The crystal structure of the photoprotein aequorin at 2.3 A resolution

Aequorin is a calcium-sensitive photoprotein originally obtained from the jellyfish Aequorea aequorea. Because it has a high sensitivity to calcium ions and is biologically harmless, aequorin is widely used as a probe to monitor intracellular levels of free calcium. The aequorin molecule contains four helix-loop-helix 'EF-hand' domains, of which three can bind calcium. The molecule also contains coelenterazine as its chromophoric ligand. When calcium is added, the protein complex decomposes into apoaequorin, coelenteramide and CO2, accompanied by the emission of light. Apoaequorin can be regenerated into active aequorin in the absence of calcium by incubation with coelenterazine, oxygen and a thiol agent. Cloning and expression of the complementary DNA for aequorin were first reported in 1985 (refs 2, 6), and growth of crystals of the recombinant protein has been described; however, techniques have only recently been developed to prepare recombinant aequorin of the highest purity, permitting a full crystallographic study. Here we report the structure of recombinant aequorin determined by X-ray crystallography. Aequorin is found to be a globular molecule containing a hydrophobic core cavity that accommodates the ligand coelenterazine-2-hydroperoxide. The structure shows protein components stabilizing the peroxide and suggests a mechanism by which calcium activation may occur.     

A first-order liquid-liquid phase transition in phosphorus

First-order structural phase transitions are common in crystalline solids, whereas first-order liquid-liquid phase transitions (that is, transitions between two distinct liquid forms with different density and entropy) are exceedingly rare in pure substances. But recent theoretical and experimental studies have shown evidence for such a transition in several materials, including supercooled water and liquid carbon. Here we report an in situ X-ray diffraction observation of a liquid-liquid transition in phosphorus, involving an abrupt, pressure-induced structural change between two distinct liquid forms. In addition to a known form of liquid phosphorus--a molecular liquid comprising tetrahedral P4 molecules--we have found a polymeric form at pressures above 1 GPa. Changing the pressure results in a reversible transformation from the low-pressure molecular form into the high-pressure polymeric form. The transformation is sharp and rapid, occurring within a few minutes over a pressure range of less than 0.02 GPa. During the transformation, the two forms of liquid coexist. These features are strongly suggestive of a first-order liquid-liquid phase transition.     

Gene silencing in cancer by histone H3 lysine 27 trimethylation independent of promoter DNA methylation

Epigenetic silencing in cancer cells is mediated by at least two distinct histone modifications, polycomb-based histone H3 lysine 27 trimethylation (H3K27triM) and H3K9 dimethylation. The relationship between DNA hypermethylation and these histone modifications is not completely understood. Using chromatin immunoprecipitation microarrays (ChIP-chip) in prostate cancer cells compared to normal prostate, we found that up to 5% of promoters (16% CpG islands and 84% non-CpG islands) were enriched with H3K27triM. These genes were silenced specifically in prostate cancer, and those CpG islands affected showed low levels of DNA methylation. Downregulation of the EZH2 histone methyltransferase restored expression of the H3K27triM target genes alone or in synergy with histone deacetylase inhibition, without affecting promoter DNA methylation, and with no effect on the expression of genes silenced by DNA hypermethylation. These data establish EZH2-mediated H3K27triM as a mechanism of tumor-suppressor gene silencing in cancer that is potentially independent of promoter DNA methylation.     

Genome sequencing and analysis of Aspergillus oryzae

The genome of Aspergillus oryzae, a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. The ability to secrete large amounts of proteins and the development of a transformation system have facilitated the use of A. oryzae in modern biotechnology. Although both A. oryzae and Aspergillus flavus belong to the section Flavi of the subgenus Circumdati of Aspergillus, A. oryzae, unlike A. flavus, does not produce aflatoxin, and its long history of use in the food industry has proved its safety. Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and Aspergillus fumigatus. Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae-specific blocks (lacking synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.     

