Showing papers by "DSM published in 2004"

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

Abstract: The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

Global-Scale Turbulent Convection and Magnetic Dynamo Action in the Solar Envelope

Abstract: The operation of the solar global dynamo appears to involve many dynamical elements, including the generation of fields by the intense turbulence of the deep convection zone, the transport of these fields into the tachocline region near the base of the convection zone, the storage and amplification of toroidal fields in the tachocline by differential rotation, and the destabilization and emergence of such fields due to magnetic buoyancy. Self-consistent magnetohydrodynamic (MHD) simulations that realistically incorporate all of these processes are not yet computationally feasible, although some elements can now be studied with reasonable fidelity. Here we consider the manner in which turbulent compressible convection within the bulk of the solar convection zone can generate large-scale magnetic fields through dynamo action. We accomplish this through a series of three-dimensional numerical simulations of MHD convection within rotating spherical shells using our anelastic spherical harmonic (ASH) code on massively parallel supercomputers. Since differential rotation is a key ingredient in all dynamo models, we also examine here the nature of the rotation profiles that can be sustained within the deep convection zone as strong magnetic fields are built and maintained. We find that the convection is able to maintain a solar-like angular velocity profile despite the influence of Maxwell stresses, which tend to oppose Reynolds stresses and thus reduce the latitudinal angular velocity contrast throughout the convection zone. The dynamo-generated magnetic fields exhibit a complex structure and evolution, with radial fields concentrated in downflow lanes and toroidal fields organized into twisted ribbons that are extended in longitude and achieve field strengths of up to 5000 G. The flows and fields exhibit substantial kinetic and magnetic helicity although systematic hemispherical patterns are only apparent in the former. Fluctuating fields dominate the magnetic energy and account for most of the back-reaction on the flow via Lorentz forces. Mean fields are relatively weak and do not exhibit systematic latitudinal propagation or periodic polarity reversals as in the Sun. This may be attributed to the absence of a tachocline, i.e., a penetrative boundary layer between the convection zone and the deeper radiative interior possessing strong rotational shear. The influence of such a layer will await subsequent studies.

High-energy particle acceleration in the shell of a supernova remnant.

Abstract: A significant fraction of the energy density of the interstellar medium is in the form of high-energy charged particles (cosmic rays)1. The origin of these particles remains uncertain. Although it is generally accepted that the only sources capable of supplying the energy required to accelerate the bulk of Galactic cosmic rays are supernova explosions, and even though the mechanism of particle acceleration in expanding supernova remnant (SNR) shocks is thought to be well understood theoretically2,3, unequivocal evidence for the production of high-energy particles in supernova shells has proven remarkably hard to find. Here we report on observations of the SNR RX J1713.7 - 3946 (G347.3 - 0.5), which was discovered by ROSAT4 in the X-ray spectrum and later claimed as a source of high-energy γ-rays5,6 of TeV energies (1 TeV = 1012 eV). We present a TeV γ-ray image of the SNR: the spatially resolved remnant has a shell morphology similar to that seen in X-rays, which demonstrates that very-high-energy particles are accelerated there. The energy spectrum indicates efficient acceleration of charged particles to energies beyond 100 TeV, consistent with current ideas of particle acceleration in young SNR shocks.

Dynamics of Femtosecond Laser Interactions with Dielectrics

Abstract: Femtosecond laser pulses appear as an emerging and promising tool for processing wide bandgap dielectric materials for a variety of applications. This article aims to provide an overview of recent progress in understanding the fundamental physics of femtosecond laser interactions with dielectrics that may have the potential for innovative materials applications. The focus of the overview is the dynamics of femtosecond laser-excited carriers and the propagation of femtosecond laser pulses inside dielectric materials.

