This Week in Science

Science  17 Apr 1998:
Vol. 280, Issue 5362, pp. 353
  1. T cell specificity and cathepsins

    The repertoire of CD4+ T cells that eventually circulate through the body are a result of careful culling to prevent autoreactivity or immunodeficiency. This selection process is initiated by major histocompatibility complex class II-expressing antigen presenting cells (APCs) in the thymus: The cortical epitheliuim initiates maturation of those T cells with helpful specificities, and the hematopoietically derived APCs identify autoreactive T cells that will ultimately die. Nakagawa et al. (p. 450 see the commentary by Creswell p. 394) have found that the cysteine protease cathepsin L is critical for the degradation of the invariant chain (Ii) of class II-but only in thymic cortical epithelium. Because Ii occupies the peptide binding site of class II molecules, the cathepsin L-deficient cortical epithelium was apparently unable to present the appropriate peptides to developing T cells. The lack of a positive selection signal led to a reduction in the number of mature CD4+ T cells. The activity of the various cathepsin family proteases was different in different tissues, so this result may offer some explanation for how stimulation of T cells by different types of APCs can have different consequences: The array of peptides that ultimately are presented may depend on the activity of the particular cathepsin active in that particular APC.

  2. Stormy clusters

    Clusters of galaxies are huge, gravitationally bound systems composed of about 1 percent visible galaxies, 15 percent intracluster gas, and 84 percent unseen matter (some form of dark matter that holds the entire cluster together). Burns (p. 400) reviews observations and modeling of these clusters which indicate that clusters have structure; complicated clumps of galaxies are woven together by irregular filaments, sheets, or walls into a weblike pattern with huge, empty void spaces (see cover). High, non-equilibrium temperatures and high relative velocities between galaxies indicate that clusters have collided, increasing the stormy conditions within the clusters. Many more collisions will occur until clusters will settle down into spherical balls of galaxies and gas in equilibrium with their dark matter.

  3. Strange matter

    Strange matter can be described as a soup of quarks, which are the elementary particles that make up protons and neutrons. Cheng et al. (p. 407) have developed a model for the unusual hard x-ray burster GRO J1744-28 (discovered by the Compton Gamma-Ray Observatory) that includes the formation of some strange matter. In their model, a star that accretes too much mass can cause the ‘crust’ of the star to crack, and the released mass is converted to strange matter that subsequently produces a fireball that expands outward. The relativistically expanding fireball interacts with the surrounding interstellar medium, which then creates shock waves that produce a burst of x-ray radiation. The intensity, duration, and spectrum of the modeled x-ray burst is consistent with recent observations of GRO J1744-28, which indicate that the x-ray burster may be associated with a strange star.

  4. Refractory inclusions: All together then

    Calcium and aluminum-rich inclusions (CAIs) found in carbonaceous chondrites and more rarely in ordinary chondrites have been inferred to represent some of the first solid particles formed in the solar nebula. The abundances of oxygen isotopes in CAIs from carbonaceous chondrites have been used to determine their spatial and temporal origin in the solar nebula. Now, McKeegan et al. (p. 414) measured the oxygen isotopic abundances of three CAIs from ordinary chondrites. They found a similar enrichment of oxygen-16 in the ordinary chondrite CAIs as had been found in the carbonaceous chondrite CAIs. This result suggests that the CAIs in all chondrites formed in a similar and restricted region of the solar nebula. Because ordinary chondrites are assumed to have been formed in a different region of the solar nebula than the carbonaceous chondrites, these CAIs must be distributed unevenly into different parts of the solar nebula.

  5. Carbonates tainting meteorites

    The Tatahouine meteorite fell in southern Tunisia on a limestone hill slope covered with a sandy soil on 27 June 1931. Samples were recovered that day and again in 1994. Barrat et al. (p. 412) compared the samples and found that the 1994 fragments contained carbonate within the fractures, whereas the 1931 fragments did not. They measured the carbon isotopes of the carbonates and found the isotopic data consistent with contamination from the sandy soil in which the samples were recovered.

