Stacking Interactions in RNA and DNA: Roll-Slide Energy Hyperspace for Ten Unique Dinucleotide Steps

Understanding dinucleotide sequence directed structures of nuleic acids and their variability from experimental observation remained ineffective due to unavailability of statistically meaningful data. We have attempted to understand this from energy scan along twist, roll, and slide degrees of freedom which are mostly dependent on dinucleotide sequence using ab initio density functional theory. We have carried out stacking energy analysis in these dinucleotide parameter phase space for all ten unique dinucleotide steps in DNA and RNA using DFT-D by B97X-D/6-31G(2d,2p), which appears to satisfactorily explain conformational preferences for AU/AU step in our recent study. We show that values of roll, slide, and twist of most of the dinucleotide sequences in crystal structures fall in the low energy region. The minimum energy regions with large twist values are associated with the roll and slide values of B-DNA, whereas, smaller twist values correspond to higher stability to RNA and A-DNA like conformations. Incorporation of solvent effect by CPCM method could explain the preference shown by some sequences to occur in B-DNA or A-DNA conformations. Conformational preference of BII sub-state in B-DNA is preferentially displayed mainly by pyrimidine-purine steps and partly by purine-purine steps. The purine-pyrimidine steps show largest effect of 5-methyl group of thymine in stacking energy and the introduction of solvent reduces this effect significantly. These predicted structures and variabilities can explain the effect of sequence on DNA and RNA functionality. (c) 2014 Wiley Periodicals, Inc. Biopolymers 103: 134-147, 2015.

Unique nanoporous antibacterial membranes derived through crystallization induced phase separation in PVDF/PMMA blends

In this study, a unique method was adopted to design porous membranes through crystallization induced phase separation in PVDF/PMMA (poly(vinylidene fluoride)/poly(methyl methacrylate)) blends. By etching out PMMA, which segregates either in the interlamellar and/or in the interspherulitic regions of the blends, nanoporous hierarchical structures can be derived. Different nanoparticles like titanium dioxide (TiO2), silver nanoparticle (Ag) decorated carbon nanotubes (Ag-CNTs), TiO2 decorated CNTs (TiO2-CNTs), Ag decorated TiO2 (Ag-TiO2) and Ag-TiO2 decorated CNTs (Ag@TiO2-CNTs) were synthesized and melt mixed with 80/20 PVDF/PMMA blends to render antibacterial activity to the membranes. Scanning electron microscopy (SEM) was used to study the crystalline morphology of the membranes. A significant improvement in the trans-membrane flux was obtained in the blends with Ag@TiO2 decorated CNTs as compared to the membranes derived from the neat blends, which can be attributed to the interconnected pores in these membranes. Both qualitative and quantitative studies of antifouling and antibacterial activity (using E. coli as a model bacterium) were performed using the standard plate count method. SEM micrographs clearly showed that the antifouling activity of the membranes was improved with addition of Ag@TiO2-CNTs. In the quantitative standard plate count method, the bacterial colony significantly decreased with the addition of Ag@TiO2-CNTs as against neat blends. This study opens a new avenue in the fabrication of polymer blend based membranes for water filtration.

A unique strategy towards high dielectric constant and low loss with multiwall carbon nanotubes anchored onto graphene oxide sheets

Multiwall carbon nanotubes (MWNTs) were anchored onto graphene oxide sheets (GOs) via diazonium and C-C coupling reactions and characterized by spectroscopic and electron microscopic techniques. The thus synthesized MWNT-GO hybrid was then melt mixed with 50/50 polyamide6-maleic anhydride-modified acrylonitrile-butadiene-styrene (PA6-mABS) blend to design materials with high dielectric constant (30) and low dielectric loss. The phase morphology was studied by SEM and it was observed that the MWNT-GO hybrid was selectively localized in the PA6 phase of the blend. The 30 scales with the concentration of MWNT-GO in the blends, which interestingly showed a very low dielectric loss (< 0.2) making them potential candidate for capacitors. In addition, the dynamic storage modulus scales with the fraction of MWNT-GO in the blends, demonstrating their reinforcing capability as well.

