Appearance of de Gennes length in force-induced transitions.

Using Langevin dynamic simulations, a simple coarse-grained model of a DNA protein construct is used to study the DNA rupture and the protein unfolding. We identify three distinct states: (i) zipped DNA and collapsed protein, (ii) unzipped DNA and stretched protein, and (iii) unzipped DNA and collapsed protein. Here, we find a phase diagram that shows these states depending on the size of the DNA handle and the protein. For a less stable protein, unfolding is solely governed by the size of the linker DNA, whereas if the protein's stability increases, complete unfolding becomes impossible because the rupture force for DNA has reached a saturation regime influenced by the de Gennes length. We show that unfolding occurs via a few intermediate states by monitoring the force-extension curve of the entire protein. We extend our study to a heterogeneous protein system, where similar intermediate states in two systems can lead to different protein unfolding paths.

A rare histopathological variant of Schwannoma with rosette-like arrangements and epithelioid cells: a case report from a histopathologist's perspective.

Schwannomas exhibit histopathological variation that leads to diagnostic dilemmas, although less frequent in the oral cavity. We describe a case with unique histopathology and no relevant clinical history that adds to the breadth of literature on the diversity presented by Schwannoma. A 60-year-old female patient presented with a small dome-shaped, asymptomatic swelling on the alveolar ridge 6 years in duration. Histopathologically, it showed rich cellular pathology with a unique arrangement of tumor cells forming irregular rosettes. Each rosette presented with a central core of fibrincollagenous material and the tumor cells were arranged on the periphery, exhibiting epithelioid change with evidence of mild cellular and nuclear pleomorphism. On immunohistochemical evaluation, the cells were strongly and diffusely positive for S-100 and negative for Ki-67. A diagnosis of benign Schwannoma with a rosette-like arrangement with epithelioid change was made. The case report emphasizes the risk of misdiagnosis and the importance of awareness regarding rare histopathological variants of Schwannoma.

Force-induced melting of DNA hairpin: Unfolding pathways and phase diagrams.

Using the exact enumeration technique, we have studied the force-induced melting of a DNA hairpin on the face centered cubic lattice for two different sequences which differ in terms of loop closing base pairs. The melting profiles obtained from the exact enumeration technique is consistent with the Gaussian network model and Langevin dynamics simulations. Probability distribution analysis based on the exact density of states revealed the microscopic details of the opening of the hairpin. We showed the existence of intermediate states near the melting temperature. We further showed that different ensembles used to model single-molecule force spectroscopy setups may give different force-temperature diagrams. We delineate the possible reasons for the observed discrepancies.

Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges.

Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.

Oral soft-tissue myxoma.

Oral soft-tissue myxomas of the oral cavity have been sparsely cited in the medical literature worldwide. This could be due to other clinically and/or histologically similar lesions requiring accurate differential diagnosis by experienced physicians and pathologists. Although myxomas are benign and do not metastasise, they have higher rates of recurrence and deserve proper attention and to be reported as well. Soft-tissue myxomas of the oral cavity are extremely rare and very few cases have been reported in the literature. The article describes a soft-tissue myxoma in a male patient in his 40s and review of published cases.

Delayed collapse transitions in a pinned polymer system.

Employing Langevin dynamics simulations, we investigated the kinetics of the collapse transition for a polymer of length N when a particular monomer at a position 1≤X≤N is pinned. The results are compared with the kinetics of a free polymer. The equilibrium θ-point separating the coil from the globule phase is located by a crossover in 〈R_{g}^{2}〉/N plots of different chain lengths. Our simulation supports a three-stage mechanism for free and pinned polymer collapse: the formation of pearls, the coarsening of pearls, and the formation of a compact globule. Pinning the central monomer has negligible effects on the kinetics as it does not break the symmetry. However, pinning a monomer elsewhere causes the process to be delayed by a constant factor ϕ_{X} depending linearly upon X. The total collapse time scales with N as τ_{c}∼ϕ_{X}N^{1.60±0.03}, which implies τ_{c} is maximum when an end monomer is pinned (X=1 or N), while when pinning the central monomer (X=N/2) it is minimum and identical to that of a free polymer. The average cluster size N_{c}(t) grows in time as t^{z}, where z=1.00±0.04 for a free particle, whereas we identify two time regimes separated by a plateau for pinned polymers. At longer times, z=1.00±0.04, while it deviates in early time regimes significantly, depending on the value of X.

Role of Hoogsteen interaction in the stability of different phases of triplex DNA.

