WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets.

BackgroundSharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software.ResultsWe here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages.ConclusionsWith these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called "Smiley2png 1.0") can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu

Novel Precursors for Boron Nanotubes: The Competition of Two-Center and Three-Center Bonding in Boron Sheets

We present a new class of boron sheets, composed of triangular and hexagonal motifs, that are more stable than structures considered to date and thus are likely to be the precursors of boron nanotubes. We describe a simple and clear picture of electronic bonding in boron sheets and highlight the importance of three-center bonding and its competition with two-center bonding, which can also explain the stability of recently discovered boron fullerenes. Our findings call for reconsideration of the literature on boron sheets, nanotubes, and clusters.Comment: 4 pages, 4 figures, 1 tabl

Novel cruzain inhibitors for the treatment of Chagas' disease.

The protozoan parasite Trypanosoma cruzi, the etiological agent of Chagas' disease, affects millions of individuals and continues to be an important global health concern. The poor efficacy and unfavorable side effects of current treatments necessitate novel therapeutics. Cruzain, the major cysteine protease of T. cruzi, is one potential novel target. Recent advances in a class of vinyl sulfone inhibitors are encouraging; however, as most potential therapeutics fail in clinical trials and both disease progression and resistance call for combination therapy with several drugs, the identification of additional classes of inhibitory molecules is essential. Using an exhaustive virtual-screening and experimental validation approach, we identify several additional small-molecule cruzain inhibitors. Further optimization of these chemical scaffolds could lead to the development of novel drugs useful in the treatment of Chagas' disease

Evaluation of Surface State Mediated Charge Recombination in Anatase and Rutile TiO2

In nanostructured thin films, photogenerated charge carriers can access the surface more easily than in dense films and thus react more readily. However, the high surface area of these films has also been associated with enhanced recombination losses via surface states. We herein use transient absorption spectroscopy to compare the ultrafast charge carrier kinetics in dense and nanostructured TiO2 films for its two most widely used polymorphs: anatase and rutile. We find that nanostructuring does not enhance recombination rates on ultrafast timescales, indicating that surface state mediated recombination is not a key loss pathway for either TiO2 polymorph. Rutile shows faster, and less intensity-dependent recombination than anatase, which we assign to its higher doping density. For both polymorphs, we conclude that bulk rather than surface recombination is the primary determinant of charge carrier lifetime

A kinetic and theoretical study of the borate catalysed reactions of hydrogen peroxide: the role of dioxaborirane as the catalytic intermediate for a wide range of substrates

Our recent work has provided new insights into the equilibria and species that exist in aqueous solution at different pHs for the boric acid – hydrogen peroxide system, and the role of these species in oxidation reactions. Most recently, (M. C. Durrant, D. M. Davies and M. E. Deary, Org. Biomol. Chem., 2011, 9,7249–7254), we have produced strong theoretical and experimental evidence for the existence of a previously unreported monocyclic three membered peroxide species, dioxaborirane, that is the likely catalytic species in borate mediated electrophilic reactions of hydrogen peroxide in alkaline solution. In the present paper, we extend our study of the borate–peroxide system to look at a wide range of substrates that include substituted dimethyl anilines, methyl-p-tolyl sulfoxide, halides, hydrogen sulfide anion, thiosulfate ,thiocyanate, and hydrazine. The unusual selectivity–reactivity pattern of borate catalysed reactions compared with hydrogen peroxide and inorganic or organic peracids previously observed for theorganic sulfides (D. M. Davies, M. E. Deary, K. Quill and R. A. Smith, Chem.–Eur. J., 2005, 11, 3552–3558) is also seen with substituted dimethyl aniline nucleophiles. This provides evidence that the pattern is not due to any latent electrophilic tendency of the organic sulfides and further supports dioxaborirane being the likely reactive intermediate, thus broadening the applicability of this catalytic system. Moreover, density functional theory calculations on our proposed mechanism involving dioxaborirane are consistent with the experimental results for these substrates. Results obtained at high concentrations of both borate and hydrogen peroxide require the inclusion the diperoxodiborate dianion in the kinetic analysis .A scheme detailing our current understanding of the borate–peroxide system is presented

