Identification of 10 novel snoRNA gene clusters from Arabidopsis thaliana

Ten novel small nucleolar RNA (snoRNA) gene clusters, consisting of two or three snoRNA genes, respectively, were identified from Arabidopsis thaliana. Twelve of the 25 snoRNA genes in these clusters are homologous to those of yeast and mammals according to the conserved antisense sequences that guide 2′-O-ribose methylation of rRNA. The remaining 13 snoRNA genes, including two 5.8S rRNA methylation guides, are new genes identified from A.thaliana. Interestingly, seven methylated nucleotides, predicted by novel snoRNAs Z41a–Z46, are methylated neither in yeast nor in vertebrates. Using primer extension at low dNTP concentration the six methylation sites were determined as expected. These snoRNAs were recognized as specific guides for 2′-O-ribose methylation of plant rRNAs. Z42, however, did not guide the expected methylation of 25S rRNA in our assay. Thus, its function remains to be elucidated. The intergenic spacers of the gene clusters are rich in uridine (up to 40%) and most of them range in size from 35 to 100 nt. Lack of a conserved promoter element in each spacer and the determination of polycistronic transcription from a cluster by RT–PCR assay suggest that the snoRNAs encoded in the clusters are transcribed as a polycistron under an upstream promoter, and individual snoRNAs are released after processing of the precursor. Numerous snoRNA gene clusters identified from A.thaliana and other organisms suggest that the snoRNA gene cluster is an ancient gene organization existing abundantly in plants.

Even-odd alternation in mass spectrum of thymine and uracil clusters: Evidence of intracluster photodimerization

Multiphoton ionization of thymine and uracil clusters generated by a supersonic molecular beam gave rise to a remarkable alternation of mass spectral intensities between even- and odd-numbered clusters. Such alternation was observed in clusters of up to 30 molecules. Excitation to the two lowest electronically excited states seemed to be a strong prerequisite. In view of the well known photodimerization reaction of thymine and uracil in the bulk phase, it is proposed that such alternation in the mass spectral intensity resulted from formation of photodimer units within the cluster on intense UV irradiation. Several analogues of thymine with no known propensity for photodimerization in the bulk phase did not exhibit any sign of such alternation in the cluster mass spectrum. The intrinsic UV window for photodimerization, and hence photoinduced mammalian mutagenesis, was estimated to be approximately 210–280 nm, significantly narrower than the previously reported bulk values of 150–300 nm.

Differential fluorescence labeling of cysteinyl clusters uncovers high tissue levels of thionein

The isolation of thionein (T) from tissues has not been reported heretofore. T contains 20 cysteinyl residues that react with 7-fluorobenz-2-oxa-1,3-diazole-4-sulfonamide to form fluorescent adducts. In metallothionein (MT) the cysteinyl residues, which are bound to zinc, do not react. However, they do react in the presence of a chelating agent such as EDTA. The resultant difference in chemical reactivity provides a means to measure T in the absence of EDTA, (MT + T) in its presence, and, of course, MT by difference. The 7-fluorobenz-2-oxa-1,3-diazole-4-sulfonamide derivative of T can be isolated from tissue homogenates by HPLC and quantified fluorimetrically with a detection limit in the femtomolar range and a linear response over 3 orders of magnitude. Analysis of liver, kidney, and brain of rats reveals almost as much T as MT. Moreover, in contrast to earlier views, MT in tissue extracts appears to be less stable than T. The existence of T in tissues under normal physiological conditions has important implications for its function both in zinc metabolism and the redox balance of the cell.

Globular clusters, Hipparcos, and the age of the galaxy

We discuss the impact of the results from the recent Hipparcos astrometric satellite on distance estimates of galactic globular clusters. Recalibrating the clusters not only implies a relatively small change in the distance to the Large Magellanic Cloud, and hence a rescaling of several estimates of the Hubble constant, but also leads to significantly younger cluster ages. Although the data are not yet conclusive, the results so far point to a likely resolution of the apparent paradox of a universe younger than its constituents, without requiring significant modifications to simple cosmological models.

