This Week in Science

Science  22 Jul 2005:
Vol. 309, Issue 5734, pp. 532
  1. Bear's Witness


    The study of DNA in ancient remains can be hampered by contamination that ranges from bacterial to human. However, Noonan et al. (p. 597, published online 2 June 2005) present the results of a metagenomic approach to analyze large amounts of ancient genomic DNA sequence from extracts of 40,000-year-old cave bear bones. Because of the extensive information that is already available from comparative genomics, the genuine bear sequences could be distinguished from contaminants. In addition, the evolutionary relationship between extinct and modern bears was elucidated.

  2. Management Opportunities in Land Use

    Human activities now appropriate more than one-third of the Earth's terrestrial ecosystem production. Foley et al. (p. 570) review the local and global impacts of land-use change on ecosystem function and services, the latter including the provision of fresh water and maintenance of soil fertility. Although increasing land use has caused deterioration in the capacity of ecosystems to provide such services, certain land-use strategies could lead to win-win-win opportunities for conservation, economics, and social development.

  3. Mantle Versus Meteorites

    Earth's silicate composition is thought to be similar to that of chondritic meteorites, the likely building blocks of the terrestrial planets. Thus, differences in isotopic composition of the crust from that of chondrites have been interpreted as requiring complementary reservoirs in Earth's mantle, and these data, particular for Nd isotopes, have been the basis of many models of Earth's interior. Boyet and Carlson (p. 576, published online 16 June 2005; see the 17 June news story by Kerr) now show that chondritic meteorites have a different relative abundance of 142Nd—the daughter of short-lived 146Sm—than sampled rocks on Earth, Moon, and Mars. The best explanation for this finding is that Earth's mantle was differentiated within about 30 million years of its formation. A small portion of the mantle, enriched in certain elements, has remained isolated and has not formed additional crust. The bulk of the mantle, now with a different composition from that of chondrites, formed Earth's continental and oceanic crust, as well as the Moon.

  4. Solid-State Quantum Computing Made Simple?

    Proposals for solid-state quantum computing have so far relied on two-qubit gates as the elementary units, but controlling the coupling interaction between qubits presents a significant challenge for real implementations. Taking cues from the quantum optics community, which has shown that quantum information processing could be carried out using only linear optics, Engel and Loss (p. 586; see the Perspective by Egues) propose a solid-state protocol that does not require interacting two-qubit gates. Using electron spins in a double quantum dot system, they argue that a Bell-state measurement of the spin-parity (converted to a charge-state for easy readout) should allow for a simpler and scalable solid-state quantum computer scheme.

  5. Olefin Metathesis at Metal Surfaces

    Stable bonding of organic molecules to metals is often achieved via thiol-gold chemistry. Although robust, it is difficult to do any further reactions with this saturated bonding arrangement. Two groups report on olefin metathesis reaction performed at carbene groups attached to metallic substrates. Siaj and McBreen (p. 588) attached cyclopentylidene groups on Mo2C surfaces, which are stable to very high temperatures. They can grow polynorbornene from this alkylidene site through ring-opening metathesis conducted at ~230°C. Tulevski et al. (p. 591) reacted diazomethane derivatives with clean ruthenium films to form surface carbene groups that are stable under ambient conditions to temperatures of 160°C. When formed on Ru particles, these carbene groups underwent olefin metathesis reactions. These reaction chemistries may also find application in forming surface polymers.

  6. Toll-Like Receptor Structure Revealed

    Binding of diverse ligands initiates various signaling pathways that play a role in the immune response. Human Toll-like receptor 3 (TLR3) is activated by double-stranded RNA, such as those associated with many viruses. The lack of a three-dimensional structure for any TLR has hampered the design of experiments to define their mode of signaling. Choe et al. (p. 581, published online 16 June 2005; see the cover) have determined the TLR3 ectodomain structure at 2.1 angstrom resolution. The ectodomain forms a horseshoe-shaped solenoid that comprises 23 leucine-rich repeats. The inner concave surface and a large portion of the outer surface are covered by carbohydrate. One face is glycosylation-free, which suggests that it may play a role in ligand binding and oligomerization.

  7. Overcoming Cultural Barriers


    Hepatitis C virus (HCV) is a major cause of chronic liver disease, with over 170 million persistently infected individuals worldwide. The development of drugs for HCV has been slowed by the absence of a cell culture system for studying viral replication. Lindenbach et al. (p. 623, published online 9 June 2005) constructed a full-length HCV genome using sequences from two different viral strains and found that the chimeric virus can replicate to high titers in cultured human liver cells. The virus spread from cell to cell and could be partially neutralized by an antibody against a viral glycoprotein and by a soluble form of a cellular surface protein involved in viral entry.

  8. Room to Roam

    An evaluation by Ceballos et al. (p. 603; see the news story by Stokstad) of global conservation priorities and conflicts for an entire animal group, the land mammals, shows that at least 15% of Earth's land surface is needed for the conservation of 10% of the geographic ranges of the great majority of mammal species. A variety of approaches to conservation will be necessary in different areas and for different taxa, ranging from protected reserves to management of human-dominated landscapes. How is animal population size regulated? Sibly et al. (p. 607; see the Perspective by Reynolds and Freckleton) analyze population time series from 1780 data sets that cover four of the major taxonomic groups of animals. Most populations do not grow exponentially to carrying capacity, as previously assumed. Instead, growth rate is strongly adjusted by density-dependent factors and slows long before carrying capacity is achieved. Despite the differences in evolutionary history, metabolism, and body size, species in all four groups generally show strong density dependence at low population levels that falls off at high population levels.

