Estimation of vortex density after superconducting film quench

This paper addresses the problem of vortex formation during a rapid quench in a superconducting film. It builds on previous work showing that in a local gauge theory there are two distinct mechanisms of defect formation, based on fluctuations of the scalar and gauge fields, respectively. We show how vortex formation in a thin film differs from the fully two-dimensional case, on which most theoretical studies have focused. We discuss ways of testing theoretical predictions in superconductor experiments and analyse the results of recent experiments in this light.Comment: 7 pages, no figure

An ecological characterization of Salt River Bay National Historical Park and Ecological Preserve, U.S. Virgin Islands

Salt River Bay National Historical Park and Ecological Preserve (hereafter, SARI or the park) was created in 1992 to preserve, protect, and interpret nationally significant natural, historical, and cultural resources (United States Congress 1992). The diverse ecosystem within it includes a large mangrove forest, a submarine canyon, coral reefs, seagrass beds, coastal forests, and many other natural and developed landscape elements. These ecosystem components are, in turn, utilized by a great diversity of flora and fauna. A comprehensive spatial inventory of these ecosystems is required for successful management. To meet this need, the National Oceanic and Atmospheric Administration (NOAA) Biogeography Program, in consultation with the National Park Service (NPS) and the Government of the Virgin Islands Department of Planning and Natural Resources (VIDPNR), conducted an ecological characterization. The characterization consists of three complementary components: a text report, digital habitat maps, and a collection of historical aerial photographs. This ecological characterization provides managers with a suite of tools that, when coupled with the excellent pre-existing body of work on SARI resources, enables improved research and monitoring activities within the park (see Appendix F for a list of data products)

Structural studies of human acidic fibroblast growth factor mutants to be used in anticancer therapy

Lectins are carbohydrate-binding proteins present ubiquitously in nature. They play a role in biological recognition phenomena involving cells and proteins. The interaction lectin-carbohydrate is highly specific, and can be exploited for the development of nanoparticles containing on their surface specific lectins that are directed to carbohydrate residues present only on malignant cells and absent on healthy ones [1].Lectins have been found to possess several anticancer properties and they are proposed as therapeutic agents, binding to cancer cell membrane receptors, causing cytotoxicity, apoptosis and inhibition of tumor growth. Some lectins are able to prevent the proliferation of malignant tumor cells because they recognize the T-antigen (Gal \u3b2 1\u20133GalNAc) found specifically on the surface of tumor cells [2]. The main problem is that their use as a detection agent for the T-antigen in clinical studies is not possible because the immune system can recognize them as foreign molecules and develop an immune response.Previous studies in our laboratory have characterized a lectin found in Boletus edulis mushrooms called BEL \u3b2-trefoil which has antiproliferative activity on tumor cell lines, because it contains three binding sites for the T-antigen. Unlike other lectins with this property, BEL \u3b2-trefoil shows structural homology with a human protein, acidic Fibroblast Growth Factor (FGF1) [3]. Superposition of the two structures suggests that the human protein could be mutated to contain at least one of the binding sites for the T-antigen. Such mutations should create in FGF1 the potential capacity of recognizing tumor cells with less immunogenicity than the fungal protein.FGF1 is a mitogenic and chemotactic protein that mediates cellular functions by binding to transmembrane receptors, which are activated by ligand-induced dimerization requiring heparin as co-receptor.To reach our purpose FGF1 cDNA was cloned into a bacterial plasmid and then mutated in two positions to prevent its binding to the natural receptor, thus suppressing its physiological activity. Loss of function was tested in fibroblast growth tests and then site-directed mutagenesis was performed in three specific positions to produce an FGF1 capable to bind T-antigen. Ligand-protein binding affinity was measured using fluorimetric and isothermal titration calorimetric techniques. Attempts to crystalize the mutants of FGF1 were made using the hanging drop technique with the final aim to carry out their structural characterization by X-ray diffraction analysis of the crystals

High resolution structures of mutants of residues that affect access to the ligand-binding cavity of human lipocalin-type prostaglandin D synthase

