Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules

Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this problem by combining experiments and theory. A new experimental method allows us to make a mapping of the opening of the guanines along the sequence as a function of temperature. The results indicate that non-local effects may be important in DNA because an AT-rich region is able to influence the opening of a base pair which is about 10 base pairs away. An earlier mesoscopic model of DNA is modified to correctly describe the time scales associated to the opening of individual base pairs well below melting, and to properly take into account the sequence. Using this model to analyze some characteristic sequences for which detailed experimental data on the melting is available [Montrichok et al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce non-local effects of AT-rich regions to get acceptable results. This brings a second indication that the influence of these highly fluctuating regions of DNA on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte

Mini Max Wallpaper

Mini Max company formulated a problem for the automatic calculation of the number of wallpaper rolls necessary for decorating a room with wallpaper. The final goal is the development of a web-based calculator open for use to both Mini Max staff and the general public. We propose an approach for reducing the studied problem to the one-dimensional cutting-stock problem. We show this in details for the case of plain wallpapers as well as for the case of patterned wallpapers with straight match. The one-dimensional cutting-stock problem can be formulated as a linear integer programming problem. We develop an approach for calculating the needed number of wallpapers for relatively small problems, create an algorithm in a suitable graphical interface and make different tests. The tests show the efficiency of the proposed approach compared with the existent (available) wallpapers’ calculators

Chemical Composition and Energy Nutritional Value of the Meat of Guinea Fowls (Numidameleagris), Fattened to different Ages

The aim of the study was to investigate the chemical composition and energy content of the meat of young Guinea-fowls, with different duration of the fattening period, raised in a free-range, semi-intensive production system. The authors establish the following data: dry matter content- from 27.08 to 28.82% in breast muscle and from 23.83 to 26.56% in thigh muscle; crude protein in dry matter –from 86.19to 93.54% in breastand from 82.02 to 87.84% in thigh muscle; crude fat in dry matter - from 5.64 to 7.58% in breast and from 9.02 to 11.05% in thigh muscles. The average energy content in 100 g dry matter varies from 23.7 (breast muscle, 16 weeks of age) to 25.07 kJ (thigh muscle, 24 weeks of age)

On the muon neutrino mass

During the runs of the PS 179 experiment at LEAR of CERN, we photographed an event of antiproton-Ne absorption, with a complete pi+ -> mu+ ->e+ chain. From the vertex of the reaction a very slow energy pi+ was emitted. The pi+ decays into a mu+ and subsequently the mu+ decays into a positron. At the first decay vertex a muon neutrino was emitted and at the second decay vertex an electron neutrino and a muon antineutrino. Measuring the pion and muon tracks and applying the momentum and energy conservation and using a classical statistical interval estimator, we obtained an experimental upper limit for the muon neutrino mass: m_nu < 2.2 MeV at a 90% confidence level. A statistical analysis has been performed of the factors contributing to the square value of the neutrino mass limit.Comment: 18 pages, 5 eps figure

Properties of the Volume Operator in Loop Quantum Gravity II: Detailed Presentation

The properties of the Volume operator in Loop Quantum Gravity, as constructed by Ashtekar and Lewandowski, are analyzed for the first time at generic vertices of valence greater than four. The present analysis benefits from the general simplified formula for matrix elements of the Volume operator derived in gr-qc/0405060, making it feasible to implement it on a computer as a matrix which is then diagonalized numerically. The resulting eigenvalues serve as a database to investigate the spectral properties of the volume operator. Analytical results on the spectrum at 4-valent vertices are included. This is a companion paper to arXiv:0706.0469, providing details of the analysis presented there.Comment: Companion to arXiv:0706.0469. Version as published in CQG in 2008. More compact presentation. Sign factor combinatorics now much better understood in context of oriented matroids, see arXiv:1003.2348, where also important remarks given regarding sigma configurations. Subsequent computations revealed some minor errors, which do not change qualitative results but modify some numbers presented her

Modelling DNA at the mesoscale: a challenge for nonlinear science?

Invited paper, in the series "Open Problems" of NonlinearityInternational audienceWhen it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be used as a guide to improve them. There are nevertheless many open problems, particularly to describe DNA at the scale of a few tens of base pairs, which is relevant for many biological phenomena

CLINICAL, ELECTROENCEPHALOGRAPHIC AND RHEOENCEPHALOGRAPHIC CORRELATIONS IN RELATIVES OF STROKE PATIENTS

No abstrac

Synthesis of structurally diverse major groove DNA interstrand crosslinks using three different aldehyde precursors

DNA interstrand crosslinks (ICLs) are extremely cytotoxic lesions that block essential cellular processes, such as replication and transcription. Crosslinking agents are widely used in cancer chemotherapy and form an array of structurally diverse ICLs. Despite the clinical success of these agents, resistance of tumors to crosslinking agents, for example, through repair of these lesions by the cellular machinery remains a problem. We have previously reported the synthesis of site-specific ICLs mimicking those formed by nitrogen mustards to facilitate the studies of cellular responses to ICL formation. Here we extend these efforts and report the synthesis of structurally diverse major groove ICLs that induce severe, little or no distortion in the DNA. Our approach employs the incorporation of aldehyde precursors of different lengths into complementary strands and ICL formation using a double reductive amination with a variety of amines. Our studies provide insight into the structure and reactivity parameters of ICL formation by double reductive amination and yield a set of diverse ICLs that will be invaluable for exploring structure-activity relationships in ICL repairope

Spin physics with antiprotons

New possibilities arising from the availability at GSI of antiproton beams, possibly polarised, are discussed. The investigation of the nucleon structure can be boosted by accessing in Drell-Yan processes experimental asymmetries related to cross-sections in which the parton distribution functions (PDF) only appear, without any contribution from fragmentation functions; such processes are not affected by the chiral suppression of the transversity function $h_1(x)$. Spin asymmetries in hyperon production and Single Spin Asymmetries are discussed as well, together with further items like electric and magnetic nucleonic form factors and open charm production. Counting rates estimations are provided for each physical case. The sketch of a possible experimental apparatus is proposed.Comment: Presented for the proceedings of ASI "Spin and Symmetry", Prague, July 5-10, 2004, to be published in Czech. J. Phys. 55 (2005

Transition Radiation Spectroscopy with Prototypes of the ALICE TRD

We present measurements of the transition radiation (TR) spectrum produced in an irregular radiator at different electron momenta. The data are compared to simulations of TR from a regular radiator.Comment: 4 pages, 5 Figures, Proceedings for "TRDs for the 3rd millennium" (Sept. 4-7, 2003, Bari, Italy