This Week in Science

Science  19 Oct 2007:
Vol. 318, Issue 5849, pp. 355
  1. Clocks in the Corals


    Moonlight triggers the synchronized spawning of reef-building corals; however, the mechanism underlying detection of moonlight by these animals is largely unknown. Levy et al. (p. 467) now demonstrate the presence of ancient blue-light-sensing photoreceptors, cryptochromes, in the reef-building coral Acropora millepora (phylum Cnidaria). Cryptochromes regulate entrainment of the circadian clock of higher animals and plants. Expression of two coral cryptochrome genes, cry1 and cry2, was rhythmic under a light-dark cycle but not in constant darkness. Expression of cry2 varied with the full moon. This work suggests that cryptochromes not only function in the circadian clock of plants and higher animals, but may trigger the synchronized spawning of the Great Barrier Reef.

  2. Insights into Wasp Eusociality

    The observation that “worker” insects will care for their siblings rather than reproduce themselves is a hallmark of eusociality, a form of altruism that has long fascinated biologists, including Darwin. Toth et al. (p. 441, published online 27 September) tested the idea that this behavior evolved from early expression of “maternal care genes” prior to reproductive development in the wasp Polistes metricus. Unlike the better-studied honey bee, both workers and reproductives display maternal (brood provisioning) behavior in this wasp, but at different times. Similarities to the sequenced genome of the honey bee were used to identify a set of wasp genes expressed in the brain or known to be relevant to behavior. Reproductive, maternal females had gene expression patterns more like nonreproductive, maternal females (workers) than like reproductive, nonmaternal females (queens).

  3. Finite, Huge, and Complex

    Many physical systems, such as the atmosphere, transportation networks, and the Internet, are highly complex, and researchers have devoted much effort to modeling these systems mathematically. However, mathematics itself can also be a complex system, in which seemingly simple principles produce an exploding number of objects or structures. Foote (p. 410) reviews the case of finite group theory, which features such examples as the Enormous Theorem requiring 15,000 pages of proofs, and the Monster group containing 1054 elements. The ways in which mathematical concepts result in complex structures may help us understand the complexity of physical systems and vice versa.

  4. Tracing Mercury's Movements

    Mercury has many isotopes, and changes in its isotopic ratios may provide clues for tracing its movement in the environment. Bergquist and Blum (p. 417, published online 13 September; see the Perspective by Lamborg) now show that, in addition to the normal mass-dependent fractionation of isotopes that is typically seen, the odd isotopes of mercury under certain reduction conditions show evidence of a mass-independent fractionation (which has been shown previously for oxygen and sulfur). Through experiments in the lab and with fish from Lakes Michigan and Champlain, this isotopic signature was used to trace the loss of methylmercury by photoreduction.

  5. From Mussels to Multiuse Coatings


    Surface coatings often must be tailored to the substrates—hence we use different formulations to coat plaster walls versus wood trim. H. Lee et al. (p. 426) show that surfaces dipped into slightly basic dopamine solutions (inspired by the adhesives used by mussels) develop a polymeric coating that can be readily modified by secondary reactions. The polydopamine coating is generic and can be applied to surfaces of different materials (metals, polymers, and ceramics), as well as complex or patterned surfaces. The coated polydopamine surfaces can undergo two types of secondary reactions, such as metallization and self-assembled monolayer formation.

  6. The Inside Scoop on Gold Nanoparticles

    Metal nanoparticles are generally nonuniform and characterized by microscopy, but well-defined large metal clusters (more than 100 metal atoms) have been synthesized and characterized by x-ray diffraction. In the examples for platinum group metals, the metal-metal bonding is strong and dominates the packing of metal shells. Through a careful growth technique, Jadzinsky et al. (p. 430, see the cover and the Perspective by Whetten) obtained a crystalline sample of nanoparticles each containing 102 gold atoms and have solved the structure by x-ray diffraction to a resolution of 1.1 angstroms. The decahedral core geometry is consistent with prior hypotheses, but surface groups exert a strong influence on the outer gold shell and contribute to the electron count that stabilizes the cluster. The self-interactions of organosulfur-capping ligands create a rigid layer that imparts chirality to the clusters.

