Two Ecdysteroids Isolated from Micropropagated Lychnis flos-cuculi and the Biological Activity of Plant Material

Genetically uniform plant material, derived from Lychnis flos-cuculi propagated in vitro, was used for the isolation of 20-hydroxyecdysone and polypodine B and subjected to an evaluation of the antifungal and antiamoebic activity. The activity of 80% aqueous methanolic extracts, their fractions, and isolated ecdysteroids were studied against pathogenic Acanthamoeba castellani. Additionally, a Microtox^® acute toxicity assay was performed. It was found that an 80% methanolic fraction of root extract exerts the most potent amoebicidal activity at IC₅₀ of 0.06 mg/mL at the 3rd day of treatment. Both ecdysteroids show comparable activity at IC₅₀ of 0.07 mg/mL. The acute toxicity of 80% fractions at similar concentrations is significantly higher than that of 40% fractions. Crude extracts exhibited moderate antifungal activity, with a minimum inhibitory concentration (MIC) within the range of 1.25–2.5 mg/mL. To the best of our knowledge, the present report is the first to show the biological activity of L. flos-cuculi in terms of the antifungal and antiamoebic activities and acute toxicity. It is also the first isolation of the main ecdysteroids from L. flos-cuculi micropropagated, ecdysteroid-rich plant material.     

Sulphur isotope compositions of components of coal and S-isotope fractionation during its combustion and flue gas desulphurization

Sulphur isotope compositions were determined in two different Polish coals (hard coal and lignite) and by-products originating from their combustion. The desulphurization process was also investigated. It was demonstrated that desulphurization changes the isotopic composition of sulphur emitted in the form of SO(2) to the atmosphere even if the process is conducted in a different way (wet lime technology and electron beam method). This fact has to be considered in the studies regarding anthropogenic sulphur genesis and its fate in the environment.     

Arrays for the combinatorial exploration of cell adhesion

A new method for the fabrication of arrays of self-assembled monolayers (SAMs) of alkane thiols (ATs) on gold to combinatorially assay surfaces for cell adhesion is reported. A fluorous SAM, which is both cytophobic and solvophobic, was used as the background between the array features. The resulting solvophobic background permits the application of an assembly after conjugation strategy for fabrication. SAMs containing mixtures of ATs and peptide-terminated ATs were generated. Multiple cell types demonstrated differential and specific binding to these surfaces. Additionally, pluripotent human embryonic stem cells proliferated on surfaces generated by this method.     

Diversity of phage-displayed libraries of peptides during panning and amplification

The amplification of phage-displayed libraries is an essential step in the selection of ligands from these libraries. The amplification of libraries, however, decreases their diversity and limits the number of binding clones that a screen can identify. While this decrease might not be a problem for screens against targets with a single binding site (e.g., proteins), it can severely hinder the identification of useful ligands for targets with multiple binding sites (e.g., cells). This review aims to characterize the loss in the diversity of libraries during amplification. Analysis of the peptide sequences obtained in several hundred screens of peptide libraries shows explicitly that there is a significant decrease in library diversity that occurs during the amplification of phage in bacteria. This loss during amplification is not unique to specific libraries: it is observed in many of the phage display systems we have surveyed. The loss in library diversity originates from competition among phage clones in a common pool of bacteria. Based on growth data from the literature and models of phage growth, we show that this competition originates from growth rate differences of only a few percent for different phage clones. We summarize the findings using a simple two-dimensional "phage phase diagram", which describes how the collapse of libraries, due to panning and amplification, leads to the identification of only a subset of the available ligands. This review also highlights techniques that allow elimination of amplification-induced losses of diversity, and how these techniques can be used to improve phage-display selection and enable the identification of novel ligands.     

Solid-phase synthesis of alkanethiols for the preparation of self-assembled monolayers

Self-assembled monolayers (SAMs) of alkanethiols (ATs) on gold can be used to fabricate surfaces for nanoscience and biology. The chemical structure of the interface can be tailored simply by modifying the AT headgroup. To streamline access to different precursor ATs, we developed a general solid-phase synthetic route. A key feature of this route is the use of a modified resin containing an AT linker ("AT resin") because it minimizes purification steps. The precursor to the AT resin was prepared in five steps, and all of the synthetic intermediates are stable solids that can be purified by crystallization. Accordingly, the AT resin can be prepared on a multigram scale. The utility of the AT resin was evaluated by using it to generate a variety of ATs. For example, ATs presenting different types of integrin-binding ligands (linear and cyclic RGD derivatives) were prepared and used to form arrays of SAMs that support cell adhesion. Additionally, the AT resin also provides a starting point for the synthesis of ATs presenting reactive groups (e.g., an amine-reactive AT or a maleimide-containing alkanedisulfide) or protein immobilization tags (e.g., biotin-AT). Thus, our synthetic strategy provides a convenient and flexible means for the synthesis of the necessary building blocks for custom SAMs and SAM arrays.     

GlyNet: a multi-task neural network for predicting protein–glycan interactions

Advances in diagnostics, therapeutics, vaccines, transfusion, and organ transplantation build on a fundamental understanding of glycan–protein interactions. To aid this, we developed GlyNet, a model that accurately predicts interactions (relative binding strengths) between mammalian glycans and 352 glycan-binding proteins, many at multiple concentrations. For each glycan input, our model produces 1257 outputs, each representing the relative interaction strength between the input glycan and a particular protein sample. GlyNet learns these continuous values using relative fluorescence units (RFUs) measured on 599 glycans in the Consortium for Functional Glycomics glycan arrays and extrapolates these to RFUs from additional, untested glycans. GlyNet''s output of continuous values provides more detailed results than the standard binary classification models. After incorporating a simple threshold to transform such continuous outputs the resulting GlyNet classifier outperforms those standard classifiers. GlyNet is the first multi-output regression model for predicting protein–glycan interactions and serves as an important benchmark, facilitating development of quantitative computational glycobiology.

GlyNet, a neural net model of glycan-protein binding strengths. Given a glycan it outputs binding to each of several protein samples. Reproducing glycan array data, it extrapolates the binding of untested glycans against the protein samples.     

Fluorine Bonding Enhances the Energetics of Protein-Lipid Binding in the Gas Phase

This paper reports on the first experimental study of the energies of noncovalent fluorine bonding in a protein-ligand complex in the absence of solvent. Arrhenius parameters were measured for the dissociation of gaseous deprotonated ions of complexes of bovine β-lactoglobulin (Lg), a model lipid-binding protein, and four fluorinated analogs of stearic acid (SA), which contained (X =) 13, 15, 17, or 21 fluorine atoms. In all cases, the activation energies (E_a) measured for the loss of neutral XF-SA from the (Lg + XF-SA)^7– ions are larger than for SA. From the kinetic data, the average contribution of each?>?CF₂ group to E_a was found to be ~1.1 kcal mol^–1, which is larger than the ~0.8 kcal mol^–1 value reported for?>?CH₂ groups. Based on these results, it is proposed that fluorocarbon–protein interactions are inherently stronger (enthalpically) than the corresponding hydrocarbon interactions.