Analysis of the Rana catesbeiana tadpole tail fin proteome and phosphoproteome during T3-induced apoptosis: identification of a novel type I keratin

<p>Abstract</p> <p>Background</p> <p>Thyroid hormones (THs) are vital in the maintenance of homeostasis and in the control of development. One postembryonic developmental process that is principally regulated by THs is amphibian metamorphosis. This process has been intensively studied at the genomic level yet very little information at the proteomic level exists. In addition, there is increasing evidence that changes in the phosphoproteome influence TH action.</p> <p>Results</p> <p>Here we identify components of the proteome and phosphoproteome in the tail fin that changed within 48 h of exposure of premetamorphic <it>Rana catesbeiana </it>tadpoles to 10 nM 3,5,3'-triiodothyronine (T₃). To this end, we developed a cell and protein fractionation method combined with two-dimensional gel electrophoresis and phosphoprotein-specific staining. Altered proteins were identified using mass spectrometry (MS). We identified and cloned a novel Rana larval type I keratin, RLK I, which may be a target for caspase-mediated proteolysis upon exposure to T₃. In addition, the RLK I transcript is reduced during T₃-induced and natural metamorphosis which is consistent with a larval keratin. Furthermore, GILT, a protein involved in the immune system, is changed in phosphorylation state which is linked to its activation. Using a complementary MS technique for the analysis of differentially-expressed proteins, isobaric tags for relative and absolute quantitation (iTRAQ) revealed 15 additional proteins whose levels were altered upon T₃treatment. The success of identifying proteins whose levels changed upon T₃treatment with iTRAQ was enhanced through <it>de novo </it>sequencing of MS data and homology database searching. These proteins are involved in apoptosis, extracellular matrix structure, immune system, metabolism, mechanical function, and oxygen transport.</p> <p>Conclusion</p> <p>We have demonstrated the ability to derive proteomics-based information from a model species for postembryonic development for which no genome information is currently available. The present study identifies proteins whose levels and/or phosphorylation states are altered within 48 h of the induction of tadpole tail regression prior to overt remodeling of the tail. In particular, we have identified a novel keratin that is a target for T₃-mediated changes in the tail that can serve as an indicator of early response to this hormone.</p

Simple theory of extremely overdoped HTS

We demonstrate the existence of a simple physical picture of superconductivity for extremely overdoped CuO2 planes. It possesses all characteristic features of HTS, such as a high superconducting transition temperature, the $d_{x^2 - y^2}$ symmetry of order parameter, and the coexistence of a single electron Fermi surface and a pseudogap in the normal state. Values of pseudogap are calculated for different doping levels. An orbital paramagnetism of preformed pairs is predicted.Comment: 7 pages, 1 figur

MASCOT : metadata for advanced scalable video coding tools : final report

The goal of the MASCOT project was to develop new video coding schemes and tools that provide both an increased coding efficiency as well as extended scalability features compared to technology that was available at the beginning of the project. Towards that goal the following tools would be used: - metadata-based coding tools; - new spatiotemporal decompositions; - new prediction schemes. Although the initial goal was to develop one single codec architecture that was able to combine all new coding tools that were foreseen when the project was formulated, it became clear that this would limit the selection of the new tools. Therefore the consortium decided to develop two codec frameworks within the project, a standard hybrid DCT-based codec and a 3D wavelet-based codec, which together are able to accommodate all tools developed during the course of the project

Upper critical field Hc2H_{c2} calculations for the high critical temperature superconductors considering inhomogeneities

We perform calculations to obtain the $H_{c2}$ curve of high temperature superconductors (HTSC). We consider explicitly the fact that the HTSC possess intrinsic inhomogeneities by taking into account a non uniform charge density $\rho(r)$. The transition to a coherent superconducting phase at a critical temperature $T_c$ corresponds to a percolation threshold among different superconducting regions, each one characterized by a given $T_c(\rho(r))$. Within this model we calculate the upper critical field $H_{c2}$ by means of an average linearized Ginzburg-Landau (GL) equation to take into account the distribution of local superconducting temperatures $T_c(\rho(r))$. This approach explains some of the anomalies associated with $H_{c2}$ and why several properties like the Meissner and Nernst effects are detected at temperatures much higher than $T_c$.Comment: Latex text, add reference

Amine functionalization of cholecyst-derived extracellular matrix with generation 1 PAMAM dendrimer

