Infrared spectrum of an extremely cool white-dwarf star

White dwarfs are the remnant cores of stars that initially had masses of less than 8 solar masses. They cool gradually over billions of years, and have been suggested to make up much of the 'dark matter' in the halo of the Milky Way. But extremely cool white dwarfs have proved difficult to detect, owing to both their faintness and their anticipated similarity in colour to other classes of dwarf stars. Recent improved models indicate that white dwarfs are much more blue than previously supposed, suggesting that the earlier searches may have been looking for the wrong kinds of objects. Here we report an infrared spectrum of an extremely cool white dwarf that is consistent with the new models. We determine the star's temperature to be 3,500 +/- 200 K, making it the coolest known white dwarf. The kinematics of this star indicate that it is in the halo of the Milky Way, and the density of such objects implied by the serendipitous discovery of this star is consistent with white dwarfs dominating the dark matter in the halo.     

Changing the identity of a transfer RNA

A leucine transfer RNA has been transformed into a serine transfer RNA by changing 12 nucleotides. This result indicates that a limited set of residues determine tRNA identity.     

Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template

Transfer RNA nucleotidyltransferases (CCA-adding enzymes) are responsible for the maturation or repair of the functional 3' end of tRNAs by means of the addition of the essential nucleotides CCA. However, it is unclear how tRNA nucleotidyltransferases polymerize CCA onto the 3' terminus of immature tRNAs without using a nucleic acid template. Here we describe the crystal structure of the Archaeoglobus fulgidus tRNA nucleotidyltransferase in complex with tRNA. We also present ternary complexes of this enzyme with both RNA duplex mimics of the tRNA acceptor stem that terminate with the nucleotides C74 or C75, as well as the appropriate incoming nucleoside 5'-triphosphates. A single nucleotide-binding pocket exists whose specificity for both CTP and ATP is determined by the protein side chain of Arg 224 and backbone phosphates of the tRNA, which are non-complementary to and thus exclude UTP and GTP. Discrimination between CTP or ATP at a given addition step and at termination arises from changes in the size and shape of the nucleotide binding site that is progressively altered by the elongating 3' end of the tRNA.     

Functional contacts of a transfer RNA synthetase with 2'-hydroxyl groups in the RNA minor groove.

The functional analysis of determinants on RNA has been largely limited to molecules that contain naturally occurring ribonucleotides, so little is known about the role of 2'-hydroxyl groups in protein-RNA recognition. A single base pair (G3.U70) in the acceptor stem of tRNA(Ala) is the principal element for specific recognition by Escherichia coli alanine-tRNA synthetase. This tRNA synthetase aminoacylates small RNA helices that contain the G3.U70 base pair. Furthermore, removal of the G3 exocyclic 2-amino group that projects into the minor groove eliminates aminoacylation. This 2-amino group is flanked on either side by ribose 2'-hydroxyl groups that line the minor groove. Here we use chemical synthesis to construct 32 helices that make deoxy and O-methyl substitutions of individual and multiple 2'-hydroxyl groups near and beyond the G3.U70 base pair and find that functional 2'-hydroxyl contacts are clustered within a few ?ngstroms of the critical 2-amino group. These contacts are highly specific and make a thermodynamically significant contribution to RNA recognition.     

A simple structural feature is a major determinant of the identity of a transfer RNA

Analysis of a series of mutants of an Escherichia coli alanine transfer RNA shows that substitution of a single G-U base pair in the acceptor helix eliminates aminoacylation with alanine in vivo and in vitro. Introduction of that base pair into the analogous position of a cysteine and a phenylalanine transfer RNA confers upon each the ability to be aminoacylated with alanine. Thus, as little as a single base pair can direct an amino acid to a specific transfer RNA.     

