This Week in Science

Science  12 Feb 2010:
Vol. 327, Issue 5967, pp. 757
  1. Standing High


      Sea-level rises and falls as Earth's giant ice sheets shrink and grow. It has been thought that sea level around 81,000 years ago—well into the last glacial period—was 15 to 20 meters below that of today and, thus, that the ice sheets were more extensive. Dorale et al. (p. 860; see the Perspective by Edwards) now challenge this view. A speleothem that has been intermittently submerged in a cave on the island of Mallorca was dated to show that, historically, sea level was more than a meter above its present height. This data implies that temperatures were as high as or higher than now, even though the concentration of CO2 in the atmosphere was much lower.

    1. Homing in on Hotspots

        The clustering of recombination in the genome, around locations known as hotspots, is associated with specific DNA motifs. Now, using a variety of techniques, three studies implicate a chromatin-modifying protein, the histone-methyltransferase PRDM9, as a major factor involved in human hotspots (see the Perspective by Cheung et al.). Parvanov et al. (p. 835, published online 31 December) mapped the locus in mice, and analyzed allelic variation in mice and humans, whereas Myers et al. (p. 876, published online 31 December) used a comparative analysis between human and chimpanzees to show that the recombination process leads to a self-destructive drive in which the very motifs that recruit hotspots are eliminated from our genome. Baudat et al. (p. 836, published online 31 December) took this analysis a step further to identify human allelic variants within Prdm9 that differed in the frequency at which they used hotspots. Furthermore, differential binding of this protein to different human alleles suggests that this protein interacts with specific DNA sequences. Thus, PDRM9 functions in the determination of recombination loci within the genome and may be a significant factor in the genomic differences between closely related species.

      1. Superconducting Quantum Optics

          The coherence properties of superconducting circuits enable them to be developed as qubits in quantum information processing applications. Astafiev et al. (p. 840) now show that these macroscopic superconducting devices also behave as artificial atoms and can exhibit quantum optical effects. The ability to fabricate and integrate these superconducting devices in electronic circuitry may help toward developing a fully controlled quantum optics system on a chip.

        1. Wave-Particle Duality

            The dual-wave nature of particles is nowhere more evident than in a confined space, where standing waves are formed with wavelengths that depend on particle energy. This so-called quantum interference has been observed in nanostructures using surface probes such as scanning tunneling microscopy. Now, Oka et al. (p. 843) use the spin-polarized version of this technique to study spin-dependent quantum interference on a triangular nanoscale cobalt island deposited on a copper surface. They observe the modulation of the magnetization, with the pattern depending on the energy of the interfering electrons. The experimental results are in good agreement with simulations, which indicate that the magnetization at a given energy and position largely depends on which of two electron spin states present dominates.

          1. Colliding in the Cold

              Chemical reactions occur through molecular collisions, which, in turn, are governed by the distributions of energy in each colliding partner. What happens when molecules are cooled so that they no longer have sufficient energy to collide? Ospelkaus et al. (p. 853; see the Perspective by Hutson) explored this question by preparing a laser-cooled sample of potassium rubidium (KRb) diatomics with barely any residual energy in any form (translational, rotational, vibrational, or electronic). By monitoring heat release over time, evidence was gathered for exothermic atom exchange reactivity through quantum mechanical tunneling. As predicted by theory, these reactions were exquisitely sensitive to the molecular states, with rates changing by orders of magnitude on varying minor factors such as nuclear spin orientation.

            1. Many Mixed Linkers in MOFs

                CREDIT: DENG ET AL.

                Crystallization can separate different molecules because different molecules cannot generally be accommodated equally well in the same crystal lattice. However, in metal-organic framework (MOF) compounds, the organic linkers do not pack closely to other parts of the lattice, so it may be possible to mix several linkers that are derivatives of a parent compound with the same end groups. Deng et al. (p. 846) show that zinc-based MOFs can be made that mix 1,4-benzenedicarboxylate and up to eight of its derivatives in a random fashion. The effects of such mixing on porosity and absorption characteristics is nonlinear; in one case, a mixed-linker compound was four times better for selecting CO2 versus CO compared with the best MOF bearing only one of the component linkers.

              1. Salty Stretch

                  What happens at the molecular level when salt dissolves in water? Much of the data characterizing the geometry and dynamics of ion solvation shells has come from indirect observation of the surrounding water structure. Using a time domain Raman technique based on the interference of four ultrashort polarized light pulses, Heisler and Meech (p. 857) have now mapped directly the stretching vibrations associated with the weak hydrogen bonding interactions between bulk water molecules and chloride, bromide, or iodide ions.

