Ozone versus particulates
Ozone and fine airborne particles are the focus of new standards recently proposed by the United States Environmental Protection Agency, and emissions of volatile organic compounds (VOCs) and nitrogen oxides (NOx) affect the formation of both pollutants. Meng et al. (p. 116) used a three-dimensional model of the metropolitan Los Angeles air basin, which takes into account a large set of gas-phase and aerosol species and their interactions, to study pollution-reduction strategies. Controlling VOC and NOx emissions reduced ozone formation but had much less effect on particulates because of the effects of chemical coupling with other precursor species.
Studies of very young stars can provide clues to the origin of our sun and solar system. The closest well-studied region, about 150 parsecs away, contains large dark clouds of cold hydrogen and helium and is an x-ray source. Kastner et al. (p. 67) found that a much closer system containing the young sunlike star TW Hya and several other young stars, but lacking dark clouds, is a strong x-ray source and is about 20 million years old. Molecules of CO and HCN orbit the stars in a solar-system-like disk.
Not all of the current-carrying electrons in a superconductor are in the electron-paired Bose condensate. At finite temperatures, some of these electrons are in quasi-particle (QP) excited states, and their dynamics can reveal much about the superconducting state. Because QPs respond strongly to temperature gradients, Krishana et al. (p. 83; see the Perspective by Lee, p. 50) studied the thermal conductivity of Bi2Sr2CaCu2O8 using a bridge-balancing method to measure thermal gradients. An anomalous plateau behavior at low temperatures (near 20 kelvin) was found, which they suggest could be an abrupt phase transition of the superconducting condensate to a superconducting state in which the QP heat current vanishes.
Bismuth double bonds
Double bonds between nonmetals are seen for the lighter main group elements of the periodic table, but for heavier elements, overlap between the atomic p-orbitals becomes increasingly difficult and destabilizes the formation of the molecular π orbitals. Tokitoh et al. (p. 78) show that a double bond between two bismuth atoms, a sixth row element, can be stabilized in a highly sterically crowded compound. Relativistic electronic effects may be important for forming such a bond.
Quantum dot spectra
In quantum dots (QDs), small structure sizes or applied potentials or both confine and localize electrons. Gammon et al. (p. 85) have developed a technique that allows optical and nuclear magnetic resonance spectra to be recorded from semiconductor QDs with a lateral resolution of 10 nanometers. Such measurements can provide insights into the effects of local strain and composition.
The first migration of people to North America from Asia evidently occurred at the end of the last glaciation when sea level was much lower. Accurate local sea-level histories are necessary to track likely migration routes. Josenhans et al. (p. 71) used detailed bathymetry, seismic data, cores, and radiocarbon dates to reconstruct the sea-level history of the continental shelf of British Columbia. Sea level rose rapidly by up to 5 centimeters per year during the time of early occupation, and the shelf edge was available for human migration from about 14,500 to 10,000 years ago.
Cytochrome bc1 complex
An essential part of the respiration chain is the mitochondrial cytochrome bc1 complex. Xia et al. (p. 60) crystallized this complex and were able to construct atomic models of several of its protein components from x-ray studies. The four iron centers and two inhibitor binding sites were located, and other aspects of the structure could be interpreted with respect to physiological data.
More than just prions at work
The reports of a human variant of bovine spongiform encephalopathy (BSE) has made the understanding of the transmission of these agents even more imperative. Prions are protein agents with a protease-resistant conformation that propagates by inducing abnormal conformational changes in the normal protein and are suspected to cause diseases such as BSE and Creutzfeldt-Jakob disease (CJD). Manuelidis et al. (p. 94) found that, after numerous serial passages of a strain of CJD in guinea pigs and Syrian hamsters, a strain capable of inducing a disease in rats similar to BSE was observed. Disease pathology was seen in the absence of the protease-resistant form of the prion protein, which suggests that other features may be important for inducing disease.
What effect does leaf litter from streamside vegetation have on aquatic ecosystems? Wallace et al. (p. 102) excluded detritus for 3 years from a long stretch of a stream and found that for habitats composed of cobble, pebble, and gravel substrate, the effects were dramatic. The abundance and biomass of invertebrates, from detritivores to predators, declined greatly. Removal of detritus had no effect on the inhabitants of moss-covered bedrock, illustrating the use of different energy sources by neighboring in-stream invertebrate assemblages.
Downstream effects of rapamycin
The mammalian target of the immunosuppressant rapamycin (mTOR) is a member of an intriguing group of proteins that function in the cell division cycle and DNA repair. The mTOR molecule and related proteins are similar to phosphoinositide kinases, but whether their physiological targets are phosphoinositides or proteins has been unclear. Brunn et al. (p. 99) present evidence that mTOR functions as a protein kinase to phosphorylate the eukaryotic initiation factor (eIF)-4E-binding protein PHAS-1. PHAS-1 inhibits translation initiation by binding to eIF-4E, and this binding is inhibited when PHAS-1 is phosphorylated by mTOR.