This document is the unedited author's version of a Submitted Work that was subsequently accepted for publication in Biomacromolecules, copyright © American Chemical Society after peer review. To access the final edited and published work, see http://pubs.acs.org/doi/pdf/10.1021/bm701055k.A method to functionalize cholecyst-derived extracellular matrix (CEM) with free amine groups was established in an attempt to improve its potential for tethering of bioactive molecules. CEM was incorporated with Generation-1 polyamidoamine (G1 PAMAM) dendrimer by using N-(3-dimethylaminopropyl)-N′-ethylcarbodiimide and N-hydroxysuccinimide cross-linking system. The nature of incorporation of PAMAM dendrimer was evaluated using shrink temperature measurements, Fourier transform infrared (FTIR) assessment, ninhydrin assay, and swellability. The effects of PAMAM incorporation on mechanical and degradation properties of CEM were evaluated using a uniaxial mechanical test and collagenase degradation assay, respectively. Ninhydrin assay and FTIR assessment confirmed the presence of increasing free amine groups with increasing quantity of PAMAM in dendrimer-incorporated CEM (DENCEM) scaffolds. The amount of dendrimer used was found to be critical in controlling scaffold degradation, shrink temperature, and free amine content. Cell culture studies showed that fibroblasts seeded on DENCEM maintained their metabolic activity and ability to proliferate in vitro. In addition, fluorescence cell staining and scanning electron microscopy analysis of cell-seeded DENCEM showed preservation of normal fibroblast morphology and phenotype

Cellular and synaptic phenotypes lead to disrupted information processing in Fmr1-KO mouse layer 4 barrel cortex

Sensory hypersensitivity is a common and debilitating feature of neurodevelopmental disorders such as Fragile X Syndrome (FXS). How developmental changes in neuronal function culminate in network dysfunction that underlies sensory hypersensitivities is unknown. By systematically studying cellular and synaptic properties of layer 4 neurons combined with cellular and network simulations, we explored how the array of phenotypes in Fmr1-knockout (KO) mice produce circuit pathology during development. We show that many of the cellular and synaptic pathologies in Fmr1-KO mice are antagonistic, mitigating circuit dysfunction, and hence may be compensatory to the primary pathology. Overall, the layer 4 network in the Fmr1-KO exhibits significant alterations in spike output in response to thalamocortical input and distorted sensory encoding. This developmental loss of layer 4 sensory encoding precision would contribute to subsequent developmental alterations in layer 4-to-layer 2/3 connectivity and plasticity observed in Fmr1-KO mice, and circuit dysfunction underlying sensory hypersensitivity.</p

Aortic distensibility and coronary artery bypass graft patency

<p>Abstract</p> <p>Background</p> <p>Aortic distensibility is an elasticity index of the aorta, and reflects aortic stiffness. Coronary artery disease has been found to be substantially associated with increased aortic stiffness. In this study we aimed to retrospectively analyze the association of angiographically determined aortic distensibility with the patency rates of coronary bypass grafts</p> <p>Methods</p> <p>The study was conducted in the Cardiology department of the Applied Research Centre for Health of Uludağ University. The coronary angiograms of 53 consecutive coronary bypass patients were analysed retrospectively. Aortic distensibility was calculated using the formula: 2 × (change in aortic diameter)/(diastolic aortic diameter) × (change in aortic pressure). The number of stenosed and patent bypass grafts and the patient characteristics like age, risk factors were noted.</p> <p>Results</p> <p>There were 44 male (83%) and 9 female (17%) cases. Eighteen cases had only one saphenous vein grafting. The number of cases with two, three and four saphenous grafting were 18, 11 and 1; respectively. In the control angiograms the number of cases with one, two, three and four saphenous vein graft obstruction were 15 (31.3%), 7 (14.6%), 1 (2.1%) and 1 (2.1%) respectively. The aortic distensibility did not differ in cases with and without saphenous graft occlusion (p > 0.05). Also left internal mammary artery (LIMA) graft patency was not related to the distensibility of the aorta (p > 0.05). We also evaluated the data for cut-off values of 50 and 70 mmHg of pulse pressure and did not see any significant difference between the groups in terms of saphenous or LIMA grafts.</p> <p>Conclusion</p> <p>In this study we failed to show association of angiographically determined aortic distensibility with coronary bypass graft patency in consecutive 53 patients with coronary artery bypass graft surgery (CABG).</p

Developments in the negative-U modelling of the cuprate HTSC systems

The paper deals with the many stands that go into creating the unique and complex nature of the HTSC cuprates above Tc as below. Like its predecessors it treats charge, not spin or lattice, as prime mover, but thus taken in the context of the chemical bonding relevant to these copper oxides. The crucial shell filling, negative-U, double-loading fluctuations possible there require accessing at high valent local environment as prevails within the mixed valent, inhomogeneous two sub-system circumstance of the HTSC materials. Close attention is paid to the recent results from Corson, Demsar, Li, Johnson, Norman, Varma, Gyorffy and colleagues.Comment: 44 pages:200+ references. Submitted to J.Phys.:Condensed Matter, Sept 7 200

On the Geodesic Nature of Wegner's Flow

Wegner's method of flow equations offers a useful tool for diagonalizing a given Hamiltonian and is widely used in various branches of quantum physics. Here, generalizing this method, a condition is derived, under which the corresponding flow of a quantum state becomes geodesic in a submanifold of the projective Hilbert space, independently of specific initial conditions. This implies the geometric optimality of the present method as an algorithm of generating stationary states. The result is illustrated by analyzing some physical examples.Comment: 8 pages, no figures. The version published in Foundations of Physic