Proposal for a photoacoustic ultrasonic generator based on Tamm plasmon structures

The scheme of a generation of ultrasound waves based on optically excited Tamm plasmon structures is proposed. It is shown that Tamm plasmon structures can provide total absorption of a laser pulse with arbitrary wavelength in a metallic layer providing the possibility of the use of an infrared semiconductor laser for the excitation of ultrasound waves. Laser pulse absorption, heat transfer and dynamical properties of the structure are modeled, and the optimal design of the structure is found. It is demonstrated that the Tamm plasmon-based photoacoustic generator can emit ultrasound waves in the frequency band up to 100 MHz with predefined frequency spectrum.

Enhancement of light emission in Bragg monolayer-thick quantum well structures

Control over spontaneous emission rate is important for improving efficiency in different semiconductor applications including lasers, LEDs and photovoltaics. Usually, an emitter should be placed inside the cavity to increase the spontaneous emission rate, although it is technologically challenging. Here we experimentally demonstrate a phenomenon of super-radiance observed in a cavity-less periodic Bragg structure based on InAs monolayer-thick multiple quantum wells (MQW). The collective super-radiant mode shows enhanced emission rate for specific angles and frequencies. This behaviour correlates with the calculations demonstrating individual spots of the enhanced Purcell coefficient near the Bragg condition curve. This study provides a perspective for realization of surface emitting cavity-less lasers with distributed feedback.

Different regimes of the Purcell effect in disordered photonic crystals

We demonstrate that disorder in photonic crystals could lead to pronounced modification of spontaneous emission rate in the frequency region corresponding to the photonic band gap (PBG). Depending on the amount of disorder, two different regimes of the Purcell effect occurs. We provide statistical analysis of Purcell coefficient on the frequency of the emitter and its position within the sample. For the moderate disorder, an enhancement of spontaneous emission occurs at the edge of PBG due to the modification of properties of the edge state. This effect is responsible for recently observed mirrorless lasing in photonic crystals at the edge of PBG. When the level of disorder increases, the spontaneous emission rate enhances within the PBG due to the appearance of the high quality factor states. This effect is likely responsible for a superlinear dependence of emissions on pumping observed in synthetic opals.

Enhancement of spontaneous emission in Tamm plasmon structures

It was theoretically and experimentally demonstrated that in metal/semiconductor Tamm plasmon structures the probability of spontaneous emission can be increased despite losses in metal, and theoretical analysis of experimental results suggested that the enhancement could be as high as one order of magnitude. Tamm plasmon structure with quantum dots has been fabricated and the emission pattern has been measured. Electromagnetic modes of the structure have been analyzed and modification of spontaneous emission rates has been calculated showing a good agreement with experimentally observed emission pattern.

Major genetic marker of nidoviruses encodes a replicative endoribonuclease

Coronaviruses are important pathogens that cause acute respiratory diseases in humans. Replication of the approximately 30-kb positive-strand RNA genome of coronaviruses and discontinuous synthesis of an extensive set of subgenome-length RNAs (transcription) are mediated by the replicase-transcriptase, a barely characterized protein complex that comprises several cellular proteins and up to 16 viral subunits. The coronavirus replicase-transcriptase was recently predicted to contain RNA-processing enzymes that are extremely rare or absent in other RNA viruses. Here, we established and characterized the activity of one of these enzymes, replicative nidoviral uridylate-specific endoribonuclease (NendoU). It is considered a major genetic marker that discriminates nidoviruses (Coronaviridae, Arteriviridae, and Roniviridae) from all other RNA virus families. Bacterially expressed forms of NendoU of severe acute respiratory syndrome coronavirus and human coronavirus 229E were revealed to cleave single-stranded and double-stranded RNA in a Mn(2+)-dependent manner. Single-stranded RNA was cleaved less specifically and effectively, suggesting that double-stranded RNA is the biologically relevant NendoU substrate. Double-stranded RNA substrates were cleaved upstream and downstream of uridylates at GUU or GU sequences to produce molecules with 2'-3' cyclic phosphate ends. 2'-O-ribose-methylated RNA substrates proved to be resistant to cleavage by NendoU, indicating a functional link with the 2'-O-ribose methyltransferase located adjacent to NendoU in the coronavirus replicative polyprotein. A mutagenesis study verified potential active-site residues and allowed us to inactivate NendoU in the full-length human coronavirus 229E clone. Substitution of D6408 by Ala was shown to abolish viral RNA synthesis, demonstrating that NendoU has critical functions in viral replication and transcription.

Human coronavirus 229E nonstructural protein 13: characterization of duplex-unwinding, nucleoside triphosphatase, and RNA 5'-triphosphatase activities

The human coronavirus 229E (HCoV-229E) replicase gene-encoded nonstructural protein 13 (nsp13) contains an N-terminal zinc-binding domain and a C-terminal superfamily 1 helicase domain. A histidine-tagged form of nsp13, which was expressed in insect cells and purified, is reported to unwind efficiently both partial-duplex RNA and DNA of up to several hundred base pairs. Characterization of the nsp13-associated nucleoside triphosphatase (NTPase) activities revealed that all natural ribonucleotides and nucleotides are substrates of nsp13, with ATP, dATP, and GTP being hydrolyzed most efficiently. Using the NTPase active site, HCoV-229E nsp13 also mediates RNA 5'-triphosphatase activity, which may be involved in the capping of viral RNAs.

