A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation

The complexity ofmany RNA processing pathways is such that a conventional systemsmodelling approach is inadequate to represent all themolecular species involved. We demonstrate that rule-based modelling permits a detailed model of a complex RNA signalling pathway to be defined. Phosphorylation of the RNApolymerase II (RNAPII)C-terminal domain (CTD; a flexible tail-like extension of the largest subunit) couples pre-messenger RNA capping, splicing and 30 end maturation to transcriptional elongation and termination, and plays a central role in integrating these processes. The phosphorylation states of the serine residues of many heptapeptide repeats of the CTD alter along the coding region of genes as a function of distance from the promoter. From a mechanistic perspective, both the changes in phosphorylation and the location atwhich they take place on the genes are a function of the time spent byRNAPII in elongation as this interval provides the opportunity for the kinases and phosphatases to interactwith theCTD.On this basis,we synthesize the available data to create a kinetic model of the action of the known kinases and phosphatases to resolve the phosphorylation pathways and their kinetics.</p

Synergistic Ca^(2+) Responses by Gα_i- and Gα_q-coupled G-protein-coupled Receptors Require a Single PLCβ Isoform That Is Sensitive to Both Gβ_γ and Gα_q

Cross-talk between Gα_i- and Gα_q-linked G-protein-coupled receptors yields synergistic Ca^(2+) responses in a variety of cell types. Prior studies have shown that synergistic Ca^(2+) responses from macrophage G-protein-coupled receptors are primarily dependent on phospholipase Cβ3 (PLCβ3), with a possible contribution of PLCβ2, whereas signaling through PLCβ4 interferes with synergy. We here show that synergy can be induced by the combination of Gβγ and Gαq activation of a single PLCβ isoform. Synergy was absent in macrophages lacking both PLCβ2 and PLCβ3, but it was fully reconstituted following transduction with PLCβ3 alone. Mechanisms of PLCβ-mediated synergy were further explored in NIH-3T3 cells, which express little if any PLCβ2. RNAi-mediated knockdown of endogenous PLCβs demonstrated that synergy in these cells was dependent on PLCβ3, but PLCβ1 and PLCβ4 did not contribute, and overexpression of either isoform inhibited Ca^(2+) synergy. When synergy was blocked by RNAi of endogenous PLCβ3, it could be reconstituted by expression of either human PLCβ3 or mouse PLCβ2. In contrast, it could not be reconstituted by human PLCβ3 with a mutation of the Y box, which disrupted activation by Gβγ, and it was only partially restored by human PLCβ3 with a mutation of the C terminus, which partly disrupted activation by Gα_q. Thus, both Gβγ and Gα_q contribute to activation of PLCβ3 in cells for Ca^(2+) synergy. We conclude that Ca^(2+) synergy between Gα_i-coupled and Gα_q-coupled receptors requires the direct action of both Gβγ and Gαq on PLCβ and is mediated primarily by PLCβ3, although PLCβ2 is also competent

3D simulations of turbulent mixing in a simplified slab-divertor geometry

Three-dimensional simulations of plasma turbulence have been run using the STORM module of BOUT  + + in a simple slab geometry aimed at representing a single, isolated tokamak divertor leg. Turbulence is driven primarily by the Kelvin-Helmholtz mechanism due to the sheared ExB flow that forms around the separatrix due to strong radial gradients in the sheath potential which arise from strong radial gradients in the electron temperature. The turbulence forms a mixing layer around the separatrix which spreads heat and particles into the private-flux region. The resulting spread of the electron heat flux is within the experimental range measured on MAST. An effective thermal transport coefficient which is approximately 10% of the Bohm value is measured from the simulations. When a transport coefficient of this magnitude is used in a diffusive axisymmetric simulation, the time-averaged radial profiles share similar features to the full turbulence simulation

Arctic shipping and polar seaways

Climate change in the Arctic triggered a series of discourses about the opening-up of a previously unreachable region. Navigation remains however difficult in the Arctic, transits are still very limited, as sea-ice still is a major constraint. How did the development policies of both the North West Passage and the Northern Sea Route unfold ? What are the recent trends in Arctic shipping ?

Grand unified theory constrained supersymmetry and neutrinoless double beta decay

We analyze the contributions to the neutrinoless double $\beta$ decay ($0\nu\beta\beta$-decay) coming from the Grand Unified Theory (GUT) constrained Minimal Supersymmetric Standard Model (MSSM) with trilinear R-parity breaking. We discuss the importance of two-nucleon and pion-exchange realizations of the quark-level $0\nu\beta\beta$-decay transitions. In this context, the questions of reliability of the calculated relevant nuclear matrix elements within the Renormalized Quasiparticle Random Phase Approximation (pn-RQRPA) for several medium and heavy open-shell nuclei are addressed. The importance of gluino and neutralino contributions to $0\nu\beta\beta$-decay is also analyzed. We review the present experiments and deduce limits on the trilinear R-parity breaking parameter $\lambda_{111}'$ from the non-observability of $0\nu\beta\beta$-decay for different GUT constrained SUSY scenarios. In addition, a detailed study of limits on the MSSM parameter space coming from the $B \to X_s \gamma$ processes by using the recent CLEO and OPAL results is performed. Some studies in respect to the future $0\nu\beta\beta$-decay project GENIUS are also presented.Comment: 29 pages, 8 figure

