This Week in Science

Science  29 Jun 2012:
Vol. 336, Issue 6089, pp. 1616
  1. The Immune System in Three Dimensions

    Immune cells must traffic within the tissues in which they reside and also through the bloodstream and lymphatic system in order to defend the host against infection. Until 10 years ago, immunologists had very little idea about how the immune response was coordinated in three dimensions. This all changed with the application of two-photon microscopy, applied intravitally or on tissue explants, to the immune system. Germain et al. (p. 1676) review how studies using this technology have informed our knowledge of immune system dynamics and discuss how to apply this technology in the future to gather further insights.

  2. Go with the Flow

    Effective absorption or filtration can be achieved by having a material with multiple levels of porosity, so that the main flow can occur in the larger channels, while smaller passageways can be used to sequester a secondary material. It can be difficult to make these materials because the pores need to be different sizes, but still fully connected to each other. Zhang et al. (p. 1684) show that a hierarchical zeolite can be made through a simple process using a single structure-directing agent that causes repetitive branching. This leads to a material with improved transport and catalytic properties.

  3. The Sedimentary Life of Earthquakes


    Estimating the hazards associated with possible large earthquakes depends largely on evidence of prior seismic activity. The relatively new global seismic networks installed to monitor earthquakes, however, have only captured the very recent history of fault zones that can remain active for thousands of years. To understand the recurrence of large earthquakes along the Alpine Fault in New Zealand, Berryman et al. (p. 1690) looked to the sediments near an old creek for evidence of surface ruptures and vertical offset. Along this fault segment, 24 large earthquakes seem to have occurred over the last 6000 years, resulting in a recurrence interval of ∼329 years. The activity is more regular than other similar strike-slip faults, such as the San Andreas Fault in California.

  4. Dating Wood Rot


    Specific lineages within the basidiomycete fungi, white rot species, have evolved the ability to break up a major structural component of woody plants, lignin, relative to their non–lignin-decaying brown rot relatives. Through the deep phylogenetic sampling of fungal genomes, Floudas et al. (p. 1715; see the Perspective by Hittinger) mapped the detailed evolution of wood-degrading enzymes. A key peroxidase and other enzymes involved in lignin decay were present in the common ancestor of the Agaricomycetes. These genes then expanded through gene duplications in parallel, giving rise to white rot lineages.

  5. Early Burrowers

    Direct fossil evidence of animals from Ediacaran period—the time in Earth's history just before extensive animal diversification in the Cambrian—is scant. However, the remains of animal activity in sediment, which remain intact through geologic time can provide clues about animal behavior and evolution. Pecoits et al. (p. 1693; see the Perspective by Droser and Gehling) found a suite of fossil animal burrows in sedimentary rocks in Uruguay. Radiometric dating places the age of the structures at ∼585 million years old, coinciding with the likely emergence of stem-group bilaterians. The complex morphologies of the fossil burrows suggest that these animals actively grazed and had the ability to burrow deep within sediments.

  6. Spinning Backwards

    When atoms and molecules collide, the energy embedded in the reaction products gets distributed among translations, vibrations, and rotations. Decades of meticulous experiments have mapped out the quantum mechanical rules underlying this distribution process, particularly in simple systems comprising just three light atoms. Now, Jankunas et al. (p. 1687; see the Perspective by Yang et al.) describe a previously unappreciated wrinkle in the elementary reaction of an H atom with deuterium. Typically, products with low vibrational and rotational excitation tend to scatter backwards from the collision, whereas the spinning products scatter sideways. Above a certain vibrational threshold, however, spinning HD products were observed to scatter backwards.

  7. Pots and Crocks

    The invention of pottery allowed for more secure storage of food than was provided by baskets or hide pouches, and the vessels could also be used in cooking. The earliest pottery has been thought to have appeared in China and Japan ∼18,000 years ago, several thousands of years before the advent of agriculture. Wu et al. (p. 1696); see the Perspective by Shelach) have now dated broken pieces of pottery from a cave in China, the earliest of which date to ∼20,000 years ago, the time of the Last Glacial Maximum. Scorch marks on many pieces imply that the pottery was used in cooking.

