This Week in Science

Science  05 Sep 2003:
Vol. 301, Issue 5638, pp. 1285
  1. Sorting Proteins via Mass Spectrometry

    Two workhorse analytical techniques that are often used in combination are chromatography and mass spectrometry. The former is used to separate different compounds, and the latter is used mainly for their identification. Ouyang et al. (p. 1351) have harnessed mass spectrometers to do the job of separating proteins to create microarrays. Although the proteins must be exposed to vacuum conditions and ionized to perform the separation, they can still be recovered and landed on soft substrates such as glycerol. Proteins such as cytochrome c, lysozyme, and protein kinase A retained their activity in biochemical assays.

  2. Probing the Interstellar Medium with Pulsars

    Unlike most pulsars, Geminga (a rapidly rotating neutron star) is relatively isolated in the sky, and the lack of a complicating star field makes it a useful probe of the interstellar medium. Observations of Geminga with XMM-Newton by Caraveo et al. (p. 1345; see the cover) reveal two diffuse tails of x-ray emission aligned with the pulsar's proper motion. The tails are produced by the electron-synchrotron emission caused by the compression of the interstellar medium's magnetic field lines from the bow shock of the pulsar winds as Geminga moves supersonically across our field of view. Modeling of the bow shock yields the proper motion of Geminga and the density of the interstellar medium.

  3. Switching on to Quantum Currents

    When current is passed through semiconductors or metals, energy is dissipated in the form of heat. Such irreversible processes in any physical system have limiting and perhaps dire consequences for applications in quantum information processing. However, Murakami et al. (p. 1348; see the Perspective by Fertig) present calculations based on a generalized description of the quantum Hall effect in higher dimensions that predict the existence of a dissipationless spin current that could be extremely useful in spintronics and quantum computing. This spin current should be observable at room temperature when ordinary semiconductors such as silicon, germanium, and gallium arsenide are subjected to an electric field.

  4. A Hard Climate Record

    Several different chronologies have been developed using polar ice cores for the large and rapid climate change events called interstadials that occurred during the last glacial period. However, uncertainties in annual-layer counting and ice-flow modeling have resulted in disagreements in timing as large as thousands of years for some intervals. Burns et al. (p. 1365; see the Perspective by Sirocko) have analyzed a stalagmite from the northwestern Indian Ocean. They could date this sample precisely for the period from 42,000 to 55,000 using U234/Th230 dating and use its oxygen isotope record as a proxy of monsoon activity. The pattern of changes is similar to those of the Greenland ice records, so these results could help resolve the disagreements between different ice core-based age models for this period.

  5. The Root Cause of an Invading Plant

    Certain plants, when introduced into new environments, can be much more pesky than they ever were in their original environment. Spotted knapweed was accidentally introduced from Eastern Europe to North America some time ago, and in the western United States is an aggressive weed that diminishes the productivity of pastures. Bais et al. (p. 1377; see the Perspective by Fitter) show that knapweed exudes a chemical from its roots that initiates a cell-death cascade in the roots of nearby susceptible plants. Thus, the roots of knapweed's invasiveness lie not so much in lack of predators or unused ecological niches, but rather in the weak defenses of its new plant neighbors.

  6. As Hard As It Gets

    For metals and alloys, smaller crystallite sizes usually lead to harder materials because grain boundaries hinder the motion of dislocations. However, at very small grain sizes, this mechanism can no longer operate and hardness decreases with decreasing grain size. Using large-scale molecular dynamics simulations, Schiotz and Jacobsen (p. 1357) identify a transition region in nanocrystalline copper between grain sizes of 10 to 15 nanometers where the maximum hardness should occur.

  7. Life Under the Snow

    It has generally been assumed that there is little microbial activity in cold soils, especially under a blanket of snow. Schadt et al. (p. 1359; see the news story by Pennisi) show that microbial communities can reach a peak of biomass and turnover under snow in cold tundra soils in North America. Many of the fungi in these systems are previously undescribed. Thus, significant and hitherto undetected biological activity may be occurring across a huge area during winter.

  8. Only a Minority of B Cells Make the Cut

    B cells that produce antibodies against the body's own proteins and DNA are for the most part purged from the repertoire. They are either forced into a state of unresponsiveness or made to undergo a process of receptor editing. Wardemann et al. (p. 1374) now determine that the number of the autoreactive B cells in the preselected repertoire is surprisingly large and can make up as many as three-fourths of the total. Predominantly, these cells bear antibody specificities that are skewed toward polyreactive and anti-DNA specificities, seen, for example, in lupus and some other autoimmune conditions. Thus, the generation of high B cell diversity comes at the cost of burdening the systems for repertoire selection with applicants who are mostly destined to fail the test.

  9. Cryptic Cuprous Ions

    Copper is an essential cofactor in several Escherichia coli enzymes, but its potential cytotoxicity requires cytoplasmic copper concentration to be strictly regulated. The metal responsive regulator CueR controls expression of proteins that remove free Cu+ from the cytosol into the periplasm. Changela et al (p. 1383) show that CueR has a zeptomolar (10−21 M) sensitivity for free Cu+. A comparison of the structures of CueR and a Zn2+-sensing homolog, ZntR, shows how CueR discriminates against divalent metal ions while binding monovalent transition metals with high affinity.