Multiple enzymatic activities associated with severe acute respiratory syndrome coronavirus helicase

Severe acute respiratory syndrome coronavirus (SARS-CoV), a newly identified group 2 coronavirus, is the causative agent of severe acute respiratory syndrome, a life-threatening form of pneumonia in humans. Coronavirus replication and transcription are highly specialized processes of cytoplasmic RNA synthesis that localize to virus-induced membrane structures and were recently proposed to involve a complex enzymatic machinery that, besides RNA-dependent RNA polymerase, helicase, and protease activities, also involves a series of RNA-processing enzymes that are not found in most other RNA virus families. Here, we characterized the enzymatic activities of a recombinant form of the SARS-CoV helicase (nonstructural protein [nsp] 13), a superfamily 1 helicase with an N-terminal zinc-binding domain. We report that nsp13 has both RNA and DNA duplex-unwinding activities. SARS-CoV nsp13 unwinds its substrates in a 5'-to-3' direction and features a remarkable processivity, allowing efficient strand separation of extended regions of double-stranded RNA and DNA. Characterization of the nsp13-associated (deoxy)nucleoside triphosphatase ([dNTPase) activities revealed that all natural nucleotides and deoxynucleotides are substrates of nsp13, with ATP, dATP, and GTP being hydrolyzed slightly more efficiently than other nucleotides. Furthermore, we established an RNA 5'-triphosphatase activity for the SARS-CoV nsp13 helicase which may be involved in the formation of the 5' cap structure of viral RNAs. The data suggest that the (d)NTPase and RNA 5'-triphosphatase activities of nsp13 have a common active site. Finally, we established that, in SARS-CoV-infected Vero E6 cells, nsp13 localizes to membranes that appear to be derived from the endoplasmic reticulum and are the likely site of SARS-CoV RNA synthesis.

Mechanisms and enzymes involved in SARS coronavirus genome expression

A novel coronavirus is the causative agent of the current epidemic of severe acute respiratory syndrome (SARS). Coronaviruses are exceptionally large RNA viruses and employ complex regulatory mechanisms to express their genomes. Here, we determined the sequence of SARS coronavirus (SARS-CoV), isolate Frankfurt 1, and characterized key RNA elements and protein functions involved in viral genome expression. Important regulatory mechanisms, such as the (discontinuous) synthesis of eight subgenomic mRNAs, ribosomal frameshifting and post-translational proteolytic processing, were addressed. Activities of three SARS coronavirus enzymes, the helicase and two cysteine proteinases, which are known to be critically involved in replication, transcription and/or post-translational polyprotein processing, were characterized. The availability of recombinant forms of key replicative enzymes of SARS coronavirus should pave the way for high-throughput screening approaches to identify candidate inhibitors in compound libraries.

[To the role of computed tomography in the algorithm of diagnosis of lung cancer]

The paper summarizes the results of examination of 100 patients with malignant tumors of the lung. The results of X-ray study, linear tomography, and computed tomography (CT) used in the examination of patients with lung cancer were compared by using as an indicator the following parameters: to make diagnosis of lung cancer, to reveal mediastinal intergrowths, to detect enlarged lymph nodes, pulmonary metastases, and pleural lesions, to obtain information on tumor spread into the chest, to reveal growths into the vascular walls. To evaluate the efficiency of the techniques in solving the above diagnostic tasks, a statistical analysis including the estimation of their accuracy, specificity, and sensitivity was made. Recommendations for examination of patients with lung cancer were drawn up for therapeutic institutions of different types.

Non-canonical functions of aminoacyl-tRNA synthetases

The basic function of aminoacyl-tRNA synthetases (aaRSs) is an activation of the amino acids and their transfer to specific RNAs. In addition to this key role in protein biosynthesis, the enzymes of this group participate in other cell processes. aaRSs regulate the expression of some genes, not only their own. The regulation is carried out on the level of transcription, processing of mRNA, and translation. They catalyze the synthesis of dinucleoside oligophosphates and thus indirectly influence many other cell functions. Tyrosyl-tRNA synthetase was shown to have cytokine activities. Some aaRSs interact specifically with other proteins. Thus, aminoacyl-tRNA synthetases are involved in the regulation of the multiple processes of living cells. In this review we summarize the available data on unusual activities of aaRSs.

Phenylalanyl-tRNA synthetase interacts with DNA: studies on activity using deoxyribooligonucleotides

Phenylalanyl-tRNA synthetase from Thermus thermophilus complexes with short (up to 30 nucleotide length) single-stranded DNA fragments more efficiently than with double-stranded fragments. The complexing between DNA and the protein significantly increases with deoxyribooligonucleotide longer than 20 nucleotides. Using affinity labeling, the binding site of DNA was located near the interface of the alpha- and beta-subunits. The binding sites of DNA and tRNAPhe do not overlap. Phenylalanyl-tRNA synthetase from E. coli also binds DNA.