  7. Warming from the Cold Places

    The details of how the different parts of the climate system act and interact during changes from glacial to interglacial states are still being resolved. Stott et al. (p. 435; published online 27 September; see the 28 September news story by Kerr) construct a chronology of high- and low-latitude climate change at the last glacial termination, in order to help answer the questions of where warming originated, and why. Their data, derived from both benthic and planktonic foraminifera recovered from the same marine sediment core, indicate that deep-sea temperatures in the western tropical Pacific warmed about 1500 years before the surface waters did, a result of the earlier warming of the high-latitude surface water from where the deep water originated. The deep-sea warming also preceded the rise in atmospheric CO2, which suggests that increasing insolation at high southern latitudes caused a retreat of sea ice that led to warming there and further a field.

  8. Unwinding and Priming DNA


    Most DNA polymerases can only initiate DNA synthesis on a primed single-stranded (ss) DNA substrate. In eubacterial cells, DNA unwinding and priming is achieved by a complex of the DnaB helicase and the DnaG primase. The interaction between DnaB and DnaG stimulates both of their activities, but how this is achieved has been unclear. Bailey et al. (p. 459) report crystal structures of unliganded hexameric DnaB and its complex with the helicase binding domain (HBD) of DnaG. The two domains of DnaB pack with different symmetries to provide a two-layered ring structure. Three bound HBDs stabilize the hexamer in a conformation that may increase its processivity, and a potential ssDNA binding site on DnaB may guide the DNA to the DnaG active site.

  9. More Different Than Expected

    A method for identifying genomic structural variants (SVs, a type of variation including copy-number variants) is described by Korbel et al. (p. 420, published online 27 September). Paired-end mapping can quickly identify the location of the breakpoints at high resolution and determine in most cases exactly where in the genome they occur. With this method, the analysis of DNA from two individuals of different ethnic backgrounds shows unexpected amounts of SVs between individuals, which indicates that people are more genetically diverse than previously realized. Among the important findings is the observation that SVs are associated with certain (but not all) types of repeats, as well as unique sequences; insights also emerge into mechanisms by which SVs arise.

  10. Off with the Methyl Marks

    The methylation of histones, proteins that make up the bulk of chromatin in eukaryotes, plays a critical role in the epigenetic regulation of gene expression. Although the enzymes that put this mark onto chromatin are well known, the class of enzymes that take it off again, the Jumonji C (JmjC) family of demethylases, are a more recent discovery (see the Perspective by Rivenbark and Strahl). Although several JmjC lysine demethylases are known, no JmjC protein has been identified that can remove methyl groups from arginine residues in histones. Chang et al. (p. 444) now report the discovery of an enzyme, JMJD6, that demethylates histone H3 at arginine 2 and histone H4 at arginine 3, marks that are likely a critical part of the “histone code” that modulates chromatin function. Di- and trimethylation of histone H3 on lysine 27 (H3K27me2-3) are exclusively repressing signals and are implicated in X-chromosome inactivation, imprinting, stem cell maintenance, circadian rhythms, and cancer. The enzyme that places the marks has been known, and now M. G. Lee et al. (p. 447, published online 30 August) have identified the human enzyme, UTX (ubiquitously transcribed mouse X-chromosome gene), a JmjC domain-containing protein (similar to other demethylase enzymes), responsible for removing the H3K27me2-3 marks and promoting the activation of gene expression.

  11. All the Same

    During the processes that release solar wind particles from the Sun's surface, some changes in element or isotopic compositions may be imprinted. Characteristic isotope ratio variations between solar wind regimes might indicate particular physical processes. In three types of solar wind samples returned to Earth by the Genesis space mission, Meshik et al. (p. 433; see the Perspective by Marti) find no significant differences in either 20Ne/22Ne or 36Ar/38Ar between sample regimes, which rules out various models for solar wind production. Relative to Earth's atmosphere, however, 36Ar/38Ar is enriched by a factor of more than three, which suggests loss of the lighter isotope from the terrestrial atmosphere.