A simple coarse-grained model of DNA which includes both Watson-Crick and Hoogsteen base pairing has been used to study the melting and unzipping of triplex DNA. Using Langevin dynamics simulations, we reproduce the qualitative features of one-step and two-step thermal melting of triplex as seen in experiments. The thermal melting phase diagram shows the existence of a stable interchain three-strand complex (bubble-bound state). Our studies based on the mechanical unzipping of a triplex revealed that it is mechanically more stable compared to an isolated duplex-DNA.

Can one detect intermediate denaturation states of DNA sequences by following the equilibrium open-close dynamic fluctuations of a single base pair?

Melting of DNA sequences may occur through a few major intermediate states, whose influence on the melting curve has been discussed previously, while their effect on the kinetics has not been explored thoroughly. Here, we chose a simple DNA sequence, forming a hairpin in its native (zipped) state, and study it using molecular dynamic (MD) simulations and a model integrating the Gaussian network model with bond-binding energies-the Gaussian binding energy (GBE) model. We find two major partial denaturation states, a bubble state and a partial unzipping state. We demonstrate the influence of these two states on the closing-opening base pair dynamics, as probed by a tagged bond auto-correlation function (ACF). We argue that the latter is measured by fluorescence correlation spectroscopy experiments, in which one base of the pair is linked to a fluorescent dye, while the complementary base is linked to a quencher, similar to the experiment reported by Altan-Bonnet et al. [Phys. Rev. Lett. 90, 138101 (2003)]. We find that tagging certain base pairs at temperatures around the melting temperature results in a multi-step relaxation of the ACF, while tagging other base pairs leads to an effectively single-step relaxation, albeit non-exponential. Only the latter type of relaxation has been observed experimentally, and we suggest which of the other base pairs should be tagged in order to observe multi-step relaxation. We demonstrate that this behavior can be observed with other sequences and argue that the GBE can reliably predict these dynamics for very long sequences, where MD simulations might be limited.

Dynamics of a polymer chain translocating through varying cone-shaped channels.

By employing the exact enumeration technique, we study consequences of different apex angles of a wedge-shaped channel on the mean first passage time and free-energy profile of a linear polymer chain translocating from the cis- to the trans-side through an interacting pore. We investigate effects of asymmetry arising in the free-energy profile due to the change in apex angles and its dependence on the first passage time. We report the combined effect of entropy (arising due to apex angles) and pore interaction on the nonmonotonic behavior of the translocation time. The effect of different solvent quality across the channel has also been explored. We show that the increase in monomer-monomer interaction leads to the formation of globules near the pore, which drives the process faster.

Polymer in wedge-shaped confinement: Effect on the θ temperature.

The equilibrium properties of a finite-length linear polymer chain confined in an infinite wedge composed of two perfectly reflecting hard walls meeting at a variable apex angle (α) are presented. One end of the polymer is anchored a distance y from the apex on the conical axis of symmetry, while the other end is free. We report here, the nonmonotonic behavior of θ temperature as a function of y for a finite-length chain. Data collapse for different chain lengths indicates that such behavior will exist for all finite lengths. We delineate the origin of such nonmonotonic behavior, which may have potential applications in understanding the cellular process occurring in nanoconfined geometries.

Odontogenic keratocyst arising in the maxillary sinus: A rare case report.

Odontogenic keratocyst is an aggressive cystic lesion and a common type of tooth derived cyst due to presence of odontogenic epithelial remnants in different regions of jaw. In majority of cases, it is located in mandibular posterior region. But it can also be found in the maxilla especially in the canine region. We present a rare case of OKC in maxillary sinus which associated with ectopic third molar. Also, it can be easily confused with other lesions of maxillary sinus like sinusitis or antral polyps, which usually resemble symptomatically. There can be malignant transformation of this benign condition towards squamous cell carcinoma or ameloblastoma. So an early and accurate diagnosis of odontogenic keratocyst is a challenge for pathologists.

Role of mast cells in inflammatory and reactive pathologies of pulp, periapical area and periodontium.

Mast cells (MCs) have been discovered over 130 years ago; their function was almost exclusively linked to allergic affections. At the time being, it is well known that MCs possess a great variety of roles, in both physiologic and pathologic conditions. In the oral tissues, MCs release different pro-inflammatory cytokines and tumor necrosis factor-alpha that promote leukocyte infiltration in various inflammatory states of the oral cavity. These cells play a key role in the inflammatory process and, as a consequence, their number changes in different pathologic conditions of the oral cavity, such as gingivitis and periodontitis. By understanding the role of MCs in the pathogenesis of different inflammatory diseases of the oral cavity, these cells may become therapeutic targets that could possibly improve the prognosis. Therefore, this review summarizes the current understanding of the role of MCs in various inflammatory pulpal, periapical and periodontal pathophysiological conditions.