Coevolution of codon usage and transfer RNA abundance

The use of synonymous codons is strongly biased in the bacterium Escherichia coli and yeast, comprising both bias between codons recognized by the same transfer RNA and bias between groups of codons recognized by different synonymous tRNAs. A major determinant of the second sort of bias is tRNA content, codons recognized by abundant tRNAs being used more often than those recognised by rare tRNAs, particularly in highly expressed genes, probably owing to selection at the level of translation against codons recognized by rare tRNAs. Conversely, codon usage is likely to exert selection pressure on tRNA abundance. Here I develop a model for the coevolution of codon usage and tRNA abundance which explains why there are unequal abundances of synonymous tRNAs leading to biased usage between groups of codons recognized by them in unicellular organisms.     

Use of photoelectron energy spectrum transfer equation for the measurement of a narrowband XUV pulse

To study the time evolution of a molecular state in an ultra-fast chemical reaction,the use of shorter pulses with higher photon energy and narrower bandwidth for both pump and probe is necessary.However,quick and precise measurement of their detailed time structures is a challenge.Over the last decade,great efforts have been made to measure an attosecond extreme ultraviolet (XUV) pulse.To date,several methods have been developed to measure the pulse duration and completely reconstruct it.The attosecond spectral phase interferometry for direct electric field reconstruction (SPIDER) and attosecond frequency-resolved optical gating (FROG) techniques are often used.However,these methods use state-of-the-art experimental set-ups and complicated data analysis procedures.To develop attosecond metrology for practical use (e.g.timing,measurement,evaluation,calibration,optimization,pumping,probing),we propose a quick and analytical method to precisely observe an attosecond XUV pulse with laser-assisted photo-ionization.The method is based on determining the laser-related phase of each streaked electron and using a transfer equation for one-step pulse reconstruction without any time-resolved measurements,iterative calculations,or data fitting procedures.Temporal errors of the pulse reconstruction are calculated from the XUV bandwidth.Because the transfer equation establishes a direct connection between the XUV pulse properties,the crucial laser parameters (peak intensity,phase,carrier envelope phase),the atomic ionization potential,and the measured photoelectron energy spectrum,we can use it to study any one of these properties from other known information and probe the dynamic processes of an ultra-fast reaction.     

A spectrum of an extrasolar planet

Of the over 200 known extrasolar planets, 14 exhibit transits in front of their parent stars as seen from Earth. Spectroscopic observations of the transiting planets can probe the physical conditions of their atmospheres. One such technique can be used to derive the planetary spectrum by subtracting the stellar spectrum measured during eclipse (planet hidden behind star) from the combined-light spectrum measured outside eclipse (star + planet). Although several attempts have been made from Earth-based observatories, no spectrum has yet been measured for any of the established extrasolar planets. Here we report a measurement of the infrared spectrum (7.5-13.2 microm) of the transiting extrasolar planet HD 209458b. Our observations reveal a hot thermal continuum for the planetary spectrum, with an approximately constant ratio to the stellar flux over this wavelength range. Superposed on this continuum is a broad emission peak centred near 9.65 microm that we attribute to emission by silicate clouds. We also find a narrow, unidentified emission feature at 7.78 microm. Models of these 'hot Jupiter' planets predict a flux peak near 10 microm, where thermal emission from the deep atmosphere emerges relatively unimpeded by water absorption, but models dominated by water fit the observed spectrum poorly.     

Tetramerization of an RNA oligonucleotide containing a GGGG sequence.

Poly rG can form four-stranded helices. The Hoogsteen-paired quartets of G residues on which such structures depend are so stable that they will form in 5'-GMP solutions, provided that Na+ or K+ are present (see for example, refs 2-4). Telomeric DNA sequences, which are G-rich, adopt four-stranded antiparallel G-quartet conformations in vitro, and parallel tetramerization of G-rich sequences may be involved in meiosis. Here we show that RNAs containing short runs of Gs can also tetramerize. A 19-base oligonucleotide derived from the 5S RNA of Escherichia coli (strand III), 5'GCCGAUGGUAGUGUGGGGU3', forms a K(+)-stabilized tetrameric aggregate that depends on the G residues at its 3' end. This complex is so stable that it would be surprising if similar structures do not occur in nature.