X-ray emission from clusters and groups of galaxies

Recent major advances in x-ray imaging and spectroscopy of clusters have allowed the determination of their mass and mass profile out to ≈1/2 the virial radius. In rich clusters, most of the baryonic mass is in the gas phase, and the ratio of mass in gas/stars varies by a factor of 2–4. The baryonic fractions vary by a factor of ≈3 from cluster to cluster and almost always exceed 0.09 h50−[3/2] and thus are in fundamental conflict with the assumption of Ω = 1 and the results of big bang nucleosynthesis. The derived Fe abundances are 0.2–0.45 solar, and the abundances of O and Si for low redshift systems are 0.6–1.0 solar. This distribution is consistent with an origin in pure type II supernova. The amount of light and energy produced by these supernovae is very large, indicating their importance in influencing the formation of clusters and galaxies. The lack of evolution of Fe to a redshift of z ≈ 0.4 argues for very early enrichment of the cluster gas. Groups show a wide range of abundances, 0.1–0.5 solar. The results of an x-ray survey indicate that the contribution of groups to the mass density of the universe is likely to be larger than 0.1 h50−2. Many of the very poor groups have large x-ray halos and are filled with small galaxies whose velocity dispersion is a good match to the x-ray temperatures.

The chaperone/usher pathways of Pseudomonas aeruginosa: Identification of fimbrial gene clusters (cup) and their involvement in biofilm formation

Pseudomonas aeruginosa, an important opportunistic human pathogen, persists in certain tissues in the form of specialized bacterial communities, referred to as biofilm. The biofilm is formed through series of interactions between cells and adherence to surfaces, resulting in an organized structure. By screening a library of Tn5 insertions in a nonpiliated P. aeruginosa strain, we identified genes involved in early stages of biofilm formation. One class of mutations identified in this study mapped in a cluster of genes specifying the components of a chaperone/usher pathway that is involved in assembly of fimbrial subunits in other microorganisms. These genes, not previously described in P. aeruginosa, were named cupA1–A5. Additional chaperone/usher systems (CupB and CupC) have been also identified in the genome of P. aeruginosa PAO1; however, they do not appear to play a role in adhesion under the conditions where the CupA system is expressed and functions in surface adherence. The identification of these putative adhesins on the cell surface of P. aeruginosa suggests that this organism possess a wide range of factors that function in biofilm formation. These structures appear to be differentially regulated and may function at distinct stages of biofilm formation, or in specific environments colonized by this organism.

Characterizations of diverse residue clusters in protein three-dimensional structures.

We present new methods for identifying and analyzing statistically significant residue clusters that occur in three-dimensional (3D) protein structures. Residue clusters of different kinds occur in many contexts. They often feature the active site (e.g., in substrate binding), the interface between polypeptide units of protein complexes, regions of protein-protein and protein-nucleic acid interactions, or regions of metal ion coordination. The methods are illustrated with 3D clusters centering on four themes. (i) Acidic or histidine-acidic clusters associated with metal ions. (ii) Cysteine clusters including coordination of metals such as zinc or iron-sulfur structures, cysteine knots prominent in growth factors, multiple sets of buried disulfide pairings that putatively nucleate the hydrophobic core, or cysteine clusters of mostly exposed disulfide bridges. (iii) Iron-sulfur proteins and charge clusters. (iv) 3D environments of multiple histidine residues. Study of diverse 3D residue clusters offers a new perspective on protein structure and function. The algorithms can aid in rapid identification of distinctive sites, suggest correlations among protein structures, and serve as a tool in the analysis of new structures.

Clusters of charged residues in protein three-dimensional structures.

Statistically significant charge clusters (basic, acidic, or of mixed charge) in tertiary protein structures are identified by new methods from a large representative collection of protein structures. About 10% of protein structures show at least one charge cluster, mostly of mixed type involving about equally anionic and cationic residues. Positive charge clusters are very rare. Negative (or histidine-acidic) charge clusters often coordinate calcium, or magnesium or zinc ions [e.g., thermolysin (PDB code: 3tln), mannose-binding protein (2msb), aminopeptidase (1amp)]. Mixed-charge clusters are prominent at interchain contacts where they stabilize quaternary protein formation [e.g., glutathione S-transferase (2gst), catalase (8act), and fructose-1,6-bisphosphate aldolase (1fba)]. They are also involved in protein-protein interaction and in substrate binding. For example, the mixed-charge cluster of aspartate carbamoyl-transferase (8atc) envelops the aspartate carbonyl substrate in a flexible manner (alternating tense and relaxed states) where charge associations can vary from weak to strong. Other proteins with charge clusters include the P450 cytochrome family (BM-3, Terp, Cam), several flavocytochromes, neuraminidase, hemagglutinin, the photosynthetic reaction center, and annexin. In each case in Table 2 we discuss the possible role of the charge clusters with respect to protein structure and function.

