A Liquid Crystal Model of Viral DNA Encapsidation

A liquid crystal continuum modeling framework for icosahedra bacteriophage viruses is developed and tested. The main assumptions of the model are the chromonic columnar hexagonal structure of confined DNA, the high resistance to bending and the phase transition from solid to fluid-like states as the concentration of DNA in the capsid decreases during infection. The model predicts osmotic pressure inside the capsid and the ejection force of the DNA as well as the size of the isotropic volume at the center of the capsid. Extensions of the model are discussed

Fine Structure of Viral dsDNA Encapsidation

In vivo configurations of dsDNA of bacteriophage viruses in a capsid are known to form hexagonal chromonic liquid crystal phases. This article studies the liquid crystal ordering of viral dsDNA in an icosahedral capsid, combining the chromonic model with that of liquid crystals with variable degree of orientation. The scalar order parameter of the latter allows us to distinguish regions of the capsid with well-ordered DNA from the disordered central core. We employ a state-of-the-art numerical algorithm based on the finite element method to find equilibrium states of the encapsidated DNA and calculate the corresponding pressure. With a data-oriented parameter selection strategy, the method yields phase spaces of the pressure and the radius of the disordered core, in terms of relevant dimensionless parameters, rendering the proposed algorithm into a preliminary bacteriophage designing tool. The presence of the order parameter also has the unique role of allowing for non-smooth capsid domains as well as accounting for knot locations of the DNA

“ESTADO ACTUAL DEL DIAGNÓSTICO Y TRATAMIENTO FARMACOLÓGICO DE LA ENFERMEDAD INFLAMATORIA INTESTINAL: (REVISIÓN DE LA LITERATURA)”

La enfermedad inflamatoria intestinal (EII), es un conjunto de trastornos gastrointestinales idiopóticos con episodios de remisión y exacerbación de duración variable, los cuales incluyen una amplia variedad de presentaciones y manifestaciones clínicas, cuya característica principal es la inflamación crónica del tubo digestivo en diferentes localizaciones

Tangle analysis of DNA unlinking by the Xer/FtsK system(Knots and soft-matter physics: Topology of polymers and related topics in physics, mathematics and biology)

この論文は国立情報学研究所の電子図書館事業により電子化されました。DNAに作用する部位特異的組み換え酵素の働きは、タングルを用いてモデル化され、得られるタングル方程式を数学の結果を用いて解くことにより、部位特異的酵素の働きのトポロジーの特徴付けが出来る。ここでは、Grainge等(2007)によって示された部位特異的Xer/FtsKシステムによるDNA絡み目解消操作の解析を行い、その特徴付けを述べる。特にその作用を特徴付ける主要なタングルが有理タングルとなることを示す。The action of site-specific recombinases can be analyzed using the tangle method, where the reaction is characterized topologically by solving the corresponding tangle equations. We here analyze unlinking of DNA catenanes by the site-specific recombination system Xer/FtsK (Grainge et al., 2007). In particular we show that the key tangle involved in this reaction is rational. Therefore all solutions to the tangle equations can be computed using tangle calculus

The Rabl configuration limits topological entanglement of chromosomes in budding yeast.

The three dimensional organization of genomes remains mostly unknown due to their high degree of condensation. Biophysical studies predict that condensation promotes the topological entanglement of chromatin fibers and the inhibition of function. How organisms balance between functionally active genomes and a high degree of condensation remains to be determined. Here we hypothesize that the Rabl configuration, characterized by the attachment of centromeres and telomeres to the nuclear envelope, helps to reduce the topological entanglement of chromosomes. To test this hypothesis we developed a novel method to quantify chromosome entanglement complexity in 3D reconstructions obtained from Chromosome Conformation Capture (CCC) data. Applying this method to published data of the yeast genome, we show that computational models implementing the attachment of telomeres or centromeres alone are not sufficient to obtain the reduced entanglement complexity observed in 3D reconstructions. It is only when the centromeres and telomeres are attached to the nuclear envelope (i.e. the Rabl configuration) that the complexity of entanglement of the genome is comparable to that of the 3D reconstructions. We therefore suggest that the Rabl configuration is an essential player in the simplification of the entanglement of chromatin fibers

Modeling RNA:DNA Hybrids with Formal Grammars

R-loops are nucleic acid structures consisting of a DNA:RNA hybrid and a DNA single strand. They form naturally during transcription when the nascent RNA hybridizes to the template DNA, forcing the coding DNA strand to wrap around the RNA:DNA duplex. Although formation of R-loops can have deleterious effects on genome integrity, there is evidence of their role as potential regulators of gene expression and DNA repair. Here we initiate an abstract model based on formal grammars to describe RNA:DNA interactions and the formation of R-loops. Separately we use a sliding window approach that accounts for properties of the DNA nucleotide sequence, such as C-richness and CG-skew, to identify segments favoring R-loops. We evaluate these properties on two DNA plasmids that are known to form R-loops and compare results with a recent energetics model from the Chédin Lab. Our abstract approach for R-loops is an initial step toward a more sophisticated framework which can take into account the effect of DNA topology on R-loop formation