Phage display: selecting straws instead of a needle from a haystack

An increasing number of peptides with specific binding affinity to various protein and even non-protein targets are being discovered from phage display libraries. The power of this method lies in its ability to efficiently and rapidly identify ligands with a desired target property from a large population of phage clones displaying diverse surface peptides. However, the search for the needle in the haystack does not always end successfully. False positive results may appear. Thus instead of specific binders phage with no actual affinity toward the target are recovered due to their propagation advantages or binding to other components of the screening system, such as the solid phase, capturing reagents, contaminants in the target sample or blocking agents, rather than the target. Biopanning experiments on different targets performed in our laboratory revealed some previously identified and many new target-unrelated peptide sequences, which have already been frequently described and published, but not yet recognized as target-unrelated. Distinguishing true binders from false positives is an important step toward phage display selections of greater integrity. This article thoroughly reviews and discusses already identified and new target-unrelated peptides and suggests strategies to avoid their isolation.     

α-Amino acid derived enaminones and their application in the synthesis of N-protected methyl 5-substituted-4-hydroxypyrrole-3-carboxylates and other heterocycles

A new and simple synthesis of novel N-protected methyl 5-substituted-4-hydroxypyrrole-3-carboxylates, which exist in equilibrium with their 4-oxo tautomers, has been developed in two steps starting from N-protected α-amino acids. The key intermediates are enaminones, which can also be isolated, characterized, and used for the construction of other functionalized heterocycles, before they spontaneously decompose to pyrrole products. 4-Hydroxypyrroles are prone to partial aerial oxidation but can be efficiently alkylated or reduced to stable polysubstituted pyrrolidine derivatives.     

GMO quantification: valuable experience and insights for the future

Cultivation and marketing of genetically modified organisms (GMOs) have been unevenly adopted worldwide. To facilitate international trade and to provide information to consumers, labelling requirements have been set up in many countries. Quantitative real-time polymerase chain reaction (qPCR) is currently the method of choice for detection, identification and quantification of GMOs. This has been critically assessed and the requirements for the method performance have been set. Nevertheless, there are challenges that should still be highlighted, such as measuring the quantity and quality of DNA, and determining the qPCR efficiency, possible sequence mismatches, characteristics of taxon-specific genes and appropriate units of measurement, as these remain potential sources of measurement uncertainty. To overcome these problems and to cope with the continuous increase in the number and variety of GMOs, new approaches are needed. Statistical strategies of quantification have already been proposed and expanded with the development of digital PCR. The first attempts have been made to use new generation sequencing also for quantitative purposes, although accurate quantification of the contents of GMOs using this technology is still a challenge for the future, and especially for mixed samples. New approaches are needed also for the quantification of stacks, and for potential quantification of organisms produced by new plant breeding techniques.     

Structural and water-repellent properties of a urea/poly(dimethylsiloxane) sol-gel hybrid and its bonding to cotton fabric

A novel diureapropyltriethoxysilane [bis(aminopropyl)-terminated-poly(dimethylsiloxane) (1000)] (PDMSU) sol-gel hybrid was synthesized and applied on cotton to make it water repellent. Surface-energy values of PDMSU deposited on an aluminum substrate were determined, and the contact angle for water was assessed for impregnated cotton fabrics. The stability of the coatings was determined by repetitive washing, and their degradation was investigated with the help of the infrared attenuated total reflection (ATR) technique. The structure of PDMSU was studied by ATR and 29Si NMR spectroscopy. The results showed the active role of the urea groups in PDMSU/cotton interface bonding, but washing led to the relaxation of the urea-urea associations, as inferred from the appearance of a new amide II band at 1541 cm(-1).     

Ferroelectric mesophase with randomized interlayer structure

We present the experimental and theoretical evidence that a new Sm X phase made of asymmetric bent-shaped molecules has a layered, nontilted, optically uniaxial and polarly ordered structure with random direction of the layer polarization. The randomness results from the sign degeneracy of the difference in polarization directions in neighboring layers, although the magnitude of the phase difference is constant. Lifting the degeneracy by external fields two additional structures of the Sm X phase are possible.     

Enzyme immobilization on epoxy- and 1,1'-carbonyldiimidazole-activated methacrylate-based monoliths

Monolithic Convective Interaction Media (CIM) have been activated with epoxide and imidazole carbamate functionalities and used as supports for covalent immobilization of protein A, deoxyribonuclease I, and trypsin. The efficiency of immobilization for these proteins was determined from the amount of bound IgG, degradation of DNA, and hydrolysis of Nalpha-benzoyl-L-arginine ethyl ester, respectively. The respective biological activities of trypsin and the binding capacity of protein A immobilized via imidazole carbamate groups were 11.45 and 2.25 times higher than those obtained for epoxide matrix while they were practically equal for deoxyribonuclease I. The kinetics of immobilization was studied in detail for trypsin under dynamic conditions and revealed that the enzyme immobilized via imidazole carbamate groups already reached its highest activity in 5 min. In contrast, a much longer time was required for immobilization via epoxy groups.     

High-speed photorefraction at telecommunication wavelength 1.55 microm in Sn2P2S6:Te

We demonstrated for what is the first time to our knowledge photorefractive two-wave mixing in a bulk ferroelectric crystal using cw light at the telecommunication wavelength 1.55 microm. In the Te-doped ferroelectric semiconductor Sn2P2S6 with absorption constant <0.1 cm(-1) at 1.55 microm, grating recording times of 10 ms and a two-beam coupling gain of 2.8 cm(-1) have been measured at 350 mW power (intensity 440 W/cm(2)) without a necessity to apply an external electric field. With a moving grating technique, a maximal gain of 6.0 cm(-1) has been obtained.     

New nonlinear optical polyamides: Influence of binding mode of side-chains and rigidity of main-chains on temporal stability

New nonlinear optical rigid polyamides were synthesized and the influence of the binding mode between nonlinear optical chromophores and oxybutyl spacers, as well as of the rigidity of the main-chain on the second-order nonlinearity were investigated. The polyamides with side-on binding mode exhibit higher temporal stability of the polar order than analogous polyamide with end-on binding mode. By decreasing the rigidity of the main-chain of side-on polyamides, polyamide with 4,4’-methylenedianiline reveals enhanced solubility and processability, still keeping a high temporal stability compared to the relatively rigid polyamide with 1,4-phenylenediamine.