MACiE: a database of enzyme reaction mechanisms.

SUMMARY: MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction. AVAILABILITY: http://www-mitchell.ch.cam.ac.uk/macie/.EPSRC (G.L.H. and J.B.O.M.), the BBSRC (G.J.B. and J.M.T.—CASE studentship in association with Roche Products Ltd; N.M.O.B. and J.B.O.M.—grant BB/C51320X/1), the Chilean Government’s Ministerio de Planificacio´n y Cooperacio´n and Cambridge Overseas Trust (D.E.A.) for funding and Unilever for supporting the Centre for Molecular Science Informatics.application note restricted to 2 printed pages web site: http://www-mitchell.ch.cam.ac.uk/macie

Pair distribution function in a two-dimensional electron gas

We calculate the pair distribution function, $g(r)$, in a two-dimensional electron gas and derive a simple analytical expression for its value at the origin as a function of $r_s$. Our approach is based on solving the Schr\"{o}dinger equation for the two-electron wave function in an appropriate effective potential, leading to results that are in good agreement with Quantum Monte Carlo data and with the most recent numerical calculations of $g(0)$. [C. Bulutay and B. Tanatar, Phys. Rev. B {\bf 65}, 195116 (2002)] We also show that the spin-up spin-down correlation function at the origin, $g_{\uparrow \downarrow}(0)$, is mainly independent of the degree of spin polarization of the electronic system.Comment: 5 figures, pair distribution dependence with distance is calculate

Ultra-high energy cosmic ray investigations by means of EAS muon density measurements

A new approach to investigations of ultra-high energy cosmic rays based on the ground-level measurements of the spectra of local density of EAS muons at various zenith angles is considered. Basic features of the local muon density phenomenology are illustrated using a simple semi-analytical model. It is shown that muon density spectra are sensitive to the spectrum slope, primary composition, and to the features of hadronic interaction. New experimental data on muon bundles at zenith angles from 30 degrees to horizon obtained with the coordinate detector DECOR are compared with CORSIKA-based simulations. It is found that measurements of muon density spectra in inclined EAS give possibility to study characteristics of primary cosmic ray flux in a very wide energy range from 10^15 to 10^19 eV.Comment: 7 pages, 7 figures. Presented at CRIS-2006, Catania, Italy, May 29 - June 2, 2006. Accepted for publication in Nucl. Phys. B (Proc. Suppl.

Fungal diversity in deep-sea sediments associated with asphalt seeps at the Sao Paulo Plateau

We investigated the fungal diversity in a total of 20 deep-sea sediment samples (of which 14 samples were associated with natural asphalt seeps and 6 samples were not associated) collected from two different sites at the Sao Paulo Plateau off Brazil by Ion Torrent PGM targeting ITS region of ribosomal RNA. Our results suggest that diverse fungi (113 operational taxonomic units (OTUs) based on clustering at 97% sequence similarity assigned into 9 classes and 31 genus) are present in deep-sea sediment samples collected at the Sao Paulo Plateau, dominated by Ascomycota (74.3%), followed by Basidiomycota (11.5%), unidentified fungi (7.1%), and sequences with no affiliation to any organisms in the public database (7.1%). However, it was revealed that only three species, namely Penicillium sp., Cadophora malorum and Rhodosporidiwn diobovatum, were dominant, with the majority of OTUs remaining a minor community. Unexpectedly, there was no significant difference in major fungal community structure between the asphalt seep and non-asphalt seep sites, despite the presence of mass hydrocarbon deposits and the high amount of macro organisms surrounding the asphalt seeps. However, there were some differences in the minor fungal communities, with possible asphalt degrading fungi present specifically in the asphalt seep sites. In contrast, some differences were found between the two different sampling sites. Classification of OTUs revealed that only 47 (41.6%) fungal OTUs exhibited >97% sequence similarity, in comparison with pre-existing ITS sequences in public databases, indicating that a majority of deep-sea inhabiting fungal taxa still remain undescribed. Although our knowledge on fungi and their role in deep-sea environments is still limited and scarce, this study increases our understanding of fungal diversity and community structure in deep-sea environments.Japan Society for the Promotion of ScienceJapan Agcy Marine Earth Sci & Technol, 2-15 Natsushima Cho, Yokosuka, Kanagawa 2370061, JapanUniv Vale Itajal, Dept Biol Sci, CTTMar, R Uruguai 458, BR-88302202 Itajal, SC, BrazilUniv Fed Sao Paulo, Rua Prof Artur Riedel 275, BR-09972270 Diadema, SP, BrazilUniv Sao Paulo, Inst Oceanog, 191 Praca Oceanog, BR-05508120 Sao Paulo, SP, BrazilUniv Fed Sao Paulo, Rua Prof Artur Riedel 275, BR-09972270 Diadema, SP, BrazilJSPS: 23770098JSPS: 15K18601Web of Scienc

