This Week in Science

Science  01 Jul 2011:
Vol. 333, Issue 6038, pp. 11
  1. Get Knotted

    CREDIT: SIMON ČOPAR/FACULTY OF MATHEMATICS AND PHYSICS, UNIVERSITY OF LJUBLJANA

    Topologically, loops and knots cannot be converted one to the other through simple twisting or stretching. These differences make knots and loops interesting objects to study, but it can be difficult to manipulate polymers into predefined shapes. Tkalec et al. (p. 62; see the Perspective by Kamien) immersed surface-treated colloidal particles in a chiral nematic liquid crystal. When the liquid crystal molecules were aligned normal to the surface of the particles, defect lines formed around each particle. By choosing different arrays of colloidal particles that could be manipulated using optical tweezers, structures where neighboring defect loops cross each other were generated allowing the production of knots of arbitrary complexity.

  2. Rotation Can Be Such a Drag

    The speed of light is reduced as it passes through a transparent medium, with the extent of the reduction dependent on the refractive index. A spinning window will rotate an image because of photon drag. However, for most materials the effect is minute—typically less than one-millionth of a degree. Franke-Arnold et al. (p. 65) show that using a spinning slow-light medium—a ruby rod with an optically induced, highly effective refractive index—can enhance the optical drag effect such that it can be visualized by eye or captured on camera.

  3. Superelasticity Set Point

    Shape metal alloys can undergo much larger reversible strain deformations than other metals or alloys. This superelasticity is caused by a reversible phase transformation between the parent phase, stable under zero applied stress, and the stress-stabilized martensite phase. A shortcoming of current superelastic alloys is a strong temperature sensitivity to the transformation-inducing stress. Omori et al. (p. 68) show that the addition of a small amount of Ni to a Fe-Mn-Al alloy leads to an alloy with almost temperature-invariant superelastic properties.

  4. Mobile Electrons in Oxide Melts and Glasses

    Electrons often have a short lifetime in solution before they undergo a reaction, but in some solvents, they dissolve and act like anions. The classic example is sodium dissolved in liquid ammonia, forming Na+ and a free electron. Some solids, called electrides, can also host free electrons. Kim et al. (p. 71; see the Perspective by Edwards) studied [Ca24Al28O64]4+·4e-, which has an internal cage structure and forms an electride when oxygen anions are displaced. Metallic conductivity persisted in the melt and in a quenched glass, where the electrons formed a paired state that moved through a hopping mechanism.

  5. Whys and Warfares

    Centuries of social and philosophical analysis have been dedicated to the general question of “how will a given war evolve?” Johnson et al. (p. 81) analyzed publicly available data on fatalities from the wars in Afghanistan and Iraq, suicide bombing data for Hezbollah and Pakistani militants, and fatalities that resulted from global terrorism between 1968 and 2008. The analysis reveals common patterns in the timing of attacks by insurgents in different geographical regions and by global terrorist groups. A linear relationship was observed between the escalation rate for attacks and the time interval between the first 2 days of fatalities in a region.

  6. Bacteria with a Bigger Bias

    When sulfate-reducing bacteria use sulfur compounds instead of oxygen during respiration, the chemical reactions that generate energy are biased toward specific natural isotopes of sulfur. The sulfite produced is thus depleted in sulfur isotopes relative to its natural abundance—often by only a few additional atoms per thousand reactions. Sim et al. (p. 74) found that a marine bacterium isolated from coastal sediments can produce a remarkably high signal of isotopic fractionation—up to 68 times per thousand reactions. Similar high values that have been observed in sedimentary rocks were thought to require additional cycling of sulfur and oxygen; however, these results suggest that this may not always be the case.

  7. Pros and Contrails

    CREDIT: HEYMSFIELD ET AL.

    Contrails—the long, thin clouds produced by high-flying aircraft—are a familiar sight in the skies, and most people would think (correctly) that their formation is the primary influence of planes on cloudiness. However, planes can also decrease cloudiness in certain cases. Heymsfield et al. (p. 77) describe the appearance of aircraft-induced voids in existing clouds, produced by ice particle formation upon passage of an aircraft through a cloud and the resulting convection due to latent heating from ice growth. This phenomenon can also induce local snowfall, and may account for some of the observations previously ascribed to cloud seeding.

  8. Chronic Fatigue

    A 2009 report that patients with chronic fatigue syndrome (CFS) are infected with a retrovirus called xenotropic murine leukemia virus (XMRV) (Science 326, 585) attracted considerable interest, but other work has failed to detect XMRV in independent groups of CFS patients. Now, two studies support the view that the purported association between XMRV and CFS is most likely due to contamination of laboratories and research reagents with the virus. Paprotka et al. (p. 97, published online 2 June) provide evidence that XMRV arose by recombination of two mouse leukemia viruses during laboratory passage of a human prostate tumor xenograft in mice in the 1990s. They conclude that contamination with XMRV produced by a cell line (22Rv1) derived from these early xenograft experiments is the most likely explanation for detection of the virus in patient samples. Knox et al. (p. 94, published online 2 June) examined blood samples from 61 CFS patients, 43 of whom had been diagnosed previously as XMRV positive. Sensitive assays for viral nucleic acids, infectious virus, and virus-specific antibodies revealed no evidence of XMRV in any of the samples.

