Dynamic scaffolds for neuronal signaling: in silico analysis of the TANC protein family

AbstractThe emergence of genes implicated across multiple comorbid neurologic disorders allows to identify shared underlying molecular pathways. Recently, investigation of patients with diverse neurologic disorders found TANC1 and TANC2 as possible candidate disease genes. While the TANC proteins have been reported as postsynaptic scaffolds influencing synaptic spines and excitatory synapse strength, their molecular functions remain unknown. Here, we conducted a comprehensive in silico analysis of the TANC protein family to characterize their molecular role and understand possible neurobiological consequences of their disruption. The known Ankyrin and tetratricopeptide repeat (TPR) domains have been modeled. The newly predicted N-terminal ATPase domain may function as a regulated molecular switch for downstream signaling. Several putative conserved protein binding motifs allowed to extend the TANC interaction network. Interestingly, we highlighted connections with different signaling pathways converging to modulate neuronal activity. Beyond a known role for TANC family members in the glutamate receptor pathway, they seem linked to planar cell polarity signaling, Hippo pathway, and cilium assembly. This suggests an important role in neuron projection, extension and differentiation.</jats:p

Suppression of cell-spreading and phagocytic activity on nano-pillared surface: in vitro experiment using hemocytes of the colonial ascidian Botryllus schlosseri.

Nano-scale nipple array on the body surface has been described from various invertebrates including endoparasitic and mesoparasitic copepods, but the functions of the nipple array is not well understood. Using the hydrophilized nanopillar sheets made of polystyrene as a mimetic material of the nipple arrays on the parasites\u2019 body surface, we assayed the cell spreading and phagocytosis of the hemocytes of the colonial ascidian Botryllus schlosseri. On the pillared surface, the number of spreading amebocytes and the number of phagocytizing hemocytes per unit area were always smaller than those on the flat surface (Mann-Whitney test, p < 0.05 - 0.001), probably because the effective area for the cell attachment on the pillared surface is much smaller than the area on the flat sheet. The present results supports the idea that the nipple array on the parasites' body surface reduces the innate immune reaction from the host hemocytes

Performance of a large limited streamer tube cell in drift mode

The performance of a large (3x3 $cm^2$) streamer tube cell in drift mode is shown. The detector space resolution has been studied using cosmic muons crossing an high precision silicon telescope. The experimental results are compared with a GARFIELD simulation.Comment: 18 pages, 7 figures. Accepted by Nucl. Instr. and Methods

Enhancement of superconductivity near the ferromagnetic quantum critical point in UCoGe

We report a high-pressure single crystal study of the superconducting ferromagnet UCoGe. Ac-susceptibility and resistivity measurements under pressures up to 2.2 GPa show ferromagnetism is smoothly depressed and vanishes at a critical pressure $p_c = 1.4$ GPa. Near the ferromagnetic critical point superconductivity is enhanced. Upper-critical field measurements under pressure show $B_{c2}(0)$ attains remarkably large values, which provides solid evidence for spin-triplet superconductivity over the whole pressure range. The obtained $p-T$ phase diagram reveals superconductivity is closely connected to a ferromagnetic quantum critical point hidden under the superconducting `dome'.Comment: 4 pages, 3 figures; accepted for publication in PR

Muon spin rotation and relaxation in the superconducting ferromagnet UCoGe

We report zero-field muon spin rotation and relaxation measurements on the superconducting ferromagnet UCoGe. Weak itinerant ferromagnetic order is detected by a spontaneous muon spin precession frequency below the Curie temperature $T_C = 3$ K. The $\mu^+$ precession frequency persists below the bulk superconducting transition temperature $T_{sc} = 0.5$ K, where it measures a local magnetic field $B_{loc} = 0.015$ T. The amplitude of the $\mu$SR signal provides unambiguous proof for ferromagnetism present in the whole sample volume. We conclude ferromagnetism coexists with superconductivity on the microscopic scale.Comment: 4 pages, 3 figures, accepted for publication in PR

Scaling of the superfluid density in superfluid films

We study scaling of the superfluid density with respect to the film thickness by simulating the $x-y$ model on films of size $L \times L \times H$ ($L >> H$) using the cluster Monte Carlo. While periodic boundary conditions where used in the planar ($L$) directions, Dirichlet boundary conditions where used along the film thickness. We find that our results can be scaled on a universal curve by introducing an effective thickness. In the limit of large $H$ our scaling relations reduce to the conventional scaling forms. Using the same idea we find scaling in the experimental results using the same value of $\nu = 0.6705$.Comment: 4 pages, one postscript file replaced by one Latex file and 5 postscript figure

Transcribed ultraconserved noncoding RNAs (T-UCR) are involved in Barrett's esophagus carcinogenesis.