Early p53 alterations in mouse skin carcinogenesis by UVB radiation: immunohistochemical detection of mutant p53 protein in clusters of preneoplastic epidermal cells.

High levels of the p53 protein are immunohistochemically detectable in a majority of human nonmelanoma skin cancers and UVB-induced murine skin tumors. These increased protein levels are often associated with mutations in the conserved domains of the p53 gene. To investigate the timing of the p53 alterations in the process of UVB carcinogenesis, we used a well defined murine model (SKH:HR1 hairless mice) in which the time that tumors appear is predictable from the UVB exposures. The mice were subjected to a series of daily UVB exposures, either for 17 days or for 30 days, which would cause skin tumors to appear around 80 or 30 weeks, respectively. In the epidermis of these mice, we detected clusters of cells showing a strong immunostaining of the p53 protein, as measured with the CM-5 polyclonal antiserum. This cannot be explained by transient accumulation of the normal p53 protein as a physiological response to UVB-induced DNA damage. In single exposure experiments the observed transient CM-5 immunoreactivity lasted for only 3 days and was not clustered, whereas these clusters were still detectable as long as 56 days after 17 days of UVB exposure. In addition, approximately 70% of these patches reacted with the mutant-specific monoclonal antibody PAb240, whereas transiently induced p53-positive cells did not. In line with indicative human data, these experimental results in the hairless mouse model unambiguously demonstrate that constitutive p53 alterations are causally related to chronic UVB exposure and that they are a very early event in the induction of skin cancer by UVB radiation.

Competitividade em clusters de alta tecnologia: estudo comparativo de clusters de ciências da saúde no Brasil e na Inglaterra

Este trabalho teve como objetivo desenvolver um modelo específico para analisar a competitividade de clusters de alta tecnologia. Foi realizado um estudo de casos múltiplos em que foram analisados os clusters de ciências da saúde de Ribeirão Preto, no Brasil, e de Oxfordshire, na Inglaterra. Coletaram-se dados primários e secundários. Os dados primários foram coletados por meio de entrevistas em ambos os clusters e os dados secundários por meio de relatórios, papers, websites, além de coleta realizada nos bancos de dados Fame e Orbis. O modelo Zaccarelli et al. (2008), utilizado como ponto de partida para o desenvolvimento do modelo, foi aprimorado de três maneiras: i. Por meio do ajustamento das métricas utilizadas para avaliar cada fundamento, o que incluiu, dentre outras coisas, uma adaptação do modelo para mapeamento de clusters desenvolvido por Todeva (2008); ii. Pela verificação da aderência de seus fundamentos aos clusters de alta tecnologia analisados; e iii. Pela identificação de fatores emergentes, importantes para competitividade de clusters de alta tecnologia. Os resultados mostram evidências de que entre os onze fundamentos do modelo original, nove se mostraram relevantes aos clusters de alta tecnologia, ratificando sua importância para a análise da competitividade de clusters. Além dos fundamentos originais, os resultados sugerem a inclusão de dois fundamentos emergentes: \"Inserção em cadeias globais\" e \"Disponibilidade de investimentos financeiros\", até então ignorados pelo modelo Zaccarelli et al. (2008). A pesquisa traz como contribuição teórica o desenvolvimento de um modelo específico para clusters de alta tecnologia; como contribuição metodológica as novas métricas, incluindo a incorporação da adaptação da metodologia de Todeva (2008); como contribuição empírica traz a comparação entre clusters de ciências da saúde reconhecidamente competitivos, mas pertencentes a países de realidades culturais e econômicas distintas; e como contribuição gerencial um modelo que pode ser utilizado por empresários e instituições pertencentes a clusters e que desejam analisar fatores que influenciam a sua competitividade.