  9. Hippocampal Memory Formation Revisited


    What is the role of the hippocampus in spatial representation versus representation of episodic and other nonspatial information? Leutgeb et al. (p. 619; see the Perspective by Buzsáki) find that hippocampal neurons have independent coding schemes for location and for what happens at a location. Changes in spatial location are represented as changes in location of firing in hippocampal place cells, whereas changes in cue configuration at a single location are represented by changes in firing rate. These results explain how, depending on the choice of dependent variables, different results have been obtained. The combination and integration of spatial and nonspatial information in the hippocampal output may form the neural basis for the role of the hippocampus in episodic memory.

  10. Considering Chromosome Rearrangements

    What are the causes, constraints, and consequences of chromosome rearrangements? Murphy et al. (p. 613) used genome sequences and high-density comparative maps from eight species within five mammalian orders to infer evolutionary processes influencing chromosome dynamics. Chromosomal breakpoints tended to be reused during evolution, and there has been an increase in the rates of mammalian chromosome breakage since the Late Cretaceous period. Centromeres tended to be associated with reuse breakpoints. Forty breakpoints were identified as primate-specific, and nearly all involved segmental duplications.

  11. Drab and Glam Together

    The males and females of Eclectus roratus, a parrot of the Australian rainforest, are so different in their plumage that they were long regarded as separate species. In contrast to the normal pattern in sexually dimorphic birds, males are drab while females are brightly colored. An 8-year field study by Heinsohn et al. (p. 617) has revealed that the reversed sexual dichromatism in Eclectus is not a result of sex-role reversal, the standard explanation for this phenomenon. Instead, it seems that contrasting selection pressures are acting on males (avoiding predation) and females (competition with other females).

  12. Just in Time

    A circadian clock serves to manage internal physiology in a cyclical manner. Dodd et al. (p. 630) now investigate the advantages conferred by having a circadian clock. Arabidopsis plants with cycles closely matched to their environmental light-dark cycle showed improved fitness relative to plants whose cycles did not fit well. The mechanisms may involve production of certain proteins in a “just in time” manner, anticipating daylight soon enough to produce the photosynthetic machinery, but not so much in advance that certain unstable proteins start to degrade.

  13. Cool Martian Surfaces

    More than 30 meteorites from Mars have been identified, and many of these have been dated by different isotopic systems. Shuster and Weiss (p. 594) point out that for one type of martian meteorite, the nakhlites, as well as a few others, the ages based on radiogenic argon accumulation agree with those for other systems. By modeling the diffusion of argon in minerals, which is highly temperature dependent, they show that these meteorites could not have been heated to above about 0°C since near the time of their crystallization. These data thus imply that the surface of Mars has long been cold for the last 4 billion years.

  14. A Long, Hot Streak

    The Eocene was an extended interval of warm climate that lasted from 55 million years ago (Ma) until 34 Ma, when permanent ice sheets developed in Antarctica. Pagani et al. (p. 600, published online 16 June 2005) present a proxy record of atmospheric CO2 concentration for the middle Eocene to the late Oligocene (~45 to 25 Ma), based on the stable carbon isotopic composition of alkenones, a type of molecule produced by certain marine algae. The levels of CO2 during the Eocene ranged from 1000 to 1500 parts per million (ppm), and then rapidly decreased to modern levels of 200 to 300 ppm by the end of the Oligocene. These data have implications for understanding issues such as the expansion of ice sheets and the development of terrestrial C4 photosynthesis.

  15. Predator-Prey Interactions

    A combination of experiment and modeling suggests a simple mechanism for the stabilization of an interaction between a prey species and its natural enemy. Murdoch et al. (p. 610) show that experimentally induced outbreaks of the California red scale insect on individual trees were stabilized within a few months by the parasitoid Aphytis, the biological control agent widely used to protect citrus crops. The key to stabilization is the interaction of life-history characteristics of the two partners in the interaction. The actual stabilizing mechanism can be modeled as differential vulnerability at different stages of the pest's life cycle, combined with the fast developmental rate of the parasitoid. The mechanism may be quite general because a large proportion of interactions of prey and natural enemies share these characteristics.

  16. A Place for Every Nucleosome, and Every Nucleosome in Its Place

    The protein component of chromatin, which consists of nucleosome octamers for the most part, is much more than a passive packing material—it plays an active role in controlling both the accessibility and activity of the DNA it sequesters. Yuan et al. (p. 626, published online 16 June 2005; see the 17 June News story by Marx) present a genome-wide analysis of chromatin structure at the level of individual nucleosomes, using tiled microarrays to determine the positions of nucleosomes along the length of an entire yeast chromosome, as well as many additional regulatory regions. The majority of nucleosome positions are remarkably well preserved, especially over genes, except for those undergoing high levels of transcription. Furthermore, functional transcription binding sites and yeast promoters are mainly nucleosome-free. These nucleosome-free intergenic regions are highly conserved among yeast species, and enriched in poly(dA-dT), hinting at a causal role in nucleosome positioning.