N-Methylmesoporphyrin IX Fluorescence As A Reporter Of Strand Orientation In Guanine Quadruplexes

Guanine quadruplexes (GQ) are four-stranded DNA structures formed by guanine-rich DNA sequences. The formation of GQs inhibits cancer cell growth, although the detection of GQs invivo has proven difficult, in part because of their structural diversity. The development of GQ-selective fluorescent reporters would enhance our ability to quantify the number and location of GQs, ultimately advancing biological studies of quadruplex relevance and function. N-methylmesoporphyrin IX (NMM) interacts selectively with parallel-stranded GQs; in addition, its fluorescence is sensitive to the presence of DNA, making this ligand a possible candidate for a quadruplex probe. In the present study, we investigated the effect of DNA secondary structure on NMM fluorescence. We found that NMM fluorescence increases by about 60-fold in the presence of parallel-stranded GQs and by about 40-fold in the presence of hybrid GQs. Antiparallel GQs lead to lower than 10-fold increases in NMM fluorescence. Single-stranded DNA, duplex, or i-motif, induce no change in NMM fluorescence. We conclude that NMM shows promise as a turn-on\u27 fluorescent probe for detecting quadruplex structures, as well as for differentiating them on the basis of strand orientation

Transcriptomic, Functional, and Network Analyses Reveal Novel Genes Involved in the Interaction between \u3ci\u3eCaenorhabditis elegans\u3c/i\u3e and \u3ci\u3eStenotrophomonas maltophilia\u3c/i\u3e

The bacterivorous nematode Caenorhabditis elegans is an excellent model for the study of innate immune responses to a variety of bacterial pathogens, including the emerging nosocomial bacterial pathogen Stenotrophomonas maltophilia. The study of this interaction has ecological and medical relevance as S. maltophilia is found in association with C. elegans and other nematodes in the wild and is an emerging opportunistic bacterial pathogen. We identified 393 genes that were differentially expressed when exposed to virulent and avirulent strains of S.maltophilia and an avirulent strain of E. coli. We then used a probabilistic functional gene network model (WormNet) to determine that 118 of the 393 differentially expressed genes formed an interacting network and identified a set of highly connected genes with eight or more predicted interactions.We hypothesized that these highly connected genes might play an important role in the defense against S. maltophila and found that mutations of six of seven highly connected genes have a significant effect on nematode survival in response to these bacteria. Of these genes, C48B4.1, mpk-2, cpr-4, clec-67, and lys-6 are needed for combating the virulent S. maltophilia JCMS strain, while dod-22 was solely involved in response to the avirulent S. maltophilia K279a strain. We further found that dod-22 and clec-67 were up regulated in response to JCMS vs. K279a, while C48B4.1, mpk-2, cpr-4, and lys-6 were down regulated. Only dod-22 had a documented role in innate immunity, which demonstrates the merit of our approach in the identification of novel genes that are involved in combating S. maltophilia infection

Influence of a mutltistrand cable design on its quench development process and stability

The quench development process was studied with two six-strand superconducting cable samples with insulated strands and different cabling design. One sample was the traditional ‘six-around-one’ cable, the other was of the ‘round-braid’ type. Quench was initiated by a heating pulse applied to a single strand. A significant difference was observed in the current redistribution among strands due to the different cabling designs. It has an important influence on the stability of multistrand cables. A new concept of the ‘single-strand stability’ was proposed and corresponding stability criteria were offered. A possible way to improve cable stability by using special cabling design is discussed

Eхperience of the Baile-Felix tourist system (Romania) for the protection and promotion of the grey seal as a brend on the Hel Peninsular (Poland)

The Pârâul Pețea Nature Reserve is located in Bihor County (Romania), in the area of the Băile-Felix rural tourist system. It has gained international popularity due to the existence of an ecosystem with thermal waters. Thermal springs are the habitat of rare fauna (Scardinius racovitzai, Melanopsis parreyssi) and flora species including the unique Nymphaea lotus var. thermalis, a tertiary relict lotus flower. Situated on the Hel Peninsula of the Baltic Sea, Hel Marine Station (HMS) is one of the most interesting tourist attractions thanks to the project aimed at the protection of the grey seal in the Polish waters. We employed a number of tools and methods (including observation and monitoring) over a period of three years for the creation of a comprehensive database. We studied the actual condition of separate elements of the two tourist systems and compared the two tourist destinations. We identified differences and similarities between the two places. The lotus flower and the grey seal have become an integral part of the local, national and international collective mentality. Special attention was paid to the causes of almost total extinction of rare species despite being indispensable elements in the promotion and rebranding of the two tourist destinations. We explored the degree of knowledge and the awareness of their value in the local mentality

Revisiting the Quantum Group Symmetry of Diatomic Molecules

We propose a q-deformed model of the anharmonic vibrations in diatomic molecules. We analyse the applicability of the model to the phenomenological Dunham's expansion by comparing with experimental data. Our methodology involves a global consistency analysis of the parameters that determine the q-deformed system, when compared with fitted vibrational parameters to 161 electronic states in diatomic molecules. We show how to include both the positive and the negative anharmonicities in a simple and systematic fashion.Comment: 15 pages, 3 Table

Anomalous Suppression of Valley Splittings in Lead Salt Nanocrystals without Inversion Center

Atomistic sp3d5s* tight-binding theory of PbSe and PbS nanocrystals is developed. It is demonstrated, that the valley splittings of confined electrons and holes strongly and peculiarly depend on the geometry of a nanocrystal. When the nanocrystal lacks a microscopic center of inversion and has T_d symmetry, the splitting is strongly suppressed as compared to the more symmetric nanocrystals with O_h symmetry, having an inversion center.Comment: 5 pages, 4 figures, 1 tabl

Electronic states in heterostructures formed by ultranarrow layers

Low-energy electronic states in heterosrtuctures formed by ultranarrow layer (single or several monolayers thickness) are studied theoretically. The host material is described within the effective mass approximation and effect of ultranarrow layers is taken into account within the framework of the transfer matrix approach. Using the current conservation requirement and the inversion symmetry of ultranarrow layer, the transfer matrix is written through two phenomenological parameters. The binding energy of localized state, the reflection (transmission) coefficient for the single ultranarrow layer case, and the energy spectrum of superlattice are determined by these parameters. Spectral dependency of absorption in superlattice due to photoexcitation of electrons from localized states into minibands is strongly dependent on the ultranarrow layers characteristics. Such a dependency can be used for verification of the transfer matrix parameters.Comment: 7 pages, 7 figure

A white dwarf-neutron star relativistic binary model for soft gamma-ray repeaters

A scenario for SGRs is introduced in which gravitational radiation reaction effects drive the dynamics of an ultrashort orbital period X-ray binary embracing a high-mass donor white dwarf (WD) to a rapidly rotating low magnetised massive neutron star (NS) surrounded by a thick, dense and massive accretion torus. Driven by GR reaction, sparsely, the binary separation reduces, the WD overflows its Roche lobe and the mass transfer drives unstable the accretion disk around the NS. As the binary circular orbital period is a multiple integer number ($m$) of the period of the WD fundamental mode (Pons et al. 2002), the WD is since long pulsating at its fundamental mode; and most of its harmonics, due to the tidal interaction with its NS orbital companion. Hence, when the powerful irradiation glows onto the WD; from the fireball ejected as part of the disk matter slumps onto the NS, it is partially absorbed. This huge energy excites other WD radial ($p$-mode) pulsations (Podsiadlowski 1991,1995). After each mass-transfer episode the binary separation (and orbital period) is augmented significantly (Deloye & Bildsten 2003; Al\'ecyan & Morsink 2004) due to the binary's angular momentum redistribution. Thus a new adiabatic inspiral phase driven by GR reaction starts which brings the binary close again, and the process repeats. This model allows to explain most of SGRs observational features: their recurrent activity, energetics of giant superoutbursts and quiescent stages, and particularly the intriguing subpulses discovered by BeppoSAX (Feroci et al. 1999), which are suggested here to be {\it overtones} of the WD radial fundamental mode (see the accompanying paper: Mosquera Cuesta 2004b).Comment: This paper was submitted as a "Letter to the Editor" of MNRAS in July 17/2004. Since that time no answer or referee report was provided to the Author [MNRAS publication policy limits reviewal process no longer than one month (+/- half more) for the reviewal of this kind of submission). I hope this contribution is not receiving a similar "peer-reviewing" as given to the A. Dar and A. De Rujula's "Cannonball model for gamma-ray bursts", or to the R.K. Williams' "Penrose process for energy extraction from rotating black holes". The author welcomes criticisms and suggestions on this pape

Surface scattering velocities in III-nitride quantum well laser structures via the emission of hybrid phonons

We have theoretically and numerically studied nitride-based quantum well (QW) laser structures. More specifically, we have used a QW made with III-nitride where the width of the barrier region is large relative to the electron mean free path, and we have calculated the electron surface capture velocities by considering an electron flux which is captured into the well region. The process is assisted by the emission of the longitudinal optical phonons as predicted by the hybrid (HB) model. The results of surface capture velocities via the emission of HB phonons are compared to the emission of the dielectric continuum phonons (Zakhleniuk et al 1999 Phys. Status Solidi a 176 79). Our investigation shows that the two different phonon models predict almost the same results for the non-retarded limit. Furthermore, the surface capture velocities strongly depend on the size of the structure and the heterostructure materials. Lastly, a comparison to the recent experimental values shows that our model could accurately describe the experimentally measured parameters of the quantum capture processes

Nonlinear evolution of surface morphology in InAs/AlAs superlattices via surface diffusion

Continuum simulations of self-organized lateral compositional modulation growth in InAs/AlAs short-period superlattices on InP substrate are presented. Results of the simulations correspond quantitatively to the results of synchrotron x-ray diffraction experiments. The time evolution of the compositional modulation during epitaxial growth can be explained only including a nonlinear dependence of the elastic energy of the growing epitaxial layer on its thickness. From the fit of the experimental data to the growth simulations we have determined the parameters of this nonlinear dependence. It was found that the modulation amplitude don't depend on the values of the surface diffusion constants of particular elements.Comment: 4 pages, 3 figures, published in Phys. Rev. Lett. http://link.aps.org/abstract/PRL/v96/e13610