                1. Of Mice and Men

                    Just how closely must mouse models replicate the known features of human disorders to be accepted as useful for mechanistic and therapeutic studies? Soliman et al. (p. 863, published online 14 January) compared mice that vary only in their allelic composition at one position within the gene encoding brain-derived neurotrophic factor (BDNF) with humans exhibiting the same range of allelic variation. Individuals (mice and humans) carrying the allele that codes for a methionine-containing variant of BDNF retained a fearful response to a threatening stimulus even after its removal in comparison to those with the valine variant. Furthermore, in both cases, this linkage was mediated by diminished activity in the ventral-medial region of the prefrontal cortex. This deficit in extinction learning may contribute to differential responses to extinction-based therapies for anxiety disorders.

                  1. Decoding a Second-Messenger's Message

                      CREDIT: KRASTEVA ET AL.

                      Biofilms are aggregates of bacteria on a surface often associated with increased resistance to antibiotics and stress. In Vibrio cholerae, the bacterial species that causes cholera, biofilm formation is promoted by the bacterial second-messenger cyclic diguanylate (c-di-GMP) and involves the transcription regulator, VpsT. Krasteva et al. (p. 866) show that VpsT is itself a receptor for c-di-GMP and that binding of the small signaling molecule promotes VpsT dimerization, which is required for DNA recognition and transcriptional regulation. As well as activating components of the biofilm pathway, VpsT also down-regulates motility genes in a c-di-GMP–dependent manner.

                    1. DNA-less Evolution

                        Prions are proteinaceous infectious elements involved in a variety of neurodegenerative diseases, including scrapie in sheep and so-called mad cow disease in cattle. Now Li et al. (p. 869, published online 31 December) show that, when propagated in tissue culture cells, cloned prion populations become diverse by mutational events and can undergo selective amplification. Thus, even though devoid of a coding genome, prions, when propagated under a particular selection regime, can be subject to rapid evolution.

                      1. Viral Superspreaders

                          Viruses are thought to spread across a lawn of cells by an iterative process of infection, replication, and release. If this were the case, the rate of spread would be limited by the viral replication kinetics. Now, Doceul et al. (p. 873, published online 21 January; see the Perspective by Pickup) describe a spreading mechanism used by vaccinia virus that is not restricted by viral replication kinetics and that causes a dramatic acceleration of spread. Early after infection, vaccinia virus proteins A33 and A36 are expressed as a complex on the cell surface. This marks the cell as infected and causes superinfecting virions to be repelled by the formation of actin projections beneath the virus particle. Virions are repelled from infected cells repeatedly until an uninfected cell is reached and are thus pushed further away from the origin of infection to accelerate dissemination.

                        1. It's All About Self-Renewal

                            The Lmo2 oncogene was identified as a contributing factor in human T cell acute lymphoblastic leukemia (T-ALL) nearly two decades ago, but the gene rose to prominence in 2003 when its inadvertent activation by a retroviral vector was shown to cause leukemia in two patients in a gene therapy trial. The cellular mechanism by which the gene product of Lmo2, a transcriptional regulator, induces T-ALL is poorly understood. Studying transgenic mice, McCormack et al. (p. 879, published online 21 January) now show that Lmo2 confers self-renewal activity to committed T cells in the thymus without affecting their capacity for T cell differentiation. These self-renewing cells, which were detectable 8 months prior to the onset of overt leukemia in the mice, expressed genes in common with hematopoietic stem cells (HSCs), suggesting that Lmo2 might reactivate an HSC-specific transcriptional program.

                          1. From Steps to Clusters

                              When a flat surface of a single crystal is formed by cutting or cleavage, the atoms may move little from their bulk positions, or the surface may reconstruct as the atoms move to more energetically favorable positions. The adsorption of molecules can also change the energetic landscape and cause reconstruction. Tao et al. (p. 850; see the Perspective by Altman) examined “stepped” platinum surfaces, the (557) and (332) surfaces in which flat terraces are connected by atomic steps. Scanning tunneling microscopy and x-ray photoelectron spectroscopy revealed a reversible breakup into nanometer-scale clusters when CO surface coverages were very high. Density functional theory calculations suggest that this new morphology increases the number of edge sites for adsorption and relieves unfavorable CO-CO repulsions.

                            1. Pinpointing Genetic Selection

                                The human genome contains hundreds of regions with evidence of recent positive natural selection, yet, for all but a handful of cases, the underlying advantageous mutation remains unknown. Current methods to detect the signal of selection often results in the identification of a broad genomic region containing many candidate regions that vary among individuals. By combining existing statistical methods, Grossman et al. (p. 883, published online 7 January) developed a method, termed Composite of Multiple Signals, which can increase the ability to pinpoint the specific variant under selection. Several candidate regions under selection in human populations were identified.