Selective hydrosilylation of 1,3-diynes catalyzed by titania-supported platinum

Titania-supported platinum (mainly as Pt(II)) has been found to effectively catalyze the hydrosilylation of 1,3-diynes at 70 °C with low catalyst loading (0.25 mol %) under solvent-free conditions. Monohydrosilylation was achieved for diaryl-substituted diynes, whereas dialkyl-substituted diynes were transformed into the corresponding dihydrosilylated products in good yields. In every case, the process was proven to be highly stereoselective, with syn addition of the silicon–hydrogen bond, and regioselective, with the silicon moiety exclusively bonded to the most internal carbon atom of the 1,3-diyne (β-E product), as confirmed by X-ray crystallography.

Spin alignment of extra electrons in K-phenanthrene clusters taken from the crystalline tripotassium-intercalated phenanthrene structure

The appearance of ferromagnetic correlations among π electrons of phenanthrene (C14H10) molecules in the herringbone structure is proven for K doped clusters both by ab initio quantum-chemistry calculations and by the direct solution of the many-body Pariser-Parr-Pople Hamiltonian. Magnetic ground states are predicted for one or three additional electrons per phenanthrene molecule. These results are a consequence of the small overlap between the lowest unoccupied molecular orbitals (and lowest unoccupied molecular orbitals + 1) of neutral neighboring phenanthrene molecules, which makes the gain in energy by delocalization similar to the corresponding increase due to the Coulomb interaction.

NGC 7419 as a template for red supergiant clusters

Context. The open cluster NGC 7419 is known to contain five red supergiants and a very high number of Be stars. However, there are conflicting reports about its age and distance that prevent a useful comparison with other clusters. Aims. We intend to obtain more accurate parameters for NGC 7419, using techniques different from those of previous authors, so that it may be used as a calibrator for more obscured clusters. Methods. We obtained Strömgren photometry of the open cluster NGC 7419, as well as classification spectroscopy of ~20 stars in the area. We then applied standard analysis and classification techniques. Results. We find a distance of 4 ± 0.4 kpc and an age of 14 ± 2 Myr for NGC 7419. The main-sequence turn-off is found at spectral type B1, in excellent agreement. We identify 179 B-type members, implying that there are more than 1200 M⊙ in B stars at present. Extrapolating this to lower masses indicates an initial cluster mass of between 7000 and 10 000 M⊙, depending on the shape of the initial mass function. We find a very high fraction (≈40%) of Be stars around the turn-off, but very few Be stars at lower masses. We also report for the first time a strong variability in the emission characteristics of Be stars. We verified that the parameters of the red supergiant members can be used to obtain accurate cluster parameters. Conclusions. NGC 7419 is sufficiently massive to serve as a testbed for theoretical predictions and as a template to compare more obscured clusters. The distribution of stars above the main-sequence turn-off is difficult to accommodate with current evolutionary tracks. Though the presence of five red supergiants is marginally consistent with theoretical expectations, the high number of Be stars and very low number of luminous evolved B stars hint at some unknown physical factor that is not considered in current synthesis models.

Massive open star clusters using the VVV survey III. A young massive cluster at the far edge of the Galactic bar

Context. Young massive clusters are key to map the Milky Way’s structure, and near-infrared large area sky surveys have contributed strongly to the discovery of new obscured massive stellar clusters. Aims. We present the third article in a series of papers focused on young and massive clusters discovered in the VVV survey. This article is dedicated to the physical characterization of VVV CL086, using part of its OB-stellar population. Methods. We physically characterized the cluster using JHKS near-infrared photometry from ESO public survey VVV images, using the VVV-SkZ pipeline, and near-infrared K-band spectroscopy, following the methodology presented in the first article of the series. Results. Individual distances for two observed stars indicate that the cluster is located at the far edge of the Galactic bar. These stars, which are probable cluster members from the statistically field-star decontaminated CMD, have spectral types between O9 and B0 V. According to our analysis, this young cluster (1.0 Myr < age < 5.0 Myr) is located at a distance of 11+5-6 kpc, and we estimate a lower limit for the cluster total mass of (2.8+1.6-1.4) · 103 M⊙. It is likely that the cluster contains even earlier and more massive stars.