This Week in Science

Science  07 Aug 2009:
Vol. 325, Issue 5941, pp. 651
  1. << Focusing on Fibrin


      Vascular injury initiates biochemical reactions that cause the blood protein, fibrin, to polymerize and help to stop bleeding and support wound healing. Fibrin can also be a scaffold for thrombi that lead to cardiovascular diseases. To maintain homeostasis, fibrin clots must be stiff, plastic, and, so that the network can be decompsed, permeable. Brown et al. (p. 741) investigated the behavior of fibrin clots at the macroscopic, single-fiber, and molecular scale. At relatively low strains, fibers aligned and formed bundles, and at higher strains, protein unfolding occurred. An integrated model provides a molecular basis for fibrin elasticity and extensibility.

    1. The Melting Is in the Details

        Global sea level rises and falls as ice sheets and glaciers melt and grow, providing an integrated picture of the changes in ice volume but little information about how much individual ice fields are contributing to those variations. Knowing the regional structure of ice variability during glaciations and deglaciations will clarify the mechanisms of the glacial cycle. Clark et al. (p. 710) compiled and analyzed more than 5000 radiocarbon and cosmogenic surface exposure ages in order to develop a record of maximum regional ice extent around the time of the Last Glacial Maximum. The responses of the Northern and Southern Hemispheres differed significantly, which reveals how the evolution of specific ice sheets affected sea level and provides insight into how insolation controlled the deglaciation.

      1. Honing Bivalve History

          What are the lasting effects of extinction, both persistent background extinctions and major events, on surviving lineages? Roy et al. (p. 733) examined the excellent fossil record of marine bivalves over the past 200 million years, which spans the end-Cretaceous extinction. Background extinctions tended to be higher within certain lineages and depended on the previous history of extinctions within those lineages. Cenozoic taxa are still reflecting the end-Cretaceous event.

        1. Codifying Maize Modifications

            Maize, one of our most important crop species, has been the target of genetic investigation and experimentation for more than 100 years. Crossing two inbred lines tends to result in “better” offspring, in a process known as heterosis. Attempts to map the genetic loci that control traits important for farming have been made, but few have been successful (see the Perspective by Mackay). Buckler et al. (p. 714) and McMullen et al. (p. 737) produced a genomic map of maize that relates recombination to genome structure. Even tremendous adaptations in very diverse species were produced by numerous, small additive steps. Differences in flowering time in maize among inbred lines were not caused by a few genes with large effects, but by the cumulative effects of numerous quantitative trait loci—each of which has only a small impact on the trait.

          1. Cosmic Shock Waves

              Cosmic rays are high-energy charged particles that bombard Earth from all directions in the sky; those originating from within our Galaxy are thought to be accelerated in the shockwaves produced by supernova explosions. Helder et al. (p. 719, published online 25 June; see the Perspective by Raymond) measured the velocity of a section of the blast wave created by supernova RCW 86, an exploding star believed to have been witnessed by Chinese astronomers in 185 A.D., and the post-shock proton temperature. The post-shock proton temperature was much lower than would be expected without any cosmic ray acceleration, which implies that the pressure induced by cosmic ray exceeds the thermal pressure behind the shock.

            1. Higher-Level Quantum Emulation

                At the heart of a quantum computer is the device on which information is to be encoded. This is typically done with a qubit, a two-level quantum system analogous to the two-level bit that encodes 0 and 1 in classical computers. However, there need not be just two quantum energy levels. There could be three (a qutrit), or more generally, d-levels (a qudit) in the device. Neeley et al. (p. 722; see the Perspective by Nori) demonstrate a five-level quantum device and show that their qudit can be used to emulate the processes involved in manipulating quantum spin. The use of multilevel qudits may also have potential in quantum information processing by simplifying certain computational tasks and simplifying the circuitry required to realize the quantum computer itself.

              1. Stressful Self-Assembly

                  CREDIT: HENRIK DIETZ

                  One way to control shape during the assembly of an object is to design in stresses that cause a planned amount of deformation. Dietz et al. (p. 725; see the Perspective by Liu and Yan) designed DNA helix bundles, arranged in honeycomb lattices, in which some of the helices have insertions or deletions relative to the other helices in the bundles. The stresses help the bundles assemble into objects on the scale of tens of nanometers. Both the direction and degree of bending could be controlled, and curvatures as tight as 6 nanometers achieved. Complex shapes, such as square-toothed gears, could be created by combining multiple curved elements.

                1. No NO

                    Isoprene, a five-carbon diene produced by plants, is the most abundant nonmethane hydrocarbon released into the atmosphere and plays an important role in tropospheric chemistry. Isoprene is also thought to affect climate by acting as a source of atmospheric aerosols. Paulot et al. (p. 730; see the Perspective by Kleindienst) now describe how isoprene may lead to the formation of secondary organic aerosols. In laboratory experiments, the photooxidation of isoprene in low-NO conditions, such as those which occur in vegetated regions far from anthropogenic influence, produced high yields of dihydroxy epoxides, a suspected precursor of the aerosols. This discovery could help to explain some of the more puzzling aspects of isoprene chemistry in remote regions.

