This Week in Science

Science  26 May 2000:
Vol. 288, Issue 5470, pp. 1297
  1. Oscillating Sunspots

    Some sunspots show oscillations in the shape and strength of spectral lines in the chromosphere above the sunspot umbrae; these umbral flashes occur with periods of about 3 minutes. Socas-Navarro et al. (p. 1396) observed anomalous circular polarization profiles for two sunspots and developed a model that inverts for the characteristics of the spectral lines of the umbral flashes by including nonthermal emissions. From their model, they suggest that umbral flashes result from the periodic formation of a downward-flowing magnetized region, and all sunspots may have umbral flashes but that some go unseen because of a lack of spectral resolution.

  2. Poles Apart

    Loss of stratospheric ozone at the poles depends on the presence of polar stratospheric clouds (PSCs) that promote formation of the “active” chlorine that catalytically destroys ozone molecules. An important step in this process is denitrification. Tabazadeh et al. (p. 1407) have evaluated satellite measurements of Antarctic stratospheric nitric acid and water vapor and introduce the concept of “PSC lifetime” to show why denitrification is more severe there than in the Arctic. This idea can be used to help explain why the Arctic has not developed an ozone hole like the one in the Antarctic and suggests that widespread Arctic ozone loss could occur if further stratospheric cooling were to accompany changes in the concentrations of greenhouse gases.

  3. Excited on the Surface

    Measurements of the dynamics of excited electrons on metal surfaces, which can control electronic processes and chemical reactions, must overcome the role of defects and the strong interactions with other electrons. Two reports present experimental approaches to overcoming these difficulties (see the Perspective by Wolf and Ertl). When an electron is excited and leaves behind a positively charge hole, it can roam the surface until it recombines with another electron. Various experimental and theoretical studies have given differing surface hole lifetimes. Kliewer et al. (p. 1399) used scanning probe microscopy to measure the hole lifetime on microscopic regions of the surface. Previous techniques were macroscopic in that they averaged across the surface and did not take into proper account scattering in the surface region. When scattering in the surface is properly taken into account, the discrepancies between theory and experiment can be resolved. When atoms or molecules adsorbed on a surface are excited electronically (for example, with light of suitable wavelength) chemical reactions may occur. The associated structural changes usually occur on time scales of femtoseconds, too fast to be resolved even by ultrafast diffraction techniques. Petek et al. (p. 1402) exploit an unusually long-lived electronic state for cesium on a copper surface to study the changes in surface electronic structure with time. Their “movie,” with 13.4-femtosecond frames, indicates that the cesium-copper bond is extended by 0.35 angstrom as a result of laser excitation before it relaxes back to its equilibrium position.

  4. Helical Inversion

    Changes in chirality can be induced photochemically and reversibly in certain small chemical compounds. Redox-driven chirality changes have also been investigated, but with less success. Zahn and Canary (p. 1404) have synthesized copper complexes that undergo complete and reversible helix inversion of the orientation of the two chromophores in these propeller-shaped molecules as a result of oxidation and reduction between CuI and CuII. The change is driven by the reorientation of one of the chromophores caused by a change in ligand.

  5. The Flip Side of Ion Pumping

    The membrane protein bacteriorhodopsin uses the energy from one photon of visible light to transport one proton from the interior of Halobacterium to the external medium. Halorhodopsin, also found in Halobacterium, bears about 30% sequence identity to bacteriorhodopsin but uses one photon to pump a chloride ion inward. How such a similar protein can catalyze such an apparently different reaction is now clearer as a result of the structure presented by Kolbe et al. (p. 1390; see the Perspective by Spudich). The photon-driven cis-trans isomerization of retinal serves to flip the Schiff's base and to drag the chloride ion to a site that provides access to the cytoplasmic space. Subsequent relaxation and reisomerization allow the chloride-binding site to be refilled from the external medium.

  6. Growing Together

    Tropical forests contain a very high diversity of tree species, but there is little baseline information that describes the population structure and dispersion of individual tree species, many of which are rare. Condit et al. (p. 1414) now present a massive survey of all stems greater than 1 centimeter in diameter, in forest plots 25 to 52 hectares in area, at six sites in Asia and Central America. This large sample of more than 1000 species shows that most tree species are aggregated and not randomly distributed or overdispersed, as many previous reports have suggested. Aggregation is maintained even among very large trees, and rare species are more aggregated than common ones. This new wealth of data paves the way for greater understanding of the factors controlling diversity in tropical forests.

  7. Getting a Grip

    Messenger RNAs are transcribed from their complementary gene in the DNA by the enzyme RNA polymerase II plus a host of additional transcription factors. One of these, transcription factor IIH, is a 3'-5' DNA helicase and is required for melting the double-stranded DNA at the transcription start site so that RNA polymerase, which acts only on single-stranded DNA, can gain access. Rather than acting directly on the start site to cause unwinding and melting, Kim et al. (p. 1418) show that IIH actually acts at a distance and binds to DNA 3 to 25 nucleotides downstream of the start site. From this adjacent position, the authors suggest, IIH acts as a “molecular wrench” to exert torque on the DNA helix. Separation of the DNA strands slightly upstream forms the start-site transcription bubble.

