CYANOS: a data management system for natural product drug discovery efforts using cultured microorganisms

A software package, termed "CYANOS", has been developed to facilitate the data management and mining for natural product drug discovery efforts. This system allows for the management of data associated with field collections, culture conditions, harvests, extractions, chemical separations, and biological evaluation. This software utilizes a MySQL database for data storage, which allows for reporting and data mining via third party tools. In addition, a Web-based interface was constructed to allow for multiuser access from a variety of desktop platforms. The code for this system is freely available and has been released under the Illinois Open Source license.     

Development and validation of a rapid method for microcystins in fish and comparing LC-MS/MS results with ELISA

Microcystins (MCs) are the most common cyanotoxins found worldwide in freshwater, brackish, and marine environments. The rapid and accurate analysis of MCs and nodularin (Nod-R) in fish tissue is important for determining occurrence, following trends, and monitoring exposure for risk assessment and other purposes. The aim of this study was to develop a streamlined and reliable sample preparation method for eight MCs (MC-RR, MC-YR, MC-LR, MC-WR, MC-LA, MC-LY, MC-LW, and MC-LF) and Nod-R in fish, and conduct a validation of the new method using liquid chromatography–tandem mass spectrometry (LC-MS/MS) for analysis and compare the results with a commercial enzyme-linked immunosorbent assay (ELISA) kit. Different sample preparation methods were compared, and a simple extraction protocol with acidified acetonitrile/water (3:1) followed by hexane partitioning cleanup was found to be most effective. Thorough validation of the final method was conducted, and 90–115% recoveries were achieved for all analytes except for MC-RR, which gave 130% average recovery (isotopically labeled internal standards were unavailable to correct for possible biases). The use of electrospray ionization in the negative mode gave few interferences and minimal matrix effects in the LC-MS/MS analysis overall. Precision was typically 10–20% RSD among multiple days in experiments, detection limits were <10 ng/g in the fish tissue (catfish, basa, and swai filets), and no false-positives or false-negatives occurred in blind analyses of many spiked samples. The ELISA was unable to distinguish between MCs but was found to correctly assess the presence or absence of MCs and Nod-R in the blind-fortified fish tissues. The capability of these approaches to measure covalently bound MCs was not assessed.     

The weighted Grammar constraint

We introduce the WeightedGrammar constraint and propose propagation algorithms based on the CYK parser and the Earley parser. We show that the traces of these algorithms can be encoded as a weighted negation normal form (WNNF), a generalization of NNF that allows nodes to carry weights. Based on this connection, we prove the correctness and complexity of these algorithms. Specifically, these algorithms enforce domain consistency on the WeightedGrammar constraint in time O(n ³). Further, we propose that the WNNF constraint can be decomposed into a set of primitive arithmetic constraint without hindering propagation.     

Univariate hyperbolic tangent neural network approximation

Here we study the univariate quantitative approximation of real and complex valued continuous functions on a compact interval or all the real line by quasi-interpolation hyperbolic tangent neural network operators. This approximation is derived by establishing Jackson type inequalities involving the modulus of continuity of the engaged function or its high order derivative. Our operators are defined by using a density function induced by the hyperbolic tangent function. The approximations are pointwise and with respect to the uniform norm. The related feed-forward neural network is with one hidden layer.     

Forcing operators on MTL‐algebras

We study the forcing operators on MTL‐algebras, an algebraic notion inspired by the Kripke semantics of the monoidal t ‐norm based logic (MTL). At logical level, they provide the notion of the forcing value of an MTL‐formula. We characterize the forcing operators in terms of some MTL‐algebras morphisms. From this result we derive the equality of the forcing value and the truth value of an MTL‐formula (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Tunneling currents that increase with molecular elongation

We present a model molecular system with an unintuitive transport-extension behavior in which the tunneling current increases with forced molecular elongation. The molecule consists of two complementary aromatic units (1,4-anthracenedione and 1,4-anthracenediol) hinged via two ether chains and attached to gold electrodes through thiol-terminated alkenes. The transport properties of the molecule as it is mechanically elongated in a single-molecule pulling setting are computationally investigated using a combination of equilibrium molecular dynamics simulations of the pulling with gDFTB computations of the transport properties in the Landauer limit. Contrary to the usual exponential decay of tunneling currents with increasing molecular length, the simulations indicate that upon elongation electronic transport along the molecule increases 10-fold. The structural origin of this inverted trend in the transport is elucidated via a local current analysis that reveals the dual role played by H-bonds in both stabilizing π-stacking for selected extensions and introducing additional electronic couplings between the complementary aromatic rings that also enhance tunneling currents across the molecule. The simulations illustrate an inverted electromechanical single-molecule switch that is based on a novel class of transport-extension behavior that can be achieved via mechanical manipulation and highlight the remarkable sensitivity of conductance measurements to the molecular conformation.     