A re-examination of otoconia from the Shaker mouse

We have studied saccular and utricular otoconia from Shaker-1 and Shaker-2 mice by X-ray diffraction and scanning electron microscopy. In contrast to previous reports, we found that the crystals were composed of calcite rather than poly crystalline hydroxylapatite. These crystals were indistinguishable mineralogically and morphologically from normal mouse otoconia. The reported occurrence of hydroxylapatite otoconia in the Shaker mouse is probably false.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47271/1/405_2004_Article_BF00464412.pd

Large-scale collaboration reveals landscape-level effects of land-use on turtle demography

Freshwater turtles and tortoises are declining worldwide and currently represent one of the most imperiled major vertebrate groups. Identifying the conditions that promote long-term viable populations is a critical conservation need. However, for most species, there is relatively little or no empirical information about the factors influencing population demographics. Large-scale population monitoring efforts necessary to acquire such information remain rare due to the logistic challenges associated with low and variable detectability, which generally preclude large monitoring initiatives by any single entity. The development of collaborative population monitoring programs represents one potential strategy for overcoming these challenges. Our goal was to leverage partnerships to identify the potential factors and relevant scales affecting wood turtle (Glyptemys insculpta) population demographics. Through a large-scale collaborative multi-institutional monitoring effort, we conducted 983 spring stream surveys at 293 sites across the northeastern United States. Wood turtle abundance was negatively associated with agriculture (300 m and 5500 m) and road traffic (5500 m) and positively associated with mature forest (5500 m). Juvenile proportion displayed strong negative relationships with stream gradient and imperviousness (300 m). Sex ratios were more male-skewed with higher mature forest cover (90 m) and road density (5500 m) and less undeveloped land (300 m). These findings suggest that effective conservation of demographically robust turtle populations will require consideration of multiple spatial scales. Landscape-level conservation may be particularly important for ensuring long-term viable populations. This study highlights the valuable role that collaboration across institutions and jurisdictions can play in the conservation of cryptic taxa

PIK3CA dependence and sensitivity to therapeutic targeting in urothelial carcinoma

Background Many urothelial carcinomas (UC) contain activating PIK3CA mutations. In telomerase-immortalized normal urothelial cells (TERT-NHUC), ectopic expression of mutant PIK3CA induces PI3K pathway activation, cell proliferation and cell migration. However, it is not clear whether advanced UC tumors are PIK3CA-dependent and whether PI3K pathway inhibition is a good therapeutic option in such cases. Methods We used retrovirus-mediated delivery of shRNA to knock down mutant PIK3CA in UC cell lines and assessed effects on pathway activation, cell proliferation, migration and tumorigenicity. The effect of the class I PI3K inhibitor GDC-0941 was assessed in a panel of UC cell lines with a range of known molecular alterations in the PI3K pathway. Results Specific knockdown of PIK3CA inhibited proliferation, migration, anchorage-independent growth and in vivo tumor growth of cells with PIK3CA mutations. Sensitivity to GDC-0941 was dependent on hotspot PIK3CA mutation status. Cells with rare PIK3CA mutations and co-occurring TSC1 or PTEN mutations were less sensitive. Furthermore, downstream PI3K pathway alterations in TSC1 or PTEN or co-occurring AKT1 and RAS gene mutations were associated with GDC-0941 resistance. Conclusions Mutant PIK3CA is a potent oncogenic driver in many UC cell lines and may represent a valuable therapeutic target in advanced bladder cancer

Brain lesions disrupting addiction map to a common human brain circuit

Drug addiction is a public health crisis for which new treatments are urgently needed. In rare cases, regional brain damage can lead to addiction remission. These cases may be used to identify therapeutic targets for neuromodulation. We analyzed two cohorts of patients addicted to smoking at the time of focal brain damage (cohort 1 n = 67; cohort 2 n = 62). Lesion locations were mapped to a brain atlas and the brain network functionally connected to each lesion location was computed using human connectome data (n = 1,000). Associations with addiction remission were identified. Generalizability was assessed using an independent cohort of patients with focal brain damage and alcohol addiction risk scores (n = 186). Specificity was assessed through comparison to 37 other neuropsychological variables. Lesions disrupting smoking addiction occurred in many different brain locations but were characterized by a specific pattern of brain connectivity. This pattern involved positive connectivity to the dorsal cingulate, lateral prefrontal cortex, and insula and negative connectivity to the medial prefrontal and temporal cortex. This circuit was reproducible across independent lesion cohorts, associated with reduced alcohol addiction risk, and specific to addiction metrics. Hubs that best matched the connectivity profile for addiction remission were the paracingulate gyrus, left frontal operculum, and medial fronto-polar cortex. We conclude that brain lesions disrupting addiction map to a specific human brain circuit and that hubs in this circuit provide testable targets for therapeutic neuromodulation.Lesions resulting in addiction remission occur in multiple different brain locations but map to a specific brain circuit and that hubs in this circuit provide testable targets for therapeutic neuromodulation.</p