Brownian dynamics simulation of nucleocytoplasmic transport: a coarse-grained model for the functional state of the nuclear pore complex

The nuclear pore complex (NPC) regulates molecular traffic across the nuclear envelope (NE). Selective transport happens on the order of milliseconds and the length scale of tens of nanometers; however, the transport mechanism remains elusive. Central to the transport process is the hydrophobic interactions between karyopherins (kaps) and Phe-Gly (FG) repeat domains. Taking into account the polymeric nature of FG-repeats grafted on the elastic structure of the NPC, and the kap-FG hydrophobic affinity, we have established a coarse-grained model of the NPC structure that mimics nucleocytoplasmic transport. To establish a foundation for future works, the methodology and biophysical rationale behind the model is explained in details. The model predicts that the first-passage time of a 15 nm cargo-complex is about 2.6±0.13 ms with an inverse Gaussian distribution for statistically adequate number of independent Brownian dynamics simulations. Moreover, the cargo-complex is primarily attached to the channel wall where it interacts with the FG-layer as it passes through the central channel. The kap-FG hydrophobic interaction is highly dynamic and fast, which ensures an efficient translocation through the NPC. Further, almost all eight hydrophobic binding spots on kap-β are occupied simultaneously during transport. Finally, as opposed to intact NPCs, cytoplasmic filaments-deficient NPCs show a high degree of permeability to inert cargos, implying the defining role of cytoplasmic filaments in the selectivity barrier.     

Regulation of phagocyte NADPH oxidase by hydrogen peroxide through a Ca2+/c-Abl signaling pathway

The importance of H₂O₂ as a cellular signaling molecule has been demonstrated in a number of cell types and pathways. Here we explore a positive feedback mechanism of H₂O₂-mediated regulation of the phagocyte respiratory burst NADPH oxidase (NOX2). H₂O₂ induced a dose-dependent stimulation of superoxide production in human neutrophils, as well as in K562 leukemia cells overexpressing NOX2 system components. Stimulation was abrogated by the addition of catalase, the extracellular Ca²⁺ chelator BAPTA, the T-type Ca²⁺ channel inhibitor mibefradil, the PKCδ inhibitor rottlerin, or the c-Abl nonreceptor tyrosine kinase inhibitor imatinib mesylate or by overexpression of a dominant-negative form of c-Abl. H₂O₂ induced phosphorylation of tyrosine 311 on PKCδ and this activating phosphorylation was blocked by treatment with rottlerin, imatinib mesylate, or BAPTA. Rac GTPase activation in response to H₂O₂ was abrogated by BAPTA, imatinib mesylate, or rottlerin. In conclusion, H₂O₂ stimulates NOX2-mediated superoxide generation in neutrophils and K562/NOX2 cells via a signaling pathway involving Ca²⁺ influx and c-Abl tyrosine kinase acting upstream of PKCδ. This positive feedback regulatory pathway has important implications for amplifying the innate immune response and contributing to oxidative stress in inflammatory disorders.     

In silico biophysics and hemorheology of blood hyperviscosity syndrome

Hyperviscosity syndrome (HVS) is characterized by an increase of the blood viscosity by up to seven times the normal blood viscosity, resulting in disturbances to the circulation in the vasculature system. HVS is commonly associated with an increase of large plasma proteins and abnormalities in the properties of red blood cells, such as cell interactions, cell stiffness, and increased hematocrit. Here, we perform a systematic study of the effect of each biophysical factor on the viscosity of blood by employing the dissipative particle dynamic method. Our in silico platform enables manipulation of each parameter in isolation, providing a unique scheme to quantify and accurately investigate the role of each factor in increasing the blood viscosity. To study the effect of these four factors independently, each factor was elevated more than its values for a healthy blood while the other factors remained constant, and viscosity measurement was performed for different hematocrits and flow rates. Although all four factors were found to increase the overall blood viscosity, these increases were highly dependent on the hematocrit and the flow rates imposed. The effect of cell aggregation and cell concentration on blood viscosity were predominantly observed at low shear rates, in contrast to the more magnified role of cell rigidity and plasma viscosity at high shear rates. Additionally, cell-related factors increase the whole blood viscosity at high hematocrits compared with the relative role of plasma-related factors at lower hematocrits. Our results, mapped onto the flow rates and hematocrits along the circulatory system, provide a correlation to underpinning mechanisms for HVS findings in different blood vessels.     

Circulating microRNAs as diagnostic and therapeutic biomarkers in gastric and esophageal cancers

Gastric and esophageal cancers are as main cancers of the gastrointestinal (GI) tract, which are associated with poor diagnosis and survival. Several efforts were made in the past few decades to finding effective therapeutic approaches, but these approaches had several problems. Finding new biomarkers is a critical step in finding new approaches for the treatment of these cancers. Finding new biomarkers that cover various aspects of the diseases could provide a choice of suitable therapies and better monitoring of patients with these cancers. Among several biomarkers tissue specific and circulating microRNAs (miRNAs) have emerged as powerful candidates in the diagnosis of gastric and esophageal cancers. MiRNAs are small noncoding single‐stranded RNA molecules that are found in the blood and regulate gene expression. These have numerous characteristics that make them suitable for being used as ideal biomarkers in cancer diagnosis. Research has indicated that the level and profile of miRNA in serum and plasma are very high. They are potentially noninvasive and sensitive enough to detect tumors in their primary stages of infection. Multiple lines of evidence indicate that the presence, absence, or deregulation of several circulating miRNAs (i.e., let‐7a, miR‐21, miR‐93, miR‐192a, miR‐18a, and miR‐10b for gastric cancer, and miR‐21, miR‐375, miR‐25‐3p, miR‐151a‐3p, and miR‐100‐3p for esophageal cancer) are associated with initiation and progression of gastric and esophageal cancers. The aim of this review is to highlight the recent advances in the roles of miRNAs in diagnosis and treatment of gastric and esophageal cancers.