Fluoroalkyl and alkyl chains have similar hydrophobicities in binding to the "hydrophobic wall" of carbonic anhydrase

The hydrophobic effect, the free-energetically favorable association of nonpolar solutes in water, makes a dominant contribution to binding of many systems of ligands and proteins. The objective of this study was to examine the hydrophobic effect in biomolecular recognition using two chemically different but structurally similar hydrophobic groups, aliphatic hydrocarbons and aliphatic fluorocarbons, and to determine whether the hydrophobicity of the two groups could be distinguished by thermodynamic and biostructural analysis. This paper uses isothermal titration calorimetry (ITC) to examine the thermodynamics of binding of benzenesulfonamides substituted in the para position with alkyl and fluoroalkyl chains (H(2)NSO(2)C(6)H(4)-CONHCH(2)(CX(2))(n)CX(3), n = 0-4, X = H, F) to human carbonic anhydrase II (HCA II). Both alkyl and fluoroalkyl substituents contribute favorably to the enthalpy and the entropy of binding; these contributions increase as the length of chain of the hydrophobic substituent increases. Crystallography of the protein-ligand complexes indicates that the benzenesulfonamide groups of all ligands examined bind with similar geometry, that the tail groups associate with the hydrophobic wall of HCA II (which is made up of the side chains of residues Phe131, Val135, Pro202, and Leu204), and that the structure of the protein is indistinguishable for all but one of the complexes (the longest member of the fluoroalkyl series). Analysis of the thermodynamics of binding as a function of structure is compatible with the hypothesis that hydrophobic binding of both alkyl and fluoroalkyl chains to hydrophobic surface of carbonic anhydrase is due primarily to the release of nonoptimally hydrogen-bonded water molecules that hydrate the binding cavity (including the hydrophobic wall) of HCA II and to the release of water molecules that surround the hydrophobic chain of the ligands. This study defines the balance of enthalpic and entropic contributions to the hydrophobic effect in this representative system of protein and ligand: hydrophobic interactions, here, seem to comprise approximately equal contributions from enthalpy (plausibly from strengthening networks of hydrogen bonds among molecules of water) and entropy (from release of water from configurationally restricted positions).     

Wettability control and patterning of PDMS using UV-ozone and water immersion

We demonstrate a simple method to tune and pattern the wettability of polydimethylsiloxane (PDMS) to generate microfluidic mimics of heterogeneous porous media. This technique allows one to tailor the capillary forces at different regions within the PDMS channel to mimic multi-phase flow in oil reservoirs. In this method, UV-ozone treatment is utilized to oxidize and hydrophilize the surface of PDMS. To maintain a stable surface wettability, the oxidized surfaces are immersed in water. Additionally, the use of a photomask makes it convenient to pattern the wettability in the porous media. A one-dimensional diffusive reaction model is established to understand the UV-ozone oxidation as well as hydrophobic recovery of oxidized PDMS surfaces. The modeling results show that during UV-ozone, surface oxidation dominates over diffusion of low-molecular-weight (LMW) species. However, the diffusivity of LMW species plays an important role in wettability control of PDMS surfaces.     

Synthesis and anion-exchange reactions of a new anionic clay, α-magnesium hydroxide

A new anionic clay, α-magnesium hydroxide, was synthesized by hydrolysis of magnesium acetate in propylene glycol. The structure of this α-hydroxide is similar to that of hydrotalcites. It consists of positively charged magnesium hydroxide layers arising out of partial protonation of the hydroxyl groups of the [Mg(OH)(2)] layers and loosely held anions in the interlayer region. As expected it ages readily in water to give β-magnesium hydroxide, brucite. While anion-exchange reactions of α-magnesium hydroxide could not be carried out in aqueous medium a number of anion-exchange reactions could be carried out successfully in ethanol medium.