Fusion of NUP214 to ABL1 on amplified episomes in T-cell acute lymphoblastic leukemia

Abstract: In T-cell acute lymphoblastic leukemia (T-ALL), transcription factors are known to be deregulated by chromosomal translocations, but mutations in protein tyrosine kinases have only rarely been identified. Here we describe the extrachromosomal (episomal) amplification of ABL1 in 5 of 90 (5.6%) individuals with T-ALL, an aberration that is not detectable by conventional cytogenetics. Molecular analyses delineated the amplicon as a 500-kb region from chromosome band 9q34, containing the oncogenes ABL1 and NUP214 (refs. 5,6). We identified a previously undescribed mechanism for activation of tyrosine kinases in cancer: the formation of episomes resulting in a fusion between NUP214 and ABL1. We detected the NUP214-ABL1 transcript in five individuals with the ABL1 amplification, in 5 of 85 (5.8%) additional individuals with T-ALL and in 3 of 22 T-ALL cell lines. The constitutively phosphorylated tyrosine kinase NUP214-ABL1 is sensitive to the tyrosine kinase inhibitor imatinib. The recurrent cryptic NUP214-ABL1 rearrangement is associated with increased HOX expression and deletion of CDKN2A, consistent with a multistep pathogenesis of T-ALL. NUP214-ABL1 expression defines a new subgroup of individuals with T-ALL who could benefit from treatment with imatinib.

SN 2003lw and GRB 031203: A Bright Supernova for a Faint Gamma-Ray Burst

Abstract: Optical and near-infrared observations of the gamma-ray burst GRB 031203, at z = 0.1055, are reported. A very faint afterglow is detected superposed onto the host galaxy in our first infrared JHK observations, carried out ~9 hr after the burst. Subsequently, a rebrightening is detected in all bands, peaking in the R band about 18 rest-frame days after the burst. The rebrightening closely resembles the light curve of a supernova like SN 1998bw, assuming that the GRB and the SN went off almost simultaneously, but with a somewhat slower evolution. Spectra taken close to the maximum of the rebrightening show extremely broad features as in SN 1998bw. The determination of the absolute magnitude of this SN (SN 2003lw) is difficult owing to the large and uncertain extinction, but likely this event was brighter than SN 1998bw by 0.5 mag in the VRI bands, reaching an absolute magnitude MV = -19.75 ± 0.15.

Proposal to elevate the genetic variant MAC-A, included in the Mycobacterium avium complex, to species rank as Mycobacterium chimaera sp. nov.

Abstract: The possibility that the strains included within the Mycobacterium avium complex (MAC), but not belonging either to M. avium or to Mycobacterium intracellulare, may be members of undescribed taxa, has already been questioned by several taxonomists. A very homogeneous cluster of 12 strains characterized by identical nucleotide sequences both in the 16S rDNA and in the 16S–23S internal transcribed spacer was investigated. Similar strains, previously reported in the literature, had been assigned either to the species M. intracellulare on the basis of the 16S rDNA similarity or to the group of MAC intermediates. However, several phenotypical and epidemiological characteristics seem to distinguish these strains from all other MAC organisms. The unique mycolic acid pattern obtained by HPLC is striking as it is characterized by two clusters of peaks, instead of the three presented by all other MAC organisms. All of the strains have been isolated from humans and all but one came from the respiratory tract of elderly people. The clinical significance of these strains, ascertained for seven patients, seems to suggest an unusually high virulence. The characteristics of all the strains reported in the literature, genotypically identical to the ones described here, seem to confirm our data, without reports of isolations from animals or the environment or, among humans, from AIDS patients. Therefore, an elevation of the MAC variant was proposed and characterized here, with the name Mycobacterium chimaera sp. nov.; this increases the number of species included in the M. avium complex. The type strain is FI-01069T (=CIP 107892T=DSM 44623T).

Development and evaluation of a quality-controlled ribosomal sequence database for 16S ribosomal DNA-based identification of Staphylococcus species.

Abstract: To establish an improved ribosomal gene sequence database as part of the Ribosomal Differentiation of Microorganisms (RIDOM) project and to overcome the drawbacks of phenotypic identification systems and publicly accessible sequence databases, both strands of the 5′ end of the 16S ribosomal DNA (rDNA) of 81 type and reference strains comprising all validly described staphylococcal (sub)species were sequenced. Assuming a normal distribution for pairwise distances of all unique staphylococcal sequences and choosing a reporting criterion of ≥98.7% similarity for a “distinct species,” a statistical error probability of 1.0% was calculated. To evaluate this database, a 16S rDNA fragment (corresponding to Escherichia coli positions 54 to 510) of 55 clinical Staphylococcus isolates (including those of the small-colony variant phenotype) were sequenced and analyzed by the RIDOM approach. Of these isolates, 54 (98.2%) had a similarity score above the proposed threshold using RIDOM; 48 (87.3%) of the sequences gave a perfect match, whereas 83.6% were found by searching National Center for Biotechnology Information (NCBI) database entries. In contrast to RIDOM, which showed four ambiguities at the species level (mainly concerning Staphylococcus intermedius versus Staphylococcus delphini), the NCBI database search yielded 18 taxon-related ambiguities and showed numerous matches exhibiting redundant or unspecified entries. Comparing molecular results with those of biochemical procedures, ID 32 Staph (bioMerieux, Marcy I'Etoile, France) and VITEK 2 (bioMerieux) failed to identify 13 (23.6%) and 19 (34.5%) isolates, respectively, due to incorrect identification and/or categorization below acceptable values. In contrast to phenotypic methods and the NCBI database, the novel high-quality RIDOM sequence database provides excellent identification of staphylococci, including rarely isolated species and phenotypic variants.

