This Week in Science

Science  08 Jun 2001:
Vol. 292, Issue 5523, pp. 1793
  1. Making Messenger RNA

    RNA polymerase II is the molecular machine responsible for all messenger RNA (mRNA) synthesis in eukaryotes. Cramer et al. (p. 1863) describe the structure of this large enzyme at 2.8 angstrom resolution, which allows the identification of most amino acid side chains, and Gnatt et al. (p. 1876) describe the structure of a complex caught in the act of transcription at 3.3 angstrom resolution (see the cover and the Perspective by Klug). The complex shows the position of the DNA duplex and the RNA-DNA hybrid. The polymerase is divided into four mobile modules that allow a clamp to be open in the uncomplexed structure, so that promoter DNA can enter, but that can close over the RNA and DNA in the complex. Together, the structures reveal protein features crucial in transcription and provide insight into how transcription is initiated, how the mRNA transcript is elongated, and how transcription factors are likely to interact with the polymerase.

  2. Not-So-Clear Skies

    The hydroxyl radical OH, the principal chemical oxidant in the atmosphere, reacts with organic hydrocarbons, carbon monoxide, methane, and most other trace constituents with appreciable lifetimes. Although OH can be measured directly at the local scale, estimates of its hemispheric or worldwide distribution must be made by measuring the concentration of an atmospheric species with which it reacts at a known rate. Measurements by Prinn et al. (p. 1882) of one such species, methyl chloroform, show that the concentration of OH has been higher in the Southern Hemisphere than in the Northern Hemisphere for the past 20 years. Global OH concentrations rose during most of the 1980s but have declined to below 1978 concentrations during the past 10 years. This trend, whose origins are still poorly understood, implies that the ability of the atmosphere to cleanse itself of anthropogenic greenhouse gases is decreasing.

  3. Nanowire Lasers

    Wide-band gap metal oxides prepared as low-dimensional structures could be used to create novel opto-electronic devices. Huang et al. (p. 1897) demonstrate room-temperature ultraviolet lasing from self-organized, oriented zinc oxide nanowire arrays deposited on sapphire substrates and synthesized using a simple vapor transport and condensation process. Grown in a preferred direction, these wide-band gap semiconductor nanowires form natural laser cavities with diameters varying from 20 to 150 nanometers and lengths up to 10 micrometers. Under optical excitation, surface-emitting lasing action is observed at a near-ultraviolet wavelength of ∼385 nanometers with emission linewidth of less than 0.3 nanometer. This performance was achieved at a fairly low threshold of 40 kilowatts per square centimeter.

  4. Making Diamond Shine

    In addition to the desirable structural and thermal properties of diamond, its wide band gap makes it an attractive material for opto-electronic applications in the ultraviolet regime. Natural diamond is a p-type conductor (the charge carriers are “holes”), but the creation of its counterpart, n-type diamond (in which the carriers are electrons), has been particularly difficult because of problems in artificially doping diamond. This limitation has so far hindered the development of diamond-based opto-electronics. Koizumi et al. (p. 1899; see the Perspective by John) report on the preparation of n-type diamond grown epitaxially on a p-type diamond substrate that exhibits the electrical characteristics of a good pn junction. They show that the junction emits ultraviolet light when placed under forward bias.

  5. Overkill of Pleistocene Megafauna

    The majority of species of large land mammals, reptiles, and birds (mostly greater than 45 kilograms in weight and referred to as the megafauna) on the major continents, such as Australia and North America, went extinct over a time period of thousands of years. This extinction has usually been attributed to the arrival, expansion, and migration of human populations who hunted the megafauna, but it has been difficult to eliminate other possible causes for megafaunal extinction, such as climate change. Two reports provide evidence for anthropogenic overkill as a primary cause in North America and Australia (see the news story by Dayton and the book review by Pimm). Roberts et al. (p. 1888) dated megafaunal burial sites across the Australian continent and estimated extinction around 46,400 years ago; 10,000 years after the arrival of humans, but about 23,000 years before the Last Glacial Maximum. The rapid extinction of some 30 large mammalian herbivore species in North America at the end of the Pleistocene 12,000 to 13,000 years ago has been attributed both to climate change and to hunting by humans. Using a computer simulation model, Alroy (p. 1893) shows that given simple assumptions about human and prey species distributions and ecology, the inference of a major mass extinction caused by hunting might be hard to avoid. The simulation model, which unites population dynamics, ecology, conservation, and anthropology, shows that humans even at low densities are capable of precipitating the collapse of prey populations.

