Updates in Rhea--a manually curated resource of biochemical reactions.

Rhea (http://www.ebi.ac.uk/rhea) is a comprehensive and non-redundant resource of expert-curated biochemical reactions described using species from the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules. Rhea has been designed for the functional annotation of enzymes and the description of genome-scale metabolic networks, providing stoichiometrically balanced enzyme-catalyzed reactions (covering the IUBMB Enzyme Nomenclature list and additional reactions), transport reactions and spontaneously occurring reactions. Rhea reactions are extensively curated with links to source literature and are mapped to other publicly available enzyme and pathway databases such as Reactome, BioCyc, KEGG and UniPathway, through manual curation and computational methods. Here we describe developments in Rhea since our last report in the 2012 database issue of Nucleic Acids Research. These include significant growth in the number of Rhea reactions and the inclusion of reactions involving complex macromolecules such as proteins, nucleic acids and other polymers that lie outside the scope of ChEBI. Together these developments will significantly increase the utility of Rhea as a tool for the description, analysis and reconciliation of genome-scale metabolic models.

Miniaturized spectrometer with intrinsic long-term image memory.

Miniaturized spectrometers have great potential for use in portable optoelectronics and wearable sensors. However, current strategies for miniaturization rely on von Neumann architectures, which separate the spectral sensing, storage, and processing modules spatially, resulting in high energy consumption and limited processing speeds due to the storage-wall problem. Here, we present a miniaturized spectrometer that utilizes a single SnS2/ReSe2 van der Waals heterostructure, providing photodetection, spectrum reconstruction, spectral imaging, long-term image memory, and signal processing capabilities. Interface trap states are found to induce a gate-tunable and wavelength-dependent photogating effect and a non-volatile optoelectronic memory effect. Our approach achieves a footprint of 19 µm, a bandwidth from 400 to 800 nm, a spectral resolution of 5 nm, and a > 104 s long-term image memory. Our single-detector computational spectrometer represents a path beyond von Neumann architectures.

Preclinical evaluation of drug combinations identifies co-inhibition of Bcl-2/XL/W and MDM2 as a potential therapy in uveal melanoma.

INTRODUCTION: Uveal melanoma (UM) is a rare and malignant intraocular tumour with a dismal prognosis. Despite a good control of the primary tumour by radiation or surgery, up to 50% of patients subsequently develop metastasis for which no efficient treatment is yet available. METHODOLOGY: To identify therapeutic opportunities, we performed an in vitro screen of 30 combinations of different inhibitors of pathways that are dysregulated in UM. Effects of drug combinations on viability, cell cycle and apoptosis were assessed in eight UM cell lines. The best synergistic combinations were further evaluated in six UM patient-derived xenografts (PDXs). RESULTS: We demonstrated that the Bcl-2/XL/W inhibitor (ABT263) sensitised the UM cell lines to other inhibitors, mainly to mammalian target of rapamycin (mTOR), mitogen-activated protein kinase kinase (MEK) and murine double minute 2 (MDM2) inhibitors. mTOR (RAD001) and MEK1/2 (trametinib) inhibitors were efficient as single agents, but their combinations with ABT263 displayed no synergism in UM PDXs. In contrast, the combination of ABT263 with MDM2 inhibitor (HDM201) showed a trend for a synergistic effect. CONCLUSION: We showed that inhibition of Bcl-2/XL/W sensitised the UM cell lines to other treatments encouraging investigation of the underlying mechanisms. Furthermore, our findings highlighted Bcl-2/XL/W and MDM2 co-inhibition as a promising strategy in UM.

Parameterization of an empirical model for the prediction of n-octanol, alkane and cyclohexane/water as well as brain/blood partition coefficients.

