This Week in Science

Science  14 May 2010:
Vol. 328, Issue 5980, pp. 787
  1. siRNA Movement in Plant Tissues


      Long-distance movement of RNA interference (RNAi)–derived signals in plants plays an important role in development and in defense against viral attack. The nature of the signals that spread from cell to cell is not known, although evidence suggests that they are nucleic acids of some sort (see the Perspective by Martienssen). Molnar et al. (p. 872, published online 22 April) and Dunoyer et al. (p. 912, published online 22 April) now show that in Arabidopsis, both exogenous and endogenous small interfering RNAs (siRNAs), rather than their long double-stranded precursor RNAs, are the molecules that transfer information between plant cells. A viral protein that counters RNAi though sequestering siRNAs blocked spreading of a transgene RNAi silencing signal. Furthermore, siRNA-processing enzymes were required in the source, and not the recipient, cells for spreading, and bombardment of plants with double-stranded siRNAs directly showed siRNA spread between cells. Endogenous siRNAs also spread between tissues and were capable of directing DNA methylation of target sequences in distant tissues.

    1. All and Nothing

        Entanglement, where a system can be in a superposition of a number of distinct states simultaneously, is a principle at the foundation of quantum mechanics (recall Schrödinger's cat, which is both dead and alive). It can also be used in many applications—imaging, communication, patterning, and metrology—with the effect being amplified by entangling larger systems. However, the systematic generation of “large” entangled systems is challenging. Afek et al. (p. 879; see the Perspective by Wildfeuer) present a technique for generating many-photon entanglement in so-called NOON states, where there are two possible paths and N photons in one path and 0 in the other—the system being a superposition of “all and nothing” states. Mixing of entangled pairs with classical light at a beam splitter formed up to five photon-entangled states. The technique should be generally applicable to generate higher-order entangled states.

      1. Stop or Go on Oxide Surfaces

          Direct studies of surface diffusion with instruments such as the scanning tunneling microscope (STM) have often focused on species on metal surfaces, but surface diffusion can play an important role for reactions on metal oxide surfaces. Li et al. (p. 882) used STM and density functional theory calculations to study how catechol (a benzene ring bearing two −OH groups) diffuses on the surface of the rutile phase of titanium dioxide. Both mobile and immobile species were observed on the time scale of minutes while making repeated STM scans. Hydrogen atom transfers between surface OH groups and the molecule changed the interaction energy between the molecule and the surface, and hence the barrier for diffusion.

        1. Earth's Silver Lining

            The age of the oldest rocks on Earth's surface is controversial, but, even if they are at their oldest estimate, hundreds of millions of years in our planet's earliest history are still missing. However, in some rocks that until relatively recently resided in the mantle, the isotopic signature from the time of Earth's formation is still preserved. Schönbächler et al. (p. 884) exploited this preservation to constrain models that describe the early material that assembled together to form Earth. Because the isotopic profile of silver in these rocks is nearly identical to that measured in a class of primitive meteorites, the earliest material probably had high volatile content. However, the fractionation of other isotopes suggests that the volatile content probably decreased over time in subsequent accretion events. With these isotopic model constraints, it is possible that one of the last major collisions—the Moon-forming giant impact—added considerable amounts of water and other volatile elements to Earth.

          1. Poor Flight of the Ancients

              In order to fly, the feathers of birds must be strong enough to support the bird's weight without breaking or bending. The main part of a feather providing structural support is its central shaft, which stiffens the feather along its length. In modern birds, this is hollow to reduce weight. Nudds and Dyke (p. 887) show that the cross-section of the shaft of the Mesozoic birds Archaeopteryx and Confuciusornis was much smaller than that of modern birds. Calculations imply that even if it was solid, it would have been too weak to support powered flight and barely strong enough to allow gliding. Thus, powered flight probably arose later in the evolution of birds and these early birds were poor fliers.

            1. Network Notation

                CREDIT: MUCHA ET AL.

                Networks are often characterized by clusters of constituents that interact more closely with each other and have more connections to one another than they do with the rest of the components of the network. However, systematically identifying and studying such community structure in complicated networks is not easy, especially when the network interactions change over time or contain multiple types of connections, as seen in many biological regulatory networks or social networks. Mucha et al. (p. 876) developed a mathematical method to allow detection of communities that may be critical functional units of such networks. Application to real-world tasks—like making sense of the voting record in the U.S. Senate—demonstrated the promise of the method.

              1. Bring Out the β-Barrel

                  The assembly of β-barrel membrane proteins, which are found in the outer membrane of Gram-negative bacteria and in the mitochondria and chloroplasts of eukaryotes, is poorly understood. Now Hagan et al. (p. 890, published online 8 April; see the Perspective by Stroud et al.) describe the development of a reconstituted system that recapitulates the process of assembly of β-barrel membrane proteins by the Escherichia coli Bam complex. The assembly of a protein substrate required the purified five-protein Bam complex and several subcomplexes and a chaperone, but did not require an external input of energy.