  8. Recognizing More than DNA Sequences

    The multiprotein complex TFIID has sequence-specific DNA binding activity and mediates regulation of transcription. The largest subunit of TFIID, TAFII250, has activities that give it a potential role in chromatin targeting or remodeling. Jacobson et al. (p. 1422; see the news story by Pennisi) present the crystal structure at 2.1 angstroms of the double bromodomain from human TAFII250. The structure reveals two four-helix bundles, each of which contains a hydrophobic central pocket that is likely to bind acetyllysine. Comparison of binding affinities for mono-, di-, or multiply-acetylated histone H4 peptides showed that binding was tightest for two acetyllysines separated by seven residues, a separation consistent with the distance of 25 angstroms between the binding pockets. The structure also displays localized patches of positive and negative charge that could be involved in nucleic acid and histone binding. Thus, the authors propose that the double bromodomains may recognize diacetylated H4 tails and target TFIID to specific chromatin-bound promoters.

  9. Profile of a Killer

    The Nipah virus, which was responsible for an outbreak of encephalitis that caused the deaths of 105 people in Singapore and Malaysia, has now been characterized by Chua et al. (p. 1432). The virus was classified as a member of the Paramyxoviridae family by electron microscopic analyses of the nucleocapsid structure and replication, as well as by serologic and sequence criteria. Epidemiological evidence had indicated that the infections occurred in people who came in contact with pigs and the virus was found in pig respiratory tracts. The authors suggest that Nipah virus and the recently discovered Hendra virus form part of a new genus; these viruses are unusual in the number of species that they can infect and potentially kill.

  10. Microbacterial Virulence Genes

    Some mycobacteria are responsible for severe and persistent human disease. Mycobacterium marinum, a close relative of the tuberculosis (TB)-causing species, infects a range of ectotherms and can cause disease to the cooler extremities of humans. Ramakrishnan et al. (p. 1436; see the news story by Wickelgren) have used differential fluorescence induction to show that in living organisms (leopard frogs infected with M. marinum), the pathogen expresses a specific set of genes during chronic infection within granulomas and that a particular subset of these genes are essential for the organism to subvert and parasitize cells of the host's immune system. Although known to exist, these genes had not previously been ascribed any function. Moreover, the same genes in M. tuberculosis can now be targeted against TB.

  11. To B Cell, or Not to B Cell

    The transcription factor PU.1 is essential in B cell and macrophage development and proliferation. DeKoter and Singh (p. 1439) show that the level of expression of PU.1 can control which cell fate will result. At low levels, PU.1 protein caused precursor cells to differentiate into B lymphocytes (the cells involved in producing antibodies), whereas at high levels of PU.1 the same cells differentiated into macrophages (the cells that engulf invading organisms).

  12. Slow Diffusion

    Regional metamorphic reaction rates can be estimated by measuring the rate of diffusion of the isotopes of strontium between the fluid and the rock. Baxter and DePaolo (p. 1411) measured the strontium-87/strontium-86 ratio in garnets from metamorphic rocks near Simplon Pass, Switzerland, and found the inferred rates of reaction to be much slower than rates measured in laboratory settings. These results suggest that natural rates of reaction may be much closer to the strain rates inferred in the rocks, which would imply that these reaction rates may record the chemical history of the rock over tens of millions of years.

  13. Nuclear Envelope Assembly

    After cell division, a new nuclear envelope forms around the segregated chromosomes. Zhang and Clarke (p. 1429) have created a cell-free system to study this process in extracts of Xenopus oocytes. They demonstrate that the small guanosine triphosphatase Ran can directly stimulate assembly of a nuclear envelope in the absence of chromatin. They used a fusion protein of Ran with glutathione-S transferase that bound to the surface of beads made with glutathione. Assembly of nuclear envelopes around such beads was promoted by the nucleotide exchange factor RCC1 and appeared to require guanosine triphosphate hydrolysis by Ran. The experimental system promises to be useful for analysis of other factors that control nuclear envelope assembly.

  14. The Pause that Repairs

    When cells acquire DNA damage through exposure to ultraviolet (UV) light, they pause in the cell cycle to allow repair before cell division proceeds. One such checkpoint mechanism acts through the p53 tumor suppressor protein to increase the synthesis of the cyclin-dependent kinase inhibitor p21CIP1/WAF1. Mailand et al. (p. 1425) show another mechanism by which cells are prevented from undergoing DNA replication. In cells exposed to UV radiation, the phosphatase Cdc25A (which dephosphorylates and activates Cdk2) becomes ubiquitinated and is degraded in a proteasome-dependent manner. This process causes cells to pause in the G1 phase of the cell cycle before DNA synthesis occurs. Phosphorylation of Cdc25A by the protein kinase Chk1 may target the phosphatase for degradation. This pathway of signaling through Cdc25A and the one mediated by p53 though p21 appear to cooperate to prevent genomic instability. Improper function of either pathway could contribute to genomic damage and formation of cancer cells.

  15. Reversibility of HIV Drug Resistance

    To predict the effectiveness of antiretroviral therapy (ART) in preventing human immunodeficiency virus (HIV) infections in the San Francisco gay community, Blower et al. (Reports, 28 Jan., p. 650) developed a mathematical model that encompassed the effects of ART, potential increases in risky behavior, and the rate of emergence of drug resistance. Davenport comments that, because the model assumes that “patients with drug-resistant virus who cease treatment…will revert to being drug sensitive…within a short period,” few patients in the model remained drug resistant and untreated. “Because this group is expected both to have a high death rate…and to exert an influence on the spread of resistant virus,” says Davenport, “their absence is significant.” Blower et al. respond that their intention was to develop a “first, simple model to provide general insights,” and that more refined future models will address such variables as re-treatment failure rates. Meanwhile, note Blower et al., the time-dependent sensitivity analyses even for the simple model “revealed that neither a very high rate of acquired (or reacquired) resistance…nor a very high reversion rate…significantly affected the two main outcome variables of interest.” The full text of these comments can be seen at