Quantitative information of solvation and transfer free energies is often needed for the understanding of many physicochemical processes, e.g the molecular recognition phenomena, the transport and diffusion processes through biological membranes and the tertiary structure of proteins. Recently, a concept for the localization and quantification of hydrophobicity has been introduced (Jäger et al. J Chem Inf Comput Sci 43:237-247, 2003). This model is based on the assumptions that the overall hydrophobicity can be obtained as a superposition of fragment contributions. To date, all predictive models for the logP have been parameterized for n-octanol/water (logP(oct)) solvent while very few models with poor predictive abilities are available for other solvents. In this work, we propose a parameterization of an empirical model for n-octanol/water, alkane/water (logP(alk)) and cyclohexane/water (logP(cyc)) systems. Comparison of both logP(alk) and logP(cyc) with the logarithms of brain/blood ratios (logBB) for a set of structurally diverse compounds revealed a high correlation showing their superiority over the logP(oct) measure in this context.

pyVib, a computer program for the analysis of infrared and Raman optical activity.

A new program called pyVib has been developed as a tool for the analysis of Gaussian (Gaussian 03, Gaussian Inc., Pittsburgh, PA) outputs of vibrational absorption (IR), Raman as well as vibrational optical activity (VOA) spectra calculations. This program has been designed to help the computational chemistry practitioner in the task of analyzing and visualizing molecular vibrations and cross sections. In particular, the analysis of absorption and scattering cross sections can be done using new tools such as group coupling matrices (GCMs) and atomic contribution patterns (ACPs) as either 2D or 3D representations, respectively (Hug, Chem Phys 2001, 264, 53). It reads the Hessian, the atomic polar tensors (APTs), the atomic axial tensors (AATs) (Nafie, J Chem Phys 1983, 79, 4950), and the gradients of the various polarizability tensors involved in VOA calculations and stored in Gaussian fchk ascii files. pyVib is capable of picking suitably chosen atoms or group of atoms for evaluating the contribution of each atom or defined groups of atoms to the calculated VOA scattered intensities. All the results generated by pyVib can be visualized in real-time but can also be transferred to text editors and electronic spreadsheets, which facilitate a detailed subsequent analysis and the visualization by other graphical user interfaces (GUIs).This program is coded in Python and used the visualization toolkit (VTK) library. It is freely available under the terms of the general GNU public license (GPL) for Linux platforms.

Density-Functional Theory Investigation of the Geometric, Energetic, and Optical Properties of the Cobalt(II)tris(2,2'-bipyridine) Complex in the High-Spin and the Jahn-Teller Active Low-Spin States.

State-of-the-art generalized gradient approximation (GGA) (PBE, OPBE, RPBE, OLYP, and HCTH), meta-GGA (VSXC and TPSS), and hybrid (B3LYP, B3LYP*, O3LYP, and PBE0) functionals are compared for the determination of the structure and the energetics of the D3 [Co(bpy)3](2+) complex in the (4)A2 and (4)E trigonal components of the high-spin (4)T1g([Formula: see text] [Formula: see text] ) state and in the low-spin (2)E state of octahedral (2)Eg([Formula: see text] [Formula: see text] ) parentage. Their comparison extends also to the investigation of the Jahn-Teller instability of the (2)E state through the characterization of the extrema of C2 symmetry of this spin state's potential energy surface. The results obtained for [Co(bpy)3](2+) in either spin manifold are very consistent among the functionals used and are in good agreement with available experimental data. The functionals, however, perform very differently with respect to the spin-state energetics because the calculated values of the high-spin/low-spin energy difference Δ[Formula: see text] vary between -3212 and 3919 cm(-)(1). Semilocal functionals tend to give too large Δ[Formula: see text] values and thus fail to correctly predict the high-spin state as the ground state of the isolated complex, while hybrid functionals tend to overestimate the stability of the high-spin state with respect to the low-spin state. Reliable results are, however, obtained with the OLYP, HCTH, B3LYP*, and O3LYP functionals which perform best for the description of the isolated complex. The optical properties of [Co(bpy)3](2+) in the two spin states are also analyzed on the basis of electronic excitation calculations performed within time-dependent density functional response theory. The calculated absorption and circular dichroism spectra agree well with experimental results.