                1. Demise of the Lizards

                    Despite pessimistic forecasts from recent studies examining the effects of global climate change on species, and observed extinctions in local geographic areas, there is little evidence so far of global-scale extinctions. Sinervo et al. (p. 894; see the Perspective by Huey et al.) find that extinctions resulting from climate change are currently reducing global lizard diversity. Climate records during the past century were synthesized with detailed surveys of Mexican species at 200 sites over the past 30 years. Temperature change has been so rapid in this region that rates of adaptation have not kept pace with climate change. The models were then extended to all families of lizards at >1000 sites across the globe, and suggest that climate change-induced extinctions are currently affecting worldwide lizard assemblages.

                  1. Counting Na+ Channels One by One

                      CREDIT: LORINCZ AND NUSSER

                      Understanding how nerve cells integrate their synaptic inputs and generate their output signals requires the identification of voltage-dependent ion channels on the axo-somato-dendritic surface of central neurons. Using improved ultrastructural immunocytochemistry techniques, Lorincz and Nusser (p. 906) found that a newly described voltage-gated sodium channel, Nav1.6, was present not only at nodes of Ranvier and axon initial segments but also at much lower, but functionally significant levels, in dendrites of CA1 pyramidal cells. However, other brain Na+ channels were not present in these dendrites, suggesting that dendritic sodium spikes result from somatic activation of this particular type of sodium channel.

                    1. It's a Knockout

                        The malaria parasite is one of the most important pathogens of humans. Increasing drug-resistance is an imminent public health disaster, and we urgently need to find new drugs. The recently acquired malarial genomes provide a plethora of targets. However, due to the genetic intractability of the parasite, it has been difficult to identify essential genes in the clinically relevant blood-stage of the parasite. Dvorin et al. (p. 910) investigated the function of a Plasmodium falciparum plant-like calcium-dependent protein kinase, PfCDPK5, which is expressed in the invasive blood-stage forms of the parasite. A system for conditional protein expression allowed the production of a functional knockout in the bloodstream stage of the parasite. PfCDPK5 was required for parasite egress from the human host erythrocyte, an essential step in the parasite life cycle.

                      1. Epigenetic Maps

                          Methylation of genomic DNA on cytosine bases provides critical epigenetic regulation of gene expression and is involved in silencing transposable elements (TEs) and repeated sequences, as well as regulating imprinted gene expression. Zemach et al. (p. 916, published online 15 April; see the Perspective by Jeltsch) analyzed DNA methylation in the genomes of five plants, five fungi, and seven animals by bisulfite sequencing. The data suggest that land plants and vertebrates, which have extensive DNA methylation, are under strong selective pressure to repress TEs, because of their sexual mode of reproduction. Unicellular animals and fungi that reproduce asexually are more likely to lose TE methylation. Although gene body methylation is evolutionarily ancient, it is also mutagenic, and so loss of this pathway has been relatively common and occurred early in fungal evolution and later in several plant and animal lineages.

                        1. Pedigree Weevils

                            The phenotype of an organism is related to its additive genetic phenotype, the small but numerous genetic differences between individuals affecting their phenotype, and its mutational load, which is the number of mutations an individual carries. How these two factors affect an individual's ability to leave offspring in the next generation is a major component of evolutionary theory, but evidence for a direct relationship has been lacking. By estimating the contribution of partially recessive mutations to additive genetic variation in seed-feeding cow-pea weevils over a seven-generation pedigree breeding program involving variation in levels of inbreeding, Tomkins et al. (p. 892) demonstrate an association between genetic quality and the mutational load carried, especially for males.

                          1. Nitrate for Me, Ammonium for You

                              The interdependence of plant nitrogen uptake and plant responses to carbon dioxide is well established, but the influence of inorganic nitrogen form—i.e., whether nitrate or ammonium—has been largely ignored. Bloom et al. (p. 899) present evidence from five independent methods in both a monocot and dicot species that carbon dioxide inhibition of nitrate assimilation is a major determinant of plant responses to rising atmospheric concentrations of carbon dioxide. This finding explains several phenomena, including carbon dioxide acclimation and decline in food quality. The large variation in these phenomena among species, locations, or years derives from the large variation in the relative dependence of plants on nitrate and ammonium as nitrogen sources among species, locations, or years. The relative importance of ammonium and nitrate for plant N nutrition in future cropping systems will be critical for quantity and quality of food.

                            1. Population Meltdown

                                Populations of wild animals, including deer and moose, are often actively managed by hunting. Following such harvesting, populations of some exploited animal species collapse, whereas others are able to withstand exploitation. To understand the reasons for these varied responses, Fryxell et al. (p. 903) developed a mathematical model which predicts that weak regulation causes damped population cycles with period lengths on the order of decades. The model was tested using time-series data for hunted populations of moose and deer in three ecosystems in Norway and Canada.