The 3D genome : investigating the role of Pcf11 and Pol II gene loops in mammalian cell lines

Eukaryotic transcription, from initiation to termination, is a highly complex and regulated process involving the interplay of different factors. Termination is a key step in gene expression, as it does not only delimit transcription, but also affects the localisation and stability of transcripts. One of the factors involved in the termination process is the cleavage and polyadenylation factor subunit Pcf11. Human Pcf11 is recruited by RNA Polymerase II to enhance termination of transcription and 3’ end processing. Evidence shows that the formation of chromatin loops impacts transcriptional dynamics and suggests that Pcf11 is implicated in 3’-5’ end crosstalk due to its recently discovered localisation also at the TSS of genes. Simultaneously, depletion of Pcf11 has been found to reduce transcription initiation rates. Chromatin Interaction Analysis by Paired-End Tag Sequencing (ChIA-PET) is a valuable tool in chromatin loop research as it allows for the identification of chromatin interactions bound by a specific protein of interest. The present work focuses on establishing quality of ChIA-PET libraries generated and analysed using the latest version of both the experimental protocol (in-situ ChIA-PET) and data processing pipeline. We identify and characterise gene loops bound by Pol II and Pcf11 and show that looped genes are involved in key cellular processes and are significantly more expressed than non-looped genes. Analysis of 3’ mRNA-seq data reveals that Pcf11 depletion causes significant downregulation of looped genes, providing further evidence that Pcf11 regulates aspects of transcription initiation and that its activity is crucial for the expression of looped genes

A Quantized Hill’s Dynamical System

In this paper, we present a modified version of Hill’s dynamical system that is called the quantized Hill’s three-body problem in the sense that the equations of motion for the classical Hill’s problem are now derived under the effects of quantum corrections. To do so, the position variables and the parameters that correspond to the quantum corrections of the respective quantized three-body problem are scaled appropriately, and then by taking the limit when the parameter of mass ratio tends to zero, we obtain the relevant equations of motion for the spatial quantized Hill’s problem. Furthermore, the Hamiltonian formula and related equations of motion are also derived

Equilibrium Points and Related Periodic Motions in the Restricted Three-Body Problem with Angular Velocity and Radiation Effects

The paper deals with a modification of the restricted three-body problem in which the angular velocity variation is considered in the case where the primaries are sources of radiation. In particular, the existence and stability of its equilibrium points in the plane of motion of the primaries are studied. We find that this problem admits the well-known five planar equilibria of the classical problem with the difference that the corresponding collinear points may be stable depending on the parameters of the problem. For all planar equilibria, sufficient parametric conditions for their stability have been established which are used for the numerical determination of the stability regions in various parametric planes. Also, for certain values of the parameters of the problem for which the equilibrium points are stable, the short and long period families have been computed. To do so, semianalytical expressions have been found for the determination of appropriate initial conditions. Special attention has been given to the continuation of the long period family, in the case of the classical restricted three-body problem, where we show numerically that periodic orbits of the short period family, which are bifurcation points with the long period family, are connected through the characteristic curve of the long period family

Evaluation of Different Coronal Sealing Materials in the Endodontically Treated Teeth: An In Vitro Study

In vitro studies have shown that rapid penetration of bacteria in the entire root canal system may occur after endodontic treatment without a coronal seal. A proper restorative technique is necessary to ensure a coronal seal and protection of the residual dental structure. The aim of this in vitro study was to evaluate the coronal sealing ability of the most relevant clinical materials by means of dye penetration (neutral red dye, Sigma-Aldrich, Germany), through a light spectrometric device, and to establish which one of the tested dental materials possesses the best sealing ability. Forty-two extracted teeth were prepared and used for this experiment; they were sealed with 5 different cements. The flow composite had the best absorbance value with 0.00675 ± 0.00096 (mean ± standard deviation) for monoradicular samples and 0.025 ± 0.00129 for pluriradicular samples. Under the constraints of the present study, both flowable and packable composite materials can be recommended as orifice sealing materials to prevent microleakage in an endodontically treated tooth. To assess the clinical superiority of any material, further in vivo studies are required