Lipocalin-type prostaglandin D synthase (L-PGDS) catalyzes the isomerisation of the 9,11-endoperoxide group of PGH2 (Prostaglandin H2) to produce PGD2 (Prostaglandin D2) with 9-hydroxy and 11-keto groups. The product of the reaction, PGD2, is the precursor of several metabolites involved in many regulatory events. L-PGDS, the first member of the important lipocalin family to be recognized as an enzyme, is also able to bind and transport small hydrophobic molecules and was formerly known as \u3b2-trace protein, the second most abundant protein in human cerebro-spinal fluid. Previous structural work on the mouse and human proteins has focused on the identification of the amino acids responsible and the proposal of a mechanism for catalysis. In this paper we present the X-ray structures of the apo and holo forms (bound to PEG) of the C65A mutant of human L-PGDS to 1.40 \uc5 resolution and of the double mutant C65A K59A to 1.60 \uc5 resolution. We have also studied the apo forms of the double mutants C65A W54F and C65A W112F and the triple mutant C65A W54F W112F. Mutation of the lysine residue does not seem to affect the binding of PEG to the ligand-binding cavity and mutation of a single or both tryptophanes appears to have the same effect on the position of these two aromatic residues at the entrance of the cavity. We have also identified a solvent molecule in an invariant position in the cavity of virtually all the molecules present in the 9 asymmetric units of the crystals that we have examined.Taken together our observations indicate that the residues we have mutated appear to indeed play a role in the entrance-exit process of the substrate and/or other ligands to the binding cavity of the lipocalin

High resolution structures of mutants of residues that affect access to the ligand-binding cavity of human lipocalin-type prostaglandin D Synthase

Lipocalin-type prostaglandin D synthase (L-PGDS) catalyzes the isomerisation of the 9,11-endoperoxide group of PGH2 (Prostaglandin H2) to produce PGD2 (Prostaglandin D2) with 9-hydroxy and 11-keto groups. The product of the reaction, PGD2, is the precursor of several metabolites involved in many regulatory events. L-PGDS, the first member of the important lipocalin family to be recognized as an enzyme, is also able to bind and transport small hydrophobic molecules and was formerly known as \u3b2-trace protein, the second most abundant protein in human cerebro-spinal fluid. Previous structural work on the mouse and human proteins has focused on the identification of the amino acids responsible and the proposal of a mechanism for catalysis. In this paper we present the X-ray structures of the apo and holo forms (bound to PEG) of the C65A mutant of human L-PGDS to 1.40 \uc5 resolution and of the double mutant C65A K59A to 1.60 \uc5 resolution. We have also studied the apo forms of the double mutants C65A W54F and C65A W112F and the triple mutant C65A W54F W112F. Mutation of the lysine residue does not seem to affect the binding of PEG to the ligand-binding cavity and mutation of a single or both tryptophanes appears to have the same effect on the position of these two aromatic residues at the entrance of the cavity. We have also identified a solvent molecule in an invariant position in the cavity of virtually all the molecules present in the 9 asymmetric units of the crystals that we have examined. Taken together our observations indicate that the residues we have mutated appear to indeed play a role in the entrance-exit process of the substrate and/or other ligands to the binding cavity of the lipocalin

Crystallographic studies on carp Fishelectin (FEL)

A few years ago we isolated and sequenced a novel glycoprotein present in the eggs of the carp (Cyprinus carpio). The protein, that binds to a Sepharose 4B matrix column and can be eluted with 0.4 M N-acetyl glucosamine, behaves like a lectin of molecular mass 26686 Da. On the basis of DLS experiments the lectin is present in solution as a stable dimer. We have determined its 238 amino acid long sequence, the position of its 4 disulfide bridges and the structure of its single N-linked carbohydrate chain. The lectin shows a very low agglutinating activity for human A-type erythrocytes and interacts with both Gram positive and negative bacteria, these last interactions are inhibited by N-acetyl glucosamine. A data base search shows that its amino acid sequence is significantly similar to that of the members of an invertebrate lectin family that includes tachylectin-1, present in the amebocytes of the horseshoe crab Tachypleus tridentatus, and known to participate in the innate defense system of this species and two other lectins, characterized in the plasmodium Physarum polycephalum, that are called Tectonins I and II and are located in the external surface of the plasma membrane. We have proposed the name fishelectins (by analogy with tachylectins) for this new vertebrate protein family. Homologous genes are present in other bony fish. The carp protein has 85 % identity with a gene expressed in the crucian carp (Carassius auratus gibelio) and 78 % identity with a gene in the cDNA library of the zebrafish (Danio rerio). We have prepared three different crystal forms of the apo protein and two of co-crystals with N-acetyl glucosamine. The orthorhombic form of the apoprotein belongs to space group P212121 and was solved first using the MIR method. Our poster will present the data collection statistics of the best apo and holo forms of the lectin and the refinement statistics of the holo form and will discuss the structure and similarity of this newly identified family of vertebrate proteins to a well known invertebrate protein family