Method of preparing nano-structured surface coatings and coated articles

Abstract: The invention relates to new processes for the preparation of antireflective coatings and coated substrates, as well as articles produced by these processes. These coatings can include one or more layers made of materials which form nano-structured and/or nano-porous surfaces. The process can include applying a cross-linkable hard coat to a substrate, partially curing or cross-linking the hard coat, and then applying a second coat carried by a solvent or mixture of solvents capable of swelling the partially cured hard coat. The second coat is then cross-linked and grafted to the hard coat to produce a durable coated substrate with antireflective properties.

The XMM-LSS survey. Survey design and first results

Abstract: We have designed a medium deep large area X-ray survey with XMM - the XMM Large Scale Structure survey, XMM-LSS - with the scope of extending the cosmological tests attempted using ROSAT cluster samples to two redshift bins between 0

Use of "Homeopathic" Ligand-Free Palladium as Catalyst for Aryl-Aryl Coupling Reactions

Abstract: We have previously shown that the use of ligand-free palladium employing Pd(OAc)2 as catalyst precursor in the Heck reaction of aryl bromides is possible if low catalyst loadings, typically between 0.01 – 0.1 mol % are used. We have now tested this phenomenon, which we have dubbed “homeopathic” palladium, in biaryl formation using the Suzuki, the Negishi and the Kumada cross-coupling reactions. The Suzuki reaction of aryl bromides, both activated and deactivated, is possible using 0.02–0.05 mol % of Pd(OAc)2. In this reaction turnover frequencies up to 30,000 have been reached with activated substrates. Even aryl chlorides could be reacted if strongly electron-withdrawing substituents were present. The Negishi coupling with a variety of arylzinc halides was possible on aryl bromides containing electron-withdrawing substituents. The Kumada reaction only gave low yields of products under “homeopathic' conditions.

First Insights into the Spitzer Wide-Area Infrared Extragalactic Legacy Survey (SWIRE) Galaxy Populations

Abstract: We characterize the Spitzer Wide-area Infrared Extragalactic Legacy Survey (SWIRE) galaxy populations in the SWIRE validation field within the Lockman Hole, based on the 3.6-24 μm Spitzer data and deep U, g', r', i' optical imaging within an area ~1/3 deg2 for ~16,000 Spitzer SWIRE sources. The entire SWIRE survey will discover over 2.3 million galaxies at 3.6 μm and almost 350,000 at 24 μm; ~70,000 of these will be five-band 3.6-24 μm detections. The colors cover a broad range, generally well represented by redshifted spectral energy distributions of known galaxy populations; however, significant samples of unusually blue objects in the [3.6]-[4.5] color are found, as well as many objects very red in the 3.6-24 μm mid-IR. Nine of these are investigated and are interpreted as star-forming systems, starbursts, and active galactic nuclei (AGNs) from z = 0.37 to 2.8, with luminosities from LIR = 1010.3 to 1013.7 L.

Lycopene and vitamin E interfere with autocrine/paracrine loops in the Dunning prostate cancer model

Abstract: SPECIFIC AIMSWe tested lycopene and vitamin E in the Dunning prostate cancer model to prove their efficacy in prostate cancer (PCA) prevention and to identify the mechanisms by which these nutrient...