  9. Doing Double Duty

    N-acetylglucosamine (GlcNAc)–1-phosphotransferase is the crucial enzyme in the generation of mannose 6-phosphate (M6P) residues on lysosomal enzymes required for their efficient transport to lysosomes. Defects in the GlcNAc-1-phosphotransferase lead to a fatal lysosomal storage disorder. GlcNAc-1-phosphotransferase is synthesized as an inactive precursor protein that is activated by proteolytic cleavage in the Golgi complex. Marschner et al. (p. 87; see the Perspective by Ye) now report that the protease involved in GlcNAc-1-phosphotransferase cleavage is the site-1 protease (S1P), a Golgi-localized protease that plays a central role in cholesterol homeostasis. Loss of S1P resulted in missorting of newly synthesized lysosomal enzymes due to the lack of M6P residues, which may contribute to the defective cartilage phenotype in S1P defective animals.

  10. Nuclear Membrane Protein Sieve

    En route from the outer membrane to the inner membrane of the nuclear envelope, nuclear membrane proteins must pass through the nuclear pore complex. Meinema et al. (p. 90, published online 9 June; see the Perspective by Kriwacki and Yoon) found that a natively unfolded linker that spaces the transmembrane domain and the nuclear localization signal, reaches out from the membrane to the central channel of the nuclear pore. During transport, the unfolded linker appears to “slice” through the nuclear pore complex scaffold, allowing the nuclear pore complex to act as a selective gate that regulates intranuclear levels of membrane proteins.

  11. Microbes Are What You Eat

    CREDIT: FAITH ET AL.

    The microbial community within the gut is influenced by dietary constituents. Faith et al. (p. 101, published online 19 May) attempted to define dietary influences on the microflora by using germ-free mice colonized with 10 sequenced members of the human gut microbiota and fed diets with systematically manipulated concentrations of four ingredients commonly found in human foods. Changes in the absolute abundance of community members and of the community's meta-transcriptome were monitored and the data were used in a simple linear model. Changes in the proportions of macronutrients explained half of the variation in microbial species abundance and casein intake was highly correlated with total microbial biomass.

  12. Fight, Flee, or Freeze

    The medial part of the central amygdala is involved in behavioral and physiological conditioned fear responses. Are the different types of fear responses reflected in different associations between behavioral and physiological components? Viviani et al. (p. 104) detected separate neuronal populations, with distinct projections to brain stem nuclei, in rats that steer freezing versus cardiovascular function. The neuronal populations in the medial central amygdala also exhibited distinct electrophysiological characteristics and responded differently to oxytocin agonists. In a contextual fear-conditioning paradigm, oxytocin selectively affected freezing, but not heart rate variability, which may explain reduced freezing and increased maternal aggression when rats defend their offspring.

  13. Peer Pressure

    Sometimes, firmly held memory representations in the brain are altered by external social influences in a phenomenon called “memory conformity.” Edelson et al. (p. 108; see the Perspective by Roediger and McDermott) used a behavioral paradigm in combination with brain imaging to elucidate the brain mechanisms involved. After watching a documentary and completing a memory task, individuals were presented with fake memories from other participants. Even when their original recollection was correct, a large number of participants conformed to the majority opinion and gave incorrect answers, even after being informed about the original manipulations. Such persistent errors were associated with enhanced activity in the hippocampus, as well as in the amygdala during the test.

  14. Imperfect Copies?

    Transcription of DNA into the complementary RNA sequences for translation into proteins is one of the cornerstones of genetics. However, sequences may show divergence between the DNA and RNA, such as an A-to-G transition that may be explained by deamination. Li et al. (p. 53, published online 19 May) identified over 20,000 events where the RNA sequences did not match the corresponding DNA sequences in cultured B cells, skin, and brain tissues. Multiple individuals showed the same patterns of change within specific sites. Both computational and experimental validations were performed and the discrepancies were widespread and could even be detected in protein structures. Thus, unanticipated aspects of transcriptional or posttranscriptional processing may affect genome variation.

  15. Views on the Virosphere

    The virosphere is the least understood domain of life, despite its evident impact. Traditionally culture-dependent methods are used to probe this domain. Nevertheless, we know almost nothing about virus-host dynamics in the wider environment. Tadmor et al. (p. 58, see the cover; see the Perspective by Krupovic and Bamford) developed a microfluidic digital multiplex polymerase chain reaction technique to detect co-occurrence of a phage marker gene and a universal bacterial host marker. The work reveals viral-bacterial interactions at the level of single, uncultured, bacterial cells taken from termite guts. The results from the termite microflora indicate high levels of bacterial host specificity in the viruses, despite the potential for lateral gene transfer and host switching. The experimental approach circumvents culturing hosts or viruses and should allow for the analysis of multiple virus-host interactions in nature.

  16. Damage Limitation Exercise

    Covalent interstrand cross-links (ICLs) in the genome must be repaired quickly to avoid disruption of DNA-based cellular processes and additional damage to the DNA. Vertebrates can repair ICLs during DNA replication in a process that involves Fanconi anemia (FA) proteins, and this repair process is also thought to require homologous recombination between sister chromatids. Long et al. (p. 84) used a Xenopus egg–based, cell-free system to show that in replication-coupled ICL repair, Rad51 is required for homologous recombination of the double-strand break in the incised sister chromatid. Rad51 is loaded onto stalled replication forks before double-strand break formation, likely functioning to initiate strand invasion as soon as the break occurs. The FA protein complex acts upstream of homologous recombination during ICL repair and is not required for Rad51 recruitment to chromatin.

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