Angiogenesis, the formation of new blood vessels, is regulated by both positive and negative factors. Among the positive regulatory factors is angiopoietin-1 (Ang1), a glycoprotein ligand that binds to and activates Tie2, a protein-tyrosine kinase receptor expressed primarily on vascular endothelial cells. Maisonpierre et al. have now isolated an angiogenic factor closely related in sequence to Ang1, called angiopoietin-2. In endothelial cells, Ang2 binds to but does not activate the Tie2 receptor; rather, it appears to antagonize the stimulatory activity of Ang1. Ang2 is expressed in tissues that undergo vascular remodeling in adults, and transgenic mice overexpressing this factor have severely abnormal blood vessels with frequent discontinuities. Ang2 may modulate the activity of Ang1 to effect alternative angiogenesis, stable vascularization, or vascular regression. [See the Perspective by Hanahan.]
Change in circulation
During the ice ages, the geometry and depth of the Arctic Ocean changed greatly, and most of it was surrounded by ice sheets. Bischof and Darby, by tracing ice-rafted debris in deep sea cores back to likely source areas, show that the circulation of sea ice and icebergs in the Arctic Ocean was likely different from the modern circulation. Today the circulation is primarily clockwise and ice exits through the Fram Strait, near Greenland. In contrast, during most of the last 700,000 years, the ice evidently moved directly toward the Fram Strait.
In many chemical reactions, the alignment of the reactants is important for the reaction to proceed. However, the exact collision conditions, that is, the vibration, rotation, and velocity of the reactant molecules, also influence reaction rates. Hou et al. studied the dissociative adsorption of deuterium molecules on a copper surface and found that the steric requirements for reaction depended strongly on the kinetic energy of the molecule. Strong steric preferences were seen at low collision energies but became less important as the collision energy increased.
Histone deacetylases in the nucleolus
Histones are nuclear proteins that package DNA into chromosomes, thus acting as a barrier to transcription. It is believed that histone acetylases and histone deacetylases (HDs) modify histones, and these modifications result in changes in the nucleosomal structure that affect transcription. Lusser et al. dentified a novel histone deacetylase in maize (HD2) that is not homologous to the yeast deacetylase RPD3. HD2 is an acidic phosphoprotein that is localized to the nucleolus, the nuclear compartments where ribosomal RNA is synthesized, and may participate in the regulation of ribosomal chromatin structure and function.
A new mutation, pickle, has been identified in the plant Arabidopsis thaliana by Ogas et al. Plants carrying the pickle mutation show an unusual morphology in their primary roots, although secondary and adventitious roots remain unaffected. When samples of mutant root tissue are cultured away from the ubiquitous plant hormone gibberellin, the tissue spontaneously produces new embryos and plants. The pickle mutation seems to alter responses to gibberellin and sustain an embryonic state of differentiation.
Transcription in the liver
Gene expression in the liver is regulated by several liver-enriched transcription factors. Two of these factors, hepatocyte nuclear factors 1 and 4 (HNF-1 and HNF-4), correlate with the differentiation state of liver cells. Ktistaki and Talianidis show that HNF-1 plays a central role in the regulatory network that defines the hepatic phenotype. Whereas HNF-1 and HNF-4 both activate transcription from promoters containing their respective DNA binding sites, HNF-1 represses genes that contain HNF-4 binding sites. This mechanism of repression involves protein-protein interactions between the two factors.
Cell shape and fungal disease
Fungal pathogens, such as Candida albicans, are opportunistic organisms that can be almost dormant, cause superficial infection, or can be life-threatening when tissue defense is low. Candida undergoes a morphological switch from cellular to filamentous growth that is believed to be important for pathogenesis. Braun and Johnson produced a Candida mutant that grows exclusively in the filamentous form by disrupting the homolog of the TUP1 gene of the yeast Saccharomyces cerevisiae, which acts as a general transcriptional repressor. This results suggests that genes under the negative control of the TUP1 homolog govern this morphological switch. [See the cover and the Perspective by Magee.]
Combinations of protease and reverse transcriptase inhibitors appear to hold great promise in treating HIV-1 (human immunodeficiency virus-type 1) disease. However, it is unknown to what extent the therapies can reconstitute the normal immune system. (Autran et al.) found that after 1 year of combination therapy, there was a significant decrease in HIV-1-driven CD4+ and CD8+ lymphocyte activation and a late increase in the number of naïve CD4+ cells. Improvements in the ability of the T cells to function after 6 months of therapy were also observed, as measured by antigen-specific responsiveness. Although this represents only a partial restoration, it suggests that the immune system has not been irreversibly damaged by HIV-1 infection. [See the news story by Cohen.]