in the marine samples, and bacteriorhodopsins were found in the surface water samples but none in the deep sea or in soil. The most discriminating operons were for transport of ions and inorganic components. This approach offers a pragmatic and informative route to sifting the enormous volumes of data obtained from metagenome studies.

  4. Emulsions on the Double


    Emulsions can be made by mixing one immiscible fluid with another (such as oil and water) to create metastable droplets. Double emulsions, where the core droplet contains smaller droplets of a third fluid, can be more stable but are not easy to prepare in a controlled manner. However, they are of interest to the cosmetic and pharmaceutical industries for delivering a protected liquid product to the user. Utada et al. (p. 537) have controllably and predictably fabricated double emulsions in a single-step process using a microfluidic device. By injecting fluids in a coaxial geometry, they can keep the fluid reservoirs separate. Droplet sizes are tuned by altering the flow rates.

  5. Sharpening Up One's Image

    The smallest details that can be imaged are usually limited by diffraction effects on the order of the wavelength of light used for illumination. Recent theoretical work has predicted that it may be possible to overcome the diffraction limit if the properties of the imaging material can be judiciously chosen. In particular, if the electric and magnetic response of the lens material can both be negative, then a flawless image of an object should result. Fang et al. (p. 534; see the Perspective by Smith) used a thin sheet of silver as their superlens and imaged structures with resolution around 1/6 of the wavelength of the illuminating light.

  6. Winds of Wide-Scale Change

    Climate warming is affecting atmospheric circulation, ocean circulation, and the marine biological cycle, with implications for weather as well as the global carbon cycle. Goes et al. (p. 545) provide a striking illustration of how large-scale physical changes can influence biological processes across large areas, even when they are separated by large distances. The decline of winter and spring snow cover in Eurasia that has accompanied mid-latitude warming since 1997 has caused greater continental warming there in the summer. This decline intensified sea-surface winds in the distant western Arabian Sea by creating a steeper thermal gradient. These stronger winds in turn caused intensified upwelling of nutrient-rich water along the Northeast coast of Africa, which increased biological productivity and phytoplankton biomass in the western Arabian Sea.

  7. "Promotin" Signaling by Arrestins

    The arrestin proteins got their name because they inhibit signaling from G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors like the β2 adrenergic receptor that mediates effects of catecholamines on the heart. However, the proteins β-arrestin 1 and -arestin 2 have much more versatile roles in signaling. Lefkowitz and Shenoy (p. 512) review recent studies showing that β-arrestins also serve as scaffolding proteins that actually enhance signaling by providing binding sites for other signaling proteins that help produce biological effects of receptor activation. The arrestins even appear to contribute to signaling by structurally distinct receptors, not just G protein-coupled receptors. In their scaffolding role, β-arrestins may transmit activating conformational changes from the receptor to downstream target molecules.

  8. Search and You Will Find

    Some of us work in parallel, tackling several tasks at once, and others prefer the serial approach, finishing one task before starting the next. Children searching for a red truck among many toys either examine each object individually (serial) or look first for red objects and for trucks (parallel). Bichot et al. (p. 529; see the cover and the Perspective by Wolfe) now provide evidence that helps to resolve the debate over which approach better describes how visual search operates, in neural terms. A feature-based mechanism (red, truck) operates in a top-down fashion so as to enhance the responsiveness and the synchrony of visual neurons that select for these features. Thus, red toys and trucks evoke more neural activity when a child is searching for a red truck than a brown dog. In addition, a spatial mechanism enhances the responsiveness of visual neurons that are selective for the particular place where the child looks, so that elements of both types of searching contribute.