  12. Deeper Surface Mixing

    Eight episodes of massive iceberg discharge into the North Atlantic Ocean, called Heinrich events, have occurred in the past 65,000 years. These events caused intense regional cooling, and disrupted global deep ocean circulation for hundreds to thousands of years each time they happened. Their impact on the surface waters of the North Atlantic Ocean is of special interest as those waters sustain the most biological activity and are most directly involved in climate processes. Rashid and Boyle (p. 439, published online 20 September) show that Heinrich events modified the upper water masses of the North Atlantic Ocean by causing them to increase in thickness and to deepen. Such a change would have had major impacts on the ecology of the region. The authors suggest that the change was the result of windier conditions during those times.

  13. Compact Genetic Carrying Cases

    Compact solutions to data storage problems might seem a novel innovation, but some organisms developed elegant solutions for genetic packing long ago (see the Perspective by Landweber). Cyanidioschyzon merolae, an ultrasmall unicellular red alga, likely represents an ancestral eukaryotic form and has the smallest genome of all free-living eukaryotes so far sequenced. Analysis suggested that C. merolae contained only 30 nuclear transfer RNA (tRNA) genes, an insufficient number to decode all 61 codons of the genetic code. Soma et al. (p. 450) reanalyze the genome and discover 11 tRNA genes in which the 3′-half lies 7 to 74 base pairs upstream of the 5′-half of the gene. The halves are expressed in a single RNA that is circularized such that the permuted gene is now in the correct 5′ to 3′ order. Although split tRNA genes and permuted genes are both known, circular permutation of a gene has not been observed before. The mitochondrial genome of the single-celled protist Diplonema papillatum is composed of many small, circular chromosomes. Marande and Burger (p. 415) have sequenced many of these circular mitochondrial DNAs and show that none carries a complete mitochondrial gene, only very short gene pieces. These are transcribed individually, and then put back together, in a manner apparently distinct from transsplicing, to make contiguous messenger RNAs.

  14. The Best Offense Is Someone Else's Defense

    Part of the strategy that Agrobacterium uses to attack its host plant cells includes transferring part of its genome into the plant cell's genome. This DNA transfer event has been effectively used as a tool for plant genetic transformation in the lab. In the natural interaction, Agrobacterium uses a complex of proteins, including both its own and the host's, to effect the transfer of its DNA into the plant cell nucleus. One of the plant's proteins, VIP1, was known to function for Agrobacterium DNA transfer, but its use to the host plant was unknown. Djamei et al. (p. 453) have now discovered that the plant's VIP1 is supposed to function in a pathogen defense cascade. Thus, Agrobacterium derails the plant's defense response by using one of the plant's own effectors to carry the bacterial DNA into the plant nucleus.

  15. Freedom to Find the Right Partner

    Nonhomologous end joining (NHEJ) is critical for repair of DNA double-strand breaks (DSBs) repair, because the majority of DSBs have damaged, noncomplementary ends that must be bridged, resectioned, and resynthesized. Brissett et al. (p. 456) have analyzed a NHEJ synaptic complex from Mycobacterium tuberculosis. The ancillary polymerase of the repair DNA ligase D allows the DNA ends freedom to search for sequence complementarity on the opposing break. The formation of bridging pre-synaptic structures is mediated by microhomology-directed base pairing, mispairing, and template dislocations involving base flipping. Hairpin structures at the break ends likely facilitate end resection in readiness for the polymerase-mediated end-filling steps.

  16. Unraveling Ras Interactions

    Activated signaling through the small guanosine triphosphatase Ras is often associated with abnormal proliferation of cancer cells. Stites et al. (p. 463) used a combination of mathematical modeling and experiments to gain new insights into the regulatory properties of the network of factors that influence Ras (or are regulated by it) and how these factors are altered in cancer cells. Their results offer insight into why particular activating Ras mutants, but not others, are found in cancer cells, and suggest a pharmacological strategy that may preferentially impede excessive signaling in networks containing an oncogenically mutated form of Ras while sparing normal cells.