Investigation of genomic DNA methylation by ultraviolet resonant Raman spectroscopy

Cytosine plays a preeminent role in DNA methylation, an epigenetic mechanism that regulates gene expression, the misregulation of which can lead to severe diseases. Several methods are nowadays employed for assessing the global DNA methylation levels, but none of them combines simplicity, high sensitivity, and low operating costs to be translated into clinical applications. Ultraviolet (UV) resonant Raman measurements at excitation wavelengths of 272 nm, 260 nm, 250 nm, and 228 nm have been carried out on isolated deoxynucleoside triphosphates (dNTPs), on a dNTP mixture as well as on genomic DNA (gDNA) samples, commercial from salmon sperm and non-commercial from B16 murine melanoma cell line. The 228 nm excitation wavelength was identified as the most suitable energy for enhancing cytosine signals over the other DNA bases. The UV Raman measurements performed at this excitation wavelength on hyper-methylated and hypo-methylated DNA from Jurkat leukemic T-cell line have revealed significant spectral differences with respect to gDNA isolated from salmon sperm and mouse melanoma B16 cells. This demonstrates how the proper choice of the excitation wavelength, combined with optimized extraction protocols, makes UV Raman spectroscopy a suitable technique for highlighting the chemical modifications undergone by cytosine nucleotides in gDNA upon hyper- and hypo-methylation events

Symmetries and boundary conditions with a twist

Interest in finite-size systems has risen in the last decades, due to the focus on nanotechnological applications and because they are convenient for numerical treatment that can subsequently be extrapolated to infinite lattices. Independently of the envisioned application, special attention must be given to boundary condition, which may or may not preserve the symmetry of the infinite lattice. Here we present a detailed study of the compatibility between boundary conditions and conservation laws. The conflict between open boundary conditions and momentum conservation is well understood, but we examine other symmetries, as well: we discuss gauge invariance, inversion, spin, and particle-hole symmetry and their compatibility with open, periodic, and twisted boundary conditions. We develop the reasoning in the framework of the one-dimensional half-filled Hubbard model, whose Hamiltonian displays a variety of symmetries. Our discussion includes analytical and numerical results. Our analytical survey shows that boundary conditions break one or more symmetries of the infinite-lattice Hamiltonian. The exception is twisted boundary condition with the special torsion $\Theta=\pi L/2$, where $L$ is the lattice size. Our numerical results for the ground-state energy at half-filling and the energy gap for $L=2$--$7$ show how the breaking of symmetry affects the convergence to the $L\to\infty$ limit. We compare the computed energies and gaps with the exact results for the infinite lattice drawn from the Bethe-Ansatz solution. The deviations are boundary-condition dependent. The special torsion yields more rapid convergence than open or periodic boundary conditions. For sizes as small as $L=7$, the numerical results for twisted condition are very close to the $L\to\infty$ limit. We also discuss the ground-state electronic density and magnetization at half filling under the three boundary conditions.Comment: Accepted for publication by the Brazilian Journal of Physics. The final publication is available at Springer via http://dx.doi.org/10.1007/s13538-017-0517-

Importance of Spin-Orbit Interaction for the Electron Spin Relaxation in Organic Semiconductors

Despite the great interest organic spintronics has recently attracted, there is only a partial understanding of the fundamental physics behind electron spin relaxation in organic semiconductors. Mechanisms based on hyperfine interaction have been demonstrated, but the role of the spin-orbit interaction remains elusive. Here, we report muon spin spectroscopy and time-resolved photoluminescence measurements on two series of molecular semiconductors in which the strength of the spin-orbit interaction has been systematically modified with a targeted chemical substitution of different atoms at a particular molecular site. We find that the spin-orbit interaction is a significant source of electron spin relaxation in these materials

Coulomb Drag in Coherent Mesoscopic Systems

We present a theory for Coulomb drag between two mesoscopic systems. Our formalism expresses the drag in terms of scattering matrices and wave functions, and its range of validity covers both ballistic and disordered systems. The consequences can be worked out either by analytic means, such as the random matrix theory, or by numerical simulations. We show that Coulomb drag is sensitive to localized states, which usual transport measurements do not probe. For chaotic 2D-systems we find a vanishing average drag, with a nonzero variance. Disordered 1D-wires show a finite drag, with a large variance, giving rise to a possible sign change of the induced current.Comment: 4 pages including 2 figures. Minor changes. Accepted for publication in Phys. Rev. Let

