Experimental demonstration of acoustically induced polarization-dependent fiber optical vortex inversion.

A recently proposed theoretical model of acousto-optic interaction in optical fibers with a traveling flexural acoustic wave of the fundamental order [M.A. Yavorsky, et al.

Subwavelength Diffractive Optical Elements for Generation of Terahertz Coherent Beams with Pre-Given Polarization State.

Coherent terahertz beams with radial polarization of the 1st, 2nd, and 3rd orders have been generated with the use of silicon subwavelength diffractive optical elements (DOEs). Silicon elements were fabricated by a technology similar to the technology used before for the fabrication of DOEs forming laser terahertz beams with pre-given mode content. The beam of the terahertz Novosibirsk Free Electron Laser was used as the illuminating beam.

Metalenses for the generation of vector Lissajous beams with a complex Poynting vector density.

We propose a method for the design of metalenses generating and focusing so-called vector Lissajous beams (VLBs), a generalization of cylindrical vector beams (CVBs) in the form of vector beams whose polarization vector is defined by two orders (p, q). The designed metalenses consist of subwavelength gratings performing the polarization transformation of the incident linearly polarized laser beams and a sublinearly chirped lens term for the realization of the beam focusing. The possibility of using VLBs for the realization of laser beams with a complex Poynting vector is theoretically shown.

Optical vortices and orbital angular momentum in strongly coupled optical fibers.

We have studied the effect of strong coupling on the propagation of optical vortices (OVs) and evolution of their orbital angular momentum (OAM) in parallel multimode optical fibers. Based on the perturbation theory that goes beyond the limits of weak orthogonality approximation we have established that strong coupling does not lead to alteration of the structure of supermodes as compared to the case of weak coupling. The strong coupling affects only the propagation constants of such supermodes, which we have found analytical expressions for.

GLAD-PCR Assay of R(5mC)GY Sites in the Regulatory Region of Tumor-Suppressor Genes Associated with Gastric Cancer.

At early stages of carcinogenesis, the regulatory regions of some tumor suppressor genes become aberrantly methylated at RCGY sites, which are substrates of DNA methyltransferase Dnmt3. Identification of aberrantly methylated sites in tumor DNA is considered to be the first step in the development of epigenetic PCR test systems for early diagnosis of cancer. Recently, we have developed a GLAD-PCR assay, a method for detecting the R(5mC)GY site in the genome position of interest even at significant excess of DNA molecules with a non-methylated RCGY site in this location.

Refractive twisted microaxicons.

Complex-shaped light fields with specially designed intensity, phase, and polarization distributions are highly demanded for various applications including optical tweezers, laser material processing, and lithography. Here, we propose a novel (to the best of our knowledge) optical element formed by the twisting of a conic surface, a twisted microaxicon, allowing us to controllably generate high-quality spiral-shaped intensity patterns. Performance of the proposed element was analyzed both analytically and numerically using ray approximation and the rigorous finite difference time domain (FDTD) solution of Maxwell's equation.

Metasurfaces with continuous ridges for inverse energy flux generation.

In this study, we propose a new approach to construct metasurfaces for the generation of inverse energy flux near the optical axis. We derive new equations intended to create continuous subwavelength relief for transformation of a linearly polarized input field into a radially polarized beam with an arbitrary order. Proposed metasurfaces combine the polarization converter as subwavelength gratings with a varying period and the focusing element as additional structure.

[Use of site-specific DNA endonucleases in genome-wide studies of human DNA].

During the last decades, site-specific DNA endonucleases have served as a key instrument to study primary structure of DNA and genetic engineering. Here, we describe examples of these enzyme uses in genome-wide analysis of human DNA including restriction endonucleases involvement during sample preparation for sequencing using NGS devices, as well as visualization of cleavage of DNA repeats by endonucleases. The first studies on application of DNA endonucleases in the rapidly developing area of epigenetic analysis of genomes, which is facilitated by the recent discovery of a new class of enzymes, 5-methylcytosinedependent site-specific DNA endonucleases, are of special interest.

Focused, evanescent, hollow, and collimated beams formed by microaxicons with different conical angles.

Diffraction patterns formed by axicons with different tip (vertex) angles are analytically and numerically investigated. Results show that the axicon (or tapered dielectric probe) can form an extended axial light beam, a compact evanescent field, a hollow beam, and a collimated beam, depending on the vertex angle. Two-dimensional and three-dimensional models of a tapered dielectric probe show that, with small changes to the vertex angle, light transmitted by the probe is scattered rather than focused, and vice versa.

Complete Genome Sequence and Methylome Analysis of 65.

65 is the original source strain for the restriction enzyme Acc65I. Its complete sequence and full methylome were determined using single-molecule real-time (SMRT) sequencing.

Expression and purification of the modification-dependent restriction enzyme BisI and its homologous enzymes.

The methylation-dependent restriction endonuclease (REase) BisI (G(m5)C ↓ NGC) is found in Bacillus subtilis T30. We expressed and purified the BisI endonuclease and 34 BisI homologs identified in bacterial genomes. 23 of these BisI homologs are active based on digestion of (m5)C-modified substrates.