Total loss of MHC class I is an independent indicator of good prognosis in breast cancer

Tumours can be recognised by CTL and NK cells. CTL recognition depends on expression of MHC Class I loaded with peptides from tumour antigens. In contrast, loss of MHC Class I results in NK activation. In our study a large set of samples from patients with primary operable invasive breast cancer was evaluated for the expression of MHC Class I heavy and light by immunohistochemical staining of 439 breast carcinomas in a tissue microarray. Forty-seven percent (206 of 439) of breast carcinomas were considered negative for HLA Class I heavy chain (HC10), whereas lack of anti-β2m-antibody staining was observed in 39% (167 of 424) of tumours, with only 3% of the β2m-negative tumours expressing detectable HLA Class I heavy chain. Correlation with patient outcome showed direct relationship between patient survival and HLA-negative phenotype (log rank = 0.004). A positive relationship was found between the intensity of expression of MHC Class I light and heavy chains expression and histological grade of invasive tumour (p < 0.001) and Nottingham Prognostic Index (p < 0.001). To investigate whether HLA Class I heavy and light chains expression had independent prognostic significance, Cox multivariate regression analysis, including the parameters of tumour size, lymph node stage, grade and intensity of HC10 and anti-β2m staining, was carried out. In our analysis, lymph node stage (p < 0.001), tumour grade (p = 0.005) and intensity of MHC Class I light and heavy chains expression were shown to be independent prognostic factors predictive of overall survival (p-values HC10 = 0.047 and β2m = 0.018)

Gene expression in Leishmania is regulated predominantly by gene dosage

ABSTRACT Leishmania tropica, a unicellular eukaryotic parasite present in North and East Africa, the Middle East, and the Indian subcontinent, has been linked to large outbreaks of cutaneous leishmaniasis in displaced populations in Iraq, Jordan, and Syria. Here, we report the genome sequence of this pathogen and 7,863 identified protein-coding genes, and we show that the majority of clinical isolates possess high levels of allelic diversity, genetic admixture, heterozygosity, and extensive aneuploidy. By utilizing paired genome-wide high-throughput DNA sequencing (DNA-seq) with RNA-seq, we found that gene dosage, at the level of individual genes or chromosomal “somy” (a general term covering disomy, trisomy, tetrasomy, etc.), accounted for greater than 85% of total gene expression variation in genes with a 2-fold or greater change in expression. High gene copy number variation (CNV) among membrane-bound transporters, a class of proteins previously implicated in drug resistance, was found for the most highly differentially expressed genes. Our results suggest that gene dosage is an adaptive trait that confers phenotypic plasticity among natural Leishmania populations by rapid down- or upregulation of transporter proteins to limit the effects of environmental stresses, such as drug selection. IMPORTANCE Leishmania is a genus of unicellular eukaryotic parasites that is responsible for a spectrum of human diseases that range from cutaneous leishmaniasis (CL) and mucocutaneous leishmaniasis (MCL) to life-threatening visceral leishmaniasis (VL). Developmental and strain-specific gene expression is largely thought to be due to mRNA message stability or posttranscriptional regulatory networks for this species, whose genome is organized into polycistronic gene clusters in the absence of promoter-mediated regulation of transcription initiation of nuclear genes. Genetic hybridization has been demonstrated to yield dramatic structural genomic variation, but whether such changes in gene dosage impact gene expression has not been formally investigated. Here we show that the predominant mechanism determining transcript abundance differences (>85%) in Leishmania tropica is that of gene dosage at the level of individual genes or chromosomal somy

Prospects for photon blockade in four level systems in the N configuration with more than one atom

We show that for appropriate choices of parameters it is possible to achieve photon blockade in idealised one, two and three atom systems. We also include realistic parameter ranges for rubidium as the atomic species. Our results circumvent the doubts cast by recent discussion in the literature (Grangier et al Phys. Rev Lett. 81, 2833 (1998), Imamoglu et al Phys. Rev. Lett. 81, 2836 (1998)) on the possibility of photon blockade in multi-atom systems.Comment: 8 page, revtex, 7 figures, gif. Submitted to Journal of Optics B: Quantum and Semiclassical Optic