A general catalogue of 6.7 GHz methanol masers. I: data

Abstract: Methanol masers are often detected in regions of intense star formation. Several studies in the last decade indicate that they may even be the earliest signpost of a high-mass star-forming region. Their powerful emission make them very good candidates for observations using both single--dish telescopes and interferometers, the latter allows detailed structural and dynamical studies of these objects. We have prepared a catalogue of all known 6.7-GHz methanol masers, discovered both by surveys that targeted possible associated objects and unbiased surveys covering a large fraction of galactic longitudes across the Galactic plane (-0.5deg <= b <= 0.5deg for most of the regions). The catalogue contains 519 sources which are listed with their kinematic (galactocentric and heliocentric) distances as well as possibly associated IR objects. We find that 6.7-GHz methanol masers clearly trace the molecular ring of our Galaxy, where most of the OB associations are located. The present list of masers also reports detections of other masing transitions of methanol as further information for the study of the maser phenomenon. In a further publication we will address some statistical considerations.

A cloned Bacillus halodurans multicopper oxidase exhibiting alkaline laccase activity.

Abstract: The gene product of open reading frame bh2082 from Bacillus halodurans C-125 was identified as a multicopper oxidase with potential laccase activity. A homologue of this gene, lbh1, was obtained from a B. halodurans isolate from our culture collection. The encoded gene product was expressed in Escherichia coli and showed laccase-like activity, oxidising 2,2′-azino-bis(3-ethylbenz-thiazoline-6-sulfonic acid), 2,6-dimethoxyphenol and syringaldazine (SGZ). The pH optimum of Lbh1 with SGZ is 7.5–8 (at 45°C) and the laccase activity is stimulated rather than inhibited by chloride. These unusual properties make Lbh1 an interesting biocatalyst in applications for which classical laccases are unsuited, such as biobleaching of kraft pulp for paper production.

Aggregation properties of N, N, N', N'-tetraoctyl-3-oxapentanediamide (TODGA) in n-dodecane

Abstract: N,N,N′,N′‐Tetraoctyl‐3‐oxapentanediamide (TODGA) in n‐dodecane was studied to characterize the aggregation properties of the extractant and the formation of a third‐phase when nitric acid is extracted. Tensiometry and small‐angle x‐ray and neutron scattering (SAXS and SANS) revealed the presence of small aggregates dispersed in the diluent. The aggregates are spherical reverse micelles consisting of a polar core containing water and the extracted ions and surrounded by approximately four extractant molecules. When the initial nitric acid content is increased, the aggregates remain spherical, their size increases as more water and ions are extracted and inter‐particle attraction increases. The sticky hard‐sphere model proposed by Baxter was used successfully to describe the small reverse micelles of the organic TODGA phases and quantify their interactions. These attractive interactions were found responsible for the formation of the third‐phase.

Functional Characterization of OsMADS18, a Member of the AP1/SQUA Subfamily of MADS Box Genes

Abstract: MADS box transcription factors controlling flower development have been isolated and studied in a wide variety of organisms. These studies have shown that homologous MADS box genes from different species often have similar functions. OsMADS18 from rice (Oryza sativa) belongs to the phylogenetically defined AP1/SQUA group. The MADS box genes of this group have functions in plant development, like controlling the transition from vegetative to reproductive growth, determination of floral organ identity, and regulation of fruit maturation. In this paper we report the functional analysis of OsMADS18. This rice MADS box gene is widely expressed in rice with its transcripts accumulated to higher levels in meristems. Overexpression of OsMADS18 in rice induced early flowering, and detailed histological analysis revealed that the formation of axillary shoot meristems was accelerated. Silencing of OsMADS18 using an RNA interference approach did not result in any visible phenotypic alteration, indicating that OsMADS18 is probably redundant with other MADS box transcription factors. Surprisingly, overexpression of OsMADS18 in Arabidopsis caused a phenotype closely resembling the ap1 mutant. We show that the ap1 phenotype is not caused by down-regulation of AP1 expression. Yeast two-hybrid experiments showed that some of the natural partners of AP1 interact with OsMADS18, suggesting that the OsMADS18 overexpression phenotype in Arabidopsis is likely to be due to the subtraction of AP1 partners from active transcription complexes. Thus, when compared to AP1, OsMADS18 during evolution seems to have conserved the mechanistic properties of protein-protein interactions, although it cannot complement the AP1 function.