  9. Elucidating a Plant Defense Mechanism

    Arabidopsis strains carrying the gene encoding RPS2 are resistant to infection by the bacterium Pseudomonas syringae, which introduces the protease effector AvrRpt2 into plant cells during pathogenesis. Coaker et al. (p. 548, published online 24 February 2005; see the Perspective by Schulze-Lefert and Bieri) now show that the plant's own cyclophilin activates the proteolytic activity of the bacterial effector, AvrRpt2. AvrRpt2 then destroys the intermediate target protein (RIN4) in the plant activating the plant's defensive response. It is possible that such folding of bacterial effector proteases by eukaryotic protein factors may be a common mechanism during pathogenesis.

  10. Molecular Arms Race


    Many invading viruses and transposons replicate and transpose through RNA intermediates. These intermediates can be detected by the host cell RNA interference machinery in plants and insects and used to generate small interfering RNAs (siRNAs), critical intermediates in silencing, which can then neutralize the invader. Lecellier et al. (p. 557; see the news story by Couzin) now show that mammalian cells can also use the RNA silencing machinery to help neutralize an invading mammalian virus. Curiously, rather than siRNAs derived from the viral genome being the effector molecules that target the invader for silencing, a host microRNA tags the virus. The importance of the pathway in host defense is supported by the presence of a viral protein that can suppress the silencing effect.

  11. You Scratch My Back...

    The interaction between “ant-plants” in the genus Acacia and ants in the genus Pseudomyrmex is a classic example of a specific, coevolved mutualism; the ants feed on extrafloral nectar produced by the plant, and defend the plant against herbivore attack. The chemical mechanisms underlying this relationship remain mysterious. Heil et al. (p. 560; see the news story by Pennisi) now show that the extrafloral nectar produced by Central American ant-acacias to nourish their resident ants is unattractive to generalist ants because it lacks sucrose. The specialized ants, however, feed on sucrose-free nectar, and they exhibit only very low activity of the sucrose-cleaving enzyme, invertase. The lack of sucrose in the nectar results from invertase activity in the secreted nectar itself.

  12. Antarctic De-Icing

    Surface air temperatures on the Antarctic Peninsula have risen by an average of about 2°C since the 1950s. This warming has significant implications for the rate of sea level rise because the Antarctic Peninsula contains a large volume of ice that can be lost through drainage by ice streams and the disintegration of sea ice shelves. Cook et al. (p. 541) compiled maps showing changes in the extent of marine glaciers draining the Antarctic Peninsula ice sheet. Their detailed cartography of 244 existing glaciers there reveals that 87% of glaciers have retreated during the last 50 years, and that the change from advance to retreat has occurred progressively with latitude. This loss could increase in speed as floating ice shelves continue to disappear.

  13. Activating ATM with Broken DNA

    Cells depend on a checkpoint mechanism that stops cell division when damaged DNA is detected, but which molecular sensors “see” breaks in DNA strands is unclear. DNA damage leads to activation of the protein kinase ATM, the product of the gene mutated in ataxia-telangiectasia (a human disease characterized by sensitivity to radiation and predisposition to cancer). Lee and Paull (p. 551, published online 24 March 2005; see the Perspective by Abraham and Tibbetts) describe an in vitro assay in which dimeric ATM (but not the monomeric enzyme) is activated by broken DNA molecules in the presence of the MRN complex, a complex of three other proteins. The MRN complex interacts with DNA and recruits ATM to the DNA-bound complex. Thus, adenosine triphosphate-dependent DNA unwinding by the MRN complex appears to be a necessary step in the activation of ATM.

  14. Developmental Balancing Act

    In vertebrates, somites are the developmental precursors for muscle and bone. Several signaling pathways affect somite development, and elimination of the retinoic acid (RA)-synthesizing enzyme RALDH2 yields compacted somites. Vermot et al. (p. 563, published online 24 February 2005) examined how RA contributes to the control of somite development. When RALDH2 was eliminated in mice, the coordinated left-right symmetry in somite development was affected in somite stages 8 to 15, with as many as three extra somites observed on one side relative to the other. An apparent correction in this asymmetry occurs later in development. Embryonic RA appears to coordinate the progression of somite-specific signaling and development along the left and right sides of the organism.

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