  6. Stranded crust

    The Kerguelen Plateau, one of Earth's largest oceanic plateaus, formed during the opening of the Indian Ocean when India and Australia rifted away from Antarctica. Hassler and Shimuzu (p. 418) used osmium isotope data to show that the plateau is underlain by pieces of Precambrian continental lithosphere. One possibility is that a piece of Gondwanaland was delaminated and stranded in the Indian Ocean during rifting.

  7. Optimizing operators

    In many coherent spectroscopic methods, such as nuclear magnetic resonance (NMR), the experimentalist wants to maximize the observed signal to shorten the data collection process. Such measurements are made on ensembles of quantum states rather than pure states, and the observables have imaginary parts that correspond to the action of non-real-valued, or non-Hermitian, operators. Thus the methods that would optimize Hermitian operators will in general not lead to the best solution. Glaser et al. (p. 421; see the commentary by Warren, p. 398) describe a gradient-based procedure for optimizing these transformations that also has applications in applied mathematics and control theory.

  8. Hydrogen from solar cells

    Splitting water into hydrogen and oxygen with sunlight is one of the most important goals of photoelectrochemistry. However, the p-type semiconductors most suitable for hydrogen generation often cannot produce sufficient voltage bias to actually perform the reaction. Khaselev and Turner (p. 425; see the news story by Service, p. 382) have made the sunlight do double duty-a p-type GaInP2 layer adsorbs visible light to perform the electrochemistry that generates hydrogen, and it is sandwiched to a GaAs junction that adsorbs near-infrared light to generate an electrical potential that gives the p-GaInP2 electrode sufficient bias. The authors report an efficiency greater than 12 percent.

  9. Tracked in the GI tract

    Understanding the events that occur immediately (within days or weeks) after infection with the human immunodeficiency virus (HIV) could be important in understanding and preventing the cascade of events that follow and lead to disease. Veazey et al. (p. 427) studied SIV (simian immunodeficiency virus) infection of macaques and found that before changes are apparent in peripheral lymphoid tissues (which are the most extensively studied tissues in HIV infection), the lymphoid tissues of the gastrointestinal tract are the major site of SIV replication and CD4+ T cell loss.

  10. Clathrin and AP3 adaptor complex

    Different classes of clathrin-coated vesicles are used in receptor-mediated endocytosis at the cell surface and to sort secretory and lysosomal proteins upon export from the Golgi complex. Adaptor proteins appear to mediate the sorting of membrane proteins into clathrin coats. Two types of adaptor (AP-1 and AP-2) are well known at the two sites. A third class of adaptors (AP-3) was identified recently with a role in signal-mediated protein sorting to endocytic compartments but was not thought to interact with clathrin. Dell'Angelica et al. (p. 431) now show that the AP-3 complex does in fact interact with clathrin on Golgi and endosome-associated coats.

  11. Stress and potassium channels

    Stress causes many changes in organismal physiology. Xie et al. (p. 443) examined the effects of stress hormones on the expression of a class of potassium channels in rat adrenal chromaffin tissue. Reductions in the level of the stress-related hormone adrenocorticotrophic hormone led to changes in the levels of alternatively splice variants of the messenger RNA that encoded a calcium and voltage-activated potassium channel. This process would be expected to alter the excitability properties of the chromaffin cells and thus how they secrete catecholamines-which would have further effects on many other organs, including the heart.

  12. Soil and CO2

    The effects of elevated CO2 on below-ground ecosystem processes and biota is reported by Jones et al. (p. 441). Using model ecosystems created in the Ecotron facility, they identified alterations in community composition, exemplified by changes in fungi and Collembola species, and in biogeochemistry, as indicated by enhanced cellulose decomposition. The work suggests that that rising atmospheric CO2 concentrations may significantly impact long-term feedback in soil processes.

