This Week in Science

Science  05 Apr 2002:
Vol. 296, Issue 5565, pp. 9
  1. Going with the Grain

    Two separate research groups report high-quality draft sequences of the rice genome that are expected to facilitate advances in the agriculture of this critical food grain. Yu et al. (p. 79) sequenced the indica variety of rice, and Goff et al. (p. 92) sequenced the japonica variety of rice. Comparisons will show how these two popular rice strains have diverged. The rice genome also provides a useful road map for investigating the larger genomes of related cereal grains such as wheat and maize [see also the report by Seki (p. 141) on Arabidopisis complementary DNA clones]. Related pieces include a pull-out wall chart that gives a summary of important aspects of rice genome research, the editorial discussing the agreements that govern accessibility to some of the data, and letters to the editor that call for continuing with the sequencing of rice to the point of a final, complete sequence. In the Perspectives, Bennetzen, as well as Ronald and Leung, discuss the implications for genomic and agricultural sciences, Cantrell and Reeves discuss the implications that sequencing the rice genome holds for promoting worldwide food security, and Serageldin discusses the interplay between worldwide economic development and food security. News stories discuss the background on what many of the various rice genome-sequencing groups have been doing, the Celera-type agreements that are governing release of the data for the Goff et al. paper, and a profile of the Chinese group that authored the Yu et al. paper.

  2. Sun Twists

    The Sun's 11-year cycle of magnetic activity is characterized not only by changes in sunspot concentration but also by latitudinal variations in the rotation rate of bands of plasma at the Sun's surface. Vorontsov et al. (p. 101; see the Perspective by Toomre) have used oscillations in the acoustic gravity waves in the Sun's interior collected by the Solar and Heliospheric Observatory (SOHO) to track these zonal bands over a period of almost 6 years into the Sun's interior. The entire convection zone of the Sun is involved in the differential rotation and latitudinal shifts of the zonal bands. Such measurements should help in connecting the observed surface features and the solar magnetic field with the deeper dynamo, which is thought to be located at the base of the convective zone.

  3. Dodging Asteroids

    Normally, it is difficult to predict the orbital path of asteroids beyond a few decades because of the nonlinear nature of the processes that perturb their orbits. Giorgini et al. (p. 132; see the news story by Kerr) have recognized that asteroid 29075 (1950DA) presents a special case. Extensive radar and optical data collected over decades, an inclined orbit that reduces perturbations, and a previously unrecognized gravitational resonance that modulates the uncertainty of its orbital path allow an accurate orbital path prediction that extends for hundreds of years—including a possible collision with Earth in March 2880. The largest uncertainty in the orbital path simulation is related to 29075's unknown surface characteristics because anisotropic thermal re-radiation of absorbed solar energy from the asteroid's surface (the Yarkovsky effect) can significantly alter the orbit over a long time. In Brevia, Spitale (p. 77) shows that we can potentially mitigate asteroid hazards by altering the asteroid's surface, and the Yarkovsky effect, enough to avoid a collision with Earth.

  4. Into Africa

    A record of biogenic silica accumulation from Lake Malawi assembled by Johnson et al. (p. 113; see the Perspective by Baker) suggests a connection between cold conditions in the Northern Hemisphere (between 11,000 and 25,000 years ago) and high diatom productivity caused by north winds over that part of equatorial Africa. More frequent north winds over the Malawi basin may have resulted from a more southerly migration of the Intertropical Conversion Zone. This interpretation is supported by the Nb-Ti ratio of the sediments. This ratio, which varies roughly in concert with the biogenic silica accumulation rate, is controlled by the input of windblown volcanic ash that originates from a region north of the lake.

  5. Controlling Colloids

    Insights into the formation of glasses and crystals by molecules can be gained by studying and manipulating similar processes in colloidal particles, which can be more readily imaged (see the Perspective by Frenkel). Different amorphous states of a material can be observed that have different density, as has been observed for water. Pham et al. (p. 104) confirm through a mixture of simulations, theory, and experiments that two distinct glassy phases of a colloid can form that depend on the nature of the interparticle attractions. At high colloid concentrations, the particles jam against each other and produce a glass based on repulsive interactions. The addition of a noninteracting polymer first causes the glass to melt by causing additional repulsive interactions that open up the structure. Adding more polymer, however, produces a different glassy phase that forms through attractive interactions between the colloidal particles. In binary crystals of large (L) and small (S) colloids, crystal structures can be obtained that are analogous to the atomic structures, such as an LS2 structure analogous to that of AlB2. Working with concentrated systems and a narrow range in the ratio of S:L sizes, Velikov et al. (p. 106) create colloidal crystals through a layer-by-layer deposition technique. They not only replicated the LS2 and LS structures but also managed to obtain the LS3 structure, which does not have an atomic analog. By building the crystal from two materials, they could selectively remove the small colloidal particles to leave behind a hexagonal, non-closed packed crystal.

  6. Birds, Bile, and Breeding

    Birds use a variety of physiological and environmental cues to determine when best to lay eggs, but learning also plays a role. Grieco et al. (p. 136; see the news story by Withgott) have discovered, in experiments with blue tits in a Netherlands forest, that a female bird's experience of food supply in 1 year can influence the date of egg-laying in the subsequent year. By increasing the availability of food during the nestling period, the birds were duped into laying eggs later in the following year. Female sea lampreys must travel long distances up streams to reach the nests that their male counterparts have already built. The females follow a chemical cue released by the males, but the known fish sex pheromones, which include steroids, only act at short ranges. Li et al. (p. 138) show that male lampreys release a bile acid that can signal both their location and reproductive status to females over such large migratory distances.