Simulations of Core Convection in Rotating A-Type Stars: Differential Rotation and Overshooting

Abstract: We present the results of three-dimensional simulations of core convection within A-type stars of 2 M☉, at a range of rotation rates. We consider the inner 30% by radius of such stars, thereby encompassing the convective core and some of the surrounding radiative envelope. We utilize our anelastic spherical harmonic code, which solves the compressible Navier-Stokes equations in the anelastic approximation, to examine highly nonlinear flows that can span multiple scale heights. The cores of these stars are found to rotate differentially, with central cylindrical regions of strikingly slow rotation achieved in our simulations of stars whose convective Rossby number (Roc) is less than unity. Such differential rotation results from the redistribution of angular momentum by the nonlinear convection that strongly senses the overall rotation of the star. Penetrative convective motions extend into the overlying radiative zone, yielding a prolate shape (aligned with the rotation axis) to the central region in which nearly adiabatic stratification is achieved. This is further surrounded by a region of overshooting motions, the extent of which is greater at the equator than at the poles, yielding an overall spherical shape to the domain experiencing at least some convective mixing. We assess the overshooting achieved as the stability of the radiative exterior is varied and the weak circulations that result in that exterior. The convective plumes serve to excite gravity waves in the radiative envelope, ranging from localized ripples of many scales to some remarkable global resonances.

Reliable high‐throughput screening with Pichia pastoris by limiting yeast cell death phenomena

Abstract: Comparative screening of gene expression libraries employing the potent industrial host Pichia pastoris for improving recombinant eukaryotic enzymes by protein engineering was an unsolved task. We simplified the protocol for protein expression by P. pastoris and scaled it down to 0.5-ml cultures. Optimising standard growth conditions and procedures, programmed cell death and necrosis of P. pastoris in microscale cultures were diminished. Uniform cell growth in 96-deep-well plates now allows for high-throughput protein expression and screening for improved enzyme variants. Furthermore, the change from one host for protein engineering to another host for enzyme production becomes dispensable, and this accelerates the protein breeding cycles and makes predictions for large-scale production more accurate.

Geometry of the non-thermal emission in SN 1006 - Azimuthal variations of cosmic-ray acceleration

Abstract: SN 1006 is the prototype of shell supernova remnants, in which non-thermal synchrotron emission dominates the X-ray spectrum. The non-thermal emission is due to the cosmic-ray electrons accelerated behind the blast wave. The X-ray synchrotron emission is due to the highest energy electrons, and is thus a tracer of the maximum energy electrons may reach behind a shock. We have put together all XMM-Newton observations to build a full map of SN 1006. The very low brightness above 2 keV in the interior indicates that the bright non-thermal limbs are polar caps rather than an equator. This implies that the ambient magnetic field runs southwest to northeast, along the Galactic plane. We used a combined VLA/Parkes radio map to anchor the spectrum at low energy, and model the spectra with synchrotron emission from a cut-off power-law electron distribution, plus a thermal component. We present radial and azimuthal profiles of the cut-off frequency. The cut-off frequency decreases steeply with radius towards the center and with position angle away from the maximum emission. The maximum energy reached by accelerated particles, as well as their number, must be higher at the bright limbs than elsewhere. This implies interesting constraints for acceleration at perpendicular shocks. Overall the XMM-Newton data is consistent with the model in which the magnetic field is amplified where acceleration is efficient.

The first evidence of anaerobic CO oxidation coupled with H2 production by a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent.

Abstract: From 24 samples of hydrothermal venting structures collected at the East Pacific Rise (13°N), 13 enrichments of coccoid cells were obtained which grew on CO, producing H2 and CO2 at 80°C. A hyperthermophilic archaeon capable of lithotrophic growth on CO coupled with equimolar production of H2 was isolated. Based on its 16S rRNA sequence analysis, this organism was affiliated with the genus Thermococcus. Other strains of Thermococcales species (Pyrococcus furiosus, Thermococcus peptonophilus, T. profundus, T. chitonophagus, T. stetteri, T. gorgonarius, T. litoralis, and T. pacificus) were shown to be unable to grow on CO. Searches in sequence databases failed to reveal deposited sequences of genes related to CO metabolism in Thermococcales. Our work provides the first evidence of anaerobic CO oxidation coupled with H2 production performed by an archaeon as well as the first documented case of lithotrophic growth of a Thermococcales representative.