Diffractive Contribution to the Elasticity and the Nucleonic Flux in the Atmosphere

We calculate the average elasticity considering non-diffractive and single diffractive interactions and perform an analysis of the cosmic-ray flux by means of an analytical solution for the nucleonic diffusion equation. We show that the diffractive contribution is important for the adequate description of the nucleonic and hadronic fluxes in the atmosphere.Comment: 10 pages, latex, 2 figures (uuencoded PostScript

Correlation energy of a two-dimensional electron gas from static and dynamic exchange-correlation kernels

We calculate the correlation energy of a two-dimensional homogeneous electron gas using several available approximations for the exchange-correlation kernel $f_{\rm xc}(q,\omega)$ entering the linear dielectric response of the system. As in the previous work of Lein {\it et al.} [Phys. Rev. B {\bf 67}, 13431 (2000)] on the three-dimensional electron gas, we give attention to the relative roles of the wave number and frequency dependence of the kernel and analyze the correlation energy in terms of contributions from the $(q, i\omega)$ plane. We find that consistency of the kernel with the electron-pair distribution function is important and in this case the nonlocality of the kernel in time is of minor importance, as far as the correlation energy is concerned. We also show that, and explain why, the popular Adiabatic Local Density Approximation performs much better in the two-dimensional case than in the three-dimensional one.Comment: 9 Pages, 4 Figure

Tau Neutrinos in the Auger Observatory : A New Window to UHECR Sources

The cosmic ray spectrum has been shown to extend well beyond 10^{20}eV. With nearly 20 events observed in the last 40 years, it is now established that particles are accelerated or produced in the universe with energies near 10^{21}eV. In all production models neutrinos and photons are part of the cosmic ray flux. In acceleration models (bottom-up models), they are produced as secondaries of the possible interactions of the accelerated charged particle; in direct production models (top-down models) they are a dominant fraction of the decay chain. In addition, hadrons above the GZK threshold energy will also produce, along their path in the Universe, neutrinos and photons as secondaries of the pion photo-production processes. Therefore, photons and neutrinos are very distinctive signatures of the nature and distribution of the potential sources of ultra high energy cosmic rays. In the following we describe the tau neutrino detection and identification capabilities of the Auger observatory. We show that in the range 3x10^{17}-3x10^{20}eV the Auger effective apperture reaches a few tenths of km^2.sr, making the observatory sensitive to fluxes as low as a few tau neutrinos per km^2.sr.year. In the hypothesis of nu_mu nu_tau oscillations with full mixing, this sensitivity allows to probe the GZK cutoff as well as to provide model independent constraints on the mechanisms of production of ultra high energy cosmic rays.Comment: 10 pages, 11 figures, accepted by Astroparticle physic

Joint profiling of DNA methylation and chromatin architecture in single cells.