  10. Live Lean and Live Long

    Autophagy, a process in which organisms use the degraded constituents of their own cells for nutrition, seems to be part of the way the nematode Caenorhabditis elegans survives hard times. Meléndez et al. (p. 1387) show that a nematode ortholog of a yeast gene that participates in yeast autophagy, bec-1, is required for the nematode to shift into the starvation-induced, metabolically slowed dauer state. This gene is also necessary for the nematodes to become long-lived, which the authors prompt in the worms by equipping them with a defective daf-2 gene that extends life-span. Several other yeast autophagy genes are also involved in dauer formation in the daf-2 mutant animals.

  11. Analyzing the Number of Antigenic Peptides

    The major histocompatibility complex class I-restricted T cells must react to abnormalities in the protein expression of a cell arising from cellular transformation, or infection with viruses and intracellular bacteria, but leave normal cells alone. The extent of this surveillance is the subject two reports (see the Perspective by Yewdell). Using a bicistronic transgene construct, Schwab et al. (p. 1367) initiated translation within a designated “untranslated” region of a gene starting with a nonstandard CUG codon. The peptide derived from this cryptic translation product was presented to the immune system with relatively high efficiency, inducing both immune tolerance and CD8 responses in different settings. Thus through novel modes of translation, the realm of self, or nonself, presented to the immune system may extend well beyond that made available by the coding region of a given gene. Viruses frequently avoid host detection by limiting the amount of viral antigen they produce. In the case of Epstein-Barr virus (EBV)-encoded nuclear antigen 1 (EBNA1), antigen limitation is thought to be achieved through inhibition of protein degradation by a glycine-alanine repeat (GAr) within the protein. However, such a mechanism would not be effective against non-Gar-containing defective ribosomal products (DRiPs), nonfunctional polypeptides that are thought to represent significant sources of antigens. In revisiting this question, Yin et al (p. 1371) show that GAr also auto-inhibits EBNA1 translation, and thus limits both full-length protein and DRiP translation.

  12. A Broader Role for β-Arrestins

    β-Arrestins are multifunctional proteins that desensitize heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors and help link such receptors to cellular signaling pathways, as well as promote endocytosis of the receptors. In two reports, Chen et al. (p. 1391 and 1394; see the Perspective by Spiegel) show that β-arrestins are even more versatile than previously thought. β-arrestin 2 is required to promote internalization of Frizzled proteins (the cell surface receptors for Wnt glycoproteins). In this role, β-arrestins do not bind directly to receptors, as they do with G protein-coupled receptors. Rather, β-arrestin 2 binds to a protein called disheveled (Dvl) that is recruited to activated Frizzled receptor proteins in the cell membrane. Once Dvl brings β-arrestin to Frizzled receptor protein complexes, the receptors are recruited into clathrin-coated pits for internalization. β-arrestins also promote internalization of a completely different type of receptor, the transforming growth factor-β receptor type III. In this case, β-arrestin binds to a receptor subunit that is phosphorylated by a another receptor subunit.

  13. Nailing the Nuclear Envelope

    Proteomic approaches to organelle analysis are beginning to shed light on the full complement of architectural protein involved in organelle generation and maintenance. Schirmer et al. (p. 1380) describe an essentially comprehensive analysis of integral membrane proteins specific to the nuclear envelope. Using “subtractive proteomics,” they eliminated proteins of contaminating organelles and proteins shared between the nuclear envelope and peripheral endoplasmic reticulum. All 13 previously identified nuclear envelope proteins were included in their data set. Consistent with recent findings that mutations in nuclear envelope proteins cause multiple human diseases, many of the 67 previously unidentified nuclear envelope proteins mapped to human chromosomal loci linked to a variety of dystrophies.

  14. Shining with a Steady Glow

    Semiconducting single-wall carbon nanotubes are synthesized as mixtures of different diameter and chirality. Each type exhibits a characteristic fluoresce arising from their different band gaps. Hartschuh et al. (p. 1354) obtained both fluorescence and Raman spectra from individual nanotubes. They see variations in the emission line shapes that may reflect the presence of detects, but also see continuous emission, unlike the “blinking” (“dark state”) behavior normally seen for molecules and quantum dots.

  15. Worldwide Climate Shifting

    Large and rapid climate changes that occurred at high northern latitudes during the last deglaciation were recorded most clearly in the air temperature records contained in ice cores from Greenland. These changes were accompanied by variations in the concentration of atmospheric methane, which suggests but does not prove that tropical wetlands—thought to be the primary source of that methane—also experienced dramatic climatic shifts. Lea et al. (p. 1361) present a high-resolution record of sea surface temperature derived from measurements of Mg/Ca ratios in planktonic foraminifera. This record shows that the surface water off the coast of Venezuela warmed and cooled quickly, by as much as 4°C, during two of these episodes. The authors propose that these high-latitude and tropical changes were synchronized by changes in the positions in the intertropical convergence zone.

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