Photonic nanohelix generated by a binary spiral axicon.

We demonstrate the possibility of generating a photonic nanojet with a helix shape (photonic nanohelix) at the diffraction of a Gaussian beam on a binary spiral axicon. We investigate the influence of the illuminating beam parameters on the shape and size of the generated photonic nanohelix by solving the Helmholtz equation using the finite element method. The simulated photonic nanohelix has depth of focus (DOF) of 2.

Cloning and Characterization of a New Site-Specific Methyl-Directed ElmI Endonuclease Recognizing and Cleaving C5-methylated DNA Sequence 5'-G(5mC)^NG(5mC)-3'.

Putative open reading frames of MD-endonucleases have been identified in Enterobacteria genomes as a result of the search for amino acid sequences homologous to MD-endonuclease BisI. A highly conserved DNA primary structure of these open reading frames in different genera of Enterobacteria (Escherichia, Klebsiella and Cronobacter) has allowed researchers to create primers for PCR screening, which was carried out on Enterobacteria DNA collected from natural sources. The DNA fragment, about 440 bp in length, was amplified by use of the genomic DNA of a wild E.

[Application of GLAD-PCR analysis for the methylation sites detection in the regulatory areas of tumor-suppressor genes ELMo1 and EsR1 in colorectal cancer].

Aberrant methylation of regulation regions of tumorsuppressor genes is showed for many cancer diseases. In course of this modification an enzyme DNMT3 methylates RCGY sites in CpG-islands of regulation regions producing R(5mC)GY sites. Earlier we developed GLAD-PCR assay to determine R(5mC)GY site in a definite position of human genome.

Complete Genome Sequence Analysis of Bacillus subtilis T30.

The complete genome sequence of Bacillus subtilis T30 was determined by SMRT sequencing. The entire genome contains 4,138 predicted genes. The genome carries one intact prophage sequence (37.

Medium-sized tandem repeats represent an abundant component of the Drosophila virilis genome.

Background: Previously, we developed a simple method for carrying out a restriction enzyme analysis of eukaryotic DNA in silico, based on the known DNA sequences of the genomes. This method allows the user to calculate lengths of all DNA fragments that are formed after a whole genome is digested at the theoretical recognition sites of a given restriction enzyme. A comparison of the observed peaks in distribution diagrams with the results from DNA cleavage using several restriction enzymes performed in vitro have shown good correspondence between the theoretical and experimental data in several cases.

Recombinant DNA-methyltransferase M1.BspACI from Bacillus psychrodurans AC: purification and properties.

A restriction-modification system from Bacillus psychrodurans AC (recognition sequence 5'-CCGC-3') comprises two DNA methyltransferases: M1.BspACI and M2.BspACI.

Substrate specificity and biochemical properties of M3.BstF5I DNA methyltransferase from the BstF5I restriction-modification system.

Optimal conditions for DNA methylation by the M3.BstF5I enzyme from Bacillus stearothermophilus and kinetic parameters of lambda phage DNA modification and that of a number of oligonucleotide substrates are established. Comparison of M1.

GlaI digestion of mouse gamma-satellite DNA: study of primary structure and ACGT sites methylation.

Background: Patterns of mouse DNA hydrolysis with restriction enzymes are coincided with calculated diagrams of genomic DNA digestion in silico, except presence of additional bright bands, which correspond to monomer and dimer of gamma-satellite DNA. Only small portion of mouse gamma-satellite DNA sequences are presented in databases. Methyl-directed endonuclease GlaI cleaves mouse DNA and may be useful for a detailed study of primary structure and CG dinucleotides methylation in gamma-satellite DNA.

A physical map of human Alu repeats cleavage by restriction endonucleases.

Background: Alu repetitive elements are the abundant sequences in human genome. Diversity of DNA sequences of these elements makes difficult the construction of theoretical patterns of Alu repeats cleavage by restriction endonucleases. We have proposed a method of restriction analysis of Alu repeats sequences in silico.

Substrate specificity of new methyl-directed DNA endonuclease GlaI.

Background: Recently, we have discovered site-specific endonucleases, which recognize and cleave only DNA sequences with 5-methylcytosine. Two specificities of such endonucleases have been described. Enzymes BisI, BlsI, and GluI are isoschizomers and hydrolyze the DNA sequence 5'-GCNGC-3'/3'-CGNCG-5', which is methylated in different ways.

Isolation and characterization of biochemical properties of DNA methyltransferase FauIA modifying the second cytosine in the nonpalindromic sequence 5'-CCCGC-3'.

A gene encoding DNA methyltransferase (methylase) FauIA of the restriction-modification system FauI from Flavobacterium aquatile (recognizing sequence 5'-CCCGC-3') was cloned in pJW vector. The latter was used for transformation of E. coli RRI cells followed by subsequent thermoinduction and biomass elaboration.

The molecular structure of the DNA fragments eliminated during chromatin diminution in Cyclops kolensis.

Presumptive somatic cells of the copepod Cyclops kolensis specifically eliminate a large fraction of their genome by the process of chromatin diminution. The eliminated DNA (eDNA) remains only in the germline cells. Very little is known about the nature of the sequences eliminated from somatic cells.