Unique Covering Problems with Geometric Sets

The Exact Cover problem takes a universe U of n elements, a family F of m subsets of U and a positive integer k, and decides whether there exists a subfamily(set cover) F' of size at most k such that each element is covered by exactly one set. The Unique Cover problem also takes the same input and decides whether there is a subfamily F' subset of F such that at least k of the elements F' covers are covered uniquely(by exactly one set). Both these problems are known to be NP-complete. In the parameterized setting, when parameterized by k, Exact Cover is W1]-hard. While Unique Cover is FPT under the same parameter, it is known to not admit a polynomial kernel under standard complexity-theoretic assumptions. In this paper, we investigate these two problems under the assumption that every set satisfies a given geometric property Pi. Specifically, we consider the universe to be a set of n points in a real space R-d, d being a positive integer. When d = 2 we consider the problem when. requires all sets to be unit squares or lines. When d > 2, we consider the problem where. requires all sets to be hyperplanes in R-d. These special versions of the problems are also known to be NP-complete. When parameterizing by k, the Unique Cover problem has a polynomial size kernel for all the above geometric versions. The Exact Cover problem turns out to be W1]-hard for squares, but FPT for lines and hyperplanes. Further, we also consider the Unique Set Cover problem, which takes the same input and decides whether there is a set cover which covers at least k elements uniquely. To the best of our knowledge, this is a new problem, and we show that it is NP-complete (even for the case of lines). In fact, the problem turns out to be W1]-hard in the abstract setting, when parameterized by k. However, when we restrict ourselves to the lines and hyperplanes versions, we obtain FPT algorithms.

A unique uracil-DNA binding protein of the uracil DNA glycosylase superfamily

Uracil DNA glycosylases (UDGs) are an important group of DNA repair enzymes, which pioneer the base excision repair pathway by recognizing and excising uracil from DNA. Based on two short conserved sequences (motifs A and B), UDGs have been classified into six families. Here we report a novel UDG, UdgX, from Mycobacterium smegmatis and other organisms. UdgX specifically recognizes uracil in DNA, forms a tight complex stable to sodium dodecyl sulphate, 2-mercaptoethanol, urea and heat treatment, and shows no detectable uracil excision. UdgX shares highest homology to family 4 UDGs possessing Fe-S cluster. UdgX possesses a conserved sequence, KRRIH, which forms a flexible loop playing an important role in its activity. Mutations of H in the KRRIH sequence to S, G, A or Q lead to gain of uracil excision activity in MsmUdgX, establishing it as a novel member of the UDG superfamily. Our observations suggest that UdgX marks the uracil-DNA for its repair by a RecA dependent process. Finally, we observed that the tight binding activity of UdgX is useful in detecting uracils in the genomes.

Explicit and Unique Construction of Tetrablock Unitary Dilation in a Certain Case

Consider the domain E in defined by This is called the tetrablock. This paper constructs explicit boundary normal dilation for a triple (A, B, P) of commuting bounded operators which has as a spectral set. We show that the dilation is minimal and unique under a certain natural condition. As is well-known, uniqueness of minimal dilation usually does not hold good in several variables, e.g., Ando's dilation is known to be not unique, see Li and Timotin (J Funct Anal 154:1-16, 1998). However, in the case of the tetrablock, the third component of the dilation can be chosen in such a way as to ensure uniqueness.

Aspectos antropológicos de las terapias con células madre

Resumen: Las células madre tienen dos características naturales únicas, que son su capacidad de división celular indefinida, y de regeneración y reparación de tejidos. Esto genera un gran interés en las áreas de investigación y tratamiento de enfermedades que aún no tienen cura y son motivadoras de una importante fuente de esperanza para los pacientes. Surge, entonces, el dilema ético de definir cuáles serán los recursos para obtenerlas, procesarlas y determinar la seguridad y eficacia de su uso en la aplicación clínica. Un enfoque personalista ontológico considerará la protección de todos los participantes en los procesos de investigación: los donantes de células, los participantes de la investigación y los pacientes que serán beneficiarios de estos tratamientos, de manera de proteger a todos los involucrados sin exponer a riesgos a unos para salvar a otros.