                  1. Untangling Food Webs

                      The factors affecting the stability of food webs are important in conservation and ecological restoration. Gross et al. (p. 747) used a generalized modeling approach to evaluate billions of replicates of food webs in order to reveal the properties that stabilize (or destabilize) food webs. Variability in the strength of trophic links between predator and prey strength affected stability in different ways depending on the size of the web—stabilizing only in relatively small food webs and destabilizing in larger ones. Universal topological rules were extracted for the patterns of network links that enhance food-web stability.

                    1. RNA Wars

                        CREDIT: LIU ET AL.

                        During RNA interference (RNAi), the Dicer endonuclease generates small interfering (si)RNAs that, with the help of the protein R2D2, are loaded into the siRNA-induced silencing complex (RISC). Using siRNAs as guides, RISC, and specifically its Argonaute subunit, targets complementary RNAs for destruction. In order to identify other components of the RISC complex, Liu et al. (p. 750) reconstituted the core RISC activity, using purified Drosophila Dicer, R2D2, and Ago-2. The protein C3PO (component 3 promoter of RISC), which consists of heterodimer of Translin and Translin-associated factor X (Trax), was found to enhance RISC activity in this system, and in vivo, with the Trax endonuclease activity activating RISC through the removal of siRNA passenger strand cleavage products.

                      1. Jamming Protein Translocation

                          Antibiotics are tremendously important drugs in modern medicine, yet we are still learning precisely how they work. SecY is a bacterial membrane protein that is part of a complex that allows protein secretion across the membrane. Van Stelten et al. (p. 753; see the Perspective by Breukink) found in Escherichia coli cells that if the protein translocator complex becomes jammed with a protein that cannot pass through, the SecY protein is degraded by the protease FtsH, leading to cell death. Cells could be protected by increasing amounts of an inhibitor of FtsH, the YccA protein. Antibiotics that block protein translation also caused jamming of the SecY machinery and destruction of SecY, thus contributing to cell death.

                        1. Plastic Pain Perception

                            Drugs and endocannabinoids acting on cannabinoid (CB) receptors have potential in the treatment of certain types of pain. In the spinal cord they are believed to suppress nociception, the perception of pain and noxious stimuli. Pernia-Andrade et al. (p. 760) now find that endocannabinoids, which are released in spinal cord by noxious stimulation, may promote rather than inhibit nociception by acting on CB1 receptors. Endocannabinoids not only depress transmission at excitatory synapses in the spinal cord, but also block the release of inhibitory neurotransmitters, thereby facilitating nociception.

                          1. Taking Shape

                              DNA recombination mechanisms enable certain pathogens to modify the proteins on their outer surfaces by rearranging their genes and so avoid repeated detection by the immune system. Cahoon and Seifert (p. 764) have found that antigenic variation of a single genetic locus in the human pathogen Neisseria gonorrhoeae is triggered by a specific cis-acting DNA element. This 16–base pair DNA sequence formed an unusual DNA structure in vitro; a guanine quartet (G4), which has been implicated in only a few other biological processes. The G4 forming sequence is required for processing the gene conversion reaction leading to antigenic variation. These findings have implications both for understanding mechanisms of DNA recombination and its role in microbial pathogenesis.

                            1. Transfer RNA Fix

                                Accurate protein synthesis requires that transfer RNAs (tRNAs) must be acylated with the correct amino acid. Mistranslation of serine or glycine for alanine apparently presents a particular challenge and is corrected by an editing domain of alanyl-tRNA synthetases (AlaRSs). Guo et al. (p. 744) now show that aside from the aminoacylation and editing domains, a third domain, C-Ala, plays a key role in AlaRS function. It forms a nucleic acid–binding motif that promotes binding of both aminoacylation and editing domains to tRNAAla. The coupling of these two functions was likely important in the evolution of AlaRSs.

                              1. Fine Dendrites Fire Differently

                                  The pyramidal neuron is the basic computational unit in the brain cortex. Its distal tuft dendrite is heavily innervated by horizontal fibers coursing through cortical layer-I providing long-range corticocortical and thalamocortical associational input. Larkum et al. (p. 756) investigated whether the apical tuft dendrites of layer-5 neocortical pyramidal neurons, like basal dendrites, generate n-methyl-d-aspartate (NMDA) spikes using two-photon–guided direct dendritic recording, glutamate uncaging, and modeling. NMDA spikes could be evoked in the distal tuft dendrites, while Ca2+ spikes could be triggered at the bifurcation points. Block of the hyperpolarization-activated current enhanced these NMDA spikes. Thus, the generation of NMDA spikes is a general principle of thin, basal, and tuft dendrites.