  6. Rarely Sharing Their Genes?

    The possibility of transfer of genes across species (lateral gene transfer) is of interest in understanding the evolution of species and in considering the possibility that bacterial infections can result in the transfer of genetic material to humans or other hosts. Salzberg et al. (p. 1903; see the Perspective by Andersson et al.), in a careful analysis of all available sequences of the human genome, present evidence that fewer than 50 genes are shared exclusively by bacteria and humans and are candidates for being the product of lateral transfer. This finding reduces previous estimates, but alternative explanations—sampling effects, gene loss, and rate variation within a genome—still exist.

  7. Watching While the Other Works

    Carbenes, in which a carbon atom forms only two single bonds and thus carries two nonbonding electrons, are highly reactive species that were long thought to exist only transiently, as is the case for the simplest carbene, CH2. However, carbenes can now be isolated, either as the spin-paired singlet and unpaired triplet forms, by carefully choosing the two substituent groups on the carbon atom to balance and shift electron density. Solé et al. (p. 1901; see the Perspective by Wentrup) now show that singlet carbenes can be stabilized by tuning only one of the substituents, which is designed to have both π-bond donor and σ-bond acceptor character; the other substituent is a mere spectator. This finding should greatly expand the number of stable carbenes that can be prepared and expand their synthetic utility.

  8. Helper T Cells Decide Their Own Fate

    Helper CD4 T cells (TH cells) acquire distinct phenotypes, depending on the prevailing cytokine environment, and two models exist to explain how this might occur. The first is an “instructive” model, which proposes that cytokines direct cell fate by launching a program of differentiation and gene transcription. The second is a “selective” model which suggests that T cells undergo an essentially stochastic fate determination that is then supported by the appropriate set of cytokines. Mullen et al. (p. 1907) present evidence for a selective model of TH1 development. They demonstrate that expression of the hallmark TH1 cytokine interferon-γ (IFN-γ and a recently identified master regulator gene, T-bet, are independent of interleukin-12 (IL-12) and the associated protein STAT-4 (signal transducer and activator of transcription 4). Retroviral expression of T-bet directly initiated IL-12-autonomous induction of IFN-γ expression, which could then be secured with the provision of a IL-12/Stat-4 signal. The stabilization of IFN-γ expression by IL-12/Stat-4 correlated with the activity of CBP (CREB-binding protein), a cofactor with intrinsic actyltransferase and chromatin-remodeling activity. These findings suggest that cytokines may be critical in nurturing committed TH cells, rather than dictating to those that have not yet made a decision.

  9. Extra p53 Export Route

    The tumor suppressor p53 is one of the best-characterized proteins, but it can still come up with a few surprises. Zhang and Xiong (p. 1910; see the Perspective by Gottifredi and Prives) identified a second nuclear export signal (NES) in p53. This NES, which is close to the amino-terminus of the protein, is inactivated in response to phosphorylation, which is itself stimulated by DNA damage. The work elucidates one of the mechanisms by which cellular injury controls the distribution of this key protein in the body's cellular defenses against malignancy.

  10. Clicking on a Mouse Model

    In recent years, certain human diseases have been linked to changes in particular chromosomal regions. However, many diseases involve multiple genetic loci, thus compounding the complexity of the problem. The mouse has proven to be a useful model for studying human disease. Using genotype and phenotype information from common inbred mouse strains, Grupe et al. (p. 1915; see the news story by Davenport) have developed a Web-accessible database that can be computationally analyzed to identify chromosomal regions regulating complex disease-related traits in mice. This molecular genetic analysis can be performed in milliseconds and does not require laborious, time-consuming, and costly genetic mouse studies.