Barretts esophagus (BE) involves a metaplastic replacement of native esophageal squamous epithelium (Sq) by columnar-intestinalized mucosa, and it is the main risk factor for Barrett-related adenocarcinoma (BAc). Ultra-conserved regions (UCRs) are a class non-coding sequences that are conserved in humans, mice and rats. More than 90% of UCRs are transcribed (T-UCRs) in normal tissues, and are altered at transcriptional level in tumorigenesis. To identify the T-UCR profiles that are dysregulated in Barretts mucosa transformation, microarray analysis was performed on a discovery set of 51 macro-dissected samples obtained from 14 long-segment BE patients. Results were validated in an independent series of esophageal biopsy/surgery specimens and in two murine models of Barretts esophagus (i.e. esophagogastric-duodenal anastomosis). Progression from normal to BE to adenocarcinoma was each associated with specific and mutually exclusive T-UCR signatures that included up-regulation of uc.58-, uc.202-, uc.207-, and uc.223- and down-regulation of uc.214+. A 9 T-UCR signature characterized BE versus Sq (with the down-regulation of uc.161-, uc.165-, and uc.327-, and the up-regulation of uc.153-, uc.158-, uc.206-, uc.274-, uc.472-, and uc.473-). Analogous BE-specific T-UCR profiles were shared by human and murine lesions. This study is the first demonstration of a role for T-UCRs in the transformation of Barretts mucosa

The Specific Heat of a Ferromagnetic Film.

We analyze the specific heat for the $O(N)$ vector model on a $d$-dimensional film geometry of thickness $L$ using ``environmentally friendly'' renormalization. We consider periodic, Dirichlet and antiperiodic boundary conditions, deriving expressions for the specific heat and an effective specific heat exponent, \alpha\ef. In the case of $d=3$, for $N=1$, by matching to the exact exponent of the two dimensional Ising model we capture the crossover for \xi_L\ra\infty between power law behaviour in the limit {L\over\xi_L}\ra\infty and logarithmic behaviour in the limit {L\over\xi_L}\ra0 for fixed $L$, where $\xi_L$ is the correlation length in the transverse dimensions.Comment: 21 pages of Plain TeX. Postscript figures available upon request from [email protected]

The Landlab v1.0 OverlandFlow component: a Python tool for computing shallow-water flow across watersheds

Representation of flowing water in landscape evolution models (LEMs) is often simplified compared to hydrodynamic models, as LEMs make assumptions reducing physical complexity in favor of computational efficiency. The Landlab modeling framework can be used to bridge the divide between complex runoff models and more traditional LEMs, creating a new type of framework not commonly used in the geomorphology or hydrology communities. Landlab is a Python-language library that includes tools and process components that can be used to create models of Earth-surface dynamics over a range of temporal and spatial scales. The Landlab OverlandFlow component is based on a simplified inertial approximation of the shallow water equations, following the solution of de Almeida et al. (2012). This explicit two-dimensional hydrodynamic algorithm simulates a flood wave across a model domain, where water discharge and flow depth are calculated at all locations within a structured (raster) grid. Here we illustrate how the OverlandFlow component contained within Landlab can be applied as a simplified event-based runoff model and how to couple the runoff model with an incision model operating on decadal timescales. Examples of flow routing on both real and synthetic landscapes are shown. Hydrographs from a single storm at multiple locations in the Spring Creek watershed, Colorado, USA, are illustrated, along with a map of shear stress applied on the land surface by flowing water. The OverlandFlow component can also be coupled with the Landlab DetachmentLtdErosion component to illustrate how the nonsteady flow routing regime impacts incision across a watershed. The hydrograph and incision results are compared to simulations driven by steady-state runoff. Results from the coupled runoff and incision model indicate that runoff dynamics can impact landscape relief and channel concavity, suggesting that on landscape evolution timescales, the OverlandFlow model may lead to differences in simulated topography in comparison with traditional methods. The exploratory test cases described within demonstrate how the OverlandFlow component can be used in both hydrologic and geomorphic applications

NMR quantification of 16-O-methylcafestol and kahweol in Coffea canephora var. robusta beans from different geographical origins

Diterpenes have recently received a great deal of interest as tools to investigate the botanical origin of coffee. Specifically, kahweol has been proposed as a marker of Coffea arabica while 16-O-methylcafestol (16-OMC) is a Coffea canephora specific marker and its detection and quantification allow the authenticity of pure C. arabica roasted coffee blends to be assessed. In this study, we evaluated the possibility of the industrial use of the quantification of these diterpenes to assess the relative amounts of the two coffee species in blends. The content of 16-OMC and kahweol was determined in 78 samples (i.e., 39 green and the corresponding 39 roasted beans) of C. canephora from different geographical origins using a recently published NMR approach. Our results show a small natural variability in 16-OMC content for the Asian samples (average content = 1837 \ub1 113 mg/kg) while a much larger spread was found for the African samples (average content = 1744 \ub1 322 mg/kg). This large variability prevents the use of 16-OMC to quantify C. canephora in unknown roasted coffee blends. We also show that kahweol cannot be considered a specific C. arabica marker since it was detected almost all coffees and quantified in about 30% of the C. canephora samples