  8. Alkaloid Synthetic Pathway

    Noscapine, a nonaddictive alkaloid found in the opium poppy, can be used as a cough suppressant and a tubulin-binding antitumor agent. Winzer et al. (p. 1704, published online 31 May; see the Perspective by DellaPenna and O'Connor) found that a cluster of 10 genes were key to the production of noscapine. Poppies homozygous for this gene cluster produced high levels of noscapine, heterozygous poppies produced low levels of noscapine, and those poppies lacking the gene cluster produced no noscapine. Silencing individual genes in turn and analyzing the accumulation of intermediate metabolites allowed the biosynthetic pathway of noscapine to be elucidated.

  9. Plant Hormone Modulators

    The activity and stability of several plant hormones is modulated by conjugation with various amino acids and their derivatives. Westfall et al. (p. 1708, published online 24 May) solved the crystal structures for two acyl acid amido synthetases from Arabidopsis. The findings suggest how the enzymes might discriminate between apolar and acidic amino acids and lend insight into the reaction chemistries that add functional diversity to hormone signaling pathways.

  10. Pretty or Sweet

    The grocery-store tomato that looks beautiful but tastes like tart cardboard arises from selection processes favoring phenotypes that make commercial production more reliable. Significant in that selection process was a mutation that reduced the mottled color variations of unripe green tomatoes, leaving them a uniform, pale, green. Powell et al. (p. 1711) analyzed the molecular biology of the mutation. The uniform ripening mutation turns out to disable a transcription factor called Golden 2-like (GLK2). GLK2 expression increases the fruit's photosynthetic capacity, resulting in higher sugar content.

  11. Seeing in the Dark


    Elephantnose fish are known to use electrosensing to navigate their murky freshwater environment. However, unlike some other animals from dark environments, they have retained their eyes and some dependence on vision. While most vertebrate vision optimizes either photon catch (for increased light capture) or visual acuity, Kreysing et al. (p. 1700) show that the unique structures of the grouped retinae found in the eyes of this species matches rod and cone sensitivity, which allows for the simultaneous use of both types of photoreceptors over a large range of dim light intensities.

  12. Noncanonical Pathway

    The textbook view of translation of messenger RNA to protein is that it is always initiated from open reading frames (ORFs) that begin with an AUG codon (encodes methionine) by an initiator methionine-bound transfer RNA (tRNA). There is evidence, however, that some polypeptides are produced from non–AUG-initiated ORFs. Starck et al. (p. 1719; see the Perspective by Dever) used a variety of biochemical techniques to determine the underlying mechanism for such nontraditional translation initiation. Comparison of translation initiation from AUG-initiated ORFs with those beginning with leucine CUG-initiated ORFs revealed that cells can use an elongator Leu-tRNA to initiate translation at CUG codons. CUG-initiated peptides were presented by major histocompatibility class I molecules and could activate T cells.

  13. Don't Terminate Me!

    DNA transcription progresses through three phases—initiation, elongation, and termination—of messenger RNA chains. The transcribing enzyme, RNA polymerase (Pol) II, recruits factors that assist in each of these phases. Mayer et al. (p. 1723) now show that the C-terminal domain (CTD) of actively elongating Pol II is phosphorylated at conserved tyrosine residues. This modification impairs recruitment of termination factors. Factor exchange on the transcribing polymerase enzyme may be explained by an extended CTD code that is based on differential phosphorylation of the tyrosines and two well-characterized serine residues in the CTD.

  14. Loading a Spring

    To regulate cellular RNA levels, transcription must be balanced by RNA degradation. An important player is the exosome, which can unwind and degrade structured RNA. Lee et al. (p. 1726) used single-molecule fluorescence analysis to investigate how degradation and unwinding are coupled in the catalytic subunit of the yeast exosome complex, Rrp44. Rrp44 apparently digests several base pairs without unwinding, accumulates the energy, which it then uses to unwind four to five base pairs in a burst. Similar spring-like behavior has been proposed for conventional helicases, except that the stored energy comes from hydrolysis of adenosine triphosphate rather than the RNA polymer.