Nuclear cataract caused by a lack of DNA degradation in the mouse eye lens

The eye lens is composed of fibre cells, which develop from the epithelial cells on the anterior surface of the lens. Differentiation into a lens fibre cell is accompanied by changes in cell shape, the expression of crystallins and the degradation of cellular organelles. The loss of organelles is believed to ensure the transparency of the lens, but the molecular mechanism behind this process is not known. Here we show that DLAD ('DNase II-like acid DNase', also called DNase IIbeta) is expressed in human and murine lens cells, and that mice deficient in the DLAD gene are incapable of degrading DNA during lens cell differentiation--the undigested DNA accumulates in the fibre cells. The DLAD-/- mice develop cataracts of the nucleus lentis, and their response to light on electroretinograms is severely reduced. These results indicate that DLAD is responsible for the degradation of nuclear DNA during lens cell differentiation, and that if DNA is left undigested in the lens, it causes cataracts of the nucleus lentis, blocking the light path.     

NICT/ATR Chinese-Japanese-English Speech-to-Speech Translation System

This paper describes the latest version of the Chinese-Japanese-English handheld speech-tospeech translation system developed by NICT/ATR, which is now ready to be deployed for travelers. With the entire speech-to-speech translation function being implemented into one terminal, it realizes real-time, location-free speech-to-speech translation. A new noise-suppression technique notably improves the speech recognition performance. Corpus-based approaches of speech recognition, machine translation, and speech synthesis enable coverage of a wide variety of topics and portability to other languages. Test results show that the character accuracy of speech recognition is 82%-94% for Chinese speech, with a bilingual evaluation understudy score of machine translation is 0.55-0.74 for Chinese-Japanese and Chinese-English     

Enhanced atmospheric loss on protoplanets at the giant impact phase in the presence of oceans

The atmospheric compositions of Venus and Earth differ significantly, with the venusian atmosphere containing about 50 times as much 36Ar as the atmosphere on Earth. The different effects of the solar wind on planet-forming materials for Earth and Venus have been proposed to account for some of this difference in atmospheric composition, but the cause of the compositional difference has not yet been fully resolved. Here we propose that the absence or presence of an ocean at the surface of a protoplanet during the giant impact phase could have determined its subsequent atmospheric amount and composition. Using numerical simulations, we demonstrate that the presence of an ocean significantly enhances the loss of atmosphere during a giant impact owing to two effects: evaporation of the ocean, and lower shock impedance of the ocean compared to the ground. Protoplanets near Earth's orbit are expected to have had oceans, whereas those near Venus' orbit are not, and we therefore suggest that remnants of the noble-gas rich proto-atmosphere survived on Venus, but not on Earth. Our proposed mechanism explains differences in the atmospheric contents of argon, krypton and xenon on Venus and Earth, but most of the neon must have escaped from both planets' atmospheres later to yield the observed ratio of neon to argon.     

Leptin reverses insulin resistance and diabetes mellitus in mice with congenital lipodystrophy.

Congenital generalized lipodystrophy (CGL) is a rare autosomal recessive disorder characterized by a paucity of adipose (fat) tissue which is evident at birth and is accompanied by a severe resistance to insulin, leading to hyperinsulinaemia, hyperglycaemia and enlarged fatty liver. We have developed a mouse model that mimics these features of CGL: the syndrome occurs in transgenic mice expressing a truncated version of a nuclear protein known as nSREBP-1c (for sterol-regulatory-element-binding protein-1c) under the control of the adipose-specific aP2 enhancer. Adipose tissue from these mice was markedly deficient in messenger RNAs encoding several fat-specific proteins, including leptin, a fat-derived hormone that regulates food intake and energy metabolism. Here we show that insulin resistance in our lipodystrophic mice can be overcome by a continuous systemic infusion of low doses of recombinant leptin, an effect that is not mimicked by chronic food restriction. Our results support the idea that leptin modulates insulin sensitivity and glucose disposal independently of its effect on food intake, and that leptin deficiency accounts for the insulin resistance found in CGL.     

The M/PH/1 queue with working vacations and vacation interruption

We study an M/PH/1 queue with phase type working vacation and vacation interruption where the vacation time follows a phase type distribution. The server serves the customers at a lower rate in a vacation period. The server comes back to the regular busy period at a service completion without completing the vacation. Such policy is called vacation interruption. In terms of quasi birth and death process and matrix-geometric solution method, we obtain the stationary queue length distribution. Moreover we obtain the conditional stochastic decomposition structures of queue length and waiting time when the service time distribution in the regular busy period is exponential.