We report a molecular assay, Methyl-HiC, that can simultaneously capture the chromosome conformation and DNA methylome in a cell. Methyl-HiC reveals coordinated DNA methylation status between distal genomic segments that are in spatial proximity in the nucleus, and delineates heterogeneity of both the chromatin architecture and DNA methylome in a mixed population. It enables simultaneous characterization of cell-type-specific chromatin organization and epigenome in complex tissues

CD44s and CD44v6 Expression in Head and Neck Epithelia

Background: CD44 splice variants are long-known as being associated with cell transformation. Recently, the standard form of CD44 (CD44s) was shown to be part of the signature of cancer stem cells (CSCs) in colon, breast, and in head and neck squamous cell carcinomas (HNSCC). This is somewhat in contradiction to previous reports on the expression of CD44s in HNSCC. The aim of the present study was to clarify the actual pattern of CD44 expression in head and neck epithelia. Methods: Expression of CD44s and CD44v6 was analysed by immunohistochemistry with specific antibodies in primary head and neck tissues. Scoring of all specimens followed a two-parameters system, which implemented percentages of positive cells and staining intensities from − to +++ (score = %×intensity; resulting max. score 300). In addition, cell surface expression of CD44s and CD44v6 was assessed in lymphocytes and HNSCC. Results: In normal epithelia CD44s and CD44v6 were expressed in 60–95% and 50–80% of cells and yielded mean scores with a standard error of a mean (SEM) of 249.5±14.5 and 198±11.13, respectively. In oral leukoplakia and in moderately differentiated carcinomas CD44s and CD44v6 levels were slightly increased (278.9±7.16 and 242±11.7; 291.8±5.88 and 287.3±6.88). Carcinomas in situ displayed unchanged levels of both proteins whereas poorly differentiated carcinomas consistently expressed diminished CD44s and CD44v6 levels. Lymphocytes and HNSCC lines strongly expressed CD44s but not CD44v6. Conclusion: CD44s and CD44v6 expression does not distinguish normal from benign or malignant epithelia of the head and neck. CD44s and CD44v6 were abundantly present in the great majority of cells in head and neck tissues, including carcinomas. Hence, the value of CD44s as a marker for the definition of a small subset of cells (i.e. less than 10%) representing head and neck cancer stem cells may need revision

XRCC1 Arg194Trp polymorphism, risk of nonmelanoma skin cancer and extramammary Paget’s disease in a Japanese population

The X-ray repair cross-complementing groups 1 gene plays an important role in base excision repair. At least three common single nucleotide polymorphisms frequently occur in this gene (Arg399Gln, Arg194Trp and Arg280His). Recent studies reported that these polymorphisms were associated with not only risk of visceral malignancy but also that of skin cancer such as basal cell carcinoma and squamous cell carcinoma, whereas the results of previous study vary among races. In this case–control study, we investigated whether these single nucleotide polymorphisms were associated with the risk of skin cancer in a Japanese population. The study population was composed of 197 patients with skin cancer (27 actinic keratoses, 47 basal cell carcinomas, 27 squamous cell carcinomas, 29 Bowen’s diseases, 46 malignant melanomas and 21 extramammary Paget’s diseases) and 93 control subjects. We genotyped two single nucleotide polymorphisms (Arg194Trp and Arg399Gln) using polymerase chain reaction-restriction fragments length polymorphism analysis. We found a significantly increased risk for basal cell carcinoma, squamous cell carcinoma and extramammary Paget’s disease associated with Arg194Trp [adjusted odds ratio (AOR) = 2.347, 3.587, 3.741, 95 % confidence interval (CI) 1.02–5.39, 1.19–10.8, 1.15–12.2, respectively]. We also found a significantly decreased risk for basal cell carcinoma associated with Gln399Gln (AOR = 0.259, 95 % CI 0.07–0.96). Our data suggest that the Arg194Trp polymorphism could be associated with nonmelanoma skin cancer and extramammary Paget’s disease risk in a Japanese population