Crystallographic studies on carp Fishelectin (FEL)

A few years ago we isolated and sequenced a novel glycoprotein present in the eggs of the carp (Cyprinus carpio) (1). The protein, that binds to a Sepharose 4B matrix column and can be eluted with 0.4 M N-acetyl glucosamine, behaves like a lectin of molecular mass 26686 Da. On the basis of DLS experiments the lectin is present in solution as a stable dimer. We have determined its 238 amino acid long sequence, the position of its 4 disulfide bridges and the structure of its single N-linked carbohydrate chain. The lectin shows a very low agglutinating activity for human A-type erythrocytes and interacts with both Gram positive and negative bacteria, these last interactions are inhibited by N-acetyl glucosamine. A data base search shows that its amino acid sequence is significantly similar to that of the members of an invertebrate lectin family that includes tachylectin-1, present in the amebocytes of the horseshoe crab Tachypleus tridentatus, and known to participate in the innate defense system of this species (2.3) and two other lectins, characterized in the plasmodium Physarum polycephalum, that are called Tectonins I and II and are located in the external surface of the plasma membrane (4). We have proposed the name fishelectins (by analogy with tachylectins) for this new vertebrate protein family. Homologous genes are present in other bony fish. The carp protein has 85 % identity with a gene expressed in the crucian carp (Carassius auratus gibelio) (5) and 78 % identity with a gene in the cDNA library of the zebrafish (Danio rerio). We have prepared three different crystal forms of the apo protein and two of co-crystals with N-acetyl glucosamine. The orthorhombic form of the apoprotein belongs to space group P212121 and was solved first using the MIR method. Our poster will present the data collection statistics of the best apo and holo forms of the lectin and the refinement statistics of the holo form and will discuss the structure and similarity of this newly identified family of vertebrate proteins to a well known invertebrate protein family

BEL \u3b2-TREFOIL. A NOVEL LECTIN WITH ANTITUMORAL PROPERTIES IN KING BOLETE (BOLETUS EDULIS) MUSHROOMS

A novel lectin completely different from the formerly described member of the saline soluble family of mushroom specific lectins (named BEL, Boletus edulis lectin, Bovi et al., 2011) was purified from the fruiting bodies of king bolete mushrooms (also called porcino, cep or penny bun). The lectin was structurally characterized: its amino acid sequence and three dimensional structure were determined. The protein is a homodimer and each protomer folds as \u3b2-trefoil domain and therefore we propose the name BEL \u3b2-trefoil to distinguish it from the other lectin that has been described in these mushrooms: BEL. The new lectin has potent anti-proliferative effects on human epithelial cancer cells which confers to it an interesting therapeutic potential as an antineoplastic agent. Several crystal forms of the apoprotein and of complexes with different carbohydrates were studied by X-ray diffraction. The interaction of the lectin with lactose, galactose, N-acetylgalactosamine, T-antigen disaccharide (Gal\u3b21-3GalNAc) and T-antigen (Ser-Gal\u3b21-3GalNAc) was examined in detail. All the three potential binding sites present in the \u3b2-trefoil fold are occupied in at least one crystal form. No important conformational changes are observed in the lectin when comparing its co-crystals with carbohydrates with those of the ligand free protein

D* Production in Deep Inelastic Scattering at HERA

This paper presents measurements of D^{*\pm} production in deep inelastic scattering from collisions between 27.5 GeV positrons and 820 GeV protons. The data have been taken with the ZEUS detector at HERA. The decay channel $D^{*+}\to (D^0 \to K^- \pi^+) \pi^+$ (+ c.c.) has been used in the study. The $e^+p$ cross section for inclusive D^{*\pm} production with $5<Q^2<100 GeV^2$ and $y<0.7$ is 5.3 \pms 1.0 \pms 0.8 nb in the kinematic region {$1.3<p_T(D^{*\pm})<9.0$ GeV and $| \eta(D^{*\pm}) |<1.5$}. Differential cross sections as functions of p_T(D^{*\pm}), $\eta(D^{*\pm}), W$ and $Q^2$ are compared with next-to-leading order QCD calculations based on the photon-gluon fusion production mechanism. After an extrapolation of the cross section to the full kinematic region in p_T(D^{*\pm}) and $\eta$(D^{*\pm}), the charm contribution $F_2^{c\bar{c}}(x,Q^2)$ to the proton structure function is determined for Bjorken $x$ between 2 $\cdot$ 10$^{-4}$ and 5 $\cdot$ 10$^{-3}$.Comment: 17 pages including 4 figure