  7. Cdc13 Joins the Fold

    The ends of eukaryotic chromosomes are capped by specialized nucleoprotein complexes called telomeres. The telomeric single-stranded (ss) DNA binding protein used by the budding yeast Saccharomyces cerevisiae, Cdc13, is unrelated in amino acid sequence to the telomere end-binding proteins in other organisms. Mitton-Fry et al. (p. 145) determined the solution structure of a complex containing the Cdc13 DNA binding domain and telomeric ssDNA and found that despite its distinctive primary sequence, Cdc13 uses the same structural motif for DNA binding—the so-called “OB fold”—as the other proteins.

  8. Tracking the Origins of Chromatin Acetylation

    Modulation of chromatin structure plays key role in the regulation of gene expression in eukaryotes, whereas in archaea, gene regulation is thought to be effected by simple bacteria-like repressors. Sir2, which plays an important role in chromatin dynamics in yeast, is highly conserved across prokaryotes, archaea, and eukaryotes. Bell et al. (p. 148) show that Sir2 from the archaeon Sulfolobus solfataricus modulates (and increases) the DNA binding activity of the chromatin protein Alba by deacetylating two of the lysine residues in its amino terminus. This step in turn facilitates Alba's ability to repress transcription in vitro. These results suggest that regulation of chromatin structure by acetylation arose in the common ancestor of the archaea and eukaryotes.

  9. The Outs and Ins of Signaling

    Integrins, which are central to cell adhesion, are cell surface molecules comprised of α and β transmembrane subunits. Their extracellular domains bind to external ligands containing the Arg-Gly-Asp tripeptide motif, and this results in the canonical “outside-in” signaling common to many cell surface receptors: Internal signals transmitted to their intracellular domains alter the ligand-binding competency of the external regions. Xiong et al. (p. 151) present the structure of the complex between the extracellular portions of the integrin αV-β3 and a cyclic peptide. The contacts made by the Arg-Gly-Asp residues lead to conformational changes in the relative orientations of the α and β subunits.

  10. Damage Control

    Successful repair of injured tissue relies on removal of products generated in the turnover of the extracellular matrix. Teder et al. (p. 155) offer direct evidence that CD44, a receptor for the matrix protein hyaluronan, is pivotal in this process. In a model of lung injury that usually resolves within 2 weeks, mice lacking CD44 expression developed fatal pulmonary inflammation caused by persisting inflammatory cells and low-molecular-weight hyaluronan fragments at the damaged site. Normal removal of these agents was associated with transforming growth factor-β activation and could be mostly attributed to CD44 expression on hematopoietically derived cells, rather than parenchymal cells of the lung.

  11. Structure of Intercalated C60

    The recent observation of electric-field-induced superconductivity in haloform-intercalated C60 at 117 K made it the closest competitor to the cuprate superconductors. By adding larger atoms to the C60 lattice, the intuitive picture put forward to explain the result was related to the increase of the electronic density at the Fermi level that should accompany the lattice expansion. Dinnebier et al. (p. 109) cast doubt on this simplistic scenario. They show from x-ray scattering that although the lattice does indeed expand, it is only the plane spacing that does so. The in-plane structure remains almost the same, which suggests that a more complex picture of the superconducting mechanism is required.

  12. Comparing Expressions

    A resource of great value to the Arabidopsis genome community is described by Seki et al. (p. 141). In an effort to identify all of the expressed Arabidopsis genes, the authors have cloned more than 150,000 complementary DNAs. This set of clones should account for about 60% of all Arabidopsis genes. Comparisons with expression predictions from whole-genome analysis offer a sense of how often these algorithms do, or do not, yield results that correspond with the actual genes that are actually transcribed.

  13. Outer Limits

    Restricted accessibility of DNA through association with heterochromatin is an important mechanism for gene regulation. In budding yeast, repression of genes also occurs at the periphery of the nucleus, although it is not clear if a similar mechanism exists in higher eukaryotes. Using two- and three-dimensional fluorescence in situ hybridization (FISH), Kosak et al. (p. 158) observed that B cell immunoglobulin (Ig) genes preferentially associate with the nuclear periphery in non-B cells, but were centrally disposed in B cells. The idea that these distinct nuclear locations regulate Ig gene rearrangement and expression was supported by the observation that movement away from the nuclear periphery was limited in cells that had been denied signals known to activate Ig gene rearrangement. Furthermore, compaction of the large Ig heavy chain locus occurred when it was centrally positioned, consistent with the need for the close proximity of VH gene segments during V(D)J rearrangement.

  14. The California Current, Devils Hole, and Pleistocene Climate

    Herbert et al. (Research Articles, 6 July 2001, p. 71) found that sea surface temperatures (SSTs) in the area now dominated by the California Current warmed 10,000 to 15,000 years before deglaciation at the past five glacial maxima but did not rise before deglaciation south of the modern California Current front. Thus, they concluded, early warming in this area (including the trend recorded in vein calcite at Devils Hole, Nevada) likely represented not a global signal but a regional one tied to weakening of the California Current due to growth of the Laurentide ice sheet, and that the Devils Hole record “does not pose a fundamental challenge to the orbital ('Milankovich') theory of the ice ages.” In a comment, Winograd, citing evidence of pre-deglaciation warming across a wide range of latitudes, asserts that the “intriguing notion linking California Current SSTs and the Laurentide ice sheet” is “open to question, as is [the] assertion” that the work resolves internal inconsistencies in the Milankovich theory. Herbert et al., in response, offer several arguments in support of their “basic conclusion that regional climate processes are important and are expressed in the preserved paleoclimate record.” The full text of these comments can be seen at