  13. Back and forth

    Development in higher plants alternates between diploid and haploid generations. Grossniklaus et al. (p. 446) have identified in Arabidopsis a genetic mutant that particularly affects the haploid gametophyte generation. The gene, medea, resembles genes encoding members of the Polycomb group of proteins, some of which regulate expression of homeotic genes in Drosophila.

  14. Arctic scavenging

    The Canada Basin in the Arctic Ocean has been considered an isolated, ice-covered basin with limited particle flux and scavenging related to sluggish circulation. Edmonds et al. (p. 405) measured the abundance of protactinium-231, thorium-230, and thorium-232 from unfiltered seawater samples collected on the shelf of the basin and from below the ice-covered center of the basin. These three isotopes are used as tracers of the scavenging, sedimentation, and ventilation rates of ocean basins. The abundances of protactinium-231 and thorium-230 are consistent with high particle fluxes and scavenging rates, typical of other ocean basins, and thus the Canada Basin is not as sluggish as previously suggested.

  15. Targeting bacterial virulence

    Staphylococcus areus can cause life-threatening infections such as toxic shock syndrome, “flesh-eating” skin infections, pneumonia, meningitis, and endocarditis. Because of increasing resistance to antibiotics, new strategies are being searched for to prevent or treat these infections. Balaban et al. have elucidated early events in the virulence pathway that turn on the virulence genes at the agr locus. More than 20 genes from this locus are under the control of one protein, RNAIII, and transcription of that protein is dependent on its activator, RAP (RNAIII-activating protein). When mice were injected with RAP as a vaccine, they were protected from subsequent exposure to S. aureus. The antibodies that were produced inhibited RNAIII production by bacteria in vitro and correlated with reduced lesion size in vivo. [See the news story by Strauss.]

  16. Comes out in the wash

    Sediment transport in rivers depends on the properties of the flow as well as the mix of sediment grains and grain sizes in the bed and river. Predicting the complex responses is useful for assessing how land use changes will affect siltation and erosion of watersheds. Wilcock (p. 410) shows that the transport of sediment in gravel-bed rivers can be modeled reasonably using an assumption of two grain types, sand and gravel. The results account for the observation of an abrupt transition from gravel beds to sand beds seen in many rivers.

  17. Pseudoknot structure

    The RNA pseudoknot is a structural motif in which the loop nucleotides of a stem-loop segment form base pairs to nucleotides outside of the stem region. This structural element is found in many classes of RNA and was first described in the genome of a plant virus, turnip yellow mosaic virus. Kolk et al. (p. 434) use nuclear magnetic resonance to obtain a high-resolution structure of a 44-nucleotide pseudoknot segment. They find an arrangement of single- and double-stranded interactions which suggest a transient malleability in pseudoknot conformation that may account for its ubiquity.

  18. Counting the Fingers of Birds and Dinosaurs

    A. C. Burke and A. Feduccia studied the embryonic development of fingers and wrists in extant amniotes (egg-laying animals) (Reports, 24 Oct., p. 666) and concluded that the three digits seen in birds are not homologous to the three digits seen in theropod dinosaurs. In an accompanying Perspective (p. 596), R. Hinchliffe wrote in favor of “[evolutionary] convergence (rather than common origin) as an explanation of the similarities between the structure of the forelimb of theropods and the wing of [the ancient bird] Archaeopteryx.”

    S. Chatterjee defends the birds-from-dinosaurs idea by reviewing work in several disciplines. He describes the “topographic position” of the digits in embryos as they develop and discusses ways that “digital reduction” could have occurred through evolution (in many species, fingers were reduced from five to two or three). He concludes that a “synthesis of both neontological and paleontological data” supports the theropod origin of birds. J. P. Garner and A. L. R. Thomas question “assumptions” made in the report and describe how the developmental data therein are actually “entirely consistent with a theropod origin of birds.”

    In response, Burke, Feduccia, and Hinchliffe discuss each point of criticism and describe how the theropod hand most likely developed (in the embryo) in a fashion consistent with the highly conserved pattern of development among amniotes. They maintain that the birds-from-dinosaurs idea is “inconsistent with the observations and current evidence of comparative embryology.”