A study of the perceived risks, benefits and barriers to the use of SDD in adult critical care units (the SuDDICU study)

Peer reviewedPublisher PD

Contribution of White Dwarfs to Cluster Masses

I present a literature search through 31 July 1997 of white dwarfs (WDs) in open and globular clusters. There are 36 single WDs and 5 WDs in binaries known among 13 open clusters, and 340 single WDs and 11 WDs in binaries known among 11 globular clusters. From these data I have calculated WD mass fractions for four open clusters (the Pleiades, NGC 2168, NGC 3532, and the Hyades) and one globular cluster (NGC 6121). I develop a simple model of cluster evolution that incorporates stellar evolution but not dynamical evolution to interpret the WD mass fractions. I augment the results of my simple model with N-body simulations incorporating stellar evolution (Terlevich 1987; de la Feunte Marcos 1996; Vesperini & Heggie 1997). I find that even though these clusters undergo moderate to strong kinematical evolution the WD mass fraction is relatively insensitive to kinematical evolution. By comparing the cluster mass functions to that of the Galactic disk, and incorporating plausibility arguments for the mass function of the Galactic halo, I estimate the WD mass fraction in these two populations. I assume the Galactic disk is ~10 Gyrs old (Winget et al. 1987; Liebert, Dahn, & Monet 1988; Oswalt et al. 1996) and that the Galactic halo is ~12 Gyrs old (Reid 1997b; Gratton et al. 1997; Chaboyer et al. 1998), although the WD mass fraction is insensitive to age in this range. I find that the Galactic halo should contain 8 to 9% (alpha = -2.35) or perhaps as much as 15 to 17% (alpha = -2.0) of its stellar mass in the form of WDs. The Galactic disk WD mass fraction should be 6 to 7% (alpha = -2.35), consistent with the empirical estimates of 3 to 7% (Liebert, Dahn, & Monet 1988; Oswalt et al. 1996). (abridged)Comment: 20 pages, uuencoded gunzip'ed latex + 3 postscrip figures, to be published in AJ, April, 199

First INTEGRAL Observations of Eight Persistent Neutron Star Low Mass X-ray Binaries

Early results from the INTEGRAL Core Program, for a sample of eight persistently bright neutron star low mass X-ray binaries in the energy range from 5 keV to 200 keV are presented. It is shown that INTEGRAL efficiently detects sources and that spectra may be obtained up to several hundreds of keV by combining data from three of the four INTEGRAL instruments: JEM-X, IBIS and SPI. For the source GX 17+2 it is shown that the spectrum extends well above 100 keV with a flattening of the spectrum above 30 keV. This might suggest a non-thermal comptonisation emission, but uncertainties in the current data reduction and background determination do not allow firm conclusions to be drawn.Comment: 5 pages, 6 figures, accepted for publication in Astronomy & Astrophysic

Resolving the Hard X-ray Emission of GX 5-1 with INTEGRAL

We present the study of one year of INTEGRAL data on the neutron star low mass X-ray binary GX 5-1. Thanks to the excellent angular resolution and sensitivity of INTEGRAL, we are able to obtain a high quality spectrum of GX 5-1 from ~5 keV to ~100 keV, for the first time without contamination from the nearby black hole candidate GRS 1758-258 above 20 keV. During our observations, GX 5-1 is mostly found in the horizontal and normal branch of its hardness intensity diagram. A clear hard X-ray emission is observed above ~30 keV which exceeds the exponential cut-off spectrum expected from lower energies. This spectral flattening may have the same origin of the hard components observed in other Z sources as it shares the property of being characteristic to the horizontal branch. The hard excess is explained by introducing Compton up-scattering of soft photons from the neutron star surface due to a thin hot plasma expected in the boundary layer. The spectral changes of GX 5-1 downward along the "Z" pattern in the hardness intensity diagram can be well described in terms of monotonical decrease of the neutron star surface temperature. This may be a consequence of the gradual expansion of the boundary layer as the mass accretion rate increases.Comment: 10 pages, 17 figures, accepted for publication in A&