Screening for protease substrate by polyvalent phage display

Proteases are key regulators of many physiological and pathological processes [1,2], and are recognized as important and tractable drug candidates. Consequently, knowledge of protease substrate recognition and specificity promotes identification of biologically relevant substrates, helps elucidating a protease's biological function, and the design of specific inhibitors. Traditional methods for establishing substrate recognition profiles involve the identification of the scissile bond within a given protein substrate by proteomic methods such as Edman degradation. Then, synthetic peptide variants of this sequence can be screened in an iterative fashion to arrive at more optimized substrates. Even though it can be fruitful, this iterative strategy is biased toward the original substrate sequence and it is also tremendously cumbersome. Furthermore, it is not amenable to high throughput analysis. In 1993, Matthew & Wells presented a method for the use of monovalent "substrate phage" libraries for discovering peptide substrates for proteases, in which more than 10(7) potential substrates can be tested concurrently [3]. A library of fusion proteins was constructed containing randomized substrate sequences placed between a binding domain and the gene III coat protein of the filamentous phage, M13, which displays the fusion protein and packages the gene coding for it inside. Each fusion protein was displayed as a single copy on filamentous phagemid particles (substrate phage). This method allows one to rapidly survey the substrate recognition and specificity of individual or closely related members of proteases. Over the past decade, substrate phage screening has shown terrific utility in rapidly determining protease specificity and characterization of substrate recognition profile of proteases. In some cases, the structural insights of the catalytic domain were obtained from comparison of substrate specificity among closely related family of proteases [4-6]. The number of proteases (from various classes) characterized by this approach testifies to its power. Since the initial development of substrate phage library, different versions of the substrate phage cloning vectors have been constructed to further improve the utility of substrate phage display. This review will provide an overview of the construction of substrate phage display libraries, screening of substrate phage libraries, examples of application, summary and future directions.     

Biosynthesis of Quantum Dots (CdTe) and its Effect on Eisenia fetida and Escherichia coli

Biosynthesis belongs to one of the new possibilities of nanoparticles preparation, whereas its main advantage is biocompatibility. In addition, the ability of obtaining the raw material for such synthesis from the soil environment is beneficial and could be useful for remediation. However, the knowledge of mechanisms that are necessary for the biosynthesis or effect on the bio-synthesizing organisms is still insufficient. In this study, we attempted to evaluate the effect of quantum dots (QDs) not only on a model organism of collembolans, but also on another soil organism—earthworm Eisenia fetida—and in also one widespread microorganism such as Escherichia coli. Primarily, we determined 28EC₅₀ as 72.4 μmol L⁻¹ for CdTe QDs in collembolans. Further, we studied the effect of QDs biosynthesis in E. fetida and E. coli. Using determination of QDs, low-molecular thiols and antioxidant activities, we found differences between both organisms and also between ways how they behave in the presence of Cd and/or Cd and Te. The biosynthesis in earthworms can be considered as its own protective mechanism; however, in E. coli, it is probably a by-product of protective mechanisms.

     

An original approach for Raman spectroscopy analysis of radioactive materials and its application to americium‐containing samples

An approach for Raman measurements of highly radioactive samples is presented here. The innovative part of this approach lies in the fact that no single part of the Raman equipment is in direct contact with the radioactive sample, as the sample is sealed in an alpha‐tight capsule. Raman analysis is effectively performed through the optical‐grade quartz window closing the capsule. This allows performing micro‐Raman measurements on radioactive samples with no limitations on the laser source wavelength, polarisation mode, spectrometer mode and microscope mode (provided the focal length of the microscope objective is greater than the thickness of the quartz window and with sub mg samples). Some example results are shown and discussed. In particular, some spectral features of americium‐containing oxide nuclear fuel specimens are presented. Raman spectra clearly reveal in these specimens the presence of abundant oxygen defects induced in the fcc fluorite lattice by trivalent americium. In order to complete the analysis the Raman spectrum of pure americium dioxide was also measured with a lower energy excitation source compared with previous research. The current results seem to be consistent with the possible occurrence of a photolysis process induced by the Raman laser, resulting in the formation of hyperstoichiometric americium sesquioxide Am₂O_{3 + z}. Such a photolytic process is deemed to be unavoidable when visible lasers are used as excitation sources for the Raman analysis of americium dioxide. © 2015 The Authors Journal of Raman Spectroscopy Published by John Wiley & Sons, Ltd.     

Structure determination of polytypes (I)

Crystal structure determination of polytypes with diffraction methods can be divided into two steps. The first step is the structure determination of the building unit of the polytypic substance (in most cases layers). The second step is the determination of the stacking sequence of the corresponding building units. The stacking can be ordered as well as disordered. Various methods for solving these problems are described. The aim of this paper is to treate these methods from a uniform point of view.     

Interference of Data Transmission in Access and Backbone Networks by High-Power Sensor System

Currently, individual optical fibers are mostly used for each non-data application, which is very inefficient and uneconomical. Sharing a single fiber for multiple applications is a promising solution. However, in the case of a non-data application, the situation is much more complicated compared to data because of special application´s requirements. In laboratory setup, we performed a measurement with a standard G.652D optical fiber for analyzing possible interaction of stable frequency/accurate time transmission, 1.25/10Gbps data transmission (typical bitrates for access point-to-point networks), and high-power sensor signal for different channel spacing and different pulse duration of sensor signal.     

On Domination and Bornological Product Measures

The bornological product measures via the generalized Dobrakov integral in complete bornological locally convex spaces are studied using the domination of